Dissertations / Theses on the topic 'Protein – protein interactions (PPI)'

Proteinmethylierung spielt eine immer größere Rolle in der Regulierung zellulärer Prozesse. Die Entwicklung effizienter proteomweiter Methoden zur Detektion von Methylierung auf Proteinen ist limitiert und technisch schwierig. In dieser Arbeit haben wir einen neuen Hefe-Zwei-Hybrid-Ansatz (Y2H) entwickelt, der Proteine, die miteinander wechselwirken, mit Hilfe von Sequenzierungen der zweiten Generation identifiziert (Y2H-Seq). Der neue Y2H-Seq-Ansatz wurde systematisch mit dem Y2H-Seq-Ansatz verglichen. Dafür wurde ein Bait-Set von 8 Protein-Arginin-Methyltransferasen, 17 Protein-Lysin-Methyltransferasen und 10 Demethylasen gegen 14,268 Prey-Proteine getestet. Der Y2H-Seq-Ansatz ist weniger arbeitsintensiv, hat eine höhere Sensitivität als der Standard Y2H-Matrix-Ansatz und ist deshalb besonders geeignet, um schwache Interaktionen zwischen Substraten und Protein-Methyltransferasen zu detektieren. Insgesamt wurden 523 Wechselwirkungen zwischen 22 Bait-Proteinen und 324 Prey-Pr oteinen etabliert, darunter 11 bekannte Methyltransferasen-Substrate. Netzwerkanalysen zeigen, dass Methyltransferasen bevorzugt mit Transkriptionsregulatoren, DNA- und RNA-Bindeproteinen wechselwirken. Diese Daten repräsentieren das erste proteomweite Wechselwirkungsnetzwerk über Protein-Methyltransferasen und dienen als Ressource für neue potentielle Methylierungssubstrate. In einem in vitro Methylierungsassay wurden exemplarisch mit Hilfe massenspektrometrischer Analysen die methylierten Aminosäurereste einiger Kandidatenproteine bestimmt. Von neun getesteten Proteinen waren sieben methyliert, zu denen gehören SPIN2B, DNAJA3, QKI, SAMD3, OFCC1, SYNCRIP und WDR42A. Wahrscheinlich sind viele Methylierungssubstrate im Netzwerk vorhanden. Das vorgestellte Protein-Protein-Wechselwirkungsnetzwerk zeigt, dass Proteinmethylierung sehr unterschiedliche zelluläre Prozesse beeinflusst und ermöglicht die Aufstellung neuer Hypothesen über die Regulierung Molekularer Mechanismen durch Methylierung.
Protein methylation on arginine and lysine residues is a largely unexplored posttranslational modification which regulates diverse cellular processes. The development of efficient proteome-wide approaches for detecting protein methylation is limited and technically challenging. We developed a novel workload reduced yeast-two hybrid (Y2H) approach to detect protein-protein interactions utilizing second generation sequencing. The novel Y2H-seq approach was systematically evaluated against our state of the art Y2H-matrix screening approach and used to screen 8 protein arginine methyltransferases, 17 protein lysine methyltransferases and 10 demethylases against a set of 14,268 proteins. Comparison of the two approaches revealed a higher sensitivity of the new Y2H-seq approach. The increased sampling rate of the Y2H-seq approach is advantageous when assaying transient interactions between substrates and methyltransferases. Overall 523 interactions between 22 bait proteins and 324 prey proteins were identified including 11 proteins known to be methylated. Network analysis revealed enrichment of transcription regulator activity, DNA- and RNA-binding function of proteins interacting with protein methyltransferases. The dataset represents the first proteome-wide interaction network of enzymes involved in methylation and provides a comprehensively annotated resource of potential new methylation substrates. An in vitro methylation assay coupled to mass spectrometry revealed amino acid methylation of candidate proteins. Seven of nine proteins tested were methylated including SPIN2B, DNAJA3, QKI, SAMD3, OFCC1, SYNCRIP and WDR42A indicating that the interaction network is likely to contain many putative methyltransferase substrate pairs. The presented protein-protein interaction network demonstrates that protein methylation is involved in diverse cellular processes and can inform hypothesis driven investigation into molecular mechanisms regulated through methylation.

Clarifying the physico-chemical principles of protein-protein interactions is critically important to understand the relationships between biological structures and functions in all biochemical mechanisms. In this project we aim to develop, validate and apply new computational-theoretical methods to study and predict the binding regions of proteins starting from 3D structural information and from the analysis of the conformational and physico-chemical properties of the constituting amino acids. In particular, this project entails the integrated analysis of the energetic properties of different datasets of proteins solved at high resolution. In this context, we have focused on four main subjects with different, yet highly intertwined, objectives. The first subject will address the application of an energy-based computational predictor for the identification of possible antibody-binding surfaces (epitopes) of protein antigens from the pathogen Burkholderia pseudomallei, responsible for human melioidosis. The second will focus on the expansion of the same rationale, adapting the method towards different applications, and including as a novel functionality the prediction of MHC-II coupled epitopes to elicit the intervention of T helper cells. The third objective concerns the design and characterization of peptides and peptidomimetics to optimize the properties of the identified epitopes as better vaccine candidates. The fourth one will pursue the investigation of the energetic determinants of interacting proteins in a more general context (not limited to immunogenic epitopes), aiming at the identification of an energy-based property describing the interaction event at the atomistic level of resolution. This part of the project is aimed at the development of a computational tool based on such property to help improve the understanding of the determinants of protein interactions and help predict their binding interfaces and orientation. All four subjects have been investigated in the broad spectrum of activities of an academic consortium, devoted to the identification of antigens from B. pseudomallei showing sufficient immunogenic potential to be considered as components for a vaccine against the pathogen. The computational methods developed and tested within this framework have theoretical as well as practical implications, from the physico-chemical study and characterization of protein-protein interactions, to the design of biologically active molecules.

Precisely how Hephaestin (Heph) facilitate iron release from cells is poorly understood. The work in this thesis tried to establish the role of different iron metabolic proteins, Mitoferrin (Mfrn), IRPs and Heph in iron homeostasis. Analysis of 18 tagSNPs in the Mfrn gene was carried out in an AsianCaucasian population to establish any correlation between the Mfrn tagSNPs, haemoglobin levels and birth weight in the presence of covariates such as sex of the fetus, gestational age and mother's booking weight. Two-way ANCOVA analysis was carried out to check if the covariates have any influence on the dependent variable in the presence of fixed factors. From the ANCOVA analysis of Mfrn tagSN Ps it can be concluded that neither the haemoglobin levels nor the birth weight are dependent on the genotype, fetal sex, nor on their interaction. Owing to the significance in identifying the interacting partners of IRPs and Heph to understand more about their role in iron metabolism, protein-protein interaction studies were also carried out. IRPs and Heph genes were successfully cloned with One-Strep tag. Full length clones were sequence confirmed for any variation after PCR. Before carrying out immunoprecipitation to identify the interacting partners, transfection efficiency, viability and the role of magnetic particles on K562 cells was performed by using IRPs and Heph cloned with One-Strep tag. Lipofectamine-L TX plus transfection had more viable cells and higher efficiency compared with magnetic-assisted transfection . Also, this study confirms that magnetic nanoparticles do not have any adverse or significant effect on IRPs during the transfection. An unsuccessful attempt was made to identify the interacting partners of IRPs and Heph by immunoprecipitation. The current thesis work also involved identification of a potential ferroxidase . Ceruloplasmin (Cp) was used as a postive control. Non-denaturing gel eletrophoresis of the K562, MDA-MB-231 and PNT2-C2 cell fractions confirmed the presence of the extra band establishing the ubiquitous nature of the band. Mass spectrometry analysis identified the excised band as Calreticulin (CALR). This is the first report of calreticulin having ferroxidase activity.

Using computational methods to identify protein-protein interactions (PPIs) supports experimental techniques by using less time and less resources. Identifying PPIs can be made through a template-based approach that describes how unstudied proteins interact by aligning a common structural template that exists in both interacting proteins. A pipeline that uses this is InterPred, that combines homology modelling and massive template comparison to construct coarse interaction models. These models are reviewed by a machine learning classifier that classifies models that shows traits of being true, which can be further refined with a docking technique. However, InterPred is dependent on using complex structural information, that might not be available from unstudied proteins, while it is suggested that PPIs are dependent of the shape and interface of proteins. A method that aligns structures based on the interface attributes is InterComp, which uses topological and sequence-order independent structural comparison. Implementing this method into InterPred will lead to restricting structural information to the interface of proteins, which could lead to discovery of undetected PPI models. The result showed that the modified pipeline was not comparable based on the receiver operating characteristic (ROC) performance. However, the modified pipeline could identify new potential PPIs that were undetected by InterPred.

