Contact Density Affects Protein Evolutionary Rate from Bacteria to Animals

[1]  Ron Elber,et al.  The network of sequence flow between protein structures , 2007, Proceedings of the National Academy of Sciences.

[2]  David L. Robertson,et al.  Specificity in protein interactions and its relationship with sequence diversity and coevolution , 2007, Proceedings of the National Academy of Sciences.

[3]  Wei-Lun Hsu,et al.  Proportion of solvent-exposed amino acids in a protein and rate of protein evolution. , 2007, Molecular biology and evolution.

[4]  Philip M. Kim,et al.  Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights , 2006, Science.

[5]  Todd O. Yeates,et al.  Proteins in a Small World , 2006, Science.

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

[7]  Boris E. Shakhnovich,et al.  Relative contributions of structural designability and functional diversity in molecular evolution of duplicates , 2006, ISMB.

[8]  C. Pál,et al.  An integrated view of protein evolution , 2006, Nature Reviews Genetics.

[9]  C. Wilke,et al.  A single determinant dominates the rate of yeast protein evolution. , 2006, Molecular biology and evolution.

[10]  Z. Weng,et al.  Structure, function, and evolution of transient and obligate protein-protein interactions. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[11]  C. Wilke,et al.  Why highly expressed proteins evolve slowly. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Bernardo Lemos,et al.  Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions. , 2005, Molecular biology and evolution.

[13]  A. E. Hirsh,et al.  Functional genomic analysis of the rates of protein evolution. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[14]  Jianzhi Zhang,et al.  Significant impact of protein dispensability on the instantaneous rate of protein evolution. , 2005, Molecular biology and evolution.

[15]  Matthew W. Hahn,et al.  Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. , 2005, Molecular biology and evolution.

[16]  Hunter B. Fraser,et al.  Modularity and evolutionary constraint on proteins , 2005, Nature Genetics.

[17]  Derek Huntley,et al.  Comparative analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans protein interaction networks , 2005, BMC Evolutionary Biology.

[18]  Edo Kussell,et al.  The designability hypothesis and protein evolution. , 2005, Protein and peptide letters.

[19]  Scott A. Rifkin,et al.  A Gene Expression Map for the Euchromatic Genome of Drosophila melanogaster , 2004, Science.

[20]  C. Wilke,et al.  Thermodynamic prediction of protein neutrality. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[21]  Sudhir Kumar,et al.  Gene Expression Intensity Shapes Evolutionary Rates of the Proteins Encoded by the Vertebrate Genome , 2004, Genetics.

[22]  Markus J. Herrgård,et al.  Integrating high-throughput and computational data elucidates bacterial networks , 2004, Nature.

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

[24]  S. Batalov,et al.  A gene atlas of the mouse and human protein-encoding transcriptomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[25]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[26]  Xiao Sun,et al.  The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens. , 2004, Bio Systems.

[27]  C. Adami,et al.  Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein–protein interactions data sets , 2003, BMC Evolutionary Biology.

[28]  K. Ekwall,et al.  Distinct centromere domain structures with separate functions demonstrated in live fission yeast cells , 2003, Journal of Cell Science.

[29]  D. Wall,et al.  Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia. , 2003, Microbiology.

[30]  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.

[31]  Laurence D. Hurst,et al.  Genomic function (communication arising): Rate of evolution and gene dispensability , 2003, Nature.

[32]  A. E. Hirsh,et al.  Genomic function (communication arising): Rate of evolution and gene dispensability , 2003, Nature.

[33]  Claudia Neuhauser,et al.  The Pattern of Amino Acid Replacements in α/β-Barrels , 2002 .

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

[35]  E. Koonin,et al.  Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. , 2002, Genome research.

[36]  A. E. Hirsh,et al.  Evolutionary Rate in the Protein Interaction Network , 2002, Science.

[37]  A. E. Hirsh,et al.  Protein dispensability and rate of evolution , 2001, Nature.

[38]  C. Pál,et al.  Highly expressed genes in yeast evolve slowly. , 2001, Genetics.

[39]  Laurent Duret,et al.  Synonymous Codon Usage, Accuracy of Translation, and Gene Length in Caenorhabditis elegans , 2001, Journal of Molecular Evolution.

[40]  L. Mirny,et al.  Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. , 1999, Journal of molecular biology.

[41]  Laurence D. Hurst,et al.  Do essential genes evolve slowly? , 1999, Current Biology.

[42]  L. Duret,et al.  Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[43]  Michael R. Green,et al.  Dissecting the Regulatory Circuitry of a Eukaryotic Genome , 1998, Cell.

[44]  M. Orešič,et al.  Specific correlations between relative synonymous codon usage and protein secondary structure. , 1998, Journal of molecular biology.

[45]  David C. Jones,et al.  Assessing the impact of secondary structure and solvent accessibility on protein evolution. , 1998, Genetics.

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

[47]  Ziheng Yang,et al.  PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..

[48]  P. Wolynes,et al.  Symmetry and the energy landscapes of biomolecules. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[49]  E. Ungewickell,et al.  Mechanism of clathrin basket dissociation: separate functions of protein domains of the DnaJ homologue auxilin , 1996, The Journal of cell biology.

[50]  Ross Ihaka,et al.  Gentleman R: R: A language for data analysis and graphics , 1996 .

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

[52]  R A Goldstein,et al.  Context-dependent optimal substitution matrices. , 1995, Protein engineering.

[53]  P. D’Eustachio,et al.  Separate domains of the Ran GTPase interact with different factors to regulate nuclear protein import and RNA processing , 1995, Molecular and cellular biology.

[54]  T. Creighton.  Proteins: Structures and Molecular Properties , 1986 .

[55]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[56]  J. Mandel.  Use of the Singular Value Decomposition in Regression Analysis , 1982 .

[57]  Eduardo P C Rocha,et al.  An analysis of determinants of amino acids substitution rates in bacterial proteins. , 2004, Molecular biology and evolution.

[58]  Takeshi Kawabata,et al.  GTOP: a database of protein structures predicted from genome sequences , 2002, Nucleic Acids Res..

[59]  C. Neuhauser,et al.  The Pattern of Amino Acid Replacements in a / b-Barrels , 2002 .

[60]  Michael Lappe,et al.  A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3 , 2001, Nucleic Acids Res..

[61]  L. Duret,et al.  Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. , 2000, Molecular biology and evolution.

[62]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .