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PMID: 15870208 Published · ppublish English Journal Article

Molecular dynamics and protein function.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 102 ·No. 19 ·2005-05-10 ·Pages 6679-85

Karplus M, Kuriyan J

Abstract

A fundamental appreciation for how biological macromolecules work requires knowledge of structure and dynamics. Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled with improvements in methodology makes this an exciting time for the application of simulation to structural biology. In this Perspective we survey two areas, protein folding and enzymatic catalysis, in which simulations have contributed to a general understanding of mechanism. We also describe results for the F(1) ATPase molecular motor and the Src family of signaling proteins as examples of applications of simulations to specific biological systems.

MeSH Terms
Animals Antineoplastic Agents/pharmacology Benzamides Biophysics/methods Catalysis Computational Biology/methods Computer Simulation Enzymes/chemistry Humans Hydrogen/chemistry Imatinib Mesylate Models, Molecular Monte Carlo Method Oxygen/chemistry Piperazines/pharmacology Protein Conformation Protein Folding Protein Structure, Tertiary Proteins/chemistry Proto-Oncogene Proteins c-abl/chemistry Proton-Translocating ATPases/chemistry Pyrimidines/pharmacology Software Thermodynamics Time Factors src-Family Kinases/chemistry
Chemicals
Antineoplastic Agents Benzamides Enzymes Piperazines Proteins Pyrimidines Hydrogen Imatinib Mesylate Proto-Oncogene Proteins c-abl src-Family Kinases Proton-Translocating ATPases Oxygen
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Karplus M
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA. [email protected]
Kuriyan J
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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.0408930102
Email
[email protected]
Published
2005-05-10
Epub
2005-00-03
Pages
6679-85
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC1100762
Subset
IM
External Links
PubMed source DOI: 10.1073/pnas.0408930102 PMC Full Text View journal details
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