Veränderungen in phosphorylierungsabhängigen Signalwegen, Akkumulation von Proteinaggregaten im Gehirn und neuronaler Zelltod sind Neurodegenerationskennzeichen und Indikatoren für überlappende molekulare Mechanismen. Um Einblicke in die involvierten Signalwege zu erhalten, wurde mit Hilfe eines modifizierten Hefe-Zwei-Hybrid (Y2H)-Systems für 71 Proteine, die mit neurologischen Erkrankungen assoziiert sind, proteomweit nach Protein-Protein Interaktionen (PPIs) gesucht. Für 21 dieser Proteine wurden PPIs identifiziert. Das Gesamtnetzwerk besteht aus 79 Proteinen und 90 PPIs von denen 5 phosphorylierungsabhängig sind. Ein Teil dieser PPIs wurde in unabhängigen Interaktionsassays mit einer Validierungsrate von 66 % getestet. Der netzwerkbasierte Versuch verbindet erfolgreich neurologische Erkrankungen untereinander aber auch mit zellulären Prozessen. Ser/Thr-Kinase abhängige PPIs verknüpfen zum Beispiel das Parkinson Protein 7 (PARK7, DJ1) mit den E3 Ligase Komponenten ASB3 und RNF31 (HOIP). Die Funktion dieser Proteine bekräftigt den Zusammenhang zwischen dem Ubiquitin-Proteasom-System und der Parkinson Krankheit (PD). Neurofibromin 2 (NF2, merlin) Isoformen und PARK7 interagieren mit der regulatorischen PI3K Untereinheit p55-gamma (PIK3R3). Diese PPIs basieren auf Tyr-Kinase Aktivität im modifizierten Y2H System und funktionellen PIK3R3 pTyr-Erkennungsmodulen (SH2 Domänen) in co-IP und Venus PCA Versuchen. Dies verknüpft den PI3K/AKT Überlebenssignalweg mit zwei unterschiedlichen neurologischen Erkrankungsphenotypen: dem PD assoziierten neuronalen Zelltod und der Neurofibromatose Typ 2-assoziierten Tumorentstehung. Die vergleichende Beobachtung von PIK3R3, AOF2 (KDM1A, LSD1) Interaktionen auf NF2 Isoformlevel offenbart eine Bevorzugung von Isoform 7 bei zytoplasmatischer Lokalisation, wohingegen Isoform 1 PPIs an der Membran lokalisiert sind. Das modifizierungsabhängige und isoformspezifische PPI Netzwerk ermöglichte neue Hypothesen zu molekularen Pathomechanismen.
Alterations in phosphorylation-dependent signalling pathways, accumulation of aggregated proteins in the brain and neuronal apoptosis are common to neurodegeneration and implicate overlapping molecular mechanism. To gain insight into involved pathways, a modified yeast-two hybrid (Y2H) system was applied to screen 71 proteins associated with neurological disorders in a proteome-wide manner. For 21 of these proteins interactions were identified including 5 phosphorylation-dependent ones. In total, the network connected 79 proteins through 90 protein-protein interactions (PPIs). A fraction of these Y2H PPIs was tested in secondary interaction assays with a validation rate of 66 %. The described network-based approach successfully identified proteins associated with more than one disorder and cellular functions connected to specific disorders. In particular, the network revealed Ser/Thr kinase-dependent PPIs between the Parkinson protein 7 (PARK7, DJ1) and the E3 ligase components ASB3 and RNF31 (HOIP). The function of these proteins further substantiates the established connection between Parkinson’s disease (PD) and ubiquitination-mediated proteasome (dis)functions. Neurofibromin 2 (NF2, merlin) isoforms and PARK7 were identified as PI3K regulatory subunit p55-gamma (PIK3R3) interactors. These PPIs required Tyr kinase coexpression in the modified Y2H system and functional PIK3R3 pTyr-recognition modules (SH2 domains) in co-IP and Venus PCA experiments. This finding implicates the PI3K/AKT survival pathway in PD-associated neuronal apoptosis and Neurofibromatosis type 2-associated tumour formation. Investigation of PIK3R3, AOF2 (KDM1A, LSD1) and EMILIN1 PPIs on NF2 isoform level revealed preferential isoform 7 binding and cytoplasmic or membrane localisation of these PPIs for isoform 7 or 1, respectively. The generated modification-dependent and isoform-specific PPI network triggered many hypotheses on the molecular mechanisms implicated in neurological disorders.

Protein-peptide interactions play a major role in several biological processes, such as cellproliferation and cancer cell life-cycles. Accurate computational methods for predictingprotein-protein interactions exist, but few of these method can be extended to predictinginteractions between a protein and a particularly small or intrinsically disordered peptide. In this thesis, PePIP is presented. PePIP is a pipeline for predicting where on a given proteina given peptide will most probably bind. The pipeline utilizes structural aligning to perusethe Protein Data Bank for possible templates for the interaction to be predicted, using thelarger chain as the query. The possible templates are then evaluated as to whether they canrepresent the query protein and peptide using a Random Forest classifier machine learningalgorithm, and the best templates are found by using the evaluation from the Random Forest in combination with hierarchical clustering. These final templates are then combined to givea prediction of binding site. PePIP is proven to be highly accurate when testing on a set of 502 experimentally determinedprotein-peptide structures, suggesting a binding site on the correct part of the protein- surfaceroughly 4 out of 5 times.

Doutoramento em Bioquímica
The work presented in this Thesis investigates the dynamics and molecular interactions of p22HBP and the p22HBP-tetrapyrrole complex. Specifically, the key residues involved when a tetrapyrrole binds to p22HBP were sought. Previous molecular modelling studies identified three possible charged residues R56, K64 and K177 as possibly being important in tetrapyrrole binding via electrostatic interactions with the propionate groups of the tetrapyrrole. A number of variants of murine p22HBP were therefore prepared and fluorescence quenching and NMR used to verify the integrity of the variants and their interaction with tetrapyrrole. The same molecular modelling studies identified a mobile loop Y171-R180 in p22HBP that decreased in mobility on tetrapyrrole binding, therefore to confirm this mobility change dynamics studies based on NMR relaxation experiments were carried out. Finally in order to obtain a non heme-binding form of human p22HBP a chimeric p22HBP was designed and constructed. This construct, and the resulting protein, will be important for future siRNA knockdown studies where rescue or recovery of function experiments are required to prove the knockdown results. Chapter one discusses the current state of the art in terms of the biological, structural and functional aspects of p22HBP. The main objectives of the Thesis are also introduced here. Chapter two presents a detailed description of the different expression vectors (pNJ2 and pet28-a) and procedures used for overexpression and purification of murine p22HBP and its variants and human p22HBP. All expression and purification systems used gave good yields and allowed isotopic labeling to be carried out. The fluorescence quenching results for tetrapyrrole binding to murine p22HBP and variants are presented in chapter three along with the dissociation constants that were found to be in the nanomolar range for wild type murine and human p22HBP. The same studies were performed for murine p22HBP variants, with hydrophobic and polar changes being introduced at R56, K64 and K177. The dissociation constants were found to double in some cases but no significant changes in the strength of hemin-protein interactions were observed. The tetrapyrrole interaction with p22HBP was also followed by NMR spectroscopy, where chemical shift mapping was used to identify binding pocket location. All the variants and wild type human p22HBP were found to bind at the same location. Chapter 4 contains the data from 2D and 3D experiments carried out on 15N/13C labelled human p22HBP that was used to obtain backbone assignments. Comparison with wild type murine p22HBP assignments, PPIX titrations and theoretical calculations based on chemical shifts (Talos+) allowed 82% of the backbone resonances to be assigned. The results from the relaxation experiments used to probe the dynamics of the mobile loop in p22HBP on binding to tetrapyrrole are presented in chapter 5. The overall protein was found to tumble isotropically in the free and bound forms however the results to probe mobility changes in the 171-180 loop on tetrapyrrole binding proved inconclusive as only residue could be assigned and this did not seem to become significantly less mobile. The final chapter describes the design and construction of a chimeric p22HBP. For these purpose, the alfa1-helix sequence of human p22HBP in the phHBP1 plasmid was replaced by its homologous sequence in hSOUL, a non heme-binding protein with identical 3D structure. The results however indicated that either the incorrect sequence was introduced into the plasmid or the purification procedure was inadequate.
O trabalho apresentado nesta Tese focou-se na dinâmica e nas interações moleculares da p22HBP e do complexo p22HBP-tetrapirrol, nomeadamente nos resíduos chave envolvidos nesta interação. Estudos prévios de modelação molecular identificaram três possíveis resíduos chave R56, K64 e K177 como sendo importantes na interação com os tetrapirróis, através de interações eletrostáticas com os grupos propionato do tetrapirrol. Foram desenhados e construídos variantes da p22HBP murina e foram desenvolvidos estudos de extinção de fluorescência e RMN para avaliar a integridade dos variantes e a sua interação com os tetrapirróis. Os mesmos estudos de modelação molecular identificaram ainda uma zona flexível (Y171-R180) na p22HBP que diminui a mobilidade com a interação do tetrapirrol. Para confirmar esta alteração de mobilidade, foram realizados estudos de dinâmica, baseados em RMN. Por fim, com o intuito de obter uma versão não funcional da p22HBP humana, foi planeada e construída uma versão quimérica da p22HBP humana. No futuro, esta nova versão da p22HBP quimérica, será importante para os estudos de knockdown envolvendo siRNA. O capítulo um introduz uma revisão dos aspetos biológicos da p22HBP nomeadamente os estudos estruturais e as possíveis funções que foram identificadas. Os principais objetivos da tese são também apresentados neste capítulo. No capítulo dois é apresentada uma descrição detalhada dos diferentes vectores de sobreexpressão (pNJ2 e pet28-a) e dos métodos de sobreexpressão e purificação da p22HBP murina e respectivos variantes, bem como da p22HBP humana. Todos os sistemas de sobreexpressão e purificação utilizados obtiveram bons rendimentos e permitiram a marcação isotópica das proteínas. No capítulo 3 são apresentados os resultados de extinção de fluorescência para a interação da p22HBP murina e humana com hemina através das constantes de dissociação determinadas na ordem dos nanomolar. Os mesmos estudos foram realizados para os variantes da p22HBP murina, com alterações hidrofóbicas e de polaridade nos resíduos R56, K64 e K177. Em alguns casos, as constantes de dissociação determinadas são mais elevadas, embora não se tenham verificado alterações significativas na força da interação proteína-hemo. As interações tetrapirrólicas com a p22HBP foram também estudadas por espectroscopia de RMN, onde foram mapeadas as diferenças nos desvios químicos para identificar a localização da zona de interação. A localização da zona de interação dos variantes da p22HBP e a p2HBP humana mantém-se igual à p22HBP murina. No capítulo 4 encontram-se os resultados das experiências 2D e 3D realizadas na p22HBP humana, isotopicamente marcada com 15N/13C, para identificar as ressonâncias da cadeia principal. 82% dos sistemas de spin da cadeia principal foram identificados através da comparação com a p22HBP murina, das titulações com PPIX e de cálculos teóricos baseados nos desvios químicos (Talos+). No capítulo 5 são apresentados os resultados das experiências de relaxação, usados para comprovarem a dinâmica do loop na p22HBP aquando da interação com o tetrapirrol. A proteína no seu todo move-se de uma forma isotrópica na forma livre e ligada. No entanto os resultados para comprovar as alterações de mobilidade no loop 171-180 na presença de hemo, foram inconclusivos uma vez que só a um resíduo foi atribuído um sistema de spin, e não foi indicativo da perda significativa de mobilidade. O último capítulo descreve o planeamento e a construção da p22HBP quimérica. Para tal, a sequência que codifica a hélix alfa 1 da p22HBP humana, no plasmídeo phHBP1, foi substituída pela sequência homóloga da SOUL humana, uma proteína com uma estrutura 3D semelhante mas não liga ao hemo. Os resultados no entanto demonstraram que ou a sequência não foi introduzida corretamente no plasmídeo ou o sistema de purificação não foi adequado.

