Issue 47, 2006

Conformational heterogeneity and low-frequency vibrational modes of proteins

Abstract

Molecular dynamics simulation and normal mode analysis are used to calculate the vibrational density of states of dihydrofolate reductase complexed with nicotinamide adenine dinucleotide phosphate at 120 K and the results are compared with the experimental spectrum derived from inelastic neutron scattering. The simulation results indicate that the experimental spectrum arises from an average over proteins trapped in different conformations with structural differences mainly in the loop regions, and that these conformations have significantly different low-frequency (<20 cm−1) spectra. Thus, the experimentally measured spectrum is an average over the vibrational modes of different protein conformations and is thus inhomogeneously broadened. The implications of this broadening for future neutron scattering experiments and ligand binding calculations are discussed.

Graphical abstract: Conformational heterogeneity and low-frequency vibrational modes of proteins

Article information

Article type
Paper
Submitted
14 Jul 2006
Accepted
20 Oct 2006
First published
08 Nov 2006

Phys. Chem. Chem. Phys., 2006,8, 5543-5548

Conformational heterogeneity and low-frequency vibrational modes of proteins

E. Balog, J. C. Smith and D. Perahia, Phys. Chem. Chem. Phys., 2006, 8, 5543 DOI: 10.1039/B610075A

To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements