Title: New quantitative descriptors of amino acids based on multidimensional scaling of a large number of physical-chemical properties

Author(s): Venkatarajan MS, Braun W

Source: JOURNAL OF MOLECULAR MODELING 7 (12): 445-453 2001

Document Type: Article

Language: English

Abstract: We derive new quantitative descriptors for the 20 naturally occurring amino acids based on multidimensional scaling of 237 physical-chemical properties. We show that a five-dimensional property space can be constructed such that the amino acids are in a similar spatial distribution to that in the original high-dimensional property space. Properties that correlate well with the five major components were hydrophobicity, size, preferences for amino acids to occur in alpha-helices, number of degenerate triplet codons and the frequency of occurrence of amino acid residues in beta-strands. Distances computed for pairs of amino acids in the five-dimensional property space are highly correlated with corresponding scores from similarity matrices derived from sequence and 3D structure comparison. We used the five-dimensional property distances to cluster the amino acids in groups depending on a cutoff distance. These groups define a reduced amino acid alphabet for protein folding studies. Our descriptors should provide a quantitative means to identify property motifs in sequences of protein families. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00894-001-0058-5.

Author Keywords: multidimensional scaling; amino acid; substitution matrices; BLOSUM; PAM; physical-chemical properties; cluster analysis

KeyWords Plus: DISTANCE GEOMETRY CALCULATIONS; HYDROPHOBIC PARAMETERS-PI; HIDDEN MARKOV-MODELS; PROTEIN SEQUENCES; STRUCTURE PREDICTION; GLOBULAR PROTEINS; 3-DIMENSIONAL STRUCTURE; SUBSTITUTION MATRICES; BACKBONE TOPOGRAPHY; MUTATION MATRICES

Addresses: Braun W (reprint author), Univ Texas, Med Branch, Dept Human Biol Chem & Genet, Sealy Ctr Struct Biol, 301 Univ Blvd, Galveston, TX 77555 USA
Univ Texas, Med Branch, Dept Human Biol Chem & Genet, Sealy Ctr Struct Biol, Galveston, TX 77555 USA

Publisher: SPRINGER-VERLAG, 175 FIFTH AVE, NEW YORK, NY 10010 USA

Subject Category: CHEMISTRY, MULTIDISCIPLINARY; COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS; BIOCHEMISTRY & MOLECULAR BIOLOGY; BIOPHYSICS

IDS Number: 553NT

ISSN: 0948-5023