Doenças complexas são caracterizadas por serem poligênicas e multifatoriais, o que representa um desafio em relação à busca de genes relacionados a elas. Com o advento das tecnologias de sequenciamento em larga escala do genoma e das medições de expressão gênica (transcritoma), bem como o conhecimento de interações proteína-proteína, doenças complexas têm sido sistematicamente investigadas. Particularmente, baseando-se no paradigma Network Medicine, as redes de interação proteína-proteína (PPI -- Protein-Protein Interaction) têm sido utilizadas para priorizar genes relacionados às doenças complexas segundo suas características topológicas. Entretanto, as redes PPI são afetadas pelo viés da literatura, em que as proteínas mais estudadas tendem a ter mais conexões, degradando a qualidade dos resultados. Adicionalmente, métodos que utilizam somente redes PPI fornecem apenas resultados estáticos e não-específicos, uma vez que as topologias destas redes não são específicas de uma determinada doença. Neste trabalho, desenvolvemos uma metodologia para priorizar genes e vias biológicas relacionados à uma dada doença complexa, através de uma abordagem integrativa de dados de redes PPI, transcritômica e genômica, visando aumentar a replicabilidade dos diferentes estudos e a descoberta de novos genes associados à doença. Após a integração das redes PPI com dados de expressão gênica, aplicamos as hipóteses da Network Medicine à rede resultante para conectar genes sementes (relacionados à doença, definidos a partir de estudos de associação) através de caminhos mínimos que possuam maior co-expressão entre seus genes. Dados de expressão em duas condições (controle e doença) são usados separadamente para obter duas redes, em que cada nó (gene) dessas redes é pontuado segundo fatores topológicos e de co-expressão. Baseado nesta pontuação, desenvolvemos dois escores de ranqueamento: um que prioriza genes com maior alteração entre suas pontuações em cada condição, e outro que privilegia genes com a maior soma destas pontuações. A aplicação do método a três estudos envolvendo dados de expressão de esquizofrenia recuperou com sucesso genes diferencialmente co-expressos em duas condições, e ao mesmo tempo evitou o viés da literatura. Além disso, houve uma melhoria substancial na replicação dos resultados pelo método aplicado aos três estudos, que por métodos convencionais não alcançavam replicabilidade satisfatória.
Complex diseases are characterized as being poligenic and multifactorial, so this poses a challenge regarding the search for genes related to them. With the advent of high-throughput technologies for genome sequencing and gene expression measurements (transcriptome), as well as the knowledge of protein-protein interactions, complex diseases have been sistematically investigated. Particularly, Protein-Protein Interaction (PPI) networks have been used to prioritize genes related to complex diseases according to its topological features. However, PPI networks are affected by ascertainment bias, in which the most studied proteins tend to have more connections, degrading the quality of the results. Additionally, methods using only PPI networks can provide just static and non-specific results, since the topologies of these networks are not specific of a given disease. In this work, we developed a methodology to prioritize genes and biological pathways related to a given complex disease, through an approach that integrates data from PPI networks, transcriptomics and genomics, aiming to increase replicability of different studies and to discover new genes associated to the disease. The methodology integrates PPI network and gene expression data, and then applies the Network Medicine Hypotheses to the resulting network in order to connect seed genes (obtained from association studies) through shortest paths possessing larger coexpression among their genes. Gene expression data in two conditions (control and disease) are used to obtain two networks, where each node (gene) in these networks is rated according to topological and coexpression aspects. Based on this rating, we developed two ranking scores: one that prioritizes genes with the largest alteration between their ratings in each condition, and another that favors genes with the greatest sum of these scores. The application of this method to three studies involving schizophrenia expression data successfully recovered differentially co-expressed gene in two conditions, while avoiding the ascertainment bias. Furthermore, when applied to the three studies, the method achieved a substantial improvement in replication of results, while other conventional methods did not reach a satisfactory replicability.

O Transtorno de Déficit de Atenção e Hiperatividade (TDAH) é a doença do neurodesenvolvimento mais comum na infância, afetando cerca de 5,8% de crianças e adolescentes no mundo. Muitos estudos vêm tentando investigar a suscetibilidade genética em TDAH, mas sem muito sucesso. Este estudo teve como objetivo analisar variantes raras e comuns contribuindo para a arquitetura genética do TDAH. Foram gerados os primeiros dados de exoma de TDAH de 30 trios brasileiros em que o filho foi diagnosticado com TDAH esporádico. Foram analisados tanto variações de único nucleotídeo (ou SNVs, single-nucleotide variants) quanto variações de número de cópias (ou CNVs, copy-number variants), tanto nesses trios quanto em outros conjuntos de dados, incluindo uma amostra brasileira de 503 crianças/adolescentes controles, bem como resultados previamente publicados em quatro estudos com variação de número de cópias e uma meta-análise de estudos de associação ao longo do genoma. Tanto os trios quanto os controles fazem parte da Coorte de Escolares de Alto Risco para o desenvolvimento de Psicopatologia e Resiliência na Infância do Instituto Nacional de Psiquiatria do Desenvolvimento (INPD). Os resultados de trios brasileiros mostraram três padrões marcantes: casos com variações herdadas e somente SNVs de novo ou CNVs de novo, e casos somente com variações herdadas. Embora o tamanho amostral seja pequeno, pudemos ver que diferentes comorbidades são mais frequentes em casos somente com variações herdadas. Após explorarmos a composição de variações nos probandos brasileiros, foram selecionados genes recorrentes entre amostras do nosso estudo ou em bancos de dados públicos. Além disso, usando somente genes expressos no cérebro (amostras pós-mortem dos projetos Brain Atlas e Genotype-Tissue Expression), construímos uma rede de interação proteína-proteína \"in silico\" com interações físicas confirmadas por pelo menos duas fontes. Análises topológicas e funcionais dos genes da rede mostraram genes relacionados a sinapse, adesão celular, vias glutamatérgicas e serotonérgicas, o que confirma achados de trabalhos independentes na literatura indicando ainda novos genes e variantes genéticas nessas vias.
Attention-Deficit/Hyperactivity Disorder (ADHD) is the most common neuro-developmental disorder in children, affecting 5.8% of children and adolescents in the world. Many studies have attempted to investigate the genetic susceptibility of ADHD without much success. The present study aimed to analyze rare and common variants contributing to the genetic architecture of ADHD. We generated exome data from 30 Brazilian trios where the children were diagnosed with sporadic ADHD. We analyzed both single-nucleotide variants (SNVs) and copy-number variants (CNVs) in these trios and across multiple datasets, including a Brazilian sample of 503 children/adolescent controls from the High Risk Cohort Study for the Development of Childhood Psychiatric Disorders, and also previously published results of four CNV studies of ADHD involving children/adolescent Caucasian samples. The results from the Brazilian trios showed 3 major patterns: cases with inherited variations and de novo SNVs or de novo CNVs and cases with only inherited variations. Although the sample size is small, we could see that various comorbidities are more frequent in cases with only inherited variants. After exploring the rare variant composition in our 30 cases we selected genes with variations (SNVs or located in CNV regions) in our trio analysis that are recurrent in the families analyzed or in public data sets. Moreover, using only genes expressed in brain (post-mortem samples from Brain Atlas and The Genotype-Tissue Expression project), we constructed an in silico protein-protein interaction (PPI) network, with physical interactions confirmed by at least two sources. Topological and functional analyses of genes in this network uncovered genes related to synapse, cell adhesion, glutamatergic and serotoninergic pathways, both confirming findings of previous studies and capturing new genes and genetic variants in these pathways.

