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Protein Structure Comparison Based on Fold Evolution

Natalja Kurbatova, Laura Mancinska, Juris Viksna
2007 German Conference on Bioinformatics  
The search for such mutations is based on structure evolution models suggesting that, similarly as sequences, protein folds (at least partially) evolveb yas tepwise process, where each step comprises comparatively  ...  The particular fold mutations considered in this study are based on the work by Grishin [Gr01].  ...  structure comparison based on evolutionary changes.  ... 
dblp:conf/gcb/KurbatovaMV07 fatcat:3u2npdhgarfnvahocp5aebuwny

Functional evolution of PLP-dependent enzymes based on active-site structural similarities

Jonathan Catazaro, Adam Caprez, Ashu Guru, David Swanson, Robert Powers
2014 Proteins: Structure, Function, and Bioinformatics  
Many examples of protein evolution have been constructed based solely on sequence information.  ...  In this work we present the functional evolution of PLP-dependent enzymes based on active site structures.  ...  Branch lengths represent the evolutionary distance between enzymes based on active site structure comparisons.  ... 
doi:10.1002/prot.24624 pmid:24920327 pmcid:PMC4177364 fatcat:k4d7uy4v3vf6fi6x65s7b5roju

Convergent evolution in structural elements of proteins investigated using cross profile analysis

Kentaro Tomii, Yoshito Sawada, Shinya Honda
2012 BMC Bioinformatics  
To date, several methods such as those based on the results of structure comparisons, sequence-based classifications, and sequence-based profile-profile comparisons have been applied to identify such protein  ...  segments that possess local similarities in both sequence and structure across protein folds.  ...  On one hand, comparison of sequence-based profiles based on evolutionary information is known to be highly effective for protein fold recognition [11] , even when they are constructed without including  ... 
doi:10.1186/1471-2105-13-11 pmid:22244085 pmcid:PMC3398312 fatcat:dstcxyl7fjexngmog52csezt6i

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments

L. Xie, P. E. Bourne
2008 Proceedings of the National Academy of Sciences of the United States of America  
evolution) from those that have adopted common structural constraints (convergent evolution).  ...  functional site ͉ structure T he evolutionary relationship between protein sequences, protein structures, and their associated function(s) remains a central topic of molecular biology and one resulting  ...  This work was supported by National Institutes of Health Grants GM63208 and GM078596 and the Research Collaboratory for Structural Bioinformatics Protein Data Bank.  ... 
doi:10.1073/pnas.0704422105 pmid:18385384 pmcid:PMC2291117 fatcat:ncjgup3igzafrkyfc3xbdlscge

Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: Potential implications to evolution and to protein folding

Daniel Fischer, Haim Wolfson, Shuo L. Lin, Ruth Nussinov
2008 Protein Science  
of actindin against the structural data base containing 1,191 selected proteins from the PDB Comparison of actindin against the structural data base containing 1,191 selected proteins from the PDB Is  ...  40 minutes to compare one protein against the PDB database (1994) Figure 1 - 1 Comparison of α-chymotrypsin against 170 random proteins Figure 1 -Comparison of α-chymotrypsin against 170 random proteins  ...  Further Applications • Understanding misfolded proteins • Determining residues involved in conformation changes • Compare drugs for flexible pharmacophores  ... 
doi:10.1002/pro.5560030506 pmid:8061606 pmcid:PMC2142723 fatcat:zc4fcsa34zd2ncxzanoyvamp24

Evolution and disorder

Celeste J Brown, Audra K Johnson, A Keith Dunker, Gary W Daughdrill
2011 Current Opinion in Structural Biology  
Recent assessments of disordered protein evolution at the sequence, structural and functional levels support this hypothesis.  ...  specific structural ensembles.  ...  From these comparisons, models of protein evolution can be inferred based upon the frequency with which different amino acids occur at the same position among the homologues.  ... 
doi:10.1016/ pmid:21482101 pmcid:PMC3112239 fatcat:bcdpcdahlzejvjgzttzdduooru

Imprint of evolution on protein structures

G. Tiana, B. E. Shakhnovich, N. V. Dokholyan, E. I. Shakhnovich
2004 Proceedings of the National Academy of Sciences of the United States of America  
These results present a fundamental view on protein evolution highlighting the relative roles of structural selection and evolutionary dynamics on genesis of modern proteins.  ...  We attempt to understand the evolutionary origin of protein folds by simulating their divergent evolution with a three-dimensional lattice model.  ...  This version is based on a three-dimensional lattice model representation of protein structure.  ... 
doi:10.1073/pnas.0306638101 pmid:14970345 pmcid:PMC365708 fatcat:kyvi5xt6jbbhlj52opmglufahy

MANET: tracing evolution of protein architecture in metabolic networks

Hee Shin Kim, Jay E Mittenthal, Gustavo Caetano-Anollés
2006 BMC Bioinformatics  
depicting the evolution of protein fold architecture.  ...  The Molecular Ancestry Network (MANET) project traces evolution of protein architecture in biomolecular networks.  ...  We recently used an approach based on a census of folds to study protein diversification and reconstruct universal phylogenomic trees describing the evolution of protein fold architecture [27, 30, 31]  ... 
doi:10.1186/1471-2105-7-351 pmid:16854231 pmcid:PMC1559654 fatcat:vdp6uhww7jau3nkczazhlfcnsy

