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Rozprawy doktorskie na temat „Fic Proteins”

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Data publikacji: 6 września 2023

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1

Al, Madadha Mohammad Emad. "Functional analysis of Fic domain bearing proteins in Klebsiella pneumoniae". Thesis, University of Leicester, 2017. http://hdl.handle.net/2381/39871.

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Fic domain bearing proteins are characterized with the presence of a domain carrying the conserved amino acid sequence (HPFX(D/E)GNGR). These proteins are present in all walks of life but are more concentrated within prokaryotes and more so within bacteria. In recent years these proteins have been increasingly characterized and their role in bacterial virulence is being elucidated. Fic proteins are usually secreted by bacteria and once delivered into the host cell they usually target cytoskeleton regulating G proteins that affect the target host in different ways depending on the target G protein. In Klebsiella pneumoniae, we have identified 5 homologous genes that code for five different Fic domain bearing proteins in this bacteria. Our first effort was to determine if these proteins were secreted, to verify if they adhere to the toxin-secretion system paradigm. The work then focused on determining the virulence effect of these proteins in an in vivo assay, an in vitro assay and an enzymatic assay for the Fic-RL protein. Fic- RL is one of the five proteins in K. pneumoniae have been shown to be conserved in all 80 sequenced strains of this bacteria. In our secretion assay this protein have been shown to be secreted by the bacteria, moreover, by utilizing different mutants that lacked different parts of secretion systems, we have been able to determine that the T4SS present on the Integrative and Conjugative Element 1 (icekp1) to be responsible for the secretion of this protein and not the other 4 homologs. Virulence assays showed that when this protein was expressed with eukaryotic cells by means of transfection, confocal and fluorescent microscopy revealed that cytotoxic effect are evident as cell rounding and actin cytoskeletal collapse in transfected cells, which does not occur when a mutated version of the protein is instead expressed. Survival killing assays utilizing the larvae of the Galleria mellonella wax moth, revealed significant attenuation of strains lacking the gene coding for Fic domain bearing proteins, which is partially complemented by re-introducing the genes in plasmid constructs. The enzymatic function for the Fic-RL protein was shown in a Guanine Exchange Factor assay, designed to reveal if a protein is able to utilize fluorophore bound substrates in its reaction of provided G protein targets (Cdc42, Rac1, RhoA), showed that Fic-RL is able to cause an increase in relative fluorescence measured that was similar to a known Guanine Exchange Factor (hDbs) but only when used on Cdc42 and not the other two G proteins.

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2

Veyron, Simon. "Structure et fonction des toxines bactériennes à domaine FIC". Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLS452/document.

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Les protéines à domaine FIC (Filamentation induced by cAMP) sont très répandues chez les bactéries où elles catalysent l’ajout d’une modification post-traductionnelle contenant un phosphate à une protéine cible, en utilisant différents co-substrats comme l’ATP. Certaines de ces protéines sont des toxines sécrétées par des pathogènes humains, mais la fonction de la plupart d’entre elles reste mystérieuse. Plus d’une dizaine de structures de protéines FIC ont été déterminées récemment, qui ont permis d’élucider leur mécanisme catalytique. L’une des sous-familles de protéines FIC possède un glutamate dans leur site catalytique, dont il a été proposé qu’il aurait une fonction auto-inhibitrice pour la fixation de l’ATP. Durant ma thèse, j’ai étudié la structure et les mécanismes de régulation de deux familles de protéines FIC : les protéines FIC à glutamate inhibiteur, et la toxine AnkX de la bactérie pathogène Legionella pneumophila.La première étude s’est intéressée à la protéine FIC de la bactérie pathogène Enterococcus faecalis (EfFIC), qui fait partie de la sous-famille des protéines FIC possédant un glutamate inhibiteur. J’ai résolu plusieurs structures cristallographique d’EfFIC, qui ont permis de caractériser son site catalytique et comment elle fixe l’AMP et l’ADP. En utilisant une propriété fréquemment observée d’auto-AMPylation (modification par l’AMP), j’ai montré au moyen d’ATP radioactif qu’EfFIC possède une activité basale d’auto-AMPylation, et j’ai identifié une nouvelle activité de dé-AMPylation. En m’inspirant des métaux observés dans mes structures cristallographiques, j’ai montré que l’alternance entre les activités d’AMPylation et de de-AMPylation dépend de la nature du métal fixé dans le site actif et de la présence du glutamate. Ce glutamate régulateur est également présent chez une protéine humaine, HYPE, qui possède une double activité d’AMPylation et dé-AMPylation d’ une chaperone du réticulum endoplasmique. Par un test de fluorescence, j’ai enfin montré que l’activité de HYPE était elle aussi régulée par les métaux comme celle de EfFIC. Ces résultats suggèrent un nouveau modèle de régulation partagé par des protéines FIC de la bactérie à l’homme.La seconde étude a porté sur la toxine AnkX de Legionella pneumophila, qui modifie les petites protéines G de la famille de Rab Rab1 et Rab35 (régulatrices du trafic cellulaire) par une molécule de phosphocholine (PC). En utilisant des liposomes de composition contrôlée, j’ai montré qu’AnkX interagit avec les membranes, et j’ai identifié par mutagenèse son domaine d’interaction avec les membranes. Au moyen de petites GTPases Rab ancrées artificiellement à la surface de liposomes par une queue 6his remplaçant le lipide naturel, j’ai montré que l’activité d’AnkX est stimulée par la présence de membranes. Des résultats préliminaires suggérent que Rab35 est un meilleur substrat que Rab1a, ce qui pourrait renseigner sur la fonction et le compartiment cellulaire où se trouve la toxine. J’ai ensuite mené une étude structurale d’AnkX par diffusion des rayons X aux petits angles (SAXS), qui permet d’obtenir des informations structurales en solution. AnkX est constitué d’un domaine FIC, de répétitions ankyrine et d’un domaine C-terminal. L’analyse en SAXS montre que ces domaines s’organisent en forme de fer à cheval, suggérant un modèle d’association bi-partite du complexe AnkX/Rab aux membranes. L’ensemble de ces résultats conduit à un modèle dans lequel l’activité d’AnkX est régulée spatialement par les membranes, ce qui pourrait lui permettre de cibler à la fois les petites GTPases Rab cellulaires et le compartiment membranaire
FIC (Filamentation induced by cAMP ) domain containing proteins are widespread in bacteria where they use different substrate such ATP to modify a target protein with a phosphate containing post-translational modification. Some of those proteins are secreted toxins from pathogens but the function of the majority stay unknown. Some recently resolved structures explain the catalytic mechanism. A subfamily of FIC proteins was proposed to be auto-inhibited for ATP binding by a glutamate in their active site. In my thesis, I lead a structural and biochemical study of two FIC proteins family: the auto-inhibited by a glutamate FIC proteins and the Legionella pneumophila toxin AnkX.For the first study, I focused on the pathogenic bacteria Enterococcus faecalis protein EfFIC that is an auto-inhibited FIC protein. I solved several crystallographic structures to characterize the active site and the AMP and ADP binding. Using the classic auto-AMPylation (modification with an AMP molecule) mechanism and radioactive ATP, I showed that EfFIC is active and I identified a new de-AMPylation activity. Using metals found in my crystallographic structures, I showed that the AMPylation and de-AMPylation switch is controlled by the nature of the metal bound in the active site and that this switch is inhibitory glutamate-dependent. This glutamate is found in human HYPE that shows a double AMPyaltion and de-AMPylation activity of the ER chaperone BIP. Using fluorescence assays, I showed that those two activities are alors regulated by metals as in EfFIC. Those results point on a new regulation model shared between FIC proteins from bacteria to human.The second study focused on Legionella pneumophila toxin AnkX that modifies small GTPases Rab1 and Rab35 with a phosphocholine (PC) molecule. Using controlled composition liposomes, I showed that AnkX interact with membranes and mapped the interaction domain by mutagenesis. With artificially anchored to nickel containing liposomes surface Rab GTPases, I demonstrated the stimulation of AnkX activity by the membranes. Preliminary results also suggest that Rab35 is a better substrate than Rab1a, giving information on AnkX function and localization during infection. I lead a small angle X-ray scattering (SAXS) study on AnkX that gave low-resolution structural information on AnkX in solution. The analyses of SAXS results show that AnkX is horseshoe shaped, suggesting an association with the membrane and Rab of AnkX model. In this model, membranes spatially regulate AnkX, allowing a targeting of Rab and cellular compartment targeting

