Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents.

Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents. Research Abstract Details 

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Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents. Abstract Text:

Ekta Khurana,Steven O Nielsen,Bernd Ensing,Michael L Klein,

The self-assembly of cyclic D,L-alpha-peptides into hollow nanotubes is a crucial mechanistic step in their application as antibacterial and drug-delivery agents. To understand this process, molecular dynamics (MD) simulations were performed on dimers of cyclic peptides formed from cyclo [(-L-Trp-D-N-MeLeu-)4-]2 and cyclo [(-L-Trp-D-Leu-)4-]2 subunits in nonpolar (nonane) and polar (water) solvent. The dimers were observed to be stable only in nonpolar solvent over the full 10 ns length of the MD trajectory. The behavior of the dimers in different solvents is rationalized in terms of the intersubunit hydrogen bonding, hydrogen bonding with the solvent, and planarity of the rings. It is shown that the phi and psi dihedral angles of a single uncapped ring in nonane lie in the beta-sheet region of the Ramachandran plot, and the ring stays in a flat conformation. Steered MD (SMD) simulations based on Jarzynski's equality were performed to obtain the potential of mean force as a function of the distance between the two rings of the capped dimer in nonane. It is also shown that a single peptide subunit prefers to reside close to the nonane/water interface rather than in bulk solvent because of the amphiphilic character of the peptide ring. The present MD results build the foundation for using MD simulations to study the mechanism of the formation of cyclic peptide nanotubes in lipid bilayers.

Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents. Publishing Authors By Initials

E Khurana,SO Nielsen,B Ensing,ML Klein,

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Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: The journal of physical chemistry. B

VOLUME: 110

Page Numbers: 18965-72

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ISSN: 1520-6106

DAY: 28

MONTH: Sep

YEAR: 2006

Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents. Information

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LANGUAGE: eng

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Grant and Affiliation Information for Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents.

AFFILIATION: Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA.

Country: United States

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MEDLINETA: J Phys Chem B

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