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Science 23 January 1987:
Vol. 235. no. 4787, pp. 458 - 460
DOI: 10.1126/science.235.4787.458
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Articles

Crystallographic R Factor Refinement by Molecular Dynamics

AXEL T. BRÜNGER 1, JOHN KURIYAN 1, and MARTIN KARPLUS 2

1 Department of Chemistry, Harvard University, Cambridge, MA 02138.
2 Department of Chemistry, Harvard University, Cambridge, MA 02138, and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139.

Molecular dynamics was used to refine macromolecular structures by incorporating the difference between the observed crystallographic structure factor amplitude and that calculated from an assumed atomic model into the total energy of the system. The method has a radius of convergence that is larger than that of conventional restrained least-squares refinement. Test cases showed that the need for manual corrections during refinement of macromolecular crystal structures is reduced. In crambin, the dynamics calculation moved residues that were misplaced by more than 3 angstroms into the correct positions without human intervention.

Submitted on September 2, 1986
Accepted on November 26, 1986


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Structure of Barley Grain Peroxidase Refined at 1.9-A Resolution. A PLANT PEROXIDASE REVERSIBLY INACTIVATED AT NEUTRAL pH.
A. Henriksen, K. G. Welinder, and M. Gajhede (1998)
J. Biol. Chem. 273, 2241-2248
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Three-dimensional Structure of L-2-Haloacid Dehalogenase from Xanthobacter autotrophicus GJ10 Complexed with the Substrate-analogue Formate.
I. S. Ridder, H. J. Rozeboom, K. H. Kalk, D. B. Janssen, and B. W. Dijkstra (1997)
J. Biol. Chem. 272, 33015-33022
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Immune Versus Natural Selection: Antibody Aldolases with Enzymic Rates But Broader Scope.
C. F. Barbas III, A. Heine, G. Zhong, T. Hoffmann, S. Gramatikova, R. Björnestedt, B. List, J. Anderson, E. A. Stura, I. A. Wilson, et al. (1997)
Science 278, 2085-2092
   Abstract »    Full Text »
Structural Plasticity in a Remodeled Protein-Protein Interface.
S. Atwell, M. Ultsch, A. M. De Vos, and J. A. Wells (1997)
Science 278, 1125-1128
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The crystal structure of human interferon beta  at 2.2-A resolution.
M. Karpusas, M. Nolte, C. B. Benton, W. Meier, W. N. Lipscomb, and S. Goelz (1997)
PNAS 94, 11813-11818
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Structure of the thrombin complex with triabin, a lipocalin-like exosite-binding inhibitor derived from a triatomine bug.
P. Fuentes-Prior, C. Noeske-Jungblut, P. Donner, W.-D. Schleuning, R. Huber, and W. Bode (1997)
PNAS 94, 11845-11850
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The Structure of Nitric Oxide Synthase Oxygenase Domain and Inhibitor Complexes.
B. R. Crane, A. S. Arvai, R. Gachhui, C. Wu, D. K. Ghosh, E. D. Getzoff, D. J. Stuehr, and J. A. Tainer (1997)
Science 278, 425-431
   Abstract »    Full Text »
Structure-Based Analysis of Catalysis and Substrate Definition in the HIT Protein Family.
C. D. Lima, M. G. Klein, and W. A. Hendrickson (1997)
Science 278, 286-290
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Consequences of Seven Novel Mutations on the Expression and Structure of Keratinocyte Transglutaminase.
M. Huber, V. C. Yee, N. Burri, E. Vikerfors, A. P. M. Lavrijsen, A. S. Paller, and D. Hohl (1997)
J. Biol. Chem. 272, 21018-21026
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X-ray analysis of azido-thymidine diphosphate binding to nucleoside diphosphate kinase.
Y. Xu, O. Sellam, S. Morera, S. Sarfati, R. Biondi, M. Veron, and J. Janin (1997)
PNAS 94, 7162-7165
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Vascular endothelial growth factor: Crystal structure and functional mapping of the kinase domain receptor binding site.
Y. A. Muller, B. Li, H. W. Christinger, J. A. Wells, B. C. Cunningham, and A. M. de Vos (1997)
PNAS 94, 7192-7197
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Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement.
P. D. Adams, N. S. Pannu, R. J. Read, and A. T. Brunger (1997)
PNAS 94, 5018-5023
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The crystal structure of subtilisin Carlsberg in anhydrous dioxane and its comparison with those in water and acetonitrile.
J. L. Schmitke, L. J. Stern, and A. M. Klibanov (1997)
PNAS 94, 4250-4255
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Can Enzymatic Activity, or Otherwise, Be Inferred from Structural Studies of Annexin III?.
B. Perron, A. Lewit-Bentley, B. Geny, and F. Russo-Marie (1997)
J. Biol. Chem. 272, 11321-11326
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Crystal structure of Lyme disease antigen outer surface protein A complexed with an Fab.
H. Li, J. J. Dunn, B. J. Luft, and C. L. Lawson (1997)
PNAS 94, 3584-3589
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Crystal structure of varicella-zoster virus protease.
X. Qiu, C. A. Janson, J. S. Culp, S. B. Richardson, C. Debouck, W. W. Smith, and S. S. Abdel-Meguid (1997)
PNAS 94, 2874-2879
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Structure of Recombinant Human CPP32 in Complex with the Tetrapeptide Acetyl-Asp-Val-Ala-Asp Fluoromethyl Ketone.
P. R.E. Mittl, S. Di Marco, J. F. Krebs, X. Bai, D. S. Karanewsky, J. P. Priestle, K. J. Tomaselli, and M. G. Grutter (1997)
J. Biol. Chem. 272, 6539-6547
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On the Convergent Evolution of Animal Toxins. CONSERVATION OF A DIAD OF FUNCTIONAL RESIDUES IN POTASSIUM CHANNEL-BLOCKING TOXINS WITH UNRELATED STRUCTURES.
M. Dauplais, A. Lecoq, J. Song, J. Cotton, N. Jamin, B. Gilquin, C. Roumestand, C. Vita, C. L.C. de Medeiros, E. G. Rowan, et al. (1997)
J. Biol. Chem. 272, 4302-4309
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Switch of Coenzyme Specificity of Mouse Lung Carbonyl Reductase by Substitution of Threonine 38with Aspartic Acid.
M. Nakanishi, K. Matsuura, H. Kaibe, N. Tanaka, T. Nonaka, Y. Mitsui, and A. Hara (1997)
J. Biol. Chem. 272, 2218-2222
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Regulation of product chain length by isoprenyl diphosphate synthases.
L. C. Tarshis, P. J. Proteau, B. A. Kellogg, J. C. Sacchettini, and C. D. Poulter (1996)
PNAS 93, 15018-15023
   Abstract »    Full Text »    PDF »


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