Catching a common fold

Tom L. Blundell, Mark S. Johnson
1993 Protein Science  
Attention was also distracted by an often fruitless argument on evolution. It seems likely that many protein  ...  However, such combinatorial approaches to the protein folding problem depend on correct assignment of a-helices, 0strands, and coils, and this remains a formidable challenge.  ...  Despite sharing this complex topology, the sequence identity based on structural comparisons is less than 10%.  ... 
doi:10.1002/pro.5560020602 pmid:8318893 pmcid:PMC2142408 fatcat:x4h7fjafejc5dp2upwwyjokm3u

The history of the CATH structural classification of protein domains

Ian Sillitoe, Natalie Dawson, Janet Thornton, Christine Orengo
2015 Biochimie  
We review the expansion of the CATH and SCOP resources to capture predicted domain structures in the genome sequence data and to provide information on the likely functions of proteins mediated by their  ...  This article presents a historical review of the protein structure classification database CATH.  ...  to begin classifications of protein families based on structure.  ... 
doi:10.1016/j.biochi.2015.08.004 pmid:26253692 pmcid:PMC4678953 fatcat:jb7v7o2f3fc37fjoc2lopkcy44

Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection

F. Morcos, N. P. Schafer, R. R. Cheng, J. N. Onuchic, P. G. Wolynes
2014 Proceedings of the National Academy of Sciences of the United States of America  
Under the quasiequilibrium selection hypothesis based on folding energy alone, given the physical free energy function E, the probability of any given sequence having attained a given fold can be computed  ...  T sel quantifies the importance of folded-state energetics and structural specificity for molecular evolution.  ...  To make this paper selfcontained, in SI Text, we review the corresponding statistical analyses of folding and evolution based on uncorrelated energy landscapes.  ... 
doi:10.1073/pnas.1413575111 pmid:25114242 pmcid:PMC4151759 fatcat:w3ddt3rmfrguhnrmatkfccjckm

Comparative computational structural genomics highlights divergent evolution of fungal effectors [article]

Kyungyong Seong, Ksenia V Krasileva
2022 bioRxiv   pre-print
We predicted the folds of 26,653 secreted proteins from 21 species with AlphaFold and performed structure-guided comparative analyses on two aspects of effector evolution: uniquely expanded effector families  ...  Structural comparisons revealed that the expanded structural folds further diversify through domain duplications and fusion with disordered stretches.  ...  Erin Baggs and Pierre Joubert for the critical review on the manuscript.  ... 
doi:10.1101/2022.05.02.490317 fatcat:ge7izugxqjbrrh6pnydgyotikq

Development of a motif-based topology-independent structure comparison method to identify evolutionarily related folds

Joseph M. Dybas, Andras Fiser
2016 Proteins: Structure, Function, and Bioinformatics  
However, the current structure classification systems are based on hierarchical organizations, which cannot accommodate structural relationships that span fold definitions.  ...  Here we describe a novel, supersecondary-structure motif-based, topology-independent structure comparison method (SmotifCOMP) that is able to quantitatively identify structural relationships between disparate  ...  Similar to the βpropeller domains, these three folds are also based on β-meander structures and, thus, may have followed a similar path in evolution as hypothesized for the β-propeller folds.  ... 
doi:10.1002/prot.25169 pmid:27671894 pmcid:PMC5118133 fatcat:ddl6eakfsvctlgd7gfnndwzwca

Computational structural genomics unravels common folds and novel families in the secretome of fungal phytopathogen Magnaporthe oryzae

Kyungyong Seong, Ksenia Krasileva
2021 Molecular Plant-Microbe Interactions  
These advances enabled a genome-wide computational structural biology approach to understand proteins based on their predicted folds.  ...  Recent breakthroughs in protein structure modeling have demonstrated the feasibility to predict the protein folds without depending on homologous structures.  ...  Evolution of putative ADP-ribose transferases (ARTs) informed through structural comparison.  ... 
doi:10.1094/mpmi-03-21-0071-r pmid:34415195 pmcid:PMC9447291 fatcat:rhoxvstnozavpopldp7eeu6m2q

A Structure-Centric View of Protein Evolution, Design and Adaptation [article]

Eric J. Deeds, Eugene I. Shakhnovich
2006 arXiv   pre-print
of structural evolution involves the divergence of protein sequences and structures from one another.  ...  Much of this work has focused on the question of how completely new protein structures (i.e. new folds or topologies) are discovered by protein sequences as they evolve.  ...  This model is based on the folding of 27-mer sequences into compact lattice structures and is based on a specific alphabet and potential energy function for which folding can be evaluated (which in our  ... 
arXiv:q-bio/0603028v1 fatcat:3o4cwhwf2jhghicwysyxywso2q
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