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On the transferability of atomic solvation parameters: Ab initio structural prediction of cyclic heptapeptides in DMSO
Author(s) -
Baysal Canan,
Meirovitch Hagai
Publication year - 2000
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/1097-0282(200011)54:6<416::aid-bip60>3.0.co;2-2
Subject(s) - transferability , chemistry , solvation , computational chemistry , ab initio , chemical physics , organic chemistry , molecule , machine learning , computer science , logit
A statistical mechanics methodology for predicting the solution structures and populations of peptides developed recently is based on a novel method for optimizing implicit solvation models, which was applied initially to a cyclic hexapeptide in DMSO (C. Baysal and H. Meirovitch, Journal of American Chemical Society , 1998, vol. 120, pp. 800–812). Thus, the molecule has been described by the simplified energy function E tot = E GRO + ∑ k σ k A k , where E GRO is the GROMOS force‐field energy, σ k and A k are the atomic solvation parameter (ASP) and the solvent accessible surface area of atom k , respectively. In a more recent study, these ASPs have been found to be transferable to the cyclic pentapeptide cyclo ( D ‐Pro 1 –Ala 2 –Ala 3 –Ala 4 –Ala 5 ) in DMSO (C. Baysal and H. Meirovitch, Biopolymers , 2000, vol. 53, pp. 423–433). In the present paper, our methodology is applied to the cyclic heptapeptides axinastatin 2 [ cyclo (Asn 1 –Pro 2 –Phe 3 –Val 4 –Leu 5 –Pro 6 –Val 7 )] and axinastatin 3 [ cyclo (Asn 1 –Pro 2 –Phe 3 –Ile 4 –Leu 5 –Pro 6 –Val 7 )], in DMSO, which were studied by nmr by Mechnich et al. ( Helvetica Chimica Acta , 1997, vol. 80, pp. 1338–1354). The calculations for axinastatin 2 show that special ASPs should be optimized for the partially charged side‐chain atoms of Asn while the rest of the atoms take their values derived in our previous work; this suggests that similar optimization might be needed for other side chains as well. The solution structures of these peptides are obtained ab initio (i.e., without using experimental restraints) by an extensive conformational search based on E GRO alone and E * tot , which consists of the new set of ASPs. For E * tot , the theoretical values of proton–proton distances, 3 J coupling constants, and other properties are found to agree very well with the nmr results, and they are always better than those based on E GRO . © 2000 John Wiley & Sons, Inc. Biopoly 54: 416–428, 2000