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3

Govers-Riemslag, Josepha Wilhelmina Philomena. "Protein-protein and protein-membrane interactions in prothrombin activation". Maastricht : Maastricht : Rijksuniversiteit Limburg ; University Library, Maastricht University [Host], 1994. http://arno.unimaas.nl/show.cgi?fid=6949.

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4

Barriga, Montero Marissa Cecilia, Iwamoto Almendra Mayumi Ordaya, Loayza Raúl Anibal Jesús Pinto, Osorio Mauricio Roca i Llamosas Mirella Alison Zevallos. "Kallmi Fit". Bachelor's thesis, Universidad Peruana de Ciencias Aplicadas (UPC), 2020. http://hdl.handle.net/10757/654683.

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El presente trabajo tiene como objetivo principal la elaboración y planificación correspondiente de las diferentes tareas y actividades base para iniciar la producción y comercialización de un complemento proteico en polvo especializado para cada deporte o carga física correspondiente, asimismo, será la de comprobar que la idea de negocio es rentable. Actualmente, se pueden encontrar diferentes complementos proteicos en polvo de diferentes marcas con beneficios relativamente similares. El objetivo de estos se basa en la mejoría del estado físico del individuo quien las consume. Sin embargo, se puede apreciar que estas proteínas contienen una composición regular. Por lo que, su composición no se adecua a diferentes cantidades de ejercicio o cargas físicas. Por este motivo, nuestro producto tiene como objetivo principal adecuarse a las diferentes cantidades de carga física de los diferentes tipos de consumidores, clasificándose en deportes o actividades de bajo consumo calórico como de alto consumo calórico de igual manera. Cabe mencionar, que nuestro producto está dirigido a hombres y mujeres cuyo rango de edad se encuentre entre los 18 a 45 años y que hagan deporte regularmente. Para demostrar que la idea de negocio será rentable, se realizaron diferentes análisis de factores internos y externos que pudieran beneficiar o perjudicar a nuestro proyecto. En adición a esto, se realizó el cálculo del valor actual neto proyectado del negocio para comprobar que este generará ganancias en el futuro.
The main objective of the present work is the elaboration and corresponding planning of the different tasks and activities that are the base to start the production and commercialization of a specialized protein powder supplement for each sport or corresponding physical load, as well as to demonstrate that the business idea is profitable. Nowadays, we can find different protein powder supplements from different brands with relatively similar benefits. This objective is based on the improvement of the physical state of the individual who consumes them. However, we can appreciate that these proteins contain a regular composition. Thus, their composition is not adapted to different amounts of exercise or physical loads. For this reason, our product has, as the main objective, to adapt to the different amounts of physical load of the different consumers, being classified in sports or activities of low caloric consumption as of high caloric consumption in the same way. It is worth mentioning that our product is aimed at those men and women whose age is between 18 and 45 years old and who do sports regularly. In order to demonstrate that our business idea will be profitable, different analyses of internal and external factors that could benefit or harm our project were carried out. In addition, we calculated the projected net present value of the business, to prove that it will generate profits in the future.
Trabajo de investigación

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5

Sarti, Edoardo. "Assessing the structure of proteins and protein complexes through physical and statistical approaches". Doctoral thesis, SISSA, 2015. http://hdl.handle.net/20.500.11767/4863.

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Determining the correct state of a protein or a protein complex is of paramount importance for current medical and pharmaceutical research. The stable conformation of such systems depend on two processes called protein folding and protein-protein interaction. In the course of the last 50 years, both processes have been fruitfully studied. Yet, a complete understanding is still not reached, and the accuracy and the efficiency of the approaches for studying these problems is not yet optimal. This thesis is devoted to devising physical and statistical methods for recognizing the native state of a protein or a protein complex. The studies will be mostly based on BACH, a knowledge-based potential originally designed for the discrimination of native structures in protein folding problems. BACH method will be analyzed and extended: first, a new method to account for protein-solvent interaction will be presented. Then, we will describe an extension of BACH aimed at assessing the quality of protein complexes in protein-protein interaction problems. Finally, we will present a procedure aimed at predicting the structure of a complex based on a hierarchy of approaches ranging from rigid docking up to molecular dynamics in explicit solvent. The reliability of the approaches we propose will be always benchmarked against a selection of other state-of-the-art scoring functions which obtained good results in CASP and CAPRI competitions.

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6

Schellings, Marcus Wilhelmus Maria. "Matricellular proteins essential modulators of cardiac remodeling /". Maastricht : Maastricht : Universiteit Maastricht ; University Library, Universiteit Maastricht [host], 2007. http://arno.unimaas.nl/show.cgi?fid=9446.

