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Dissertations / Theses on the topic 'Protein sequence evolution'

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Published: 14 March 2023

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1

Hollich, Volker. "Orthology and protein domain architecture evolution /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-783-9/.

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2

Kosiol, Carolin. "Markov models for protein sequence evolution." Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.614166.

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3

Warnecke, Tobias. "Determinants of coding sequence evolution- beyong protein function." Thesis, University of Bath, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.531341.

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4

Guney, Tacettin Dogacan. "Prediction Of Protein-protein Interactions From Sequence Using Evolutionary Relations Of Proteins And Species." Master's thesis, METU, 2009. http://etd.lib.metu.edu.tr/upload/12611058/index.pdf.

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Prediction of protein-protein interactions is an important part in understanding the biological processes in a living cell. There are completely sequenced organisms that do not yet have experimentally verified protein-protein interaction networks. For such organisms, we can not generally use a supervised method, where a portion of the protein-protein interaction network is used as training set. Furthermore, for newly-sequenced organisms, many other data sources, such as gene expression data and gene ontology annotations, that are used to identify protein-protein interaction networks may not be

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5

Davies, L. "Sequence database searching using structural models of protein evolution." Thesis, University of Cambridge, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.598371.

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Commonly used programs to search sequence databases such as BLAST, FASTA and SSEARCH identify sequence homology through pairwise alignment techniques. These programs are good at detecting closely related sequences but have problems accurately detecting homologous sequences with low sequence identity. This thesis describes a new approach that attempts to improve the detection of distantly related sequences by rejecting the assumption that all sites in a protein behave in an identical manner. This is done without the use of profile techniques, which require the preliminary collection of a set of

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6

Wistrand, Markus. "Hidden Markov models for remote protein homology detection /." Stockholm, 2005. http://diss.kib.ki.se/2006/91-7140-598-4/.

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7

Nordesjö, Olle. "Searching for novel protein-protein specificities using a combined approach of sequence co-evolution and local structural equilibration." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-275040.

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Greater understanding of how we can use protein simulations and statistical characteristics of biomolecular interfaces as proxies for biological function will make manifest major advances in protein engineering. Here we show how to use calculated change in binding affinity and coevolutionary scores to predict the functional effect of mutations in the interface between a Histidine Kinase and a Response Regulator. These proteins participate in the Two-Component Regulatory system, a system for intracellular signalling found in bacteria. We find that both scores work as proxies for functional muta

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8

Höglund, Pär J. "Identification, Characterization and Evolution of Membrane-bound Proteins /." Uppsala : Acta Universitatis Upsaliensis Acta Universitatis Upsaliensis, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-9329.

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9

Dubey, Anshul. "Search and Analysis of the Sequence Space of a Protein Using Computational Tools." Diss., Georgia Institute of Technology, 2006. http://hdl.handle.net/1853/14115.

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A new approach to the process of Directed Evolution is proposed, which utilizes different machine learning algorithms. Directed Evolution is a process of improving a protein for catalytic purposes by introducing random mutations in its sequence to create variants. Through these mutations, Directed Evolution explores the sequence space, which is defined as all the possible sequences for a given number of amino acids. Each variant sequence is divided into one of two classes, positive or negative, according to their activity or stability. By employing machine learning algorithms for feature selec

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10

Randall, Ryan Nicole. "Experimental phylogenetics: a benchmark for ancestral sequence reconstruction." Thesis, Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/48998.

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The field of molecular evolution has benefited greatly from the use of ancestral sequence reconstruction as a methodology to better understand the molecular mechanisms associated with functional divergence. The method of ancestral sequence reconstruction has never been experimentally validated despite the method being exploited to generate high profile publications and gaining wider use in many laboratories. The failure to validate such a method is a consequence of 1) our inability to travel back in time to document evolutionary transitions and 2) the slow pace of natural evolutionary processe

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11

Chan, Yvonne H. "The Complex Role of Sequence and Structure in the Stability and Function of the TIM Barrel Proteins." eScholarship@UMMS, 2011. http://escholarship.umassmed.edu/gsbs_diss/934.

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Sequence divergence of orthologous proteins enables adaptation to a plethora of environmental stresses and promotes evolution of novel functions. As one of the most common motifs in biology capable of diverse enzymatic functions, the TIM barrel represents an ideal model system for mapping the phenotypic manifestations of protein sequence. Limits on evolution imposed by constraints on sequence and structure were investigated using a model TIM barrel protein, indole-3-glycerol phosphate synthase (IGPS). Exploration of fitness landscapes of phylogenetically distant orthologs provides a strategy f

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12

Chan, Yvonne H. "The Complex Role of Sequence and Structure in the Stability and Function of the TIM Barrel Proteins." eScholarship@UMMS, 2017. https://escholarship.umassmed.edu/gsbs_diss/934.

