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Conformational studies of human islet amyloid peptide using molecular dynamics and simulated annealing methods
Author(s) -
Ilangovan U.,
Ramamoorthy A.
Publication year - 1998
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/(sici)1097-0282(199801)45:1<9::aid-bip2>3.0.co;2-x
Subject(s) - chemistry , molecular dynamics , conformational isomerism , hydrogen bond , aqueous solution , peptide , amide , peptide bond , crystallography , computational chemistry , molecule , organic chemistry , biochemistry
Abstract Molecular dynamics simulations and simulated annealing in vacuum, model aqueous solution, and simulated membrane were used to analyze the conformational preferences of a segment spanning 20–29 residues of human islet amyloid polypeptide, [referred to as IAPP H (20–29)]. Molecular dynamics simulations were conducted at 300 K on IAPP H (20–29). The minimum energy conformers obtained in model aqueous solution and vacuum exhibited similar structures. Even in the absence of any constraints on peptide bonds, trans conformation was preferred consistently by all the peptide bonds. Analysis of the minimum energy conformers indicated that IAPP H (20–29) showed a strong preference for turn structures in all the environments. These turn structures were stabilized by the formation of hydrogen bonds between the backbone amide and carbonyl groups. A good agreement was found between the results obtained from the molecular dynamics simulation and solid‐state nmr experimental studies. © 1998 John Wiley & Sons, Inc. Biopoly 45: 9–20, 1998