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7

Ficz, Gabriella. "Protein dynamics in the nucleus implications for gene expression /". Doctoral thesis, [S.l.] : [s.n.], 2005. http://webdoc.sub.gwdg.de/diss/2005/ficz.

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8

PACHETTI, MARIA. "Studio UV Raman Risonante sulla struttura proteica, sulla fibrillazione e sull'interazione proteina-ligando". Doctoral thesis, Università degli Studi di Trieste, 2021. http://hdl.handle.net/11368/2988326.

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Il termine "proteinopatia" è stato coniato per indicare una classe di disturbi legati al mal ripiegamento delle proteine come le malattie di Alzheimer (AD) e Parkinson (PD). Oggi, le demenze, l'AD e il diabete di tipo II sono considerati tra le prime 20 cause di morte in tutto il mondo dall'Organizzazione Mondiale della Sanità (OMS). Il mal-ripiegamento non solo induce la perdita delle funzioni biologiche delle proteine, ma promuove anche un processo termodinamicamente favorito chiamato "aggregazione", che generalmente termina con la formazione di fibrille proteiche, cioè una struttura filiforme ordinata fatta di proteine mal ripiegate. La formazione di specie proteiche non native e la formazione di depositi di fibrille all'interno o all'esterno delle cellule potrebbero compromettere le funzioni biologiche native di cellule, tessuti e organi. Nonostante la spettroscopia UV Raman Risonante (UVRR) non fornisca misure ad alta risoluzione, questa offre preziose informazioni sulla struttura nativa del campione, superando così le limitazioni di cryo-EM e ssNMR. Per citare alcuni vantaggi, la spettroscopia UVRR offre la possibilità di lavorare in condizioni acquose, diluite, senza richiedere manipolazioni chimiche del campione. Ancora più importante, la spettroscopia UVRR offre la possibilità di aumentare selettivamente la sezione d'urto Raman dei modi vibrazionali di peculiari cromofori proteici a seconda dell'energia di eccitazione scelta. Lo scopo di questa tesi di dottorato è quello di mostrare l'utilità della spettroscopia UVRR per l'indagine strutturale delle fibrille proteiche e anche delle interazioni proteina-ligando, collegando il comportamento di diversi biomarkers spettroscopici alla modifica strutturale delle proteine durante entrambi i fenomeni. In particolare: - abbiamo dimostrato la capacità della spettroscopia UVRR di ottenere importanti informazioni sulla modifica strutturale delle proteine durante la fibrillazione e durante l'interazione con i ligandi, studiando la fibrillazione del lisozima contenuto nell'albume d'uovo di gallina (HEWL) e dell'insulina umana e la loro interazione con un antiossidante, il resveratrolo. Abbiamo fornito un solido approccio spettroscopico basato sulla spettroscopia UVRR e completato da altre classiche tecniche spettroscopiche, con l'obiettivo di tradurre questo approccio multi-tecnica verso l'indagine di una classe più interessante di proteine, cioè le proteine intrinsecamente disordinate. - abbiamo caratterizzato un nuovo meccanismo di fibrillazione della diidrofolato reduttasi (DHFR) di E.Coli, indotta a pH neutro dalla presenza di spermina. Infatti, l'interazione con la spermina induce una parziale inibizione dell'attività enzimatica, stabilizzando il DHFR in un conformatore ad alta energia. Questa struttura rimane stabile per alcuni giorni, poi inizia a precipitare in fibrille insolubili. Il meccanismo di interazione tra E.Coli DHFR e la spermina è stato discusso in questa sezione, fornendo un chiaro esempio di ligando che induce la fibrillazione. -Nell'ultima sezione, il solido protocollo basato su UVRR testato con sistemi modello, e l'identificazione di peculiari biomarcatori spettrali UVRR sensibili alla fibrillazione della proteina e all'interazione con ligandi sono stati sfruttati trattando una nota proteina intrinsecamente disordinata (IDP), che è l'α-sinucleina (aS). Abbiamo proposto un metodo alternativo di analisi degli spettri UVRR basato sull'uso di un riferimento proteico esterno per chiarire la struttura di aS e la sua forma troncata al C-terminale, (1-120) aS. Abbiamo proposto un metodo alternativo di analisi degli spettri UVRR basato sull'uso di un riferimento proteico esterno per stimare approssimativamente quanti residui Tyr sono protetti dal solvente nel caso sia delle fibrille che dei monomeri di aS, ottenendo risultati in linea con la recente letteratura.
The term “proteinopathy” was coined to indicate a class of disorders related to protein misfolding such as Alzheimer’s (AD) and Parkinson’s (PD) diseases. Nowadays, dementias, AD and type II diabetes are considered within the top 20 causes of death worldwide by World Health Organization (WHO). Misfolding not only induces the loss of proteins’ biological functions, but also promotes a thermodynamically favoured process called “aggregation”, that generally ends with the formation of protein fibrils, i.e. an ordered thread-like structure made of misfolded proteins. The formation of non-native protein species as well as the formation of fibrils deposits within or outside cells could compromise the native biological functions of cells, tissues and organs. Despite UV Resonance Raman (UVRR) spectroscopy does not offer high-structural resolution measurements, it provides valuable insights on the native-like structure of the sample, thus overcoming the limitations of cryo-EM and ssNMR. To name few advantages, UVRR spectroscopy offers the possibility to work in diluted, native-like aqueous conditions, without requiring a chemical manipulation of the sample. More importantly, UVRR spectroscopy opens the possibility to selectively enhance the Raman cross section of peculiar protein chromophore vibrational modes depending on the radiation excitation energy chosen. The aim of the this Ph.D. thesis is to show the usefulness of UV Resonance Raman (UVRR) spectroscopy for the structural investigation of protein fibrils and also of protein-ligand interactions, linking the behaviour of several spectroscopic biomarkers to the structural modification of proteins during both phenomena. In particular: - we demonstrated the ability of UVRR spectroscopy to get important insights on the structural modification of proteins upon fibrillation and upon interaction with ligands, by studying the fibrillation of hen egg white lysozyme (HEWL) and human insulin and their interaction with an antioxidant, which is resveratrol. We provide a solid spectroscopic approach based on UVRR spectroscopy and complemented by other classical spectroscopic techniques, with the aim to translate this multi-technique approach towards the investigation of a more interesting class of proteins, i.e. the intrinsically disordered proteins. - we characterized a novel mechanism of fibrillation of E.Coli dihydrofolate reductase (DHFR), induced at neutral pH by the presence of spermine. In fact, the interaction with spermine induces a partial inhibition of the enzymatic activity, stabilizing DHFR in a high energy conformer. This structure remains stable for few days, then starts to precipitate into insoluble fibrils. The mechanism of interaction between E.Coli DHFR and spermine has been discussed in this section, providing a clear example of a fibrillation-inducing ligand. -in the last section, the solid UVRR-based protocol tested with model systems, and the identification of peculiar UVRR spectral biomarkers sensitive to protein fibrillation and to interaction with ligands have been exploited dealing with a well-known intrinsically disordered protein (IDP), which is α-synuclein (aS). We proposed an alternative method of UVRR spectra analysis based on the use of an external protein reference to elucidate the structure of aS and its C-terminus truncated form, (1-120) aS. We proposed an alternative method of UVRR spectra analysis based on the use of an external protein reference roughly estimate how many Tyr residues are solvent-protected in the case of both aS fibrils and monomers, obtaining results in line with the recent literature.

