Empirical potentials and functions for protein folding and binding.

Simplified models and empirical potentials are being increasingly used for the analysis of proteins, frequently augmenting or replacing molecular mechanics approaches. Recent folding simulations have employed potentials that, in addition to terms assuring proper polypeptide geometry, include only two noncovalent effects-hydrogen bonding and hydrophobicity, with extremely simple approximations to the latter. The potentials that have been used in the free-energy ranking of protein-ligand complexes have generally been more involved. These potentials have more detailed solvation models and account for both local (hydrophobic and polar) solute-solvent phenomena and long range electrostatic solvation effects. The models of solvation that have been used most frequently are surface area related atomic parameters, knowledge-based models extracted from protein-structure data, and continum electrostatics with an additional area-related parameter. The knowledge-based approaches to solvation, although convenient and accurate enough, are suspect of double counting certain free-energy terms.

[1]  Hans-Joachim Böhm,et al.  The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure , 1994, J. Comput. Aided Mol. Des..

[2]  K. Dill,et al.  A simple protein folding algorithm using a binary code and secondary structure constraints. , 1995, Protein engineering.

[3]  W. V. van Gunsteren,et al.  An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution. , 1996, Journal of molecular biology.

[4]  M J Sippl,et al.  Helmholtz free energy of peptide hydrogen bonds in proteins. , 1996, Journal of molecular biology.

[5]  H. Wolfson,et al.  Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed, sparse, points in docking. , 1995, Journal of molecular biology.

[6]  D Gilis,et al.  Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials. , 1996, Journal of molecular biology.

[7]  J M Thornton,et al.  X-SITE: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins. , 1996, Journal of molecular biology.

[8]  M. Sippl Calculation of conformational ensembles from potentials of mena force , 1990 .

[9]  I. Kuntz,et al.  Calculation of protein tertiary structure. , 1976, Journal of molecular biology.

[10]  T. Halgren,et al.  A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site. , 1995, Journal of medicinal chemistry.

[11]  D. Yee,et al.  Principles of protein folding — A perspective from simple exact models , 1995, Protein science : a publication of the Protein Society.

[12]  E I Shakhnovich,et al.  Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. , 1995, Journal of molecular biology.

[13]  S Vajda,et al.  Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments. , 1995, Protein engineering.

[14]  M. Karplus,et al.  Prediction of the folding of short polypeptide segments by uniform conformational sampling , 1987, Biopolymers.

[15]  J Moult,et al.  Local interactions dominate folding in a simple protein model. , 1996, Journal of molecular biology.

[16]  S Vajda,et al.  Prediction of protein complexes using empirical free energy functions , 1996, Protein science : a publication of the Protein Society.

[17]  R. Brasseur,et al.  Simulating the folding of small proteins by use of the local minimum energy and the free solvation energy yields native-like structures. , 1995, Journal of molecular graphics.

[18]  A Wlodawer,et al.  An approach to rapid estimation of relative binding affinities of enzyme inhibitors: application to peptidomimetic inhibitors of the human immunodeficiency virus type 1 protease. , 1996, Journal of medicinal chemistry.

[19]  D. Covell,et al.  Docking enzyme‐inhibitor complexes using a preference‐based free‐energy surface , 1996, Proteins.

[20]  D L Preston,et al.  RERF scientific agenda and DOE. , 1995, Science.

[21]  J. Skolnick,et al.  Monte carlo simulations of protein folding. I. Lattice model and interaction scheme , 1994, Proteins.

[22]  J Skolnick,et al.  Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: atomic burial position and pairwise non-bonded interactions. , 1996, Protein engineering.

[23]  B. Honig,et al.  On the formation of protein tertiary structure on a computer. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Gennady M Verkhivker,et al.  Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity. , 1995, Protein engineering.

[25]  S. Sung Folding simulations of alanine-based peptides with lysine residues. , 1995, Biophysical journal.

[26]  S Vajda,et al.  Effect of conformational flexibility and solvation on receptor-ligand binding free energies. , 1994, Biochemistry.

[27]  Michel F. Sanner,et al.  Lattice modeling: Accuracy of energy calculations , 1996, J. Comput. Chem..

[28]  S. Sun,et al.  A genetic algorithm that seeks native states of peptides and proteins. , 1995, Biophysical journal.

[29]  Robert E. Bruccoleri,et al.  Finite difference Poisson-Boltzmann electrostatic calculations: Increased accuracy achieved by harmonic dielectric smoothing and charge antialiasing , 1997, J. Comput. Chem..

[30]  R. Jernigan,et al.  Structure-derived potentials and protein simulations. , 1996, Current opinion in structural biology.

[31]  P Argos,et al.  Ab initio tertiary-fold prediction of helical and non-helical protein chains using a genetic algorithm. , 1996, International journal of biological macromolecules.

[32]  I. Kuntz,et al.  Protein docking and complementarity. , 1991, Journal of molecular biology.

[33]  R. Jernigan,et al.  Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. , 1996, Journal of molecular biology.

[34]  E. Shakhnovich,et al.  SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence , 1996 .

