Title

Secondary Structure Analysis of Small Peptides Using Molecular Dynamics (MD) and Steered Molecular Dynamics (SMD)

Lead Author Affiliation

PCSP

Introduction

Protein structure is critical for the function of proteins. Despite the high profile of the research, the formation of final protein structure and exactly how intramolecular forces drive it is still mostly a mystery, despite many experimental methods used to determine how and why these structures fold and form the way they do. Because of the ability of molecular dynamics (MD) to simulate rather large systems, while still allowing close inspection over moderately long timescales, molecular dynamics lends itself especially well in observing these phenomena from a first hand perspective. In particular, steered molecular dynamics (SMD) may provide valuable insight towards elucidating the folding process. Here we utilize SMD to study the macrodipole stabilization effect of a sodim ion on a small helical peptide.

Location

DUC Ballroom A&B

Format

Poster Presentation

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Apr 30th, 1:00 PM Apr 30th, 3:30 PM

Secondary Structure Analysis of Small Peptides Using Molecular Dynamics (MD) and Steered Molecular Dynamics (SMD)

DUC Ballroom A&B

Protein structure is critical for the function of proteins. Despite the high profile of the research, the formation of final protein structure and exactly how intramolecular forces drive it is still mostly a mystery, despite many experimental methods used to determine how and why these structures fold and form the way they do. Because of the ability of molecular dynamics (MD) to simulate rather large systems, while still allowing close inspection over moderately long timescales, molecular dynamics lends itself especially well in observing these phenomena from a first hand perspective. In particular, steered molecular dynamics (SMD) may provide valuable insight towards elucidating the folding process. Here we utilize SMD to study the macrodipole stabilization effect of a sodim ion on a small helical peptide.