Conformational studies of human islet amyloid peptide using molecular dynamics and simulated annealing methods

Biopolymers
U Ilangovan, Ayyalusamy Ramamoorthy

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 IAPPH (20-29)]. Molecular dynamics simulations were conducted at 300 K on IAPPH (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 IAPPH (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.

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Citations

Feb 9, 2006·Journal of the American Chemical Society·Hung D Nguyen, Carol K Hall
Nov 8, 2008·Biochemistry·Ravi Prakash Reddy NangaAyyalusamy Ramamoorthy
Mar 13, 2009·Journal of the American Chemical Society·Pieter E S SmithAyyalusamy Ramamoorthy
Apr 11, 2009·PLoS Computational Biology·Ping JiangYuguang Mu
Sep 1, 2012·Biochimica Et Biophysica Acta·Jun ZhaoJie Zheng
Oct 7, 2004·Biophysical Journal·Hung D Nguyen, Carol K Hall
Apr 30, 2003·Biopolymers·Alessandro MascioniGianluigi Veglia
Dec 14, 2004·The Journal of Biological Chemistry·Hung D Nguyen, Carol K Hall
May 22, 2009·Journal of the American Chemical Society·Ravi Prakash Reddy NangaAyyalusamy Ramamoorthy
Jun 30, 2005·Journal of the American Chemical Society·Veronica EspositoGiuseppe Melacini

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