%0 Journal Article %1 ISI:000229048500009 %A Karplus, M %A Kuriyan, J %C 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA %D 2005 %I NATL ACAD SCIENCES %J PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA %K function md %N 19 %P 6679-6685 %R 10.1073/pnas.0408930102 %T Molecular dynamics and protein function %V 102 %X 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.

@article{ISI:000229048500009, 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.}}, added-at = {2009-01-14T02:12:15.000+0100}, address = {{2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA}}, affiliation = {{Kuriyan, J (Reprint Author), Harvard Univ, Dept Chem \& Chem Biol, Cambridge, MA 02138 USA. Harvard Univ, Dept Chem \& Chem Biol, Cambridge, MA 02138 USA. Univ Strasbourg 1, Lab Chim Biophys, Inst Sci \& Ingn Supramol, F-67000 Strasbourg, France. Univ Calif Berkeley, Howard Hughes Med Inst, Berkeley, CA 94720 USA. Univ Calif Berkeley, Dept Mol \& Cell Biol, Berkeley, CA 94720 USA. Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA.}}, author = {Karplus, M and Kuriyan, J}, author-email = {{marci@tammy.harvard.edu kuriyan@berkeley.edu}}, biburl = {https://www.bibsonomy.org/bibtex/2e4c7c1d6200b13d67da1d2b935827056/huiyangsfsu}, cited-references = {{ABRAHAMS JP, 1994, NATURE, V370, P621. AKSIMENTIEV A, 2004, BIOPHYS J, V86, P1332. ANTES I, 2003, BIOPHYS J, V85, P695. AROLD ST, 2001, J BIOL CHEM, V276, P17199. BASRAN J, 1999, BIOCHEMISTRY-US, V38, P3218. BERNECHE S, 2001, NATURE, V414, P73. BILLETER SR, 2001, J CHEM PHYS, V114, P341. BOCKMANN RA, 2002, NAT STRUCT BIOL, V9, P198. BOLHUIS PG, 2002, ANNU REV PHYS CHEM, V53, P291. BOYER PD, 1993, BIOCHIM BIOPHYS ACTA, V1140, P215. BOYER PD, 1997, ANNU REV BIOCHEM, V66, P717. BRASHER BB, 2001, ONCOGENE, V20, P7744. BROOKS CL, 1988, PROTEINS THEORETICAL. CASE DA, 2002, ACCOUNTS CHEM RES, V35, P325. CAVALLI A, 2002, PROTEINS, V47, P305. CUI Q, 2002, J AM CHEM SOC, V124, P3093. 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A.}}, keywords = {function md}, keywords-plus = {{ABL TYROSINE KINASE; DIHYDROFOLATE-REDUCTASE; TRIOSEPHOSPHATE ISOMERASE; ATP SYNTHASE; C-ABL; ENZYME CATALYSIS; FORCE-FIELDS; CONFORMATIONAL CHANGE; ENERGY TRANSDUCTION; IMPLICIT SOLVENT}}, language = {{English}}, month = {{MAY 10}}, number = {{19}}, number-of-cited-references = {{84}}, pages = {{6679-6685}}, publisher = {{NATL ACAD SCIENCES}}, subject-category = {{Multidisciplinary Sciences}}, times-cited = {{83}}, timestamp = {2009-01-14T02:12:15.000+0100}, title = {{Molecular dynamics and protein function}}, type = {{Article}}, unique-id = {{ISI:000229048500009}}, volume = {{102}}, year = {{2005}} }