Les interactions protéine – protéine (IPP) sont essentielles à la régulation des phénomènes cellulaires. Elles impliquent deux partenaires : une protéine adaptatrice et une protéine effectrice, cette dernière étant régulée positivement ou négativement. Bien que l’inhibition des IPPs constitue une approche thérapeutique solide, la stabilisation reste encore peu étudiée, mais pourrait mener à de nouvelles modalités prometteuses. Ce projet se concentre sur la famille de protéines adaptatrices 14-3-3 qui interagit avec plus de 200 partenaires. Parmi eux, la protéine p53 est l’objet de multiples recherches dû à sa fonction régulatrice clé de nombreux processus biologiques (réparation de l’ADN, apoptose). Ces fonctions majeures sont cependant altérées dans la moitié des cancers, favorisant ainsi le développement tumoral. Des études préliminaires ont montré que la stabilisation de l’interaction entre p53 et 14-3-3 à l’aide d’une colle moléculaire permettait de restaurer l’activité antitumorale de p53. Parmi ces colles moléculaires, la fusicoccine-A (FC-A) se localise dans la vallée formée par 14-3-3 et permet d’augmenter la stabilisation du complexe protéique. Dans ce contexte, ce projet se concentre sur l’accès à des analogues simplifiés de la FC-A à travers la synthèse de squelettes tricycliques afin d’élargir la librairie de colles moléculaires. Des analogues [6-8-5] à partir d’un substrat aromatique sont envisagés, ainsi que des analogues [5-8-5] à partir d’un dérivé cyclopentane, plus proches de la structure cible. Différentes stratégies de synthèse ont été explorées afin d’accéder à ces analogues
In biological media, protein-protein interactions (PPI) are of huge importance, as they allow the regulation of many cellular events. PPI classically involve two partners: an adapter protein and its effector protein(s) regulated either in a positive or a negative manner. Inhibition of PPI has thus been considered as a solid therapeutic approach. On the other hand, stabilization of PPI remains scarcely investigated, but may lead to new promising approaches. This project focuses on the 14-3-3 family adapter protein which interacts with more than 200 protein partners. Among them, p53 protein is subjected to a lot of studies as this tumor suppressor protein regulates multiple biological processes (DNA repair, apoptosis). However, those major functions appear to be silenced in most cancer cases, thus allowing tumor cells proliferation. Some studies have shown that stabilization of the 14-3-3/p53 pair with the help of a molecular glue permitted to restore tumor suppressor activity of p53. Among the examined molecular glues, the fusicoccin-A (FC-A) natural product is shown to lodge in the valley formed by 14-3-3 and increases stabilization of the 14-3-3/p53 interaction. In this context, to enlarge the p53/14-3-3 molecular glue library, this project focuses on the access to simplified FC-A analogs through the synthesis of tricyclic scaffold. [6-8-5] analogs from an aromatic substrate are envisaged, as well as [5-8-5] analogs from a cyclopentane derivative, closer to the target structure. Various strategies have been explored in order to access these analogs

Tackling protein interfaces with small molecules capable of modulating protein-protein interactions remains a challenge in structure-based ligand design. Particularly arduous are cases in which the epitopes involved in molecular recognition have a non-structured and discontinuous nature. Here, the basic strategy of translating continuous binding epitopes into mimetic scaffolds cannot be applied, and other innovative approaches are therefore required. We present a structure-based rational approach involving the use of a regular expression syntax inspired in the well established PROSITE to define minimal descriptors of geometric and functional constraints signifying relevant functionalities for recognition in protein interfaces of non-continuous and unstructured nature. These descriptors feed a search engine that explores the currently available three-dimensional chemical space of the Protein Data Bank (PDB) in order to identify in a straightforward manner regular architectures containing the desired functionalities, which could be used as templates to guide the rational design of small natural-like scaffolds mimicking the targeted recognition site. The application of this rescaffolding strategy to the discovery of natural scaffolds incorporating a selection of functionalities of interleukin-10 receptor-1 (IL-10R1), which are relevant for its interaction with interleukin-10 (IL-10) has resulted in the de novo design of a new class of potent IL-10 peptidomimetic ligands.

Tackling protein interfaces with small molecules capable of modulating protein-protein interactions remains a challenge in structure-based ligand design. Particularly arduous are cases in which the epitopes involved in molecular recognition have a non-structured and discontinuous nature. Here, the basic strategy of translating continuous binding epitopes into mimetic scaffolds cannot be applied, and other innovative approaches are therefore required. We present a structure-based rational approach involving the use of a regular expression syntax inspired in the well established PROSITE to define minimal descriptors of geometric and functional constraints signifying relevant functionalities for recognition in protein interfaces of non-continuous and unstructured nature. These descriptors feed a search engine that explores the currently available three-dimensional chemical space of the Protein Data Bank (PDB) in order to identify in a straightforward manner regular architectures containing the desired functionalities, which could be used as templates to guide the rational design of small natural-like scaffolds mimicking the targeted recognition site. The application of this rescaffolding strategy to the discovery of natural scaffolds incorporating a selection of functionalities of interleukin-10 receptor-1 (IL-10R1), which are relevant for its interaction with interleukin-10 (IL-10) has resulted in the de novo design of a new class of potent IL-10 peptidomimetic ligands.

Proteins in Escherichia coli were compared in terms of essentiality, centrality, and conservation. The hypotheses of this study are: for proteins in Escherichia coli, (1) there is a positive, measureable correlation between protein conservation and essentiality, (2) there is a positive relationship between conservation and degree centrality, and (3) essentiality and centrality also have a positive correlation. The third hypothesis was supported by a moderate correlation, the first with a weak correlation, and the second hypotheis was not supported. When proteins that did not map to orthologous groups and proteins that had no interactions were removed, the relationship between essentality and conservation increased to a strong relationship. This was due to the effect of proteins that did not map to orthologus groups and suggests that protein orthology represented by clusters of orthologus groups does not accurately dipict protein conservation among the species studied.

RNA:protein interactions are central in many cellular processes, including activation of innate immune responses against microbial infection. Their study is essential to better understand the diverse biological events that occur within cells. However, isolation of RNA:protein complexes is often laborious and requires specialized techniques. This thesis is concerned with attempts to develop an improved purification protocol to isolate specific RNA:protein complexes. Taking advantage of the specific interaction of the Pseudomonas aeruginosa PP7 protein with its cognate RNA binding site, termed the PP7 recognition sequence (PRS), the aim was to identify cellular proteins involved in activating cell-signalling pathways, including the interferon-induction cascade, following viral infection with stocks of parainfluenza virus 5 (PIV5) rich in copyback defective interfering (DI) particles. Copyback DI genomes are powerful inducers of IFN and, here, I show they also activate the induction of IL-6, IL-8 and TNFα; cytokines that also have antiviral properties. Following the successful cloning of the PRS into a copyback DI genome, we investigated conditions for optimal in vitro capture of DI-PRS:protein complexes by PP7 on Dynabeads. When tested, the protocol led to the successful capture of ILF3 and PKR, two dsRNA binding proteins induced by IFN. We further developed a tap-tagging system to minimize the presence of non-specifically bound proteins to Dynabeads that may interfere with future mass spectrometry analysis. To isolate DI-PRS RNA:protein complexes from infected cells, attempts were made to rescue replicating DI-PRS genomes in the context of wild type PIV5. Similarly, efforts were made to isolate influenza A virus RNPs that contained the PRS in the neuraminidase (NA) gene from infected cells using the PP7-based protocol developed. However, for reasons discussed, unfortunately RNA:proteins complexes were not successfully purified from infected cells in either case.

