The structure of protein evolution and the evolution of protein structure.

The observed distribution of protein structures can give us important clues about the underlying evolutionary process, imposing important constraints on possible models. The availability of results from an increasing number of genome projects has made the development of these models an active area of research. Models explaining the observed distribution of structures have focused on the inherent functional capabilities and structural properties of different folds and on the evolutionary dynamics. Increasingly, these elements are being combined.

[1]  Eric J. Deeds,et al.  The emergence of scaling in sequence-based physical models of protein evolution. , 2004, Biophysical journal.

[2]  Erich Bornberg-Bauer,et al.  Recombinatoric exploration of novel folded structures: A heteropolymer-based model of protein evolutionary landscapes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[3]  P. Schuster,et al.  Chance and necessity in evolution: lessons from RNA , 1998, physics/9811037.

[4]  Dan S. Tawfik,et al.  Conformational diversity and protein evolution--a 60-year-old hypothesis revisited. , 2003, Trends in biochemical sciences.

[5]  Ned S. Wingreen,et al.  Designability, thermodynamic stability, and dynamics in protein folding: A lattice model study , 1998, cond-mat/9806197.

[6]  N S Wingreen,et al.  Are protein folds atypical? , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Benjamin P. Blackburne,et al.  Population dynamics simulations of functional model proteins. , 2005, The Journal of chemical physics.

[8]  Frances H Arnold,et al.  Structural determinants of the rate of protein evolution in yeast. , 2006, Molecular biology and evolution.

[9]  E. Bornberg-Bauer,et al.  How are model protein structures distributed in sequence space? , 1997, Biophysical journal.

[10]  Paul D. Williams,et al.  SELECTIVE ADVANTAGE OF RECOMBINATION IN EVOLVING PROTEIN POPULATIONS: A LATTICE MODEL STUDY. , 2006, International journal of modern physics. C, Physics and computers.

[11]  Paul D. Williams,et al.  Functionality and the evolution of marginal stability in proteins: Inferences from lattice simulations , 2006, Evolutionary bioinformatics online.

[12]  Eugene I Shakhnovich,et al.  Structural determinant of protein designability. , 2002, Physical review letters.

[13]  Dan S. Tawfik,et al.  Evolution of new protein topologies through multistep gene rearrangements , 2006, Nature Genetics.

[14]  Andrey Rzhetsky,et al.  Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome , 2001, Bioinform..

[15]  I. Shmulevich,et al.  Computational and Statistical Approaches to Genomics , 2007, Springer US.

[16]  V. Kuznetsov Statistics of the Numbers of Transcripts and Protein Sequences Encoded in the Genome , 2003 .

[17]  Teresa M. Przytycka,et al.  Scale-free networks versus evolutionary drift , 2004, Comput. Biol. Chem..

[18]  Erich Bornberg-Bauer,et al.  A structural model of latent evolutionary potentials underlying neutral networks in proteins. , 2007, HFSP journal.

[19]  P. Gettins,et al.  The role of conformational change in serpin structure and function , 1993, BioEssays : news and reviews in molecular, cellular and developmental biology.

[20]  O. White,et al.  Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.

[21]  Sebastian Bonhoeffer,et al.  Evolution of complexity in signaling pathways , 2006, Proceedings of the National Academy of Sciences.

[22]  Eugene I Shakhnovich,et al.  Physical origins of protein superfamilies. , 2005, Journal of molecular biology.

[23]  Benjamin P. Blackburne,et al.  Three-dimensional functional model proteins: Structure function and evolution , 2003 .

[24]  J. Banfield,et al.  Community structure and metabolism through reconstruction of microbial genomes from the environment , 2004, Nature.

[25]  Benjamin P. Blackburne,et al.  Evolution of functional model proteins , 2001 .

[26]  W. Fontana,et al.  Plasticity, evolvability, and modularity in RNA. , 2000, The Journal of experimental zoology.

[27]  S. Govindarajan,et al.  Why are some protein structures so common ? ( tertiary structure y protein evolution y lattice models y fitness landscapes y spin glasses ) , 1998 .

[28]  E. Nimwegen Scaling Laws in the Functional Content of Genomes , 2003, physics/0307001.

[29]  Richard A. Goldstein,et al.  Surveying determinants of protein structure designability across different energy models and amino-acid alphabets: A consensus , 2000 .

[30]  Sung-Hou Kim,et al.  Evolution of protein structural classes and protein sequence families , 2006, Proceedings of the National Academy of Sciences.

[31]  William R. Taylor,et al.  Topological accessibility shows a distinct asymmetry in the folds of βα proteins , 2006 .

[32]  Eugene I. Shakhnovich,et al.  Natural selection of more designable folds: A mechanism for thermophilic adaptation , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[33]  A. Lapedes,et al.  Exploring protein sequence space using knowledge-based potentials. , 2001, Journal of theoretical biology.

[34]  Eugene I Shakhnovich,et al.  Expanding protein universe and its origin from the biological Big Bang , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Eugene I Shakhnovich,et al.  Physics and evolution of thermophilic adaptation. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[36]  David R. Gilbert,et al.  Assessment of the probabilities for evolutionary structural changes in protein folds , 2007, Bioinform..

[37]  Jayanth R Banavar,et al.  Physics of proteins. , 2007, Annual review of biophysics and biomolecular structure.

[38]  William R. Taylor,et al.  Protein knots and fold complexity: Some new twists , 2007, Comput. Biol. Chem..

[39]  M. Gerstein,et al.  Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model. , 2001, Journal of molecular biology.

