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PMID: 3860838 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 82 ·No. 15 ·1985-08-00 ·Pages 4995-9

Brooks B, Karplus M

Abstract

A method is presented for finding particular normal modes for large molecules such as proteins and nucleic acids. The method is based on an iterative approach that extracts eigenvectors of interest from the full second-derivative matrix. Application of the method to the interdomain (hinge-bending) motion of lysozyme yields a frequency of 3.6 cm-1. This is similar to the value obtained from earlier adiabatic-energy-minimization studies. Analysis of the mode shows that the relaxation associated with the hinge bending is highly delocalized; that is, the dihedral angle and energy changes are distributed over many residues, including some (e.g., Trp-28) that are distant from the cleft and hinge region.

MeSH Terms

Animals Chickens Models, Molecular Motion Muramidase Protein Conformation Thermodynamics

Chemicals

Muramidase

Authors & Affiliations

2 authors, click to expand affiliations / ORCID

Brooks B

Karplus M

References (16)

16 references, click to expand

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Article Info

Journal

Proceedings of the National Academy of Sciences of the United States of America

Abbr.

Proc Natl Acad Sci U S A

ISSN

0027-8424

DOI

10.1073/pnas.82.15.4995

Published

1985-08-00

Pages

4995-9

Language

English

Region

United States

NLM ID

7505876

PMCID

PMC390485

Subset

External Links

PubMed source DOI: 10.1073/pnas.82.15.4995 PMC Full Text View journal details

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Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme.

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