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Sequence divergence of orthologous proteins enables adaptation to a plethora of environmental stresses and promotes evolution of novel functions. As one of the most common motifs in biology capable of diverse enzymatic functions, the TIM barrel represents an ideal model system for mapping the phenotypic manifestations of protein sequence. Limits on evolution imposed by constraints on sequence and structure were investigated using a model TIM barrel protein, indole-3-glycerol phosphate synthase (IGPS). Exploration of fitness landscapes of phylogenetically distant orthologs provides a strategy f

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13

Menlove, Kit J. "Model Detection Based upon Amino Acid Properties." BYU ScholarsArchive, 2010. https://scholarsarchive.byu.edu/etd/2253.

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Similarity searches are an essential component to most bioinformatic applications. They form the bases of structural motif identification, gene identification, and insights into functional associations. With the rapid increase in the available genetic data through a wide variety of databases, similarity searches are an essential tool for accessing these data in an informative and productive way. In our chapter, we provide an overview of similarity searching approaches, related databases, and parameter options to achieve the best results for a variety of applications. We then provide a worked e

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14

Stern, Joshua Gallant. "STORI: selectable taxon ortholog retrieval iteratively." Thesis, Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/53377.

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Speciation and gene duplication are fundamental evolutionary processes that enable biological innovation. For over a decade, biologists have endeavored to distinguish orthology (homology caused by speciation) from paralogy (homology caused by duplication). Disentangling orthology and paralogy is useful to diverse fields such as phylogenetics, protein engineering, and genome content comparison. A common step in ortholog detection is the computation of Bidirectional Best Hits (BBH). However, we found this computation impractical for more than 24 Eukaryotic proteomes. Attempting to retrieve orth

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15

Capella, Gutiérrez Salvador Jesús 1985. "Analysis of multiple protein sequence alignments and phylogenetic trees in the context of phylogenomics studies." Doctoral thesis, Universitat Pompeu Fabra, 2012. http://hdl.handle.net/10803/97289.

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Phylogenomics is a biological discipline which can be understood as the intersection of the fields of genomics and evolution. Its main focuses are the analyses of genomes through the evolutionary lens and the understanding of how different organisms relate to each other. Moreover, phylogenomics allows to make accurate functional annotations of newly sequenced genomes. This discipline has grown in response to the deluge of data coming from different genome projects. To achieve their objectives, phylogenomics heavily depends on the accuracy of different methods to generate precise phyloge

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16

Kratzer, James Timothy. "Reengineering a human-like uricase for the treatment of gout." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/52149.

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There is an unmet medical need in the treatment of gout. This type of inflammatory arthritis can be efficiently alleviated by the enzyme uricase. This enzyme breaks down uric acid, the causative agent of gout, so it can be flushed from the body. In humans and the other great apes, uricase is a pseudogene and as such is inactive. Research on therapeutic uricases has focused on using enzymes from naturally occurring sources; however, these foreign proteins can be very antigenic and present a potentially life-threatening safety risk to patients. We address the challenges of developing a safer uri

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17

WEBER, M. ELISABETH. "Transporteurs de pyrimidines chez saccharomyces cerevisiae : sequence de deux genes et prediction de structure des proteines correspondantes." Université Louis Pasteur (Strasbourg) (1971-2008), 1987. http://www.theses.fr/1987STR13197.

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18

Pond, Sergei L. "Modeling evolution of protein coding DNA sequences." Diss., The University of Arizona, 2003. http://hdl.handle.net/10150/289906.

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We develop a new class of computationally feasible stochastic models for statistical analysis of genetic sequence evolution and inference of properties of the underlying substitution processes in the context of maximum likelihood framework. Existing models for evolution of protein coding sequences allow site to site variation in non-synonymous substitution rates, but assume that the rate of synonymous substitutions is constant for all sites. New models provide a rigorous statistical framework for testing the hypothesis of synonymous rate constancy, and enable a host of data exploration and ana

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19

Gregory, Matthew Alan. "Characterisation and evolution of homoimmune Streptomyces bacteriophages." Thesis, University of Nottingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.324534.

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20

Ekman, Diana, and Arne Elofsson. "Identifying and Quantifying Orphan Protein Sequences in Fungi." Stockholms universitet, Institutionen för biokemi och biofysik, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-49277.