Human cytomegalovirus (HCMV) is a leading cause of congenital defects in humans. Currently available antivirals utilized for the therapy against HCMV infections have a series of contraindications due to their high cost, low bioavailability, high toxicity and the uprising of resistant viral strains. Furthermore no vaccine is available and no drugs are approved to prevent vertical transmission during pregnancy, therefore new, effective antiviral are highly needed. HCMV DNA polymerase accessory protein UL44 plays an essential role in viral replication, conferring processivity to the DNA polymerase catalytic subunit UL54 by tethering it to the DNA. Binding of UL44 to dsDNA occurs in the absence of ATP and clamp loaders, and depends on UL44 homodimerization. Indeed, our research group recently demonstrated that the protein can dimerize in cells and point mutations disrupting protein self-interaction also prevent DNA binding and abolish viral oriLyt-dependent DNA replication in transient transcomplementation assays. Therefore, disruption of UL44 homodimerization represents an attractive target for the development of new anti-virals. Based on these observations, using the recently published crystal structure of UL44 homodimers our research group previously performed a virtual screening with the Glide software in combination with a library of 1.3 x 10^6 small molecules (SMs) to identify SMs potentially interfering with UL44 homodimerization. After three rounds of screening (HTVS: high-throughput virtual screening, SP: standard precision, XP: extra precision), followed by an in depth analysis of compounds chemical properties, 18 SMs were selected for further analysis. Selected compounds were obtained from a commercial supplier, to be tested in a variety of assays for their ability to inhibit UL44 homodimerization both in cells and in vitro, as well as on HCMV replication. To this end, we applied a number of in cells and in vitro assays to monitor the effect of the SMs on UL44 dimerization. In cells methods included Fluorescent Resonant Energy Transfer (FRET) and Bioluminescence Resonant Energy Transfer (BRET), while as GST pull-down assays was chosen as the in vitro method. FRET acceptor photobleaching was capable of detecting both UL44 homodimerization and UL44 binding to the catalytic subunit C-terminal domain (residues 1125-1242). Such interactions were sensitive to point mutations specifically impairing the two processes, highlighting the specificity of this technique. Therefore, we were able to confirm that UL44 forms dimers in cells. However, data acquisition and analysis proved quite time consuming and dependent on high fusion proteins expression levels. BRET assays allowed to quickly and precisely quantitatively monitor UL44 self-interaction and binding to UL54 in living cells, and through saturation experiments allowed to precisely calculate Bmax and B50 values, relative to homodimerization or binding to UL54 for a number of single amino acids substitution derivatives of UL44 impaired for dimerization, binding to UL54 or to dsDNA, as well as for nuclear targeting. These data allowed gaining insights relative to the formation of HMCV DNA polymerase holoenzyme, suggesting conformational changes within UL44 upon DNA binding in complex to UL54. Furthermore, calculation of Bmax and B50 values was used to establish three different cellular systems expressing ideal amount of UL44 for screening purposes, in that they generated a BRET ratio similar to half of the Bmax. These included a fully stable expression system, whereby both RLuc-UL44 and YFP-UL44 are stably expressed in HEKA derived cells, a stable/transient system whereby YFP-UL44 is stably expressed and RLuc-UL44 is transiently expressed, or a fully transient system whereby both fusion proteins are transiently expressed. Competition assays performed overexpressing increasing amounts of FLAG-tagged UL44 as a competitor revealed that no inhibition could be obtained for the fully stably expressing system. This result highlighted the difficulty in disrupting a pre-existing protein complex and suggested to focus our attention on transient systems. Keeping this in mind, a first small-scale screening was performed to study the impact of 18 SMs on UL44 dimerization by BRET using the stable/transient system. The 18 selected SMs were resuspended in DMSO and their toxicity was evaluated in cell culture, before being added at sub-toxic concentration to the YFP-UL44 cell line, six hours post-transfection with RLuc-UL44. Our analysis identified only compounds slightly inhibiting the BRET ratio relative to UL44 homodimerization. Based on these disappointing results, we revaluated the BRET assays setup, by decreasing the time of SM incubation before assaying their effect from 42 to 18h, by switching to a completely transient system, and by decreasing the amount of expressed proteins. The last modification required a change in the substrate used for generation of bioluminescent signal from RLuc-fusion proteins from CTZ to hCTZ. A new screening was performed, which resulted in very similar results to those obtained using the original setup. Furthermore when hit candidates were re-evaluated for their effect using a negative control, their effect on BRET ratio of UL44 proved unspecific. Additionally, BRET - similarly to FRET - failed to detect a specific effect on the UL54/UL44 interaction by a SM known to disrupt such interaction. Therefore we conclude that, with our current settings, BRET and FRET are not the ideal techniques to search for SM inhibitors of protein-protein interactions We then focused on in vitro methods, starting with a GST pull-down assay, which was performed using UL44 C-terminal domain (residues 1-290), either fused to GST of a 6His-tag. Our results indicated that GST pull-down was capable of detecting differences in binding between wild-type UL44 and a dimerization-impaired mutant, suggesting a possible application for the screening of SMs. GST pull-down is currently being implemented for this purpose, and preliminary data suggest that a number of tested SMs could impair UL44 dimerization. In summary, we have developed a number of assays to monitor UL44 dimerization. Whereas in cells RET based assays confirmed that UL44 form dimers in living cells, they proved suboptimal for screening proposes. On the other hand, in vitro methods such as GST pull-down might prove more sensitive and are currently being implemented for the identification of SMs inhibitors of UL44 dimerization
Cytomegalovirus (CMV) è un importante patogeno di interesse umano. Al momento gli antivirali disponibili ed utilizzati per la terapia contro l’infezione da CMV presentano una serie di controindicazioni dovute all’alto costo, bassa biodisponibilità, alta tossicità ed il presentarsi di ceppi virali resistenti. Inoltre non è disponibile un vaccine ed ancora non è ancora stato approvato l’uso di alcun farmaco per prevenire la trasmissione verticale durante la gravidanza. Per questi motivi, sono necessari nuovi ed efficaci farmaci antivirali. La proteina accessoria UL44 della DNA polimerasi di CMV, svolge un ruolo essenziale nella replicazione virale, conferendo processività alla subunità catalitica UL54 ancorando il complesso oloenzimatico al DNA. Il legame di UL44 al dsDNA avviene in assenza di ATP e dei clamp loaders, e dipende dalla omodimerizzazione di UL44. Infatti, il nostro gruppo di ricerca ha recentemente dimostrato che la proteina può dimerizzare in cellule e che mutazioni puntiformi in grado di inficiare tale dimerizzazione prevengono il legame con il DNA ed aboliscono la replicazione del DNA virale oriLyt-dipendente in saggi di transcomplementazione transiente. Perciò, la distruzione dell’omodimerizzazione UL44 rappresenta un potenziale allettante bersaglio per lo sviluppo di nuovi anti-virali. Partendo da queste osservazioni ed usando la struttura cristallografica recentemente pubblicata degli omodimeri UL44, il nostro gruppo di ricerca ha eseguito un virtual screening con il software Glide in combinazione con una libreria di 1.3 x 10^6 piccole molecole (SMs) per identificare SMs che potenzialmente potessero interferire con l’omodimerizzazione di UL44. Dopo tre rounds di screening (HTVS: high-throughput virtual screening, SP: standard precision, XP: extra precision), seguiti da un’analisi delle proprietà chimiche dei composti, sono state selezione 18 SM per ulteriori analisi. I composti selezionati sono stati acquistati presso un fornitore commerciale, per essere testati in diversi saggi per valutare le loro abilità di inibire l’omodimerizzazione di UL44, sia in cellule che in vitro. A questo scopo, abbiamo utilizzato diversi saggi in cellule e in vitro per monitorare l’effetto delle SMs sulla dimerizzazione di UL44. Nei saggi cellulari, le tecniche utilizzate includono Fluorescent Resonant Energy Transfer (FRET) e Bioluminescence Resonant Energy Transfer (BRET), mentre per saggi in vitro è stato utilizzato il saggio GST-pull down. I nostri dati indicano che la metodica FRET acceptor photobleaching è in grado di rilevare sia l’omodimerizzazione di UL44, sia il legame con il dominio C-terminale della subunità catalitica (residui 1125-1242). Queste interazioni sono sensibili all’introduzione di mutazioni puntiformi che alterano i due processi, evidenziando la specificità di questa tecnica. Siamo stati quindi in grado di confermare che UL44 forma dimeri in un contesto cellulare. Purtroppo, l’acquisizione dei dati e la loro analisi richiedono un lungo tempo e dipendono da alti livelli di espressione delle proteine di fusione. Per contro, il saggio BRET permette un rapido e preciso monitoraggio quantitativo dell’omodimerizzazione di UL44 e il legame con UL54 in cellule viventi. Inoltre, attraverso esperimenti di saturazione, che permettono di calcolare in modo preciso i valori di Bmax e B50 relative all’omodimerizzazione o al legame con UL54 per varianti di UL44 che contengono singole sostituzioni amminoacidiche che affliggono la dimerizzazione di UL44, il suo legame a UL54 o il DNA, nonché il trasporto al nucleo della proteina. I dati ottenuti possono aiutare a comprendere il processo di formazione dell’oloenzima della DNA polimerasi di CMV, suggerendo cambiamenti conformazionali nel complesso olenzimatico in seguito a legame con il DNA. Inoltre, il calcolo di Bmax e B50 è stato usato per sviluppare tre differenti sistemi cellulari esprimenti un’ideale quantità di UL44 da utilizzare come piattaforma per lo screening di SM, poiché sono in grado di generare valori di BRET ratio simili al 50% della Bmax .Questi includono un sistema di espressione completamente stabile, in cui sia RLuc-UL44 che YFP-UL44 sono stabilmente espresse in cellule derivate da HEK293 A, un sistema ibrido stabile/transiente, in cui YFP-UL44 è stabilmente espressa e RLuc-UL44 è espressa in transiente, o un sistema completamente transiente in cui entrambe le proteine sono espresse transientemente. Saggi di competizione eseguiti sovra-esprimendo quantità crescenti di UL44 fusa a un FLAG tag hanno evidenziato che nessun inibizione può essere ottenuta per il sistema completamente stabile, probabilmente per la difficoltà di distruggere un complesso proteico preformato piuttosto che prevenirne la formazione. Per questo motive ci siamo focalizzati su sistemi transienti di espressione piuttosto che sul sistema interamente stabile. Sulla base di questi dati, un primo screening su piccolo scala è stato eseguito per studiare l’effetto di 18 SMs sulla dimerizzazione di UL44 usando il sistema BRET stabile/transiente. Le 18 piccole molecole sono state risospese in DMSO e la loro tossicità è stata valutata in coltura cellulare, prima di essere aggiunte a concentrazioni subtossiche alla linea YFP-UL44, sei ore dopo la trasfezione per esprimere RLuc-UL44. La nostra analisi ha identificato solo composti che inibivano blandamente il BRET ratio relativo alla dimerizzazione di UL44. Per questo motivo abbiamo ri-valutato il set up del saggio BRET, diminuendo il tempo d’incubazione delle SM prima di testare i valori BRET da 42 a 18 ore, utilizzando un saggio completamente transiente e diminuendo la quantità di proteine espresse. Per quest’ultima è stato necessario cambiare il substrato utilizzato per generare il segnale bioluminescente da CTZ a hCTZ. È stato eseguito un nuovo screening, con risultati molto simili a quelli ottenuti utilizzando il setup originale. Inoltre, quando i candidati migliori sono stati rivalutati usando un controllo negativo, il loro effetto sul BRET ratio è risultato aspecifico. Ulteriormente, la BRET, come la FRET, non è riuscita a rilevare uno specifico effetto nell’interazione UL44/UL54 di una SM in grado di distruggere questa interazione. Possiamo quindi concludere che BRET e FRET non sono tecniche ideali per la ricerca di SM inibitrici dell’interazione tra le proteine. Ci siamo poi focalizzati su metodi in vitro, partendo dal saggio GST-pull down, il quale è stato effettato utilizzando il dominio C-terminale (residui 1-290) di UL44, fuso o con GST o con 6His-tag. I risultati ottenuti mostrano che la tecnica GST-pull down è in grado di rilevare differenze nel legame tra UL44 wild-type e i mutanti con mutazioni nel sito di dimerizzazione, suggerendo una possibile applicazione di GST-pull down per lo screening delle SMs. Questa tecnica è stata implementata per questo studio, e i dati preliminari suggeriscono che il numero di SMs testate potrebbe portare all’inibizione della dimerizzazione di UL44. In conclusione, abbiamo sviluppato diversi saggi per monitorare la dimerizzazione di UL44. I saggi cellulari basati su RET confermano che UL44 forma dimeri in cellule viventi, e dimostrano di essere subottimali per lo screening. D’altro canto, i metodi in vitro come GST-pull down dimostrerebbero un maggiore sensibilità e sono stati implementati per l’identificazione degli inibitori della dimerizzazione di UL44.