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Kragten, Johannes Albertus. "New myocardial marker proteins in acute myocardial infarction quantitative aspects : release patterns of cellular enzymes and proteins in plasma following acute myocardial infarction /". Assen : Maastricht : Dekker & van de Vegt en Van Gorcum ; University Library, Maastricht University [Host], 1998. http://arno.unimaas.nl/show.cgi?fid=6052.

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Jie, Gerard Kon Siong. "The role of vitamin K-dependent proteins in tissue calcification". Maastricht : Maastricht : Universitaire Pers Maastricht ; University Library, Maastricht University [Host], 1995. http://arno.unimaas.nl/show.cgi?fid=8340.

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11

Schrander, Jacobus Jan Pieter. "Cow's milk protein intolerance in infants". Maastricht : Maastricht : Universitaire Pers Maastricht ; University Library, Maastricht University [Host], 1994. http://arno.unimaas.nl/show.cgi?fid=6846.

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12

Covino, Roberto. "Investigating Protein Folding Pathways at Atomistic Resolution: from a Small Domain to a Knotted Protein". Doctoral thesis, Università degli studi di Trento, 2013. https://hdl.handle.net/11572/367925.

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Although protein folding has been studied for decades many open issues still resist, and we yet lack a clear and general description of the mechanisms leading from the unfolded to the folded state. In particular, it is still under debate whether proteins fold through few well-defined pathways or trough a large multitude of independent ways. Answering these questions is made difficult by the fact that standard molecular dynamics (MD) simulations are very computationally expensive and often impracticable. Moreover, often even experimental techniques lack the necessary resolution to give a definitive answer. We will introduce and develope the Dominant Reaction Pathway (DRP), which is an approach that permits to efficiently study the thermally activated conformational dynamics of bio-molecules in atomistic detail. In particular, it can be used to characterize and portray the folding pathways of a protein once the unfolded and folded configurations are given. We firstly applied the DRP to a realistic protein studying the folding pathways of the Fip35 WW Domain, a 35 amino-acids long protein. Performing all atom simulations we were able to show that this small protein folds following only two pathways, defined by the order of formation of secondary structures. Notably, our results are compatible with ultra long MD simulations and consistent with the analysis of the experimental available data on the folding kinetics of the same system. Exploiting the efficiency of the DRP formalism, computing a folding trajectory of this protein only required about one hour on 48 CPUâ€™s. We applied then our simulation scheme to a much more challenging task: performing an all-atom folding simulation of a 82 amino-acids long protein displaying a topological knot in its native conformation. We were able to portray the folding mechanism and to identify the essential key contacts leading to the proper formation of this knot. Interestingly, we showed that non native contacts, i.e., transient contacts formed during the folding of the protein but absent in its native state, can sensibly enhance the probability of correctly forming the knot.

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Vork, Michaël Maria. "Fatty acid-binding protein in rat heart". Maastricht : Maastricht : Universitaire Pers Maastricht ; University Library, Maastricht University [Host], 1993. http://arno.unimaas.nl/show.cgi?fid=6232.

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Proefschrift Maastricht.
Samenvatting in het Nederlands. Ten dele eerder verschenen en nog te verschijnen art. Auteursnaam op rug en omslag: Michaël Vork. Met lit. opg. en een samenvatting in het Nederlands.

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14

Pannemans, Daphne Louise Elise. "Energy and protein metabolism in the elderly". Maastricht : Maastricht : Universitaire Pers Maastricht ; University Library, Maastricht University [Host], 1994. http://arno.unimaas.nl/show.cgi?fid=6814.

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Covino, Roberto. "Investigating Protein Folding Pathways at Atomistic Resolution: from a Small Domain to a Knotted Protein". Doctoral thesis, University of Trento, 2013. http://eprints-phd.biblio.unitn.it/1163/1/thesis_covino_final.pdf.

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Although protein folding has been studied for decades many open issues still resist, and we yet lack a clear and general description of the mechanisms leading from the unfolded to the folded state. In particular, it is still under debate whether proteins fold through few well-defined pathways or trough a large multitude of independent ways. Answering these questions is made difficult by the fact that standard molecular dynamics (MD) simulations are very computationally expensive and often impracticable. Moreover, often even experimental techniques lack the necessary resolution to give a definitive answer. We will introduce and develope the Dominant Reaction Pathway (DRP), which is an approach that permits to efficiently study the thermally activated conformational dynamics of bio-molecules in atomistic detail. In particular, it can be used to characterize and portray the folding pathways of a protein once the unfolded and folded configurations are given. We firstly applied the DRP to a realistic protein studying the folding pathways of the Fip35 WW Domain, a 35 amino-acids long protein. Performing all atom simulations we were able to show that this small protein folds following only two pathways, defined by the order of formation of secondary structures. Notably, our results are compatible with ultra long MD simulations and consistent with the analysis of the experimental available data on the folding kinetics of the same system. Exploiting the efficiency of the DRP formalism, computing a folding trajectory of this protein only required about one hour on 48 CPU’s. We applied then our simulation scheme to a much more challenging task: performing an all-atom folding simulation of a 82 amino-acids long protein displaying a topological knot in its native conformation. We were able to portray the folding mechanism and to identify the essential key contacts leading to the proper formation of this knot. Interestingly, we showed that non native contacts, i.e., transient contacts formed during the folding of the protein but absent in its native state, can sensibly enhance the probability of correctly forming the knot.

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16

Hollmann, Markus W. "Local anesthetic interactions with G protein-coupled receptor signaling". Aachen : Maastricht : Shaker ; University Library, Maastricht University [Host], 2001. http://arno.unimaas.nl/show.cgi?fid=7012.

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Waardenburg, Dirk Adriaan van. "Protein metabolism and nutritional requirements in critically ill children". Maastricht : Maastricht : Maastricht University ; University Library, Universiteit Maastricht [host], 2008. http://arno.unimaas.nl/show.cgi?fid=15092.

