Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum.

Structural refinement of proteins involves the minimization of a target function that combines X-ray data with a set of restraints enforcing stereochemistry and packing. Electrostatic interactions are not ordinarily included in the target function, partly because they cannot be calculated reliably without a description of dielectric screening by solvent in the crystal. With the recent development of accurate implicit solvent models to describe this screening, the question arises as to whether a more detailed target function including electrostatic and solvation terms can yield more accurate structures or somewhat different structures of equivalent accuracy. The Generalized Born (GB) model is one such model that describes the solvent as a dielectric continuum, taking into account its heterogeneous distribution within the crystal. It is used here for X-ray refinements of three protein structures with experimental diffraction data to 2.4, 2.9 and 3.2 A, respectively. In each case, a higher resolution structure is available for comparison. The new target function includes stereochemical restraints, van der Waals, Coulomb and solvation interactions, along with the usual X-ray pseudo-energy term, which employs the likelihood estimator of Pannu and Read. Multiple simulated-annealing refinements were performed in torsion-angle space with a conventional target function and the new GB target function, yielding ensembles of refined structures. The new target function yields structures of similar accuracy, as measured by the free R factor, map/model correlations and deviations from the high-resolution structures. About 10% of side-chain conformations differ between the two sets of refinements, in the sense that the two ensembles of conformations do not completely overlap. Over 75% of the differences correspond to surface side chains. For one of the proteins, the GB set has a greater dispersion, indicating that for this case the conventional target function overestimates the true precision. As GB parameterization continues to improve, we expect that this approach will become increasingly useful.

[1]  W. Hendrickson.  Stereochemically restrained refinement of macromolecular structures. , 1985, Methods in enzymology.

[2]  Thomas Simonson,et al.  Implicit solvent models: Combining an analytical formulation of continuum electrostatics with simple models of the hydrophobic effect , 1999 .

[3]  A. Brünger,et al.  Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement , 1994, Proteins.

[4]  W. C. Still,et al.  Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .

[5]  Bin Xia,et al.  Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water , 2002, Journal of biomolecular NMR.

[6]  A. Brunger.  Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. , 1992 .

[7]  Axel T Brunger,et al.  Molecular dynamics applied to X-ray structure refinement. , 2002, Accounts of chemical research.

[8]  Structure of crystalline Escherichia coli methionyl‐tRNA(f)Met formyltransferase: comparison with glycinamide ribonucleotide formyltransferase. , 1996, The EMBO journal.

[9]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[10]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[11]  R. Read,et al.  Improved Structure Refinement Through Maximum Likelihood , 1996 .

[12]  M. Karplus,et al.  A Comprehensive Analytical Treatment of Continuum Electrostatics , 1996 .

[13]  T. Simonson,et al.  Macromolecular electrostatics: continuum models and their growing pains. , 2001, Current opinion in structural biology.

[14]  D. Case,et al.  Generalized born models of macromolecular solvation effects. , 2000, Annual review of physical chemistry.

[15]  D. Moras,et al.  Crystal structure of aspartyl‐tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation , 1998, The EMBO journal.

[16]  B. Dominy,et al.  Development of a generalized Born model parameterization for proteins and nucleic acids , 1999 .

[17]  A. Roitberg,et al.  All-atom structure prediction and folding simulations of a stable protein. , 2002, Journal of the American Chemical Society.

[18]  Christian Bartels,et al.  Solution conformations of structured peptides: continuum electrostatics versus distance-dependent dielectric functions , 1999 .

[19]  D. Case,et al.  Modification of the Generalized Born Model Suitable for Macromolecules , 2000 .

[20]  P. Beroza,et al.  Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects , 1999 .

[21]  W. C. Still,et al.  The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii , 1997 .

[22]  A T Brünger,et al.  Protein hydration observed by X-ray diffraction. Solvation properties of penicillopepsin and neuraminidase crystal structures. , 1994, Journal of molecular biology.

[23]  W. Saenger,et al.  Decamer-like conformation of a nona-peptide bound to HLA-B*3501 due to non-standard positioning of the C terminus. , 1998, Journal of molecular biology.

[24]  C. Brooks,et al.  Novel generalized Born methods , 2002 .

[25]  Fabrice Leclerc,et al.  Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes , 2001, J. Comput. Chem..

[26]  P Gros,et al.  Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics. , 1990, Science.

[27]  L. Wilkinson.  Immunity , 1891, The Lancet.

[28]  R. Huber,et al.  Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement , 1991 .

[29]  M. Karplus,et al.  Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model. , 1998, Journal of molecular biology.

[30]  Gregory D. Hawkins,et al.  Pairwise solute descreening of solute charges from a dielectric medium , 1995 .

[31]  Axel T. Brunger,et al.  X-PLOR Version 3.1: A System for X-ray Crystallography and NMR , 1992 .

[32]  R. Friesner,et al.  Generalized Born Model Based on a Surface Integral Formulation , 1998 .

[33]  M. Schaefer,et al.  A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution. , 1990, Journal of molecular biology.

[34]  G. Bricogne.  [23] Bayesian statistical viewpoint on structure determination: Basic concepts and examples. , 1997, Methods in enzymology.

[35]  良二 上田.  J. Appl. Cryst.の発刊に際して , 1970 .

[36]  Axel T. Brunger,et al.  Phase Improvement by Multi-Start Simulated Annealing Refinement and Structure-Factor Averaging , 1998 .

[37]  M. Karplus,et al.  Crystallographic R Factor Refinement by Molecular Dynamics , 1987, Science.

[38]  T. Simonson,et al.  Protein molecular dynamics with the generalized born/ACE solvent model , 2001, Proteins.

[39]  Ray Luo,et al.  Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease , 2000 .

[40]  D. Case,et al.  Theory and applications of the generalized born solvation model in macromolecular simulations , 2000, Biopolymers.