Identification of functional residues and secondary structure from protein multiple sequence alignment.

Publisher Summary This chapter describes a strategy for the hierarchical analysis of residue conservation and the identification of functional residues and secondary structure from protein multiple sequence alignment. Hierarchical methods of alignment cope with large numbers of sequences and give reasonably accurate alignments. Having generated the alignment, the problem is to find out what it can tell us about the protein family. Interpretation of alignments can be, particularly difficult when there are large numbers of sequences to examine. The method allows the residue-specific similarities and differences in physicochemical properties among groups of sequences to be identified quickly. The method also highlights conserved positions across a complete alignment and, thus, can help to identify patterns characteristic of regular secondary structures. The chapter also discusses a procedure for applying these patterns in secondary structure prediction and evaluates their predictive power in six blind secondary-structure predictions.

[1]  V. Lim.  Algorithms for prediction of α-helical and β-structural regions in globular proteins , 1974 .

[2]  J. Thornton,et al.  Analysis and prediction of the different types of β-turn in proteins , 1988 .

[3]  S. Benner,et al.  Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: a prediction of the structure of the catalytic domain of protein kinases. , 1991, Advances in enzyme regulation.

[4]  P. Slonimski,et al.  Evolutionary divergence plots of homologous proteins. , 1992, Biochimie.

[5]  G J Barton,et al.  Secondary structure prediction from multiple sequence data: blood clotting factor XIII and Yersinia protein-tyrosine phosphatase. , 2009, International journal of peptide and protein research.

[6]  G. Barton,et al.  Amino acid sequence analysis of the annexin super-gene family of proteins. , 1991, European journal of biochemistry.

[7]  G. Barton,et al.  The limits of protein secondary structure prediction accuracy from multiple sequence alignment. , 1993, Journal of molecular biology.

[8]  B. Rost,et al.  Prediction of protein secondary structure at better than 70% accuracy. , 1993, Journal of molecular biology.

[9]  W. Taylor,et al.  The classification of amino acid conservation. , 1986, Journal of theoretical biology.

[10]  M. Sternberg,et al.  Prediction of protein secondary structure and active sites using the alignment of homologous sequences. , 1987, Journal of molecular biology.

[11]  C. Sander,et al.  Database of homology‐derived protein structures and the structural meaning of sequence alignment , 1991, Proteins.

[12]  I. Crawford,et al.  Prediction of secondary structure by evolutionary comparison: Application to the α subunit of tryptophan synthase , 1987, Proteins.

[13]  G. Barton,et al.  A structural analysis of phosphate and sulphate binding sites in proteins. Estimation of propensities for binding and conservation of phosphate binding sites. , 1994, Journal of molecular biology.

[14]  A A Salamov,et al.  Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignments. , 1995, Journal of molecular biology.

[15]  J. Devereux,et al.  A comprehensive set of sequence analysis programs for the VAX , 1984, Nucleic Acids Res..

[16]  R. Huber,et al.  The crystal and molecular structure of human annexin V, an anticoagulant protein that binds to calcium and membranes. , 1990, The EMBO journal.

[17]  E. Kabat.  Structural Concepts in Immunology and Immunochemistry , 1968 .

[18]  George D. Rose,et al.  Prediction of chain turns in globular proteins on a hydrophobic basis , 1978, Nature.

[19]  P. Argos,et al.  Quantification of secondary structure prediction improvement using multiple alignments. , 1993, Protein engineering.

[20]  G. Barton,et al.  Conservation analysis and structure prediction of the SH2 family of phosphotyrosine binding domains , 1992, FEBS letters.

[21]  G J Barton,et al.  ALSCRIPT: a tool to format multiple sequence alignments. , 1993, Protein engineering.

[22]  M. Sternberg.  Protein Structure Prediction: A Practical Approach , 1997 .

[23]  M. Sternberg,et al.  A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons. , 1987, Journal of molecular biology.

[24]  J. Garnier,et al.  Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. , 1978, Journal of molecular biology.