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18

Claessens, Mandy. "Dietary proteins: their effects on insulin and glucagon in relation to body weight management". Maastricht : Maastricht : Universitaire Pers Maastricht ; University Library, Universiteit Maastricht [host], 2008. http://arno.unimaas.nl/show.cgi?fid=9517.

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Knuth, Monika. "Identifizierung und Charakterisierung von FIP, einem neuen Filamin-bindenden Protein". [S.l. : s.n.], 2001. http://deposit.ddb.de/cgi-bin/dokserv?idn=963612883.

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20

Forward, Benjamin Spencer. "Characterization and expression of the Douglas-fir luminal binding protein". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/NQ58567.pdf.

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21

Matheson, Mary Ann. "Structural and immunological characterisation of FIM D, a minor fibrial protein of Bordetella pertussis". Thesis, Open University, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.309866.

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22

Galli, Monica Maria Teresa. "Involvement of protein cofactors in the expression of antiphospholipid antibodies". [Maastricht : Maastricht : Rijksuniversiteit Limburg] ; University Library, Maastricht University [Host], 1993. http://arno.unimaas.nl/show.cgi?fid=6236.

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23

Blaauw, Ivo de. "Interorgan protein and glutamine metabolism in the tumor bearing rat". Maastricht : Maastricht : Universiteit Maastricht ; University Library, Maastricht University [Host], 1996. http://arno.unimaas.nl/show.cgi?fid=6752.

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24

Lendel, Christofer. "Molecular principles of protein stability and protein-protein interactions". Doctoral thesis, Stockholm, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-480.

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25

Matei, Adriana. "Optical investigations of biological samples in far infrared". [S.l. : s.n.], 2005. http://www.bsz-bw.de/cgi-bin/xvms.cgi?SWB11814266.

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26

CHOUDHARY, DHAWAL. "Studio a livello di singola molecola del folding, misfolding e aggregazione di proteine e dell’attività chaperonica della HSPB8". Doctoral thesis, Università degli studi di Modena e Reggio Emilia, 2020. http://hdl.handle.net/11380/1199862.

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Negli ultimi decenni le pinze ottiche si sono rivelate una tecnica sperimentale estremamente efficace per eseguire studi di spettroscopia di forza a livello di singola molecola. In particolare, un’applicazione delle pinze ottiche che sta avendo una rilevanza biomedica sempre più importante è quella relativa allo studio dei processi di ripiegamento corretto (folding), non corretto (misfolding) e dell’aggregazione di proteine. Di forte rilevanza biomedica è anche la possibilità offerta dalle pinze ottiche di caratterizzare in grande dettaglio i meccanismi molecolari che mediano le interazioni tra due o più biomolecole, come ad esempio tra uno chaperone molecolare e il suo substrato. La rilevanza medica di questi studi deriva dal fatto che l'errato ripiegamento e l'aggregazione delle proteine sono processi deleteri, spesso associati a neurodegenerazione. Gli chaperoni molecolari si sono evoluti come strumento molecolare per combattere sia il misfolding che l’aggregazione proteica. Un funzionamento non corretto degli chaperoni molecolari spesso causa perdita di proteostasi e l’insorgenza di varie patologie umane. Il lavoro descritto in questa tesi spiega in maniera dettagliata l’approccio sperimentale utilizzato per utilizzare le pinze ottiche per lo studio del folding, misfolding e aggregazione di proteine. In particolare in questa tesi vengono descritti: i) i risultati di esperimenti mirati alla elucidazione del processo di ripiegamento corretto e non del sensore al calcio NCS-1 (Neuronal Calcium Sensor 1; ii) l'approccio sperimentale adottato per descrivere la dinamica strutturale e funzionale di vari chaperoni molecolari utilizzando le pinze ottiche e la microscopia a forza atomica; iii) recenti sviluppi tecnici che hanno ampliato le possibili applicazioni delle pinze ottiche in campo biologico; iv) i risultati di esperimenti mirati a far luce sui meccanismi molecolari che mediano l’attività chaperonica dello chaperone molecolare HSPB8. In quest’ultimi esperimenti abbiamo manipolato meccanicamente monomeri e tetrameri della Maltose Binding Protein (MBP) e analizzato i loro processi di folding, misfolding e aggregazione in presenza e assenza del HSPB8 wild-type e del suo mutante HSPB8-K141E. I nostri risultati dimostrano una forte attività antiaggregante (holdase activity) della HSPB8 che riduce significativamente l'aggregazione delle molecole di MBP e un’attività antiaggregante molto ridotta del mutante HSPB8-K141E. Inoltre, i nostri studi rivelano una inaspettata attività pro-folding (foldase activity) sia della forma mutata che di quella wild-type della HSPB8. Questi dati sperimentali evidenziano nuovi meccanismi di interazione tra HSPB8 e i suoi substrati e suggeriscono un ruolo fisiologico più complesso per questo chaperone molecolare di quanto precedentemente ipotizzato.
Optical tweezers have evolved as an exemplary Single Molecule Force Spectroscopy (SMFS) technique over the past three decades. A distinct and bio medically relevant application of Optical Tweezers is their ability to observe directly at single molecule level the folding, misfolding and aggregation of protein molecules. Additionally the dynamic approach of Optical Tweezer setup also allows for the isolated study of interactions between two or more biomolecules, such as chaperone-protein interactions, in real time. The medical relevance of such studies stems from the fact that misfolding and aggregation of proteins are deleterious processes and have been linked to many neurodegenerative disorders. While molecular chaperones have evolved as an evolutionarily conserved sword and shield mechanism against such deleterious processes, wherein their holdase action acts as a shield preventing further aggregation of misfolded protein species and their foldase action acts as a sword and actively assists misfolded structure to regains their natively folded state. The dysfunction of this chaperone activity is also cytotoxic and can lead to loss of proteostasis. The present thesis dwells deeper in this specific application of Optical tweezer. The thesis will elaborate upon how optical tweezers can extract the mechanistic details of the folding and misfolding of protein molecules by reviewing the experiments performed on NCS-1 (Neuronal Calcium Sensor 1). It will also discuss the experimental approach taken by SMFS techniques like Optical Tweezers and AFM (Atomic Force Microscopy) to study the structural and functional dynamics of molecular chaperones. Furthermore, the thesis will explore the recent developments in Optical Tweezers and their biological applications. Finally, I describe the results of experiments we have carried out on the maltose binding protein to elucidate the mechanism of action of the chaperone HSPB8. We have mechanically denatured homotetramers of MBP as well as single MBP molecules and analyzed their folding and aggregation processes in the presence and absence of wild-type HSPB8 and its mutant form HSPB8-K141E/N. Our results reveal a strong holdase activity of wild type HSPB8, which either prevents completely the aggregation of denatured MBP molecules or allows the substrate to form only small and mechanically weak aggregates while this holdase activity is significantly suppressed in the mutant. Moreover, and importantly, a careful analysis of the data also discloses an unexpected foldase activity of both wild type and mutated forms of HSPB8, which guides the folding process of denatured MBP molecules into their native states. Our findings highlight new mechanisms of interaction between HSPB8 and its substrates and suggest a more complex physiological role for this chaperone than previously assumed.