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For large regions of many proteins, and even entire proteins, no homology to known domains or proteins can be detected. These sequences are often referred to as orphans. Surprisingly, it has been reported that the large number of orphans is sustained in spite of a rapid increase of available genomic sequences. However, it is believed that de novo creation of coding sequences is rare in comparison to mechanisms such as domain shuffling and gene duplication; hence, most sequences should have homologs in other genomes. To investigate this, the sequences of 19 complete fungi genomes were compared.

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21

Bianchetti, Laurent. "Intégration de l'évolution pour contribuer à l'étude de la relation séquence, structure, fonction des protéines." Thesis, Strasbourg, 2019. https://publication-theses.unistra.fr/restreint/theses_doctorat/2019/bianchetti_laurent_2019_ED414.pdf.

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Intégrer l’évolution peut aider à comprendre la relation séquence, structure, fonction des protéines. Dans un 1er projet, j’ai utilisé la phylogénèse moléculaire pour montrer que les gènes Testis expressed 19 » (Tex19) et « Secreted and transmembrane 1 » (Sectm1) coévoluent. Bien que Tex19 et Sectm1 interviennent dans des processus biologiques différents, régulation des transposons et immunité respectivement, la coévolution établit entre eux un lien fonctionnel très fort. Comme Tex19 ne s’exprime que dans le testicule de l’adulte sain et en cellule cancéreuse, ce résultat pourrait présenter un

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22

Holder, Mark Travis. "Using a complex model of sequence evolution to evaluate and improve phylogenetic methods." Access restricted to users with UT Austin EID Full text (PDF) from UMI/Dissertation Abstracts International, 2001. http://wwwlib.umi.com/cr/utexas/fullcit?p3037500.

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23

Hill, E. E. "Evolution of protein families : genome sequences and three dimensional structures." Thesis, University of Cambridge, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.604054.

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The aim here is to investigate the relationship between sequence and structure for families of structurally related proteins with low sequence identity in order to determine any conserved positions and define them. We do this in two main ways: (i) Evolution of Three Dimensional Structures The members of the 4-helical cytokine superfamily of proteins have no significant sequence identity. Despite this superfamilies' low to non-existent sequence similarity their homology is inferred by their common structural and functions. We carry out an in depth analysis of the long and short chain families b

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24

Wintz, Henri. "Contribution a l'etude de l'organisation et de la structure des genes de rna de transfert mitochondriaux des plantes." Université Louis Pasteur (Strasbourg) (1971-2008), 1988. http://www.theses.fr/1988STR13008.

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Les genes codant pour le trna**(phe), trna**(trp), trna**(typ), trna**(met), trna**(pro), trna**(asp) et trna**(his) ont ete identifies a l'aide de trnas isoaccepteurs purifies et d'oligonucleotide de synthese. Localisation des genes de trna chloroplastiques presents dans le genome mitochondrial de mais. Determination de la sequence nucleotidique de deux genes de trna (trna**(cys) et trna**(ser)) et d'un pseudo-gene de trna**(pne) inactive par la presence d'une insertion dans la sequence codante du gene. Le gene de trna**(cys) fait partie d'une insertion de pna chloroplastique dans le genome m

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25

Anderson, Jon Paul. "Molecular diversity and evolution of human immunodeficiency virus type 1 /." Thesis, Connect to this title online; UW restricted, 1999. http://hdl.handle.net/1773/8049.

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26

Radó, i. Trilla Núria 1985. "Low-complexity regions in proteins as a source of evolutionary innovation." Doctoral thesis, Universitat Pompeu Fabra, 2013. http://hdl.handle.net/10803/113603.

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In this thesis we aimed to study evolutionary implications of low-complexity regions, protein sequences of very simple amino acid composition. Its uncontrolled expansion causes several human diseases, including Huntington’s disease and other neurodegenerative and developmental diseases. However, they are surprisingly abundant in proteins, which seem paradoxical given their high pathogenic potential. Moreover, experimental data has shown that the formation of novel LCRs, or the modification of existing ones, can have functional consequences. First we wanted to perform a descriptive anal

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27

Groussin, Mathieu. "Résurrection du passé à l’aide de modèles hétérogènes d’évolution des séquences protéiques." Thesis, Lyon 1, 2013. http://www.theses.fr/2013LYO10201/document.

