Environmental features are important in determining protein secondary structure

Citation
Jr. Macdonald et Wc. Johnson, Environmental features are important in determining protein secondary structure, PROTEIN SCI, 10(6), 2001, pp. 1172-1177
Citations number
23
Language
INGLESE
art.tipo
Article
Categorie Soggetti
Biochemistry & Biophysics
Journal title
PROTEIN SCIENCE
ISSN journal
0961-8368 → ACNP
Volume
10
Issue
6
Year of publication
2001
Pages
1172 - 1177
Database
ISI
SICI code
0961-8368(200106)10:6<1172:EFAIID>2.0.ZU;2-8
Abstract
We have investigated amino acid features that determine secondary structure : (1) the solvent accessibility of each side chain, and (2) the interaction of each side chain with others one to four residues apart. Solvent accessi bility is a simple model that distinguishes residue environment. The pairwi se interactions represent a simple model of local side chain to side chain interactions. To test the importance of these features we developed an algo rithm to separate alpha -helices, beta -strands, and "other" structure. Sin gle residue and pairwise probabilities were determined for 25,141 samples f rom proteins with < 30% homology. Combining the features of solvent accessi bility with pairwise probabilities allows us to distinguish the three struc tures after cross validation at the 82.0% level. We gain 1.4% to 2.0% accur acy by optimizing the propensities, demonstrating that probabilities do not necessarily reflect propensities. Optimization of residue exposures, weigh ts of all probabilities, and propensities increased accuracy to 84.0%.