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A hierarchical “nesting” approach to describe the stability of alpha helices with side‐chain interactions
Author(s) -
Robert Charles H.
Publication year - 1990
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360300311
Subject(s) - side chain , chemistry , chain (unit) , block (permutation group theory) , nesting (process) , stability (learning theory) , alpha helix , helix (gastropod) , alpha (finance) , statistical physics , protein structure , combinatorics , physics , computer science , mathematics , materials science , biochemistry , snail , ecology , construct validity , biology , polymer , machine learning , metallurgy , statistics , organic chemistry , psychometrics , astronomy
A straightforward hierarchical statistical–mechanical approach is shown to enable one to describe the stability of the alpha helix in the presence of side‐chain interactions. The formulation can be used with even the simple nearest‐neighbor models and it is demonstrated explicitly with the popular 2 × 2 Zimm‐Bragg model [B. H. Zimm and J. K. Bragg (1959) J. Chem. Physics 31 , 526–535]. It involves a conceptual dissection of the polypeptide chain into interacting blocks; the behavior of any block with side‐chain interactions is treated then with conventional binding polynomial techniques. This dissection is a manifestation of “nesting,” which is a hierarchical framework for the description of the behavior of complex macromoecules [C. H. Robert, H. Decker, B. Richey, S. J. Gill, and J. Wyman (1987) Proc. Natl. Acad. Sci. 84 , 1891–1895]. The method is demonstrated through applications to existing detailed data for the pH and salt dependences of the helix–coil transition in the S peptide and in synthetic peptides.