The gene PAX6 is located on chromosome 11 (11p13) and encodes a transcription factor (PAX6) that is expressed early in development. The PAX6 protein is expressed in the developing eye, regions of the brain, central nervous system (CNS), nasal epithelium and pancreas. PAX6 is best known for its role eye development with heterozygous mutations causing congenital ocular malformations. However, it must be remembered that PAX6 has multiple functions in the brain including specification of neuronal subtypes and axon guidance. There is growing understanding of the role of PAX6 as a transcription factor during development, and many of its DNA targets have recently been defined. However, almost nothing is known about the proteins with which PAX6 interacts. In the initial stage of my research I identified a conserved region consisting of the final 32 amino acids of the PST (proline, serine and threonine rich) domain of PAX6. Based on sequence homology and secondary structure predictions I classed this region as a novel domain, the ‘C terminal domain’. Next I used the yeast 2-hybrid system to investigate possible PAX6 protein interactions. By screening a mouse brain cDNA library with the C terminal domain and whole PST domain, I identified three novel and interesting interactors, HOMER3, DNCL1 and TRIM11. I re-confirmed these interactions in a pairwise manner using the yeast 2-hybrid system, and I showed that the C terminal domain was vital for the interactions between PAX6 and HOMER3 or DNCL1. Furthermore, certain C terminal mutations that are known to cause ocular malformations in patients are also sufficient to reduce or abolish these interactions. I attempted to further characterise the interactions by co-immunoprecipitation. However, this was not possible due to technical difficulties.

Protein-protein interactions build large networks which are essential in understanding complex diseases. Due to limitations of experimental methodology there are problems with large amounts of false negative and positive interactions; and a large gap in the amount of known interactions and structurally determined interactions. By using computational methods these problems can be alleviated. In this thesis the quality of a newly developed pipeline (InterPred) were investigated for its ability to generate coarse interaction models and score them. This ability was investigated by performing docking experiments in Rosetta on models generated in InterPred. The results suggest that InterPred is highly successful in generating good starting points for docking proteins in silico and to distinguish the quality of models.

Quenched Molecular Dynamics (QMD) used to explore molecular conformations was developed to operate in Insight II platform for two simulation engines: CHARMm and Discover. Two scripts and procedures were written for molecular minimization, dynamics, minimization of each of several hundred conformers, and cut off. Experience with Insight II/Discover versus Quanta/CHARMm, and between Insight II/CHARMm versus Quanta/CHARMm has taught that the forcefield is the key factor in QMD studies. Protein A has been used for the purification of commercial antibodies, but it is expensive. Seven peptidomimetics of protein A were designed based on the hot-spots located at the helix-loop-helix region of protein A, and synthesized via solid phase using the Fmoc approach. These peptidomimetics were characterized by MS and NMR. The conformations of four peptidomimetics were studied by NMR and CD in water/hexafluoroisopropanol (pH 4). The CD and NMR data show that addition of hexafluoroisopropanol stabilizes their a-helical conformations. The structures of these peptidomimetics in solution were generated with Quanta/CHARMm using NMR data as limits for the QMD technique. Protein G has also been used to purify antibodies, but it is expensive too. A number of protein G mimics were designed as trivalent molecules. An efficient preparation of trivalent molecules having a useful primary amine arm has been developed through solid phase synthesis. The cheap, commercially available poly(propylene imine) dendrimers were used as scaffolds which allow multimerization of functionalized compounds. A small library of trivalent compounds were synthesized using this approach. A portion of compounds in this library were tested by Amersham Biosciences. The seven amino acid modified DAB-Am-4 exhibits strong binding to the IgG/Fab, and is a potential ligand for IgG purification. The interactions between neurotrophins (ie NGF and NT-3) and their receptors are typical drug targets. Fourteen second-generation peptidomimetics showing NGF-like or NT3-like activities in a preliminary bioassay, were resynthesized and tested again. Preliminary and retested data were compared. To access a direct binding assay, five fluorescently labeled peptidomimetics 41a-e were synthesized for a fluorescence activated cell sorting (FACScan) assay. Six monomeric precursors 42 and 43 were prepared on large scales for the library of bivalent turn analogs

Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2008.
Title from electronic title page (viewed Dec. 11, 2008). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biochemistry and Biophysics Program in Molecular and Cellular Biophysics." Discipline: Biochemistry and Biophysics; Department/School: Medicine.

Proteins often depend on a-helices for binding to other biomacromolecules. Reversible control of a-helix stability was accomplished in previous studies by incorporating a photoisomerisable azobenzene cross-linker into peptides, subsequently enabling the optical control of DNA-protein interactions. This approach was extended in this study to include protein-protein and protein-RNA interactions. One of the primary regulatory components in apoptosis signalling is the antiapoptotic protein Bcl-xL which interacts with the a-helical BH3 domain of the Bak protein. The Rev/RRE interaction is crucially involved in the life cycle of Human Immunodeficiency Virus. These interactions were targeted by designing peptides based on the BH3 domain of Bak and on the RNA-binding domain of Rev these peptides are activated by external light pulses after the incorporation of the cross-linker. The ability to control cross-linker conformation and hence peptide secondary structure was demonstrated by CD and UV/Vis spectroscopy. The binding to the target structure and complex disruption was determined in the dark-adapted and irradiated states using fluorescence based assays. Structural studies using NMR spectroscopy demonstrated that the alkylated peptides bind to the same part of the target molecule as the wild-type peptide, regardless of their structure. Moreover, one of the BH3 domain-based peptides and the light-controllable transcription factor PhotoMyoD were modified with protein transduction domains to enable future in vivo studies. Overall, this work opens the possibility to interfere reversibly and specifically with protein-protein and protein-RNA interactions and to study and modulate cellular function by optical control.

Protein-DNA interactions are indispensable players in the daily activities of cells. DNA-binding proteins regulate gene expression and are responsible of DNA replication, packaging, repair and recombination. Among them, transcription factors activate/repress gene transcription by binding to specific genomic sites. Hence, the characterization of transcription factor binding sites turns out to be crucial in order to understand gene regulation. In this context, the development of computational tools is foremost. Here, I show the prediction of redundant transcription factors in yeast using a combination of homology-based tools and protein-protein interactions. The approach was automated and incorporated into ModLink+, an online and user-friendly tool to infer the fold of remote homologs. Moreover, I describe split-statistical potentials for protein-DNA interactions. Finally, I present SHAITAN, a statistical/homology-based approach that can be used to both predict transcription factor binding sites and infer the more likely transcription factors to bind a DNA sequence of interest.
Les interaccions proteïna-ADN són indispensables en l’activitat diària de les cèl•lules. Les proteïnes que participen en aquestes interaccions s’encarreguen de la regulació de l'expressió gènica i són responsables de la replicació, l'empaquetament, la reparació i la recombinació de l’ADN. Entre aquestes proteïnes, els factors de transcripció activen/reprimeixen la transcripció de gens mitjançant la unió a llocs específics dins el genoma. Per tant, la caracterització dels llocs d'unió dels diferents factors de transcripció és crucial per tal d’entendre com funciona la regulació gènica. En aquest context, desenvolupar eines computacionals és importantíssim. En aquesta tesi predict redundància entre factors de transcripció de llevat eines fent servir eines basades en homologia i interaccions proteïna-proteïna. Aquesta aproximació va ser automatitzada i incorporada a ModLink+, una eina accessible des d’internet i fàcil d'usar per a inferir el plegament de proteïnes a partir d’homòlegs remots. D'altra banda, descric potencials estadístics fraccionats per a interaccions proteïna-ADN. Finalment presento SHAITAN, una aproximació basada en homologia i potencials estadistics que pot ser utilitzada per a predir els llocs d'unió de factors de transcripció així com per saber quins factors de transcripció són més probables que s’uneixin a una determinada seqüència d'ADN.