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La reconstruction et la résurrection moléculaire de protéines ancestrales est au coeur de cette thèse. Alors que les données moléculaires fossiles sont quasi inexistantes, il est possible d'estimer quelles étaient les séquences ancestrales les plus probables le long d'un arbre phylogénétique décrivant les relations de parentés entre séquences actuelles. Avoir accès à ces séquences ancestrales permet alors de tester de nombreuses hypothèses biologiques, de la fonction des protéines ancestrales à l'adaptation des organismes à leur environnement. Cependant, ces inférences probabilistes de séquenc

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28

Wood, Natasha Tandi. "Modelling the Evolution of HIV-1 Protein-Coding Sequences with Particular focus on the early stages of Infection." Doctoral thesis, University of Cape Town, 2010. http://hdl.handle.net/11427/4352.

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Modelling the Evolution of HIV-1 Protein-Coding Sequences with Particular Focus on the Early Stages of Infection Natasha Thandi Wood, February 2010 The evolution of the viral genome sequence over the course of HIV-1 infection is of interest for vaccine and drug design, and for the development of effective treatment strategies. Characteristics of the transmitted viral genome that could render the virus more sensitive to host immune responses, are of particular interest for vaccine studies. However, sequence samples from the earliest phase of HIV infection are scarce, and inferences about the na

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29

Delorme, Marie-Odile. "Analyse des sequences biologiques par des methodes d'apprentissage numerique et symbolique." Paris 6, 1988. http://www.theses.fr/1988PA066188.

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30

Nadaradjane, Aravindan. "Exploring the use of Deep Mutational Scanning and of Evolution for the Structural Prediction of Protein Complexes." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASS014.

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L’objectif de cette thèse a été de développer des stratégies computationnelles permettant d’exploiter les informations issues des technologies de mutagenèse à haut débit (deep mutational scanning, DMS) pour prédire le mode d’assemblage des protéines. Pour cela, j’ai cherché à améliorer l’accord entre les modèles simulés par les techniques d’amarrage moléculaire et les contraintes expérimentales. Deux complexes de référence dont les structures ont été résolues expérimentalement et pour lesquels les données de DMS ont été publiées ont été utilisés pour la mise au point de ces méthodes, les compl

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31

Nosek, Ondřej. "Hardwarová akcelerace algoritmu pro hledání podobnosti dvou DNA řetězců." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2007. http://www.nusl.cz/ntk/nusl-236882.

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Methods for aproximate string matching of various sequences used in bioinformatics are crucial part of development in this branch. Tasks are of very large time complexity and therefore we want create a hardware platform for acceleration of these computations. Goal of this work is to design a generalized architecture based on FPGA technology, which can work with various types of sequences. Designed acceleration card will use especially dynamic algorithms like Needleman-Wunsch and Smith-Waterman.

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32

Buck, Michael Joseph. "Protein evolution from sequence to structure." 2003. http://www.lib.ncsu.edu/theses/available/etd-05192003-144950/unrestricted/etd.pdf.

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33

Bhaskara, Ramachandra M. "Structure, Stability and Evolution of Multi-Domain Proteins." Thesis, 2013. http://etd.iisc.ernet.in/2005/3384.

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Analyses of protein sequences from diverse genomes have revealed the ubiquitous nature of multi-domain proteins. They form up to 70% of proteomes of most eukaryotic organisms. Yet, our understanding of protein structure, folding and evolution has been dominated by extensive studies on single-domain proteins. We provide quantitative treatment and proof for prevailing intuitive ideas on the strategies employed by nature to stabilize otherwise unstable domains. We find that domains incapable of independent stability are stabilized by favourable interactions with tethered domains in the multi-doma

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34

Mohaddes, Zia. "Modeling protein evolution using secondary structures." Thèse, 2010. http://hdl.handle.net/1866/4767.

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L’évolution des protéines est un domaine important de la recherche en bioinformatique et catalyse l'intérêt de trouver des outils d'alignement qui peuvent être utilisés de manière fiable et modéliser avec précision l'évolution d'une famille de protéines. TM-Align (Zhang and Skolnick, 2005) est considéré comme l'outil idéal pour une telle tâche, en termes de rapidité et de précision. Par conséquent, dans cette étude, TM-Align a été utilisé comme point de référence pour faciliter la détection des autres outils d'alignement qui sont en mesure de préciser l'évolution des protéines. En parallèle, n

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35

Pandya, Chetanya. "Sequence- and structure-based approaches to deciphering enzyme evolution in the Haloalkonoate Dehalogenase superfamily." Thesis, 2014. https://hdl.handle.net/2144/15107.