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27

Gerken, Thomas. "Functional studies of the double-stranded beta-helix proteins FIH, FTO and Pirin". Thesis, University of Oxford, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.670070.

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28

Orioli, Simone. "Generating and Validating Transition Path Ensembles of Protein Folding". Doctoral thesis, Università degli studi di Trento, 2019. https://hdl.handle.net/11572/367639.

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This thesis proposes to provide a unified and systematic strategy to overcome the second timescale in protein folding, by exploiting qualities and drawbacks of the Bias Functional Method and proposing new theoretical approaches to overcome its limitations. The first half of the thesis is dedicated to the development of theoretical solutions to the dependence of the Bias Functional Method on an a-priori defined collective coordinate and microscopic non-reversibility of the dynamics. The second part of the manuscript is devoted to applications of the BF method on two different proteins: Canine milk lysozyme and alpha1-antitrypsin (A1AT).

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29

Nieuwenhoven, Franciscus Arnoldus van. "Heart fatty acid-binding proteins role in cardiac fatty acid uptake and marker for cellular damage /". Maastricht : Maastricht : Rijksuniversiteit Limburg ; University Library, Maastricht University [Host], 1996. http://arno.unimaas.nl/show.cgi?fid=6268.

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30

Wang, Ping. "Proteomic, transcriptomic and epidemiological analysis of adipocyte-secreted proteins towards a system biological understanding of adipocytes /". Maastricht : Maastricht : Universitaire Pers ; University Library, Universiteit Maastricht [host], 2007. http://arno.unimaas.nl/show.cgi?fid=13845.

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31

Dinjens, Winandus Nicolaas Maria. "Distribution of adenosine deaminase complexing protein in normal and neoplastic cells". Maastricht : Maastricht : Rijksuniversiteit Limburg ; University Library, Maastricht University [Host], 1988. http://arno.unimaas.nl/show.cgi?fid=5412.

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32

Giachini, Lisa <1978&gt. "Structure and dynamics of metal sites in proteins: X-ray Absorption Spectroscopy investigations". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2007. http://amsdottorato.unibo.it/334/1/tesi_giachini.pdf.

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33

Giachini, Lisa <1978&gt. "Structure and dynamics of metal sites in proteins: X-ray Absorption Spectroscopy investigations". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2007. http://amsdottorato.unibo.it/334/.

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34

Camilloni, C. "Protein Folding : a molecular dynamics study". Doctoral thesis, Università degli Studi di Milano, 2008. http://hdl.handle.net/2434/59334.

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35

Schaap, Franciscus Gerardus. "Physiological role of cytoplasmic fatty acid-binding protein for the cardiac myocyte". [Maastricht : Maastricht : Universiteit Maastricht] ; University Library, Maastricht University [Host], 1999. http://arno.unimaas.nl/show.cgi?fid=6839.

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36

Kleine, Albert Hans. "Fatty acid-binding protein as diagnostic marker of acute myocardial infarction in man". Maastricht : Maastricht : Universitaire Pers Maastricht ; University Library, Maastricht University [Host], 1993. http://arno.unimaas.nl/show.cgi?fid=5939.

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37

Orioli, Simone. "Generating and Validating Transition Path Ensembles of Protein Folding". Doctoral thesis, University of Trento, 2019. http://eprints-phd.biblio.unitn.it/3487/1/thesis.pdf.

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This thesis proposes to provide a unified and systematic strategy to overcome the second timescale in protein folding, by exploiting qualities and drawbacks of the Bias Functional Method and proposing new theoretical approaches to overcome its limitations. The first half of the thesis is dedicated to the development of theoretical solutions to the dependence of the Bias Functional Method on an a-priori defined collective coordinate and microscopic non-reversibility of the dynamics. The second part of the manuscript is devoted to applications of the BF method on two different proteins: Canine milk lysozyme and alpha1-antitrypsin (A1AT).

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38

Crabtree, Michael David. "Probing order within intrinsically disordered proteins". Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/270303.

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Decades have passed since the realisation that a protein’s amino acid sequence can contain all the information required to form a complex three-dimensional fold. Until recently, these encoded structures were thought to be crucial determinants of protein function. Much effort was directed to fully understand the mechanisms behind how and why proteins fold, with natively unfolded proteins thought to be experimental artefacts. Today, the field of natively unfolded – or so-called intrinsically disordered – proteins, is rapidly developing. Protein disorder content has been positively correlated with organismal complexity, with over thirty percent of eukaryotic proteins predicted to contain disordered regions. However, the biophysical consequences of disorder are yet to be fully determined. With the aim of addressing some of the outstanding questions, the work described in this thesis focuses on the relevance of structure within disordered proteins. Whilst populating a variety of conformations in isolation, a subset of disordered proteins can fold upon binding to a partner macromolecule. This folded state may be present within the ensemble of conformations sampled by the unbound protein, opening the question of what comes first: folding or binding? Protein engineering techniques were employed to alter the level of residual ‘bound-like’ structure within the free conformational ensemble, and the consequences on coupled folding and binding reactions were investigated. Resultant changes in the rate of association are easily imaginable; yet, this work demonstrates that the majority of the observed changes in binding affinity were due to alterations in the rate of dissociation, thus altering the lifetime of the bound complex. Promiscuous binding is a touted advantage of being disordered. If many disordered proteins, each with their own conformational ensemble, can bind and fold to the same partner, then where is the folding component encoded? Does the partner protein template the folding reaction? Or, is the folding information contained within the disordered protein sequence? Utilising phi-value analysis on the BCL-2 family of proteins, residues in the disordered sequence were probed to ascertain which form contacts at the transition state of the reaction. Comparison with phi-value analyses of alternative pairs – sharing either the ordered or disordered protein – provides insight into the encoding of these interactions. In the context of a bimolecular reaction, the amino acid sequence of the disordered protein was shown to determine the interactions within the transition state. Thus, analogous to the discovery from decades’ past, it is the sequence of the protein that folds which encodes its pathway, even when binding is a prerequisite.

