Structure and dynamics of the homologous series of alanine peptides: a joint molecular dynamics/NMR study.

Full Abstract

The phi,psi backbone angle distribution of small homopolymeric model peptides is investigated by a joint molecular dynamics (MD) simulation and heteronuclear NMR study. Combining the accuracy of the measured scalar coupling constants and the atomistic detail of the all-atom MD simulations with explicit solvent, the thermal populations of the peptide conformational states are determined with an uncertainty of <5 %. Trialanine samples mainly ( approximately 90%) a poly-l-proline II helix-like structure, some ( approximately 10%) beta extended structure, but no alphaR helical conformations. No significant change in the distribution of conformers is observed with increasing chain length (Ala(3) to Ala(7)). Trivaline samples all three major conformations significantly. Triglycine samples the four corner regions of the Ramachandran space and exists in a slow conformational equilibrium between the cis and trans conformation of peptide bonds. The backbone angle distribution was also studied for the segment Ala3 surrounded by either three or eight amino acids on both N- and C-termini from a sequence derived from the protein hen egg white lysozyme. While the conformational distribution of the central three alanine residues in the 9mer is similar to that for the small peptides Ala(3)-Ala(7), major differences are found for the 19mer, which significantly (30-40%) samples alphaR helical stuctures.

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Author information

Author/s: Graf, Jürgen (J); Nguyen, Phuong H (PH); Stock, Gerhard (G); Schwalbe, Harald (H);

Affiliation: Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, D-60438 Frankfurt/Main, Germany.

Journal and publication information

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal: Journal of the American Chemical Society (J Am Chem Soc), published in United States. (Language: eng)

Reference: 2007-Feb; vol 129 (issue 5) : pp 1179-89

Dates: Created 2007/01/31; Completed 2007/03/29;

PMID: 17263399, status: MEDLINE (last retrieval date: 12/26/2008)

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MeSH headings (categories)

This article was linked to the MESH Headings shown below.

Alanine - chemistry
Amino Acid Sequence
Computer Simulation
Hydrogen Bonding
Magnetic Resonance Spectroscopy - methods
Molecular Conformation

Molecular Conformation
Muramidase - chemistry
Peptides - chemistry
Protein Structure, Secondary
Solvents - chemistry
Spectrum Analysis

Associated Chemicals: Peptides (0) ; Solvents (0) ; Alanine (56-41-7) ; Muramidase (EC 3.2.1.17)

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