A major area of interest is the identification of proteins that play a role in hormone dependent cancers and in collaboration with the MRC Centre for Reproductive Health we studied the gonadotropin releasing hormone receptor (GnRH-R). Other targets described in the thesis are the SH3 domain of PSD-95 and the protein BLyS. In order to identify potential inhibitory small molecules we have used a variety of computational data base mining approaches as well as using and developing experimental binding assays. It has become increasingly challenging to evaluate the most representative drug like small molecule compounds when using traditional high throughput screening methods. This thesis assesses the use of in silico tools to probe key protein-protein and protein-peptide interactions. These tools provide a means to identify enriched compound datasets which can be purchased and tested in vitro in a time and cost efficient way. The transmembrane protein GnRH-R provides an interesting opportunity to identify small molecules that could inhibit the binding of its peptide ligand GnRH. This is a challenging project as there are few examples in the literature of drug-like molecules that bind to such protein-peptide interfaces. The first step involved receptor modelling using solved crystal structures of homologous proteins. The model was then validated by developing structure activity relationships for established high affinity ligands. We also performed crystallographic and biophysical studies on the native GnRH decapeptide. Two other protein-protein systems were also examined using the same virtual screening and experimental ligand binding methodology. SH3 domains play an important role in cell signalling and we used the PSD-95 protein as our target for study as a crystal structure has been published. As well as identifying potential ligands we characterised structural properties of PSD-95 fusion proteins and also developed the basis for compound assay. The third system studied was B Lymphocyte Stimulator (BLyS) which is a target for treatment of a number of autoimmune diseases. This presented an interesting target for study as the protein binds to multiple receptors depending on its multimeric state. BLyS protein was characterised using electron microscopy and other biophysical techniques.

Human embryonic kidney (HEK) 293 cells, stably expressing the rat GnRH receptor were used to investigate the mechanism of ERK activation by GnRH.  ERK activation was found to be dependent on cell adhesion to the extracellular matrix, and required an intact actin cytoskeleton. Through the use of specific pharmacological inhibitors and expression of dominant negative cDNA constructs, ERK activation was found to be mediated by the Rho family GTPase Rac1, and the non-receptor tyrosine kinases Src and focal adhesion kinase (FAK). FAK was found to function as a tyrosine phosphorylated scaffold upon which components of the ERK cascade assembled. Having established a role for Src in the activation of ERK, a proteomics study was undertaken to identify novel Src binding proteins that may be involved in the regulation of GnRH receptor signalling. Through a combination of immune-precipitation, two-dimensional gel electrophoresis, and matrix assisted laser desorption ionisation – time of flight mass spectrometry, Src was found to associate with the lipid kinase diacylglycerol kinase zeta (DGKζ). This interaction was found to be required for GnRH to stimulate DGKζ enzyme activity. By phosphorylating the second messenger molecule diacylglycerol to produce phosphatidic acid, DGKζ may play an important role in regulating GnRH receptor signalling. In this thesis, a potential mechanism of ERK activation is described for the GnRH receptor, with Src playing a key role in this pathway. In addition, Src was found to be involved in the activation of DGKζ, and is therefore implicated in the regulation of diacylglycerol signalling. This is the first report of an interaction between Src and DGKζ.

Protein aggregation is a frequently cited problem during the development of liquid protein formulations, which is especially problematic since each protein exhibits different aggregation behaviour. Aggregation can be controlled by judicious choice of solution conditions, such as salt and buffer type and concentration, pH, and small molecule additives. However, finding conditions is still a trial and error process. In order to improve formulation development, a fundamental understanding of how excipients impact upon protein aggregation would significantly contribute to the development of stable protein therapeutics. The underlying mechanisms that control effects of excipients on protein behaviour are poorly understood. This dissertation is directed at understanding how excipients alter the conformational and colloidal stability of proteins and the link to aggregation. This knowledge can be used for finding novel ways of either predicting or preventing/inhibiting protein aggregation. Experiments using static and dynamic light scattering, intrinsic fluorescence, turbidity and electrophoretic light scattering were conducted to study the effect of solution conditions such as pH, salt type and concentration on protein aggregation behaviour for three model systems: lysozyme, insulin and a monoclonal antibody. Emphasis is placed on understanding the effects of solution additives on protein-protein interactions and the link to aggregation. This understanding has allowed the rational development of stable formulations with novel additives, such as arginine containing dipeptides and polycations.

Over the past decade, knowledge of the human genome has grown exponentially. While identifying individual genes and their protein products is crucial, understanding how these entities exist within the context of other molecules within the cell provides valuable insight into their functional significance. In particular, mapping the intricate web of interactions between proteins (or the ‘interactome’), allows for an understanding the roles of individual proteins within specific cellular processes and the potentially negative implications when these processes cannot occur. At the present time, approximately 40,000 binary, protein-protein interactions have been identified in human through low- and high-throughput, lab-based experiments; however, this number represents only a fraction of the estimated 600,000 protein-protein interactions thought to occur. With the high number of potential protein-protein pairing, experimentally testing each possible interaction is a time-consuming and near-impossible task. As a result, several computational methods have been developed to predict probable interactions for experimental verification. Previously, our group developed PIPs, a predictor of protein-protein interactions in human based on a naive Bayesian framework that has undergone two version releases (Scott et al., 2007, McDowall, 2011). In this thesis, a third version of PIPs, PIPs v. 3.0, is described. In addition to an update of the included data, PIPs v. 3.0 contains a new network analysis component, the TransMCL (Z) module, that combines the previously separate Transitive module (and associated EOCT predictor) introduced in version 1.0 and Cluster module (and associated EOCM predictor) introduced in version 2.0. This new module has allowed the two previously separate PIPs predictors to be merged into one method (the EOCZ predictor). In total, the new EOCZ predictor identifies over 500K significant interactions, made up of those predicted by the EOCT and EOCM predictors individually as well as a new set of interactions.Additionally, this thesis describes the development of PIP’NN, a new protein-protein interaction predictor built on a neural network framework with the data incorporated into PIPs. Overall, PIP’NN performs slightly better than the three PIPs predictors on multiple blind tests of varying sizes. PIP’NN identifies both interactions predicted by the three PIPs methods as well as a set of new interactions. As a result, PIP’NN is able to stand on its own as a new predictor of human protein-protein interactions or in conjunction with PIPs as a method to further narrow down the set of predicted interactions. Finally, this thesis describes the practical implementation of PIPs and PIP’NN through collaborations with two groups within the University of Dundee that have identified sets of potential interactions of interest for experimental confirmation. While these interactions have yet to be confirmed, both studies offer a proof of concept of how the predictors can be incorporated into lab-based interaction identification protocols. Additionally, the new PIPs web server will allow outside groups access to the updated PIPs prediction database.Overall, the work described in this thesis has built upon previous work both within and outside of the University of Dundee to further the identification of novel protein-protein interactions in human and increase the understanding of the human interactome.

Les phénotypes de tous les organismes vivants connus sont déterminés par les interactions compliquées entre les protéines produites dans ces organismes. La compréhension des réponses des organismes aux stimuli externes ou internes est basée sur la compréhension des interactions des protéines individuelles et des structures de ses complexes. La prédiction d'un complexe de deux ou plus protéines est le problème du domaine du docking protéine-protéine. Les algorithmes du docking ont habituellement deux étapes majeurs: recherche 6D exhaustive suivi par le scoring. Dans ce travail, nous avons contribués aux deus étapes sus indiquées. Nous avons développés le nouvel algorithme pour la recherche 6D exhaustive, HermiteFit. Cela est basé sur la décomposition des fonctions 3D en base Hermite. Nous avons implémenté cet algorithme dans le programme pour le fitting (l'ajustement des donnés) des cartes de densité électronique de résolution faible. Nous avons montrés qu'il surpasse les algorithmes existants en terme de temps par point tandis qu'il maintient la même précision du modèle sortant. Nous avons aussi développés la nouvelle approche de calculation de la fonction du scoring, qui est basé sur les arguments logique simples et qui évite la calculation ambiguë de l'état de référence. Nous avons comparés cela aux fonctions de scoring existantes avec l'aide du docking protéines-protéines benchmarks bien connues. Enfin, nous avons développés une approche permettant l'inclusion des interactions eau-protéine à la fonction du scoring et nous avons validés notre méthode pendant le CAPRI (Critical Assessment of Protein Interactions) tour 47
The phenotype of every known living organism is determined mainly by the complicated interactions between the proteins produced in this organism. Understanding the orchestration of the organismal responses to the external or internal stimuli is based on the understanding of the interactions of individual proteins and their complexes structures. The prediction of a complex of two or more proteins is the problem of the protein-protein docking field. Docking algorithms usually have two major steps: exhaustive 6D rigid-body search followed by the scoring. In this work we made contribution to both of these steps. We developed a novel algorithm for 6D exhaustive search, HermiteFit. It is based on Hermite decomposition of 3D functions into the Hermite basis. We implemented this algorithm in the program for fitting low-resolution electron density maps. We showed that it outperforms existing algorithms in terms of time-per-point while maintaining the same output model accuracy. We also developed a novel approach to computation of a scoring function, which is based on simple logical arguments and avoids an ambiguous computation of the reference state. We compared it to the existing scoring functions on the widely used protein-protein docking benchmarks. Finally, we developed an approach to include water-protein interactions into the scoring functions and validated our method during the Critical Assessment of Protein Interactions round 47

