Comparison of predicted native structures of Met‐enkephalin based on various accessible‐surface‐area solvent models

We examine the variation and similarity of the native structures predicted from various accessible‐surface‐area solvent models for peptide Met‐enkephalin. Both ECEPP/2 and ECEPP/3 force fields have been used in conjunction with ten different sets of accessible‐surface‐area parameterization. The native structures were determined by an implementation of the basin hopping Monte Carlo technique. The results suggest that the implicit solvent models examined in this study should be employed in computer simulations with extreme caution. In addition, the effect of fixing or not fixing the peptide angles ω has been examined. We conclude that fixing ω generally gives rise to a poor prediction. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009

[1]  J. Doye,et al.  Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms , 1997, cond-mat/9803344.

[2]  J. Pablo,et al.  Density of states simulations of proteins , 2003 .

[3]  David J. Wales,et al.  Global optimization and folding pathways of selected α-helical proteins , 2005 .

[4]  Hsiao-Ping Hsu,et al.  Metropolis simulations of Met-Enkephalin with solvent-accessible area parametrizations. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[5]  G. Némethy,et al.  The γ Turn, a Possible Folded Conformation of the Polypeptide Chain. Comparison with the β Turn , 1972 .

[6]  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.

[7]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[9]  K. Dill.  Polymer principles and protein folding , 1999, Protein science : a publication of the Protein Society.

[10]  H. Scheraga,et al.  Global optimization of clusters, crystals, and biomolecules. , 1999, Science.

[11]  P. Kollman,et al.  Protein structure prediction with a combined solvation free energy-molecular mechanics force field , 1993 .

[12]  Yuko Okamoto,et al.  Solvation structure and stability of peptides in aqueous solutions analyzed by the reference interaction site model theory , 1997 .

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

[14]  A. Schug,et al.  Basin hopping simulations for all-atom protein folding. , 2006, The Journal of chemical physics.

[15]  R. Berry,et al.  Computer simulation of met-enkephalin using explicit atom and united atom potentials : Similarities, differences, and suggestions for improvement , 2003 .

[16]  W. Braun,et al.  Surface area included in energy refinement of proteins. A comparative study on atomic solvation parameters. , 1993, Journal of molecular biology.

[17]  C. Venkatachalam.  Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units , 1968, Biopolymers.

[18]  Charles L. Brooks,et al.  Generalized born model with a simple smoothing function , 2003, J. Comput. Chem..

[19]  Harold A. Scheraga,et al.  Structure and free energy of complex thermodynamic systems , 1988 .

[20]  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 .

[21]  Werner Braun,et al.  Efficient search for all low energy conformations of polypeptides by Monte Carlo methods , 1991 .

[22]  H. Scheraga,et al.  Monte Carlo-minimization approach to the multiple-minima problem in protein folding. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Yuko Okamoto,et al.  Combination of the Replica-Exchange Monte Carlo Method and the Reference Interaction Site Model Theory for Simulating a Peptide Molecule in Aqueous Solution , 2004 .

[24]  M. Karplus,et al.  Effective energy function for proteins in solution , 1999, Proteins.

[25]  B Honig,et al.  Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models. , 1991, Biochemistry.

[26]  J. Thornton,et al.  PROMOTIF—A program to identify and analyze structural motifs in proteins , 1996, Protein science : a publication of the Protein Society.

[27]  J. Richardson,et al.  The anatomy and taxonomy of protein structure. , 1981, Advances in protein chemistry.

[28]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[29]  Stephen R. Wilson,et al.  Simulated annealing of met-enkephalin: low energy states and their relevance to membrane-bound, solution and solid-state conformations , 1994 .

[30]  G. Rose,et al.  Turns in peptides and proteins. , 1985, Advances in protein chemistry.

[31]  K. Sanbonmatsu,et al.  Structure of Met‐enkephalin in explicit aqueous solution using replica exchange molecular dynamics , 2002, Proteins.

[32]  David J. Wales,et al.  The free energy landscape and dynamics of met-enkephalin , 2003 .

[33]  D. Eisenberg,et al.  Atomic solvation parameters applied to molecular dynamics of proteins in solution , 1992, Protein science : a publication of the Protein Society.

[34]  Ulrich H. E. Hansmann,et al.  An enhanced version of SMMP - open-source software package for simulation of proteins , 2006, Comput. Phys. Commun..

[35]  Y. Okamoto,et al.  Solvent effects on conformational stability of peptides: RISM analyses , 2001 .

[36]  Harold A. Scheraga,et al.  Stereochemical requirements for the existence of hydrogen bonds in β-bends , 1980 .

[37]  Lixin Zhan,et al.  Conformational study of Met-enkephalin based on the ECEPP force fields. , 2006, Biophysical journal.

[38]  Lixin Zhan,et al.  Fast Stochastic Global Optimization Methods and Their Applications to Cluster Crystallization and Protein Folding , 2005 .

[39]  Wing-Ki Liu,et al.  Multicanonical basin hopping: a new global optimization method for complex systems. , 2004, The Journal of chemical physics.

[40]  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.

[41]  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 .

[42]  Yuko Okamoto,et al.  Multicanonical algorithm combined with the RISM theory for simulating peptides in aqueous solution , 2000 .

[43]  Conrad C. Huang,et al.  MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance , 2003, Bioinform..

[44]  H. Scheraga,et al.  Empirical solvation models can be used to differentiate native from near‐native conformations of bovine pancreatic trypsin inhibitor , 1991, Proteins.

[45]  H. Scheraga,et al.  Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides , 1994 .

[46]  W. Liu,et al.  Computational study of the Trp‐cage miniprotein based on the ECEPP/3 force field , 2006, Proteins.

[47]  E. Milner-White,et al.  One type of gamma-turn, rather than the other gives rise to chain-reversal in proteins. , 1988, Journal of molecular biology.

[48]  Christodoulos A. Floudas,et al.  Prediction of Oligopeptide Conformations via Deterministic Global Optimization , 1997, J. Glob. Optim..

[49]  C. Anfinsen.  Principles that govern the folding of protein chains. , 1973, Science.

[50]  K. Freed,et al.  Long time dynamics of Met-enkephalin: comparison of explicit and implicit solvent models. , 2002, Biophysical journal.

[51]  P M Cullis,et al.  Affinities of amino acid side chains for solvent water. , 1981, Biochemistry.

[52]  Wing-Ki Liu,et al.  Asynchronous multicanonical basin hopping method and its application to cobalt nanoclusters. , 2005, The Journal of chemical physics.

[53]  Philip E. Gill,et al.  Practical optimization , 1981 .

[54]  Hagai Meirovitch,et al.  A Simple and Effective Procedure for Conformational Search of Macromolecules: Application to Met- and Leu-Enkephalin , 1994 .

[55]  P. Privalov.  Stability of proteins: small globular proteins. , 1979, Advances in protein chemistry.

[56]  Louis Carlacci.  Conformational analysis of [Met5]-enkephalin: Solvation and ionization considerations , 1998, J. Comput. Aided Mol. Des..

[57]  Ulrich H. E. Hansmann,et al.  SMMP) A modern package for simulation of proteins , 2001 .

[58]  Frank Eisenmenger,et al.  Variation of the Energy Landscape of a Small Peptide under a Change from the ECEPP/2 Force Field to ECEPP/3 , 1997, physics/9710020.

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

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