%0 Journal Article %1 ISI:000179530500011 %A Paci, E %A Vendruscolo, M %A Dobson, CM %A Karplus, M %C 24-28 OVAL RD, LONDON NW1 7DX, ENGLAND %D 2002 %I ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD %J JOURNAL OF MOLECULAR BIOLOGY %K AcP phi states transition value %N 1 %P 151-163 %R 10.1016/S0022-2836(02)00944-0 %T Determination of a transition state at atomic resolution from protein engineering data %V 324 %X We present a method for determining the structure of the transition state ensemble (TSE) of a protein by using phi values derived from protein engineering experiments as restraints in molecular dynamics simulations employing a realistic all-atom molecular mechanics energy function. The method uses a biasing potential to select an ensemble of structures having phi values in agreement with the experimental data set. An application to acylphosphatase (AcP), a protein for which phi values have been measured for 24 out of 98 residues, illustrates the approach. The properties of the TSE determined in this way are compared with those of a coarse-grained model obtained using a Monte Carlo (MC) sampling method based on a C-alpha representation of the structure. The two TSEs determined at different structural resolution are consistent and complementary. While the C-alpha model allows better sampling of the conformation space occupied by the transition state, the all-atom model offers a more detailed description of the structural and energetic properties of the conformations included in the TSE. The combination of low-resolution C-alpha results with all-atom molecular dynamics simulations provides a powerful and general method for determining the nature of TSEs from protein engineering data. (C) 2002 Elsevier Science Ltd. All rights reserved.

@article{ISI:000179530500011, abstract = {{We present a method for determining the structure of the transition state ensemble (TSE) of a protein by using phi values derived from protein engineering experiments as restraints in molecular dynamics simulations employing a realistic all-atom molecular mechanics energy function. The method uses a biasing potential to select an ensemble of structures having phi values in agreement with the experimental data set. An application to acylphosphatase (AcP), a protein for which phi values have been measured for 24 out of 98 residues, illustrates the approach. The properties of the TSE determined in this way are compared with those of a coarse-grained model obtained using a Monte Carlo (MC) sampling method based on a C-alpha representation of the structure. The two TSEs determined at different structural resolution are consistent and complementary. While the C-alpha model allows better sampling of the conformation space occupied by the transition state, the all-atom model offers a more detailed description of the structural and energetic properties of the conformations included in the TSE. The combination of low-resolution C-alpha results with all-atom molecular dynamics simulations provides a powerful and general method for determining the nature of TSEs from protein engineering data. (C) 2002 Elsevier Science Ltd. All rights reserved.