Molecular dynamics study of structural properties of beta-sheet assemblies formed by synthetic de novo oligopeptides

Giovanni Bellesia; Maxim V. Fedorov; Edward G. Timoshenko

doi:10.1016/j.physa.2006.06.011

Molecular dynamics study of structural properties of beta-sheet assemblies formed by synthetic de novo oligopeptides

Giovanni Bellesia, Maxim V. Fedorov, Edward G. Timoshenko

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11 Citations (Scopus)

Abstract

We study, by means of molecular dynamics (MD) simulations with explicit water, the structure and stability of beta-sheet tapes, ribbons and double ribbons formed by rationally designed oligopeptides P-11-I and P-11-II in aqueous solutions. Two different methods for the treatment of the electrostatic interactions were considered: a smoothly shifted spherical cutoff approach under spherical harmonic conditions, and the particle mesh Ewald technique. We investigate the transfer of chirality from single L-aminoacids to the molecular scale of oligopeptides and from the latter to the supramolecular scale of peptide clusters. Furthermore, we obtain structural data for the representative conformations of these clusters, as well as study various average properties of their geometry.

Original language	English
Pages (from-to)	455-476
Number of pages	22
Journal	Physica A: Statistical Mechanics and its Applications
Volume	373
DOIs	https://doi.org/10.1016/j.physa.2006.06.011
Publication status	Published - 1 Jan 2007

Keywords

peptide-based clusters
supramolecular chirality
molecular dynamics
peptides
proteins
rotation
vectors

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10.1016/j.physa.2006.06.011

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title = "Molecular dynamics study of structural properties of beta-sheet assemblies formed by synthetic de novo oligopeptides",

abstract = "We study, by means of molecular dynamics (MD) simulations with explicit water, the structure and stability of beta-sheet tapes, ribbons and double ribbons formed by rationally designed oligopeptides P-11-I and P-11-II in aqueous solutions. Two different methods for the treatment of the electrostatic interactions were considered: a smoothly shifted spherical cutoff approach under spherical harmonic conditions, and the particle mesh Ewald technique. We investigate the transfer of chirality from single L-aminoacids to the molecular scale of oligopeptides and from the latter to the supramolecular scale of peptide clusters. Furthermore, we obtain structural data for the representative conformations of these clusters, as well as study various average properties of their geometry. ",

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author = "Giovanni Bellesia and Fedorov, {Maxim V.} and Timoshenko, {Edward G.}",

year = "2007",

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doi = "10.1016/j.physa.2006.06.011",

language = "English",

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journal = "Physica A: Statistical Mechanics and its Applications",

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TY - JOUR

T1 - Molecular dynamics study of structural properties of beta-sheet assemblies formed by synthetic de novo oligopeptides

AU - Bellesia, Giovanni

AU - Fedorov, Maxim V.

AU - Timoshenko, Edward G.

PY - 2007/1/1

Y1 - 2007/1/1

N2 - We study, by means of molecular dynamics (MD) simulations with explicit water, the structure and stability of beta-sheet tapes, ribbons and double ribbons formed by rationally designed oligopeptides P-11-I and P-11-II in aqueous solutions. Two different methods for the treatment of the electrostatic interactions were considered: a smoothly shifted spherical cutoff approach under spherical harmonic conditions, and the particle mesh Ewald technique. We investigate the transfer of chirality from single L-aminoacids to the molecular scale of oligopeptides and from the latter to the supramolecular scale of peptide clusters. Furthermore, we obtain structural data for the representative conformations of these clusters, as well as study various average properties of their geometry.

AB - We study, by means of molecular dynamics (MD) simulations with explicit water, the structure and stability of beta-sheet tapes, ribbons and double ribbons formed by rationally designed oligopeptides P-11-I and P-11-II in aqueous solutions. Two different methods for the treatment of the electrostatic interactions were considered: a smoothly shifted spherical cutoff approach under spherical harmonic conditions, and the particle mesh Ewald technique. We investigate the transfer of chirality from single L-aminoacids to the molecular scale of oligopeptides and from the latter to the supramolecular scale of peptide clusters. Furthermore, we obtain structural data for the representative conformations of these clusters, as well as study various average properties of their geometry.

KW - peptide-based clusters

KW - supramolecular chirality

KW - molecular dynamics

KW - peptides

KW - proteins

KW - rotation

KW - vectors

U2 - 10.1016/j.physa.2006.06.011

DO - 10.1016/j.physa.2006.06.011

M3 - Article

SN - 0378-4371

VL - 373

SP - 455

EP - 476

JO - Physica A: Statistical Mechanics and its Applications

JF - Physica A: Statistical Mechanics and its Applications

ER -

Molecular dynamics study of structural properties of beta-sheet assemblies formed by synthetic de novo oligopeptides

Abstract

Keywords

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