ISSN:
1432-2234
Keywords:
Key words: Hydrophobic core
;
Solvent accessibility
;
Hydrophobicity
;
Folding
;
Modelling
Source:
Springer Online Journal Archives 1860-2000
Topics:
Chemistry and Pharmacology
Notes:
Abstract. The positions of a given fold always occupied by strong hydrophobic amino acids (V, I, L, F, M, Y, W), which we call “topohydrophobic positions”, were detected and their properties demonstrated within 153 non-redundant families of homologous domains, through 3D structural alignments. Sets of divergent sequences possessing at least four to five members appear to be as informative as larger sets, provided that their mean pairwise sequence identity is low. Amino acids in topohydrophobic positions exhibit several interesting features: they are much more buried than their equivalents in non-topohydrophobic positions, their side chains are far less dispersed; and they often constitute a lattice of close contacts in the inner core of globular domains. In most cases, each regular secondary structure possesses one to three topohydrophobic positions, which cluster in the domain core. Moreover, using sensitive alignment processes such as hydrophobic cluster analysis (HCA), it is possible to identify topohydrophobic positions from only a small set of divergent sequences. Amino acids in topohydrophobic positions, which can be identified directly from sequences, constitute key markers of protein folds, define long-range structural constraints, which, together with secondary structure predictions, limit the number of possible conformations for a given fold.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1007/s002140050397
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