Molecular Dynamics and Monte Carlo Simulations Favor the α-Helical Form for Alanine-Based Peptides in Water

Julian Tirado-Rives; David S. Maxwell; William L. Jorgensen

doi:10.1021/ja00077a066

Molecular Dynamics and Monte Carlo Simulations Favor the α-Helical Form for Alanine-Based Peptides in Water

Julian Tirado-Rives, David S. Maxwell, William L. Jorgensen

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101 Scopus citations

Abstract

Molecular dynamics and Monte Carlo simulations of a capped undecaalanine peptide were conducted to determine the preferred helical conformation in water. The results clearly favor the α-helical form over the 3₁₀ alternative, in contrast to recent ESR findings. A molecular dynamics simulation started at the 3₁₀ conformation converges rapidly to an α-helix, and the free energy profile calculated via Monte Carlo simulations shows the α-helix to be more stable by ca. 1.0 kcal•mol⁻¹ per residue.

Original language	English (US)
Pages (from-to)	11590-11593
Number of pages	4
Journal	Journal of the American Chemical Society
Volume	115
Issue number	24
DOIs	https://doi.org/10.1021/ja00077a066
State	Published - Dec 1 1993
Externally published	Yes

ASJC Scopus subject areas

Catalysis
General Chemistry
Biochemistry
Colloid and Surface Chemistry

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title = "Molecular Dynamics and Monte Carlo Simulations Favor the α-Helical Form for Alanine-Based Peptides in Water",

abstract = "Molecular dynamics and Monte Carlo simulations of a capped undecaalanine peptide were conducted to determine the preferred helical conformation in water. The results clearly favor the α-helical form over the 310 alternative, in contrast to recent ESR findings. A molecular dynamics simulation started at the 310 conformation converges rapidly to an α-helix, and the free energy profile calculated via Monte Carlo simulations shows the α-helix to be more stable by ca. 1.0 kcal•mol−1 per residue.",

author = "Julian Tirado-Rives and Maxwell, {David S.} and Jorgensen, {William L.}",

year = "1993",

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AU - Tirado-Rives, Julian

AU - Maxwell, David S.

AU - Jorgensen, William L.

PY - 1993/12/1

Y1 - 1993/12/1

N2 - Molecular dynamics and Monte Carlo simulations of a capped undecaalanine peptide were conducted to determine the preferred helical conformation in water. The results clearly favor the α-helical form over the 310 alternative, in contrast to recent ESR findings. A molecular dynamics simulation started at the 310 conformation converges rapidly to an α-helix, and the free energy profile calculated via Monte Carlo simulations shows the α-helix to be more stable by ca. 1.0 kcal•mol−1 per residue.

AB - Molecular dynamics and Monte Carlo simulations of a capped undecaalanine peptide were conducted to determine the preferred helical conformation in water. The results clearly favor the α-helical form over the 310 alternative, in contrast to recent ESR findings. A molecular dynamics simulation started at the 310 conformation converges rapidly to an α-helix, and the free energy profile calculated via Monte Carlo simulations shows the α-helix to be more stable by ca. 1.0 kcal•mol−1 per residue.

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Molecular Dynamics and Monte Carlo Simulations Favor the α-Helical Form for Alanine-Based Peptides in Water

Abstract

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