}}, added-at = {2009-01-07T00:44:41.000+0100}, address = {{24-28 OVAL RD, LONDON NW1 7DX, ENGLAND}}, affiliation = {{Karplus, M (Reprint Author), Univ Strasbourg 1, ISIS, Lab Chim Biophys, 4 Rue Blaise Pascal, F-67000 Strasbourg, France. Univ Strasbourg 1, ISIS, Lab Chim Biophys, F-67000 Strasbourg, France. Univ Zurich, Inst Biochem, CH-8057 Zurich, Switzerland. Univ Cambridge, Dept Chem, Cambridge CB2 1EW, England. Harvard Univ, Dept Chem \& Chem Biol, Cambridge, MA 02138 USA.}}, author = {Paci, E and Vendruscolo, M and Dobson, CM and Karplus, M}, biburl = {https://www.bibsonomy.org/bibtex/2269d9bfbe873065b8fc7fa7a890b82dd/huiyangsfsu}, cited-references = {{ASTUMIAN RD, 2001, SCI AM, V285, P45. BROOKS BR, 1983, J COMPUT CHEM, V4, P187. CHANDLER D, 1978, J CHEM PHYS, V68, P2959. CHITI F, 1998, BIOCHEMISTRY-US, V37, P1447. CHITI F, 1999, NAT STRUCT BIOL, V6, P1005. CHITI F, 1999, P NATL ACAD SCI USA, V96, P3590. COTA E, 2000, J MOL BIOL, V302, P713. DEJONG D, 2002, J MOL BIOL, V319, P229. DINNER AR, 2000, TRENDS BIOCHEM SCI, V25, P331. DOKHOLYAN NVV, 2002, PHYS REV E, V65, ARTN 061910. DU R, 1998, J CHEM PHYS, V108, P334. FERSHT AR, 1993, FEBS LETT, V325, P5. FERSHT AR, 1999, STRUCTURE MECH PROTE. FERSHT AR, 2002, CELL, V108, P573. GSPONER J, 2002, P NATL ACAD SCI USA, V99, P6719. HOOVER WG, 1985, PHYS REV A, V31, P1695. ITZHAKI LS, 1995, J MOL BIOL, V254, P260. KABSCH W, 1983, BIOPOLYMERS, V22, P2577. KORADI R, 1996, J MOL GRAPHICS, V14, P51. LAZARIDIS T, 1997, SCIENCE, V278, P1928. LAZARIDIS T, 1999, J MOL BIOL, V288, P477. LAZARIDIS T, 1999, PROTEINS, V35, P133. LI AJ, 1994, P NATL ACAD SCI USA, V91, P10430. LI L, 2001, P NATL ACAD SCI USA, P98. MARCHI M, 1999, J CHEM PHYS, V110, P3697. NERIA E, 1996, J CHEM PHYS, V105, P1902. NORTHRUP SH, 1982, P NATL ACAD SCI USA, V79, P4035. NOSE S, 1984, MOL PHYS, V52, P255. PACI E, 1999, J MOL BIOL, V288, P441. PACI E, 2001, J MOL BIOL, V306, P329. PACI E, 2002, IN PRESS BIOPHYS J. PACI E, 2002, PROTEINS, V47, P379. PASTORE A, 1992, J MOL BIOL, V224, P427. RIEF M, 1997, SCIENCE, V276, P1109. RYCKAERT JP, 1977, J COMPUT PHYS, V23, P327. SHAKHNOVICH E, 1996, NATURE, V379, P96. SHEA JE, 1999, P NATL ACAD SCI USA, V96, P12512. TADDEI N, 2000, J MOL BIOL, V300, P633. TANFORD C, 1970, ADV PROTEIN CHEM, V24, P1. VANNULAND NAJ, 1998, J MOL BIOL, V283, P883. VENDRUSCOLO M, 2001, NATURE, V409, P641. VILLEGAS V, 1998, J MOL BIOL, V283, P1027. WATANABE M, 1993, J CHEM PHYS, V99, P8063. WINTER G, 1982, NATURE, V299, P756. WUTHRICH K, 1989, SCIENCE, V243, P45.}}, doc-delivery-number = {{620JP}}, doi = {{10.1016/S0022-2836(02)00944-0}}, interhash = {33f4496017269230407407571aecb764}, intrahash = {269d9bfbe873065b8fc7fa7a890b82dd}, issn = {{0022-2836}}, journal = {{JOURNAL OF MOLECULAR BIOLOGY}}, journal-iso = {{J. Mol. Biol.}}, keywords = {AcP phi states transition value}, keywords-plus = {{SITE-DIRECTED MUTAGENESIS; MOLECULAR-DYNAMICS; CHYMOTRYPSIN INHIBITOR-2; MUSCLE ACYLPHOSPHATASE; SECONDARY STRUCTURE; SIMULATIONS; STABILITY; ENERGY; MECHANISM; RESIDUES}}, language = {{English}}, month = {{NOV 15}}, number = {{1}}, number-of-cited-references = {{45}}, pages = {{151-163}}, publisher = {{ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD}}, subject-category = {{Biochemistry \& Molecular Biology}}, times-cited = {{63}}, timestamp = {2009-01-07T00:44:41.000+0100}, title = {{Determination of a transition state at atomic resolution from protein engineering data}}, type = {{Article}}, unique-id = {{ISI:000179530500011}}, volume = {{324}}, year = {{2002}} }