Empirical solvation models can be used to differentiate native from near‐native conformations of bovine pancreatic trypsin inhibitor

Several hydration models for peptides and proteins based on solvent accessible surface area have been proposed previously. We have evaluated some of these models as well as four new ones in the context of near‐native conformations of a protein. In addition, we propose an empirical site–site distance‐dependent correction that can be used in conjuction with any of these models.

[1]  Kenneth Levenberg A METHOD FOR THE SOLUTION OF CERTAIN NON – LINEAR PROBLEMS IN LEAST SQUARES , 1944 .

[2]  D. Marquardt An Algorithm for Least-Squares Estimation of Nonlinear Parameters , 1963 .

[3]  G. N. Ramachandran,et al.  Variation of the NH–CαH coupling constant with dihedral angle in the NMR spectra of peptides , 1971 .

[4]  H. Scheraga,et al.  Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids , 1975 .

[5]  Keinosuke Fukunaga,et al.  A Graph-Theoretic Approach to Nonparametric Cluster Analysis , 1976, IEEE Transactions on Computers.

[6]  V. Parsegian,et al.  Measured work of deformation and repulsion of lecithin bilayers. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Kurt Wüthrich,et al.  1H‐nmr parameters of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H‐Gly‐Gly‐X‐L‐Ala‐OH , 1979 .

[8]  K. Kopple,et al.  Solvent-dependent conformational distributions of some dipeptides , 1980 .

[9]  J. Israelachvili,et al.  The hydrophobic interaction is long range, decaying exponentially with distance , 1982, Nature.

[10]  H. Scheraga,et al.  Computed conformational states of the 20 naturally occurring amino acid residues and of the prototype residue α-aminobutyric acid , 1983 .

[11]  M GayDavid,et al.  Algorithm 611: Subroutines for Unconstrained Minimization Using a Model/Trust-Region Approach , 1983 .

[12]  H. Scheraga,et al.  Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids , 1983 .

[13]  M. L. Connolly Analytical molecular surface calculation , 1983 .

[14]  W F van Gunsteren,et al.  Computer simulation as a tool for tracing the conformational differences between proteins in solution and in the crystalline state. , 1984, Journal of molecular biology.

[15]  H. Scheraga,et al.  Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H...O = C hydrogen bonds from packing configurations , 1984 .

[16]  M. Levitt,et al.  Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. , 1985, Journal of molecular biology.

[17]  D. F. Evans,et al.  Attractive forces between uncharged hydrophobic surfaces: direct measurements in aqueous solution. , 1985, Science.

[18]  A. Lesk,et al.  The relation between the divergence of sequence and structure in proteins. , 1986, The EMBO journal.

[19]  A. D. McLachlan,et al.  Solvation energy in protein folding and binding , 1986, Nature.

[20]  J. Israelachvili,et al.  Structuring in liquid alkanes between solid surfaces: Force measurements and mean‐field theory , 1987 .

[21]  K. D. Gibson,et al.  Exact calculation of the volume and surface area of fused hard-sphere molecules with unequal atomic radii , 1987 .

[22]  H. Scheraga,et al.  Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[23]  A Wlodawer,et al.  Comparison of two highly refined structures of bovine pancreatic trypsin inhibitor. , 1987, Journal of molecular biology.

[24]  N Go,et al.  Normal modes of vibration in bovine pancreatic trypsin inhibitor and its mechanical property , 1987, Proteins.

[25]  J. Israelachvili Solvation forces and liquid structure, as probed by direct force measurements , 1987 .

[26]  Harold A. Scheraga,et al.  Free energies of hydration of solute molecules. 3. Application of the hydration shell model to charged organic molecules , 1987 .

[27]  Harold A. Scheraga,et al.  Free energies of hydration of solute molecules. 1. Improvement of the hydration shell model by exact computations of overlapping volumes , 1987 .

[28]  R. Sharon,et al.  Accurate simulation of protein dynamics in solution. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[29]  William L. Jorgensen,et al.  Cis-trans energy difference for the peptide bond in the gas phase and in aqueous solution , 1988 .

[30]  J. Fauchère,et al.  Estimating and representing hydrophobicity potential , 1988 .

[31]  H. Scheraga,et al.  Calculation of protein conformation by the build-up procedure. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data. , 1988, Journal of biomolecular structure & dynamics.

[32]  H A Scheraga,et al.  Variable-target-function and build-up procedures for the calculation of protein conformation. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data. , 1988, Journal of biomolecular structure & dynamics.

[33]  H. Scheraga,et al.  On the multiple‐minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method—tests on poly(L‐alanine) , 1988, Biopolymers.

[34]  Harold A. Scheraga,et al.  Free energies of hydration of solute molecules. IV: Revised treatment of the hydration shell model , 1988 .

[35]  M. Karplus,et al.  Crystallographic refinement by simulated annealing: application to crambin , 1989 .

[36]  D. Marsh Water adsorption isotherms and hydration forces for lysolipids and diacyl phospholipids. , 1989, Biophysical journal.

[37]  T. Witten,et al.  Entropic orientational forces between surfaces in anisotropic liquids , 1989 .

[38]  H. Scheraga,et al.  A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. II. Phi-psi maps for N-acetyl alanine N'-methyl amide: comparisons, contrasts and simple experimental tests. , 1989, Journal of biomolecular structure & dynamics.

[39]  Harold A. Scheraga,et al.  Protein structure prediction using a combination of sequence homology and global energy minimization I. Global energy minimization of surface loops , 1990 .

[40]  William L. Jorgensen,et al.  Molecular dynamics of proteins with the OPLS potential functions. Simulation of the third domain of silver pheasant ovomucoid in water , 1990 .

[41]  Lucjan Piela,et al.  On the multiple‐minima problem in the conformational analysis of polypeptides. V. Application of the self‐consistent electrostatic field and the electrostatically driven monte carlo methods to bovine pancreatic trypsin inhibitor , 1991, Proteins.