Protein Engineering, Vol. 13, No. 3, 149-152,
March 2000
© 2000 Oxford University Press
Simplified amino acid alphabets for protein fold recognition and implications for folding
Department of Chemistry, Rutgers University, Wright-Rieman Laboratories, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
Protein design experiments have shown that the use of specific subsets of amino acids can produce foldable proteins. This prompts the question of whether there is a minimal amino acid alphabet which could be used to fold all proteins. In this work we make an analogy between sequence patterns which produce foldable sequences and those which make it possible to detect structural homologs by aligning sequences, and use it to suggest the possible size of such a reduced alphabet. We estimate that reduced alphabets containing 10–12 letters can be used to design foldable sequences for a large number of protein families. This estimate is based on the observation that there is little loss of the information necessary to pick out structural homologs in a clustered protein sequence database when a suitable reduction of the amino acid alphabet from 20 to 10 letters is made, but that this information is rapidly degraded when further reductions in the alphabet are made.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  S. Idicula-Thomas, A. J. Kulkarni, B. D. Kulkarni, V. K. Jayaraman, and P. V. Balaji A support vector machine-based method for predicting the propensity of a protein to be soluble or to form inclusion body on overexpression in Escherichia coli Bioinformatics, February 1, 2006; 22(3): 278 - 284. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Doi, K. Kakukawa, Y. Oishi, and H. Yanagawa High solubility of random-sequence proteins consisting of five kinds of primitive amino acids Protein Eng. Des. Sel., June 1, 2005; 18(6): 279 - 284. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Z. Zhang, S. Kochhar, and M. G. Grigorov Descriptor-based protein remote homology identification Protein Sci., February 1, 2005; 14(2): 431 - 444. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. C. Edgar Local homology recognition and distance measures in linear time using compressed amino acid alphabets Nucleic Acids Res., January 16, 2004; 32(1): 380 - 385. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Li, K. Fan, J. Wang, and W. Wang Reduction of protein sequence complexity by residue grouping Protein Eng. Des. Sel., May 1, 2003; 16(5): 323 - 330. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. I. Rogov and A. N. Nekrasov A numerical measure of amino acid residues similarity based on the analysis of their surroundings in natural protein sequences Protein Eng. Des. Sel., July 1, 2001; 14(7): 459 - 463. [Abstract] [Full Text] [PDF]
|
|