A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure

The correlation between the primary and secondary structures of proteins was analysed using a large data set from the Protein Data Bank. Clear preferences of amino acids towards certain secondary structures classify amino acids into four groups: α-helix preferrers, strand preferrers, turn and bend preferrers, and His and Cys (the latter two amino acids show no clear preference for any secondary structure). Amino acids in the same group have similar structural characteristics at their Cβ and Cγ atoms that predicts their preference for a particular secondary structure. All α-helix preferrers have neither polar heteroatoms on Cβ and Cγ atoms, nor branching or aromatic group on the Cβ atom. All strand preferrers have aromatic groups or branching groups on the Cβ atom. All turn and bend preferrers have a polar heteroatom on the Cβ or Cγ atoms or do not have a Cβ atom at all. These new rules could be helpful in making predictions about non-natural amino acids.

[1]  J. Witmer,et al.  Statistics for the Life Sciences , 1990 .

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

[3]  William F. DeGrado,et al.  Amino Acid Propensities are Position-dependent Throughout the Length of α-Helices , 2004 .

[4]  U. Hobohm,et al.  Enlarged representative set of protein structures , 1994, Protein science : a publication of the Protein Society.

[5]  J. Gibrat,et al.  Further developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs. , 1987, Journal of molecular biology.

[6]  A. Doig,et al.  Side-chain structures in the first turn of the alpha-helix. , 1999, Journal of molecular biology.

[7]  S. Rackovsky,et al.  On the use of secondary structure in protein structure prediction: a bioinformatic analysis , 2004 .

[8]  B. Rost.  Protein Structure Prediction in 1D, 2D, and 3D , 2002 .

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

[10]  M. Levitt,et al.  Automatic identification of secondary structure in globular proteins. , 1977, Journal of molecular biology.

[11]  G. Rose,et al.  Are proteins made from a limited parts list? , 2005, Trends in biochemical sciences.

[12]  J. Skolnick,et al.  Ab initio folding of proteins using restraints derived from evolutionary information , 1999, Proteins.

[13]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[14]  P. Y. Chou,et al.  Prediction of protein conformation. , 1974, Biochemistry.

[15]  B. Robson,et al.  Analysis of code relating sequences to conformation in globular prtoeins. Theory and application of expected information. , 1974, The Biochemical journal.

[16]  G. Crippen,et al.  Contact potential that recognizes the correct folding of globular proteins. , 1992, Journal of molecular biology.

[17]  Cheng Che Chen,et al.  Using imperfect secondary structure predictions to improve molecular structure computations , 1999, Bioinform..

[18]  B. Rost.  Review: protein secondary structure prediction continues to rise. , 2001, Journal of structural biology.

[19]  P. Schleyer.  Encyclopedia of computational chemistry , 1998 .

[20]  Anthony K. Felts,et al.  Protein tertiary structure prediction using a branch and bound algorithm , 1999, Proteins.

[21]  M. Levitt,et al.  Computer simulation of protein folding , 1975, Nature.

[22]  A. Lomize,et al.  Prediction of protein structure: The problem of fold multiplicity , 1999, Proteins.

[23]  G. Rose,et al.  Secondary structure determines protein topology , 2006, Protein science : a publication of the Protein Society.

[24]  S L Mayo,et al.  Intrinsic beta-sheet propensities result from van der Waals interactions between side chains and the local backbone. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[25]  K-L Ting,et al.  Combining the GOR V algorithm with evolutionary information for protein secondary structure prediction from amino acid sequence , 2002, Proteins.

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

[27]  M. Levitt.  Conformational preferences of amino acids in globular proteins. , 1978, Biochemistry.

[28]  V A Eyrich,et al.  Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set. , 1999, Journal of molecular biology.

[29]  Andrés Moya,et al.  Genomic determinants of protein folding thermodynamics in prokaryotic organisms. , 2004, Journal of molecular biology.

[30]  Jeremy M. Berg,et al.  Thermodynamic β -sheet propensities measured using a zinc-finger host peptide , 1993, Nature.

[31]  M. Sternberg,et al.  Enhanced genome annotation using structural profiles in the program 3D-PSSM. , 2000, Journal of molecular biology.

[32]  V. Muñoz,et al.  Position dependence of non-polar amino acid intrinsic helical propensities. , 1998, Journal of molecular biology.

[33]  P. S. Kim,et al.  Measurement of the β-sheet-forming propensities of amino acids , 1994, Nature.

[34]  Robert L. Baldwin,et al.  Relative helix-forming tendencies of nonpolar amino acids , 1990, Nature.

[35]  P. Wolynes,et al.  Self-consistently optimized energy functions for protein structure prediction by molecular dynamics. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[36]  G. Rose,et al.  Building native protein conformation from highly approximate backbone torsion angles. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[37]  R Samudrala,et al.  Constructing side chains on near-native main chains for ab initio protein structure prediction. , 2000, Protein engineering.

[38]  R. L. Baldwin.  Energetics of protein folding. , 2007, Journal of molecular biology.

[39]  W. DeGrado,et al.  A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. , 1990, Science.

[40]  Yael Mandel-Gutfreund,et al.  On the significance of alternating patterns of polar and non-polar residues in beta-strands. , 2002, Journal of molecular biology.

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