Recent developments in the theory of protein folding: searching for the global energy minimum.

Statistical mechanical theories and computer simulation are being used to gain an understanding of the fundamental features of protein folding. A major obstacle in the computation of protein structures is the multiple-minima problem arising from the existence of many local minima in the multidimensional energy landscape of the protein. This problem has been surmounted for small open-chain and cyclic peptides, and for regular-repeating sequences of models of fibrous proteins. Progress is being made in resolving this problem for globular proteins.

[1]  J. Skolnick,et al.  Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptides , 1992 .

[2]  P. Wolynes,et al.  Intermediates and barrier crossing in a random energy model , 1989 .

[3]  D. Ripoll,et al.  On the multiple‐minima problem in the conformational analysis of polypeptides. IV. Application of the electrostatically driven monte carlo method to the 20‐residue membrane‐bound portion of melittin , 1990, Biopolymers.

[4]  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.

[5]  Harold A. Scheraga,et al.  Statistical Thermodynamics of Protein Folding: Comparison of a Mean-Field Theory with Monte Carlo Simulations , 1994 .

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

[7]  H A Scheraga,et al.  Prediction of the native conformation of a polypeptide by a statistical‐mechanical procedure. III. Probable and average conformations of enkephalin , 1987, Biopolymers.

[8]  A. Tu.  Current Topics In Biochemistry. , 1973 .

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

[10]  N. Go,et al.  Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions. , 2009 .

[11]  Steven G. Louie,et al.  A Monte carlo simulated annealing approach to optimization over continuous variables , 1984 .

[12]  Harold A. Scheraga,et al.  Analysis of the Contribution of Internal Vibrations to the Statistical Weights of Equilibrium Conformations of Macromolecules , 1969 .

[13]  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.

[14]  Lucjan Piela,et al.  Mean field theory as a tool for intramolecular conformational optimization. II: Tests on the homopolypeptides decaglycine and icosalanine , 1993 .

[15]  L. Piela,et al.  Mean field theory as a tool for intramolecular conformational optimization. 1. Tests on terminally-blocked alanine and met-enkephalin , 1992 .

[16]  A Kolinski,et al.  Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics. , 1991, Journal of molecular biology.

[17]  C. D. Gelatt,et al.  Optimization by Simulated Annealing , 1983, Science.

[18]  A. Kolinski,et al.  Simulations of the Folding of a Globular Protein , 1990, Science.

[19]  H. Neurath.  The proteins : composition, structure, and function , 1963 .

[20]  E. Katchalski.  Poly-α-Amino Acids , 1951 .

[21]  R. Jernigan,et al.  Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation , 1985 .

[22]  H A Scheraga,et al.  The Electrostatically Driven Monte Carlo method: Application to conformational analysis of decaglycine , 1991, Biopolymers.

[23]  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.

[24]  Harold A. Scheraga,et al.  Conformational Energy Calculations of the Effects of Sequence Variations on the Conformations of Two Tetrapeptides , 1978 .

[25]  T Schlick,et al.  Supercoiled DNA energetics and dynamics by computer simulation. , 1992, Journal of molecular biology.

[26]  Structure and Expression. Vol. 1. From Proteins to Ribosomes. : M.H. Sarma and R.H. Sarma (Editors). Adenine Press, Guilderland, NY, 1988, ISBN 0-9400030-21-7, viii + 288 pp., US$90.00. , 1989 .

[27]  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 .

[28]  H A Scheraga,et al.  Hydrogen bonding involving the ornithine side chain of gramicidin S. , 1984, Biochemical and biophysical research communications.

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

[30]  H. Scheraga,et al.  On the multiple-minima problem in the conformational analysis of molecules: deformation of the potential energy hypersurface by the diffusion equation method , 1989 .

[31]  H. A. Scheraga,et al.  Application of the diffusion equation method of global optimization to water clusters , 1992 .

[32]  Akbar Nayeem,et al.  A comparative study of the simulated‐annealing and Monte Carlo‐with‐minimization approaches to the minimum‐energy structures of polypeptides: [Met]‐enkephalin , 1991 .

[33]  H. Scheraga,et al.  Use of buildup and energy‐minimization procedures to compute low‐energy structures of the backbone of enkephalin , 1985, Biopolymers.

[34]  H. Scheraga,et al.  Statistical mechanics of noncovalent bonds in polyamino acids. I. Hydrogen bonding of solutes in water, and the binding of water to polypeptides , 1965 .