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Understanding how changes in functional requirements of the cell select for changes in protein sequence and structure is a fundamental challenge in molecular evolution. This dissertation delineates some of the underlying evolutionary forces using as a model system, the Haloalkanoate Dehalogenase Superfamily (HADSF). HADSF members have unique cap-core architecture with the Rossmann-fold core domain accessorized by variable cap domain insertions (delineated by length, topology, and point of insertion). To identify the boundaries of variable domain insertions in protein sequences, I have dev

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36

Scherrer, Michael Paul. "From the inside out : determining sequence conservation within the context of relative solvent accessibility." 2013. http://hdl.handle.net/2152/21613.

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Evolutionary rates vary vastly across intraspecific genes and the determinants of these rates is of central concern to the field of comparative genomics. Tradition has held that preservation of protein function conserved the sequence, however mounting evidence implicates the biophysical properties of proteins themselves as the elements that constrain sequence evolution. Of these properties, the exposure of a residue to solvent is the most prevalent determinant of its evolutionary rate due to pressures to maintain proper synthesis and folding of the structure. In this work, we have developed

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37

Ptáčková, Barbora. "Strukturní charakterizace vybraných náhodných proteinových sekvencí s vysokým obsahem neuspořádanosti." Master's thesis, 2018. http://www.nusl.cz/ntk/nusl-379356.

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An infinitesimal fraction of the practically infinite sequence space has achieved enormous functional diversity of proteins during evolution. Intrinsically disordered proteins (IDPs) which lack a fully defined three-dimensional structure are the most likely precursors to today's proteins because of their flexible conformation and functional diversity. But how have these proteins evolved into often rigid and highly specialized protein structures? This evolutionary trajectory has the greatest support in the theory of induced fold whereby the development of the structure was mediated by the inter

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38

van, Hazel Ilke. "Molecular Evolution and Functional Characterization of the Visual Pigment Proteins of the Great Bowerbird (Chlamydera nuchalis) and Other Vertebrates." Thesis, 2012. http://hdl.handle.net/1807/43401.

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Visual pigments are light sensitive receptors in the eye that form the basis of sensory visual transduction. This thesis presents three studies that explore visual pigment proteins in vertebrates using a number of computational and experimental methods in an evolutionary framework. The objective is not only to identify, but also to experimentally investigate the functional consequences of genetic variation in vertebrate visual pigments. The focus is on great bowerbirds (Chlamydera nuchalis), which are a model system in visual ecology due to their spectacular behaviour of building and decoratin

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39

Tsai, Tsung Yu, and 蔡宗佑. "Analyze the relationships among functions、sequences and structures of protein folds based on structure evolution." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/82960481964409613076.

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碩士<br>國立清華大學<br>資訊系統與應用研究所<br>93<br>Central dogma of molecular biology states that DNA carries the genetic information which is transcribed to mRNA and subsequently translated to protein. And function of protein is determined from protein structure. Widespread researches all use the sequence alignment to join the structure information to find out the latent function. This method often causes not alike or relationship of evolutionary the farther sequence can't find out the function. According to this, the usage of structure alignment builds up evolutionary tree in this thesis, by the structure

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40

Dickinson, GH, IE Vega, KJ Wahl, et al. "Barnacle cement: a polymerization model based on evolutionary concepts." Thesis, 2009. http://hdl.handle.net/10161/653.

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Enzymes and biochemical mechanisms essential to survival are under extreme selective pressure and are highly conserved through evolutionary time. We applied this evolutionary concept to barnacle cement polymerization, a process critical to barnacle fitness that involves aggregation and cross-linking of proteins. The biochemical mechanisms of cement polymerization remain largely unknown. We hypothesized that this process is biochemically similar to blood clotting, a critical physiological response that is also based on aggregation and cross-linking of proteins. Like key elements of vertebrate a

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41

Shen, Yaoqing. "In silico analysis of mitochondrial proteins." Thèse, 2009. http://hdl.handle.net/1866/3766.

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Le rôle important joué par la mitochondrie dans la cellule eucaryote est admis depuis longtemps. Cependant, la composition exacte des mitochondries, ainsi que les processus biologiques qui sy déroulent restent encore largement inconnus. Deux facteurs principaux permettent dexpliquer pourquoi létude des mitochondries progresse si lentement : le manque defficacité des méthodes didentification des protéines mitochondriales et le manque de précision dans lannotation de ces protéines. En conséquence, nous avons développé un nouvel outil informatique, YimLoc, qui permet de prédire avec succès les pr

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