Protein-protein interactions (PPIs) are essential features of cellular processes including DNA replication, transcription, translation, recombination, and repair. In my study, the protein interactions of bacterial DNA topoisomerase I, an essential enzyme, were investigated. The topoisomerase I in bacteria relaxes excess negative supercoiling on DNA and maintains genomic stability. Investigating the PPI network of DNA topoisomerase I can further our understanding of the various functional roles of this enzyme. My study is focused on topoisomerase I of Escherichia coli and Mycobacterium smegmatis. Firstly, we have explored the biochemical mechanisms for an interaction between RNA Polymerase, and topoisomerase I in E. coli. Molecular docking and molecular dynamic simulations have predicted that the interactions are mediated through electrostatic, and hydrogen bonding. The predicted Lysine residues (K627, K664) of topoisomerase I that are involved in the electrostatic interactions were mutated to Alanine, and its effect on the binding efficiency with RNA polymerase was reported. In a separate study, PPI partners of topoisomerase I in mycobacteria were identified. Knowledge gained from the study can provide valuable insights into the physiological functions of a validated drug target, DNA topoisomerase I, in pathogenic mycobacteria. Co-immunoprecipitation and pull-down assays were coupled to mass spectrometry for identification of the protein partners of mycobacterial topoisomerase I. The study has identified RNA polymerase, and putative helicases (DEAD/DEAH BOX helicases) as potential protein partners of mycobacterial topoisomerase I. My results indicated that the tail region of the CTD-topoisomerase I was required for direct physical interaction with the RNAP beta’ subunit. My studies have also verified the physiological relevance of the topoisomerase I - RNA polymerase interactions for survival under antibiotic, and oxidative stress. Lastly, I report a direct physical interaction between E. coli topoisomerase I and RecA by pull-down assays. Previous studies have shown that RecA, a DNA repair protein, can stimulate the relaxation activity of E. coli topoisomerase I. Our new results showed that the stimulatory effect can be attributed to the physical interaction of topoisomerase I with RecA.

Protein-protein interactions (PPIs) are key drug targets and recent breakthroughs in this area are providing insight into the types of molecules needed to selectively and potently inhibit a target traditionally seen as untractable. The rules that have been used to design classic substratecompetitive drugs (for example Lipinski's rule of five) may not apply in this new field in the same way. Here I present work performed in three systems that are well-validated drug targets for oncogenesis: the CDK2/cyclin A complex, the PLK1 Polobox domain and MDM2. In each case the site of the protein-protein interaction is defined and understood and the rationale for pharmaceutical intervention is clear. I use these as a model system to evaluate the characteristics of drugs that target protein-protein interaction sites and present work on the development of inhibitors as potential leads for subsequent drug development. In Chapter 1 I introduce the problems, challenges and rewards of PPI drug development; in Chapter 2 I present co-crystal structures of MDM2 with isoindolinone inhibitors; in Chapter 3 I detail attempts to co-crystallise the Plk1 Polobox with inhibitors and screen potential inhibitors; in Chapter 4 I present the results of screening to identify inhibitors of Cyclin A recruitment; and in Chapter 5 I discuss other strategies for inhibition of the CDK2/cyclin A complex, including results with a covalent inhibitor. Through these projects I have been able to demonstrate the wide applicability of the PPI inhibition approach, identify key features of drugs able to inhibit PPIs and contribute to drug design in each system.

Knowledge of protein sequences has exploded, but knowledge of protein function is needed to make use of sequence information, and this lags behind. A protein's function must be understood in context and part of this is the network of interactions between proteins. What are the relationships between protein function and the structure of the interaction network? In the first part of my thesis, I investigate the functional relevance of clusters, or communities, of proteins in the yeast protein interaction network. Communities are candidates for biological modules. The work I present is the first to systematically investigate this structure at multiple scales in such networks. I develop novel tests to assess whether communities are functionally homogeneous, and demonstrate that almost every protein is found in a functionally homogeneous community at some scale. The evolution of protein sequences IS well-studied, but comparatively little is known about the evolution of protein function. Such knowledge is needed to un- derstand when it is appropriate to annotate newly sequenced proteins by transferring functional information from homologs-i.e. evolutionarily related proteins. In the sec- ond part of my thesis, I assess the success of transferring protein-protein interactions across species and use this to estimate the rate at which interactions are lost in evolu- tion. At levels of sequence similarity associated with functional annotation transfer, I demonstrate that protein-protein interaction transfer is unreliable. The relevance of community structure for understanding protein function and the low conservation of individual interactions, suggests a possible role for communities in the evolution of cellular function. I discuss this possibility in my conclusions.

Thesis (Ph.D.)--Boston University PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.
Protein-protein interactions are integral to myriad molecular biological processes as they transfer information between molecules to effect a variety of goals. These include complex formation to activate gene transcription, serial interactions in signal transduction cascades, and one-time receptor-ligand or enzyme-substrate binding. Better understanding these interactions can therefore inform our view of larger biological frameworks and may be accomplished via direct visualization studies using structural and microscopy-based platforms. Using x-ray crystallography, the complex formed by the catalytic light chain of the Clostridium botulinum Serotype A neurotoxin (BoNT/A-LC) and its physiological substrate, synaptosomal-associated protein 25 (SNAP-25), has been examined to aid future inhibitor development. While small molecule and peptidic active site directed inhibitors have been published for this zinc-dependent protease, additional binding sites outside this region may exist given the extensive binding interface between these proteins. To identify these putative sites we conducted a computational analysis of the hydration structure of BoNT/A-LC across crystal structures to identify water molecules that are highly conserved as well as those that are more easily displaced, particularly when the BoNT/A-LC:SNAP-25 complex is formed. Results of these analyses are presented, including implications for de novo inhibitor design and extending previously established chemical scaffolds. In contrast, lower-resolution time-resolved luminescence microscopy (TRLM) was employed to develop a novel probe for imaging the receptor-ligand complex formed by interleukin-1 beta (IL1β) or epidermal growth factor (EGF) and their respective receptors. While a plethora of molecular tags exist for cellular localization studies, they often rely on chemically ligating an exogenous fluorophore to a protein target or endogenously expressing large protein-based tags (e.g. green fluorescent protein) in tandem with the protein to be tracked. We aimed to develop a compact genetically encoded tag that may be detected via in vitro and in cellula visualization studies using TRLM to measure long- lived luminescence while bypassing the epifluorescence that can be observed when irradiating biological specimens. Provided a sufficient concentration of LBT-tagged ligand is localized along a surface, the luminescent signal can be detected exclusive of epifluorescence. Future efforts to improve the physicochemical properties of the LBT and the imaging platform characteristics are discussed.

2011 - 2012
Protein-protein interactions are at the basis of many of the most important molecular processes in the cell, which explains the constantly growing interest within the scientific community for the structural characterization of protein complexes.1 However, experimental knowledge of the 3D structure of the great majority of such complexes is missing, and this spurred their accurate prediction through molecular docking simulations, one of the major challenges in the field of structural computational biology and bioinformatics.2,3 My PhD work aims to contribute to the field, by providing novel computational instruments and giving useful insight on specific case studies in the field. In particular, in the first part of my PhD thesis, I present novel methods I developed: i) for analysing and comparing the 3D structure of protein complexes, to immediately extract useful information on the interaction based on a contact map visualization (COCOMAPS4 web tool, Chapter 2), and ii) for analysing a set of multiple docking solutions, to single out the key inter-residue contacts and to distinguish native-like solutions from the incorrect ones (CONS-COCOMAPS5 web tool and CONS-RANK program, Chapter 3 and 4, respectively). In the second part of the thesis, these methods have been applied, in combination with classical state-of-art computational biology techniques, to predict and analyse the binding mode in real biological systems, related to particular diseases. This part of the work has been afforded in collaboration with experimental groups, to take advantage of specific biological information on the systems under study. In particular, the interaction between proteins involved in the autoimmune response in celiac disease6,7 (Chapters 5 and 6) has been studied in collaboration with the group directed by Prof. Sblattero, University of Piemonte Orientale (Italy) and the group directed by Prof. Esposito, University of Salerno (Italy). In addition, recognition properties of 3 the FXa enzymatic system8 has been studied through dynamic characterization of a FXa pathogenic mutant that causes problems in the blood coagulation cascade (Chapter 7). This study has been performed in collaboration with the group directed by Prof. De Cristofaro, Catholic University School of Medicine, Rome (Italy) and the group directed by Prof. Peyvandi, Ospedale Maggiore Policlinico and Università degli Studi di Milano (Italy)... [edited by author]
XI n.s.

Protein-surfactant interactions in aqueous media have been investigated. The globular proteins lysozyme and bovine serum albumin (BSA) served as model proteins. Several ionic and non-ionic surfactants were used.

Fluorescence probe measurements showed that at low sodium dodecyl sulfate (SDS) concentration (< 0.1 M) one micelle-like SDS cluster is bound to lysozyme. From dynamic light scattering (DLS) results it was observed that lysozyme in the complex does not correspond to the fully unfolded protein. At high SDS concentration (> 0.1 M) one compact and one more extended lysozyme-SDS complex coexist.

The influence of surfactant alkyl chain length and headgroup on BSA-surfactant complex formation was investigated. In these studies, binding isotherms were determined by nuclear magnetic resonance (NMR), DLS was used to measure the hydrodynamic radii of the complexes and the size of the micelle-like aggregates on BSA was determined using fluorescence probe methods.

It was observed from fluorescence measurements that the number of bound SDS molecules does not depend on the presence of the disulfide bridges. Reduced proteins wrap more efficiently around the micelle-like structures, resulting in somewhat smaller complexes, as observed with DLS.

Concentrated BSA-SDS solutions and the corresponding heat-set gels were investigated using DLS and fluorescence probe methods. Correlation lengths in the gel were determined and it was concluded that SDS forms micelle-like aggregates on BSA in concentrated solution and gel phase. The gel region in the ternary phase diagram BSA-SDS-3.1 mM NaN₃ has been determined at room temperature.