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39

Lattanzi, Gianluca. "Statistical physics approach to Protein Motors". Doctoral thesis, SISSA, 2001. http://hdl.handle.net/20.500.11767/4322.

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40

Nicolaes, Gerardus Anna Franciscus. "Regulation of thrombin formation via the protein C pathway in normal and hypercoagulable states". [Maastricht : Maastricht : Universiteit Maastricht] ; University Library, Maastricht University [Host], 1997. http://arno.unimaas.nl/show.cgi?fid=8518.

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41

Hoeks, Joris. "Preserve the fire of live uncoupling protein 3 in the defence against mitochondrial lipotoxicity /". Maastricht : Maastricht : UPM, Universitaire Pers Maastricht ; University Library, Maastricht University [Host], 2006. http://arno.unimaas.nl/show.cgi?fid=7588.

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42

Bons, Judith Anna Petronella. "Proteomics as a tool for biomarker detection protein profiling in chronic and vascular disease /". [Maastricht] : Maastricht : Universitaire Pers Maastricht ; University Library, Universiteit Maastricht [host], 2008. http://arno.unimaas.nl/show.cgi?fid=10105.

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43

Manders, Ralph Johannes Francisca. "Protein supplementation as a dietary strategy to improve glycemic control in type 2 diabetes". Maastricht : Maastricht : Universitaire Pers ; University Library, Universiteit Maastricht [host], 2008. http://arno.unimaas.nl/show.cgi?fid=13484.

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44

SCALISI, SILVIA. "Quantitative single-molecule mapping of neuronal proteins at the nanoscale". Doctoral thesis, Università degli studi di Genova, 2020. http://hdl.handle.net/11567/1001622.

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The advent of super-resolution microscopy, also called nanoscopy, allowed a substantial improvement of spatial resolution, opening the door for the observation of biological structures beyond the diffraction limit impossible with conventional light microscopy. Among the super-resolution techniques, single-molecule localization microscopies have proven to be a powerful tool to address many biological issues, since they provide an imaging resolution of the order of tens of nanometers and the possibility to perform quantitative measurements. Neuroscience has been one of the fields in biology to benefit most from super-resolution microscopy. During the last years, single-molecule localization microscopies have been widely exploited to study diffraction-limited subcellular structures in neurons, allowing a deeper understanding of molecular mechanisms underlying neural network functioning and its impairments in pathologies. In this thesis, we developed a tool to investigate the distribution, spatial organization, clustering, and density of neural proteins at the nanoscale. In particular, we focused on the quantitative study of synaptic neurotransmitter receptors and focal adhesions. The knowledge of the distribution and stoichiometry of synaptic proteins is fundamental to understand the regulation of the synaptic transmission in neurons. However, a detailed characterization of the protein architecture within synapses can be achieved only by visualizing them at a nanometric level. Here we propose a quantitative approach based on stochastic optical reconstruction microscopy combined with cluster analysis to investigate the molecular rearrangement of GABAA receptors into subsynaptic domains during synaptic plasticity of the inhibitory neurotransmission. This approach was also applied to the study of the adhesion machinery of mammalian cells and neurons at the interface with single-layer graphene to investigate the interaction between cells and nanostructured materials. Due to their excellent properties and biocompatibility, graphene and its derivatives are the ideal candidates for many biomedical applications, such as neural tissue engineering. However, the adhesion processes at the graphene/neuron interface are still not clear nowadays. Our method offers an easy way to study how graphene substrates can affect adhesion and migration of different types of cells.

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45

Toffano, Alberto Antonio <1989&gt. "Protein Modelling Focused on Voltage-Gated Sodium Channel NaV 1.7". Master's Degree Thesis, Università Ca' Foscari Venezia, 2019. http://hdl.handle.net/10579/15049.

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As the state-of-the-art stands at present, it is recognised the narrow correlation between the behavior of voltage-gated sodium channel transmembrane human isoform NaV 1.7 and pain perception . Gain of function mutations are strictly related with several neurophaty (IEM, PEPD). On the other way round, loss of functions are associated with congenital insensivity to pain. Drugs actually avaiable are not able to relief effectively patients with pain disorders. It is thus necessary improve the knowledge in this sense, difficulties in obtaining these informations resides in production and purification of enough proteins to XDR analysis for each genetic variants. In order to achive these goals, computational chemistry comes in help. It allows to develop large amount of structural models of proteins of which are known only the primary sequence

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46

Bakker, Harm Marten. "Accelerin the activated form(s) of human blood coagulation factor V /". Maastricht : Maastricht : Rijksuniversiteit Limburg ; University Library, Maastricht University [Host], 1994. http://arno.unimaas.nl/show.cgi?fid=6954.

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47

Martinelli, Ida Marianna. "Clinical studies on hereditary thrombophilia a focus on resistance to activated protein C (factor V:Q506) /". Maastricht : Maastricht : Universiteit van Maastricht ; University Library, Maastricht University [Host], 1997. http://arno.unimaas.nl/show.cgi?fid=5929.

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48

Cazzolli, Giorgia. "Protein structural dynamics and thermodynamics from advanced simulation techniques". Doctoral thesis, Università degli studi di Trento, 2013. https://hdl.handle.net/11572/368954.

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In this work we apply simulation techniques, namely Monte Carlo simulations and a path integral based method called Dominant Reaction Pathways (DRP) approach, in order to study aspects of dynamics and thermodynamics in three different families of peculiar proteins. These proteins are, for reasons such as the presence of an intermediate state in the folding path or topological constraints or large size, different from ideal systems, as may be considered small globular proteins that fold in a two state manner. The first treated topic is represented by the colicin immunity proteins IM9 and IM7, very similar in structure but with an apparently different folding mechanism. Our simulations suggest that the two proteins should fold with a similar folding mechanism via a populated on-pathway intermediate state. Then, two classes of pheromones that live in temperate and arctic water respectively are investigated. The two types of pheromones, despite the high structural similarity, show a different thermodynamic behavior, that could be explained, according to our results, by considering the role played by the location of CYS-CYS bonds along the chain. Finally, the conformational changes occurring in serpin proteins are studied. The serpins are very flexible, with a large size, more than 350 residues, and slow dynamics, from hours to weeks, completely beyond the possibilities of the simulation techniques to date. In this thesis we present the first all-atom simulations, obtained with the DRP approach, of the mechanism related to serpins and a complete characterization of the serpin dynamics is performed. Moreover, important implications for what concerns medical research field, in particular in drug design, are drown from this detailed analysis.

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49

Silva, Marcos Araújo Castro e. "Evolução convergente da protease FtsH5 de Arabidopsis thaliana e seu regulador negativo putativo FIP (FtsH5 interacting protein)". Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-23042015-163556/.

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As metaloproteases AAA/FtsH são componentes chave do controle da qualidade das proteínas inseridas nas membranas de mitocôndrias e cloroplastos. Em Arabidopsis thaliana, as proteases FtsH presentes nas membranas dos tilacóides formam um complexo heterohexamérico composto pelas subunidades FtsH1/FtsH5 (tipo A) e FtsH2/FtsH8 (tipo B). Este complexo está envolvido na reciclagem de proteínas foto-danificadas, especialmente da proteína D1, centro de reação do PSII. Algumas linhas de evidências indicam ainda que existe um limiar de concentração das proteases FtsH, necessário para a correta formação e desenvolvimento dos cloroplastos. Apesar da extensiva caracterização genética e molecular das proteases FtsH, o mecanismo regulatório do complexo FtsH dos cloroplastos não foi totalmente elucidado até o momento, contudo existem evidências de que a sua ativação pode estar relacionada a alta incidência luminosa e a outras condições de estresse. A presença de fatores proteicos auxiliares, foi testada como hipótese alternativa por nosso grupo, através do uso da protease FtsH5 como isca em um ensaio de duplo híbrido de leveduras. Este ensaio identificou uma proteína interagente putativa, nomeada FIP (FtsH5 Interacting Protein), a qual comprovadamente interage com FtsH5 e está localizada nas membranas dos tilacóides. De modo a investigar o papel regulatório putativo de FIP sobre a atividade do complexo FtsH, nós analisamos os padrões de expressão em uma ampla gama de condições de estresse a partir de dados públicos de microarranjos de DNA. Os perfis de expressão indicam que FIP pode ser um regulador negativo da atividade do complexo. Os resultados também sugerem que o complexo pode estar envolvido na resposta do cloroplasto a diferentes tipos de condições de estresse. O estudo da história evolutiva das proteínas interagentes FtsH5 e FIP evidenciou que as sequências homólogas a FIP são encontradas exclusivamente em musgos e plantas superiores, sugerindo assim que a origem de FIP pode estar relacionada a colonização terrestre. Todos os genes codificantes das proteases FtsH do complexo foram usados como \"query\" na busca por sequências homólogas, permitindo a classificação das proteases FtsH nos tipos A e B por inferência filogenética Bayesiana. Análises filogenéticas Bayesianas também foram feitas para FIP e as proteases FtsH tipos A e B, independentemente. A análise Mirrortree suportou a existência de coevolução entre FIP e as proteases FtsH tipo A. Por outro lado, nenhuma correlação foi encontrada entre FIP e as proteases FtsH tipo B, o que corrobora nossas observações experimentais anteriores. Além disso, o agrupamento portador de homólogos FIP pôde ser recuperado em uma filogenia mais completa das proteases FtsH do tipo A. Análises subsequentes mostraram que ambas as proteínas interagentes estão extensivamente sobre seleção negativa e que proteases FtsH tipo A são bastante conservadas, principalmente nos seus domínios internos.
Eukaryotic AAA/FtsH metalloproteases display a key role in the protein quality control of membrane-inserted proteins in mitochondria and chloroplasts. In Arabidopsis thaliana, chloroplast thylakoidal membranes FtsH proteases form a heterohexameric complex made by FtsH1/FtsH5 (type A) and FtsH2/FtsH8 (type B) subunits. This complex is involved in protein turnover of photo-damaged proteins, in particular the D1 protein at the PSII reaction center. Several lines of evidence also indicate that a FtsH threshold level is necessary for the proper formation and development of chloroplasts. Despite extensive genetic and molecular characterization of the FtsH proteases, the regulatory mechanism of the FtsH complex in chloroplasts has not yet been fully elucidated, however, there are evidences that its activation might be related to high light incidence and other stress conditions. The presence of auxiliary protein factors, as an alternative hypothesis, was tested by our group, through the use of the protease FtsH5 as bait in a yeast two-hybrid assay. This essay identified a putative interacting protein named FIP (FtsH5 Interacting Protein), which has been proved to interact with FtsH5 and be located at the thylakoid membranes. In order to investigate a putative regulatory role of FIP on FtsH complex activity, we analyzed gene expression patterns in a wide range of stress conditions from public DNA microarray data. The expression profiles indicate that FIP could be a negative regulator of the FtsH complex activity. The results also suggest that the complex may be involved in the chloroplast response to different types of stress conditions. In order to shed some light on the evolutionary history of FtsH5 and FIP interacting proteins, we have shown that FIP\'s homologous sequences were exclusively found in mosses and higher plants, suggesting that FIP origin might be related to the plant terrestrial colonization. All Arabidopsis FtsH complex-encoding genes were used as \"query\" sequences in search for homologous sequences, allowing us to classify the FtsH proteases in type A and B by Bayesian phylogenetic inference. Bayesian phylogenetic analyses were also run for FIP and FtsH types A and B proteases, independently. Mirrortree analysis supported coevolution between FIP and type A FtsH proteases. On the other hand, no correlation was found between FIP and type B FtsH homologues, which support our previous experimental observations. In addition, the FIP bearing cluster could be recovered in a more complete type A FtsH phylogeny. Subsequent analyzes have shown that both interacting proteins are extensively under negative selection and that type A FtsH are very conserved, mainly in its inner domains.

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50

Petretto, Emanuele <1989&gt. "Computational Study of Solvent Effects on the Stability of Native Structures in Proteins". Master's Degree Thesis, Università Ca' Foscari Venezia, 2018. http://hdl.handle.net/10579/12078.

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The commonly accepted protein folding mechanism hinges upon the idea that all the information required for a protein to reach the native conformation are encoded in its primary sequence. However, an equally important role is played by the interaction with the solvent, as recent both experimental and computational studies have clarified. The present thesis will build upon these study to investigate the stability of few representative proteins in the presence of solvents of different nature, ranging from highly polar, as water, to highly non-polar, as ciclohexane. This task will be pursued using a two fold approach. In the first approach, we will collaborate with a group at the University of Kyoto to compare the solvation free energy differences for proteins folding into different solvents, as compared with a number of in-house generated decoys. Within the framework we will develop a tool capable to build several decoys with a wide variety of α-helix and β-sheet contents and three-dimensional misfolded structures. In the second approach, we will use thermodynamic integration and molecular dynamics simulations to compute the same free energy difference with the aim of disentangling the entropic and the enthalpic contributions. This will be carried out at the level of single amino acids both in water and in cyclohexane. The aim of this second part will be to back up with a detailed numerical calculations the results of the approximate calculations carried out in the first part.

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