Assessing and improving the accuracy of detecting protein adaptation with the TreeSAAP analytical software

TreeSAAP has been used in a variety of protein studies for detecting adaptation in terms of the physicochemical properties involved in amino acid replacement. The accuracy of TreeSAAP was here tested using simulated protein-coding DNA data. A sampling of 1402 simulated amino acid replacements resulted in a default accuracy of 81.1%, with most properties exhibiting >90% accuracy. More than half of the false-positive results were traced to just 11 of the 180 possible single-step amino acid exchanges. Overall accuracy increased as the number of magnitude partitions used in the analysis decreased. Sliding window size did not significantly affect accuracy.

[1]  P. Ponnuswamy,et al.  Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins. , 1980, Biochimica et biophysica acta.

[2]  P. Y. Chou,et al.  Prediction of the secondary structure of proteins from their amino acid sequence. , 2006 .

[3]  M. Michael Gromiha,et al.  Relationship Between Amino Acid Properties and Protein Compressibility , 1993 .

[4]  Minoru Kanehisa,et al.  AAindex: Amino Acid index database , 2000, Nucleic Acids Res..

[5]  N. Goldman,et al.  Codon-substitution models for heterogeneous selection pressure at amino acid sites. , 2000, Genetics.

[6]  R. Nielsen,et al.  Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. , 2002, Molecular biology and evolution.

[7]  Ziheng Yang,et al.  Statistical methods for detecting molecular adaptation , 2000, Trends in Ecology & Evolution.

[8]  C R Woese,et al.  The molecular basis for the genetic code. , 1966, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Variation of amino acid properties in protein secondary structures, α-helices and β-strands , 2009 .

[10]  Pedro A Fernandes,et al.  Comparative evolutionary genomics of the HADH2 gene encoding Aβ-binding alcohol dehydrogenase/17β-hydroxysteroid dehydrogenase type 10 (ABAD/HSD10) , 2006, BMC Genomics.

[11]  R. Grantham.  Amino Acid Difference Formula to Help Explain Protein Evolution , 1974, Science.

[12]  P K Ponnuswamy,et al.  Dynamics of amino acid residues in globular proteins. , 2009, International journal of peptide and protein research.

[13]  Mark J. Clement,et al.  Pharmacogenomics: analysing SNPs in the CYP2D6 gene using amino acid properties , 2007, Int. J. Bioinform. Res. Appl..

[14]  A. Antunes,et al.  Structural and functional implications of positive selection at the primate angiogenin gene , 2007, BMC Evolutionary Biology.

[15]  Mark J. Rowe,et al.  Evolutionary selective pressure on three mitochondrial SNPs is consistent with their influence on metabolic efficiency in Pima Indians , 2007, Int. J. Bioinform. Res. Appl..

[16]  K. McCracken,et al.  Estimating the influence of selection on the variable amino acid sites of the cytochrome B protein functional domains. , 2001, Molecular biology and evolution.

[17]  M. Pérez‐Losada,et al.  Population genetics of Neisseria gonorrhoeae in a high-prevalence community using a hypervariable outer membrane porB and 13 slowly evolving housekeeping genes. , 2005, Molecular biology and evolution.

[18]  Roger L. Lundblad,et al.  Handbook of Biochemistry and Molecular Biology, Fifth Edition , 2010 .

[19]  K. Holsinger.  The neutral theory of molecular evolution , 2004 .

[20]  Frederic M. Richards,et al.  Packing of α-helices: Geometrical constraints and contact areas☆ , 1978 .

[21]  M. Prabhakaran,et al.  The distribution of physical, chemical and conformational properties in signal and nascent peptides. , 1990, The Biochemical journal.

[22]  P. Y. Chou,et al.  Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. , 1974, Biochemistry.

[23]  R. Christensen,et al.  Physicochemical evolution and molecular adaptation of the cetacean and artiodactyl cytochrome b proteins. , 2005, Molecular biology and evolution.

[24]  R. Christensen,et al.  Genetic codes as evolutionary filters: subtle differences in the structure of genetic codes result in significant differences in patterns of nucleotide substitution. , 2004, Journal of theoretical biology.

[25]  M. Nei,et al.  Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major-histocompatibility-complex molecules. , 1990, Molecular biology and evolution.

[26]  K. Crandall,et al.  Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. , 1999, Molecular biology and evolution.

[27]  P. Sharp,et al.  In search of molecular darwinism , 1997, Nature.

[28]  P. Ponnuswamy,et al.  The spatial distribution of physical, chemical, energetic and conformational properties of amino acid residues in globular proteins. , 1979, Journal of theoretical biology.

[29]  J. M. Zimmerman,et al.  The characterization of amino acid sequences in proteins by statistical methods. , 1968, Journal of theoretical biology.

[30]  Minoru Kanehisa,et al.  AAindex: amino acid index database, progress report 2008 , 2007, Nucleic Acids Res..

[31]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[32]  Xuhua Xia,et al.  What Amino Acid Properties Affect Protein Evolution? , 1998, Journal of Molecular Evolution.

[33]  D. D. Jones,et al.  Amino acid properties and side-chain orientation in proteins: a cross correlation appraoch. , 1975, Journal of theoretical biology.

[34]  Keith A. Crandall,et al.  TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees , 2003, Bioinform..

[35]  M. Charton,et al.  The dependence of the Chou-Fasman parameters on amino acid side chain structure. , 1983, Journal of theoretical biology.

[36]  K. Crandall,et al.  Molecular characterization of crustacean visual pigments and the evolution of pancrustacean opsins. , 2006, Molecular biology and evolution.

[37]  Ziheng Yang,et al.  Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. , 2002, Molecular biology and evolution.

[38]  M. Oobatake,et al.  An analysis of non-bonded energy of proteins. , 1977, Journal of theoretical biology.