[35]  Fredy Sussman,et al.  Solvent accessibility as a predictive tool for the free energy of inhibitor binding to the HIV‐1 protease , 1995, Protein science : a publication of the Protein Society.

[36]  J. Skolnick,et al.  Monte carlo simulations of protein folding. II. Application to protein A, ROP, and crambin , 1994, Proteins.

[37]  F E Cohen,et al.  Protein model structure evaluation using the solvation free energy of folding. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[38]  R. Bruccoleri,et al.  On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5. , 1989, Biochemistry.

[39]  A. H. Juffer,et al.  Comparison of atomic solvation parametric sets: Applicability and limitations in protein folding and binding , 1995, Protein science : a publication of the Protein Society.

[40]  R. Read,et al.  Atomic solvation parameters in the analysis of protein‐protein docking results , 1995, Protein science : a publication of the Protein Society.

[41]  M. Sippl,et al.  Helmholtz free energies of atom pair interactions in proteins. , 1996, Folding & design.

[42]  Adam Godzik,et al.  Lattice representations of globular proteins: How good are they? , 1993, J. Comput. Chem..

[43]  R. Srinivasan,et al.  LINUS: A hierarchic procedure to predict the fold of a protein , 1995, Proteins.

[44]  R L Jernigan,et al.  A preference‐based free‐energy parameterization of enzyme‐inhibitor binding. Applications to HIV‐1‐protease inhibitor design , 1995, Protein science : a publication of the Protein Society.

[45]  M. Lewis,et al.  Calculation of the free energy of association for protein complexes , 1992, Protein science : a publication of the Protein Society.

[46]  K. Dill,et al.  Statistical potentials extracted from protein structures: how accurate are they? , 1996, Journal of molecular biology.

[47]  M. Levitt,et al.  Computer simulation of protein folding , 1975, Nature.

[48]  J Novotny,et al.  Empirical free energy calculations: a blind test and further improvements to the method. , 1997, Journal of molecular biology.

[49]  Adding backbone to protein folding: why proteins are polypeptides. , 1995, Folding & design.

[50]  Ajay,et al.  Computational methods to predict binding free energy in ligand-receptor complexes. , 1995, Journal of medicinal chemistry.

[51]  K. Sharp,et al.  Finite difference Poisson‐Boltzmann electrostatic calculations: Increased accuracy achieved by harmonic dielectric smoothing and charge antialiasing , 1997 .

[52]  B. Lee,et al.  Protein folding by a biased Monte Carlo procedure in the dihedral angle space , 1996, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[53]  I. Vakser Low-resolution docking: prediction of complexes for underdetermined structures. , 1998, Biopolymers.

[54]  M J Sternberg,et al.  A continuum model for protein-protein interactions: application to the docking problem. , 1995, Journal of molecular biology.

[55]  K Yue,et al.  Folding proteins with a simple energy function and extensive conformational searching , 1996, Protein science : a publication of the Protein Society.

[56]  D E Koshland,et al.  Computational method for relative binding energies of enzyme‐substrate complexes , 1996, Protein science : a publication of the Protein Society.

[57]  S. Doniach,et al.  A computer model to dynamically simulate protein folding: Studies with crambin , 1989, Proteins.

[58]  C. DeLisi,et al.  Determination of atomic desolvation energies from the structures of crystallized proteins. , 1997, Journal of molecular biology.

[59]  R. Bruccoleri,et al.  Criteria that discriminate between native proteins and incorrectly folded models , 1988, Proteins.

[60]  B Honig,et al.  An algorithm to generate low-resolution protein tertiary structures from knowledge of secondary structure. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[61]  R Abagyan,et al.  Homology modeling by the ICM method , 1995, Proteins.

[62]  A. Leslie,et al.  Refined crystal structure of type III chloramphenicol acetyltransferase at 1.75 A resolution. , 1990, Journal of molecular biology.

[63]  Daniel A. Gschwend,et al.  Molecular docking towards drug discovery , 1996, Journal of molecular recognition : JMR.

[64]  Garland R. Marshall,et al.  VALIDATE: A New Method for the Receptor-Based Prediction of Binding Affinities of Novel Ligands , 1996 .

[65]  B. Honig,et al.  Classical electrostatics in biology and chemistry. , 1995, Science.

[66]  D. Eisenberg,et al.  An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[67]  Robert E. Bruccoleri,et al.  Application of Systematic Conformational Search to Protein Modeling , 1993 .

[68]  K. Dill,et al.  Comparing folding codes for proteins and polymers , 1996, Proteins.

[69]  P. Wolynes,et al.  Self‐consistently optimized statistical mechanical energy functions for sequence structure alignment , 1996, Protein science : a publication of the Protein Society.

[70]  K. Dill,et al.  An iterative method for extracting energy-like quantities from protein structures. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[71]  M. Karplus,et al.  Kinetics of protein folding. A lattice model study of the requirements for folding to the native state. , 1994, Journal of molecular biology.

[72]  K. Sharp,et al.  Decomposition of interaction free energies in proteins and other complex systems. , 1995, Journal of molecular biology.