[40]  Lisa N Kinch,et al.  Evolution of protein structures and functions. , 2002, Current opinion in structural biology.

[41]  P. Schuster,et al.  From sequences to shapes and back: a case study in RNA secondary structures , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[42]  E. Bornberg-Bauer,et al.  Evolution of circular permutations in multidomain proteins. , 2006, Molecular biology and evolution.

[43]  F. Arnold,et al.  Protein stability promotes evolvability. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[44]  Daniel W. A. Buchan,et al.  Evolution of protein superfamilies and bacterial genome size. , 2004, Journal of molecular biology.

[45]  Eugene I Shakhnovich,et al.  Divergent evolution of a structural proteome: phenomenological models. , 2007, Biophysical journal.

[46]  Lvek,et al.  Evolution of protein structures and functions , 2022 .

[47]  M. Lynch,et al.  The evolutionary fate and consequences of duplicate genes. , 2000, Science.

[48]  A V Finkelstein,et al.  Boltzmann-like statistics of protein architectures. Origins and consequences. , 1995, Sub-cellular biochemistry.

[49]  Richard A. Goldstein,et al.  Searching for foldable protein structures using optimized energy functions , 1995 .

[50]  J. Skolnick,et al.  On the origin and highly likely completeness of single-domain protein structures. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[51]  Guido Tiana,et al.  Imprint of evolution on protein structures. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[52]  Eric J. Deeds,et al.  Protein structure and evolutionary history determine sequence space topology. , 2004, Genome research.

[53]  K. Baeck The analytic gradient for the equation-of-motion coupled-cluster energy with a reduced molecular orbital space: An application for the first excited state of formaldehyde , 2000 .

[54]  ECOLI SODF,et al.  Analogous Enzymes : Independent Inventions in Enzyme Evolution , 1998 .

[55]  Eric J. Deeds,et al.  Protein evolution within a structural space. , 2003, Biophysical journal.

[56]  Carsten Wiuf,et al.  Subnets of scale-free networks are not scale-free: sampling properties of networks. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[57]  P. Wolynes,et al.  Protein tertiary structure recognition using optimized Hamiltonians with local interactions. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[58]  Duilio Cascio,et al.  Discovery of a thermophilic protein complex stabilized by topologically interlinked chains. , 2007, Journal of molecular biology.

[59]  Michael Levitt,et al.  Roles of mutation and recombination in the evolution of protein thermodynamics , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[60]  A. Finkelstein,et al.  Why are the same protein folds used to perform different functions? , 1993, FEBS letters.

[61]  P. Wolynes,et al.  Optimal protein-folding codes from spin-glass theory. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[62]  E. Koonin,et al.  The structure of the protein universe and genome evolution , 2002, Nature.

[63]  Charlotte M. Deane,et al.  How old is your fold? , 2005, ISMB.

[64]  A. Finkelstein,et al.  Why do protein architectures have boltzmann‐like statistics? , 1995, Proteins.

[65]  Eugene I. Shakhnovich,et al.  A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds , 2007, PLoS Comput. Biol..

[66]  L A Mirny,et al.  How to derive a protein folding potential? A new approach to an old problem. , 1996, Journal of molecular biology.

[67]  E I Shakhnovich,et al.  Protein design: a perspective from simple tractable models , 1998, Folding & design.

[68]  E. Koonin,et al.  Birth and death of protein domains: A simple model of evolution explains power law behavior , 2002, BMC Evolutionary Biology.

[69]  G. Rose,et al.  A backbone-based theory of protein folding , 2006, Proceedings of the National Academy of Sciences.

[70]  Charles DeLisi,et al.  Functional fingerprints of folds: evidence for correlated structure-function evolution. , 2003, Journal of molecular biology.

[71]  David A. Lee,et al.  Exploiting protein structure data to explore the evolution of protein function and biological complexity , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

[72]  Christoph Adami,et al.  Stability and the evolvability of function in a model protein. , 2004, Biophysical journal.

[73]  Rajgopal Srinivasan,et al.  Recursive domains in proteins , 2002, Protein science : a publication of the Protein Society.

[74]  J. Hirst,et al.  The evolutionary landscape of functional model proteins. , 1999, Protein engineering.

[75]  C DeLisi,et al.  Estimating the number of protein folds. , 1998, Journal of molecular biology.

[76]  N. Grishin Fold change in evolution of protein structures. , 2001, Journal of structural biology.

[77]  C. Orengo,et al.  Protein folds and functions. , 1998, Structure.

[78]  R A Goldstein,et al.  The distribution of structures in evolving protein populations. , 2000, Biopolymers.

[79]  P D Williams,et al.  Evolution of functionality in lattice proteins. , 2001, Journal of molecular graphics & modelling.

[80]  Eugene V Koonin,et al.  Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models , 2004, BMC Evolutionary Biology.

[81]  N. Wingreen,et al.  Emergence of Preferred Structures in a Simple Model of Protein Folding , 1996, Science.

[82]  Neil P King,et al.  Identification of rare slipknots in proteins and their implications for stability and folding. , 2007, Journal of molecular biology.

[83]  E. Koonin,et al.  Birth and Death Models of Genome Evolution , 2006 .

[84]  M. Huynen,et al.  The frequency distribution of gene family sizes in complete genomes. , 1998, Molecular biology and evolution.

[85]  C. Chothia,et al.  The immunoglobulin superfamily in Drosophila melanogaster and Caenorhabditis elegans and the evolution of complexity , 2003, Development.