[35]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[36]  S. Rackovsky,et al.  Prediction of protein conformation on the basis of a search for compact structures: Test on avian pancreatic polypeptide , 1993, Protein science : a publication of the Protein Society.

[37]  T. Blundell,et al.  Conformational flexibility in a small globular hormone: X‐ray analysis of avian pancreatic polypeptide at 0.98‐Å resolution , 1983, Biopolymers.

[38]  H A Scheraga,et al.  Lattice neural network minimization. Application of neural network optimization for locating the global-minimum conformations of proteins. , 1993, Journal of molecular biology.

[39]  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 .

[40]  S Rackovsky,et al.  Unfolding and refolding of the native structure of bovine pancreatic trypsin inhibitor studied by computer simulations. , 1993, Biochemistry.

[41]  H. Scheraga,et al.  Prediction of the native conformation of a polypeptide by a statistical‐mechanical procedure. I. Backbone structure of enkephalin , 1985, Biopolymers.

[42]  A. Gronenborn,et al.  Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. , 1988, Protein engineering.

[43]  H. Scheraga,et al.  Application of the diffusion equation method for global optimization to oligopeptides , 1992 .

[44]  Harold A. Scheraga,et al.  On the Use of Classical Statistical Mechanics in the Treatment of Polymer Chain Conformation , 1976 .

[45]  Harold A. Scheraga,et al.  MONTE CARLO SIMULATION OF A FIRST-ORDER TRANSITION FOR PROTEIN FOLDING , 1994 .

[46]  H. Scheraga,et al.  Performance of the diffusion equation method in searches for optimum structures of clusters of Lennard-Jones atoms , 1991 .

[47]  K. Dill,et al.  Thermal stabilities of globular proteins. , 1989, Biochemistry.

[48]  D. Covell,et al.  Conformations of folded proteins in restricted spaces. , 1990, Biochemistry.

[49]  A Kolinski,et al.  Prediction of the folding pathways and structure of the GCN4 leucine zipper. , 1994, Journal of molecular biology.

[50]  H A Scheraga,et al.  Use of a symmetry condition to compute the conformation of gramicidin S1. , 1975, Macromolecules.

[51]  E. Shakhnovich,et al.  Implications of thermodynamics of protein folding for evolution of primary sequences , 1990, Nature.

[52]  Harold A. Scheraga,et al.  Pattern recognition in the prediction of protein structure. III. An importance‐sampling minimization procedure , 1989 .

[53]  Harold A. Scheraga,et al.  Pattern recognition in the prediction of protein structure. II. Chain conformation from a probability‐directed search procedure , 1989 .

[54]  K. Okuyama,et al.  Structure Analysis of a Collagen Model Polypeptide, (Pro–Pro–Gly)10 , 1976 .

[55]  H. Scheraga,et al.  Conformational energy studies of β‐sheets of model silk fibroin peptides. I. Sheets of poly(Ala‐Gly) chains , 1991 .

[56]  E. Shakhnovich,et al.  Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of a replica approach. , 1989, Biophysical chemistry.

[57]  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 .

[58]  K. Dill.  Theory for the folding and stability of globular proteins. , 1985, Biochemistry.

[59]  M. Karplus,et al.  How does a protein fold? , 1994, Nature.

[60]  A. Godzik,et al.  A general method for the prediction of the three dimensional structure and folding pathway of globular proteins: Application to designed helical proteins , 1993 .

[61]  H. Scheraga,et al.  Pattern recognition in the prediction of protein structure. I. Tripeptide conformational probabilities calculated from the amino acid sequence , 1989 .

[62]  Harold A. Scheraga,et al.  Calculation of the Structures of Collagen Models. Role of Interchain Interactions in Determining the Triple-Helical Coiled-Coil Conformation. 2. Poly(glycyl-prolyl-hydroxyprolyl) , 1980 .

[63]  M. Hao,et al.  STATISTICAL THERMODYNAMICS OF PROTEIN FOLDING : SEQUENCE DEPENDENCE , 1994 .

[64]  Harold A. Scheraga,et al.  The multiple-minima problem in the conformational analysis of polypeptides. III. An Electrostatically Driven Monte Carlo Method: Tests on enkephalin , 1989, Journal of protein chemistry.

[65]  Harold A. Scheraga,et al.  Calculations of Conformations of Polypeptides , 1968 .

[66]  H. Scheraga,et al.  Calculations on crystal packing of a flexible molecule, Leu-enkephalin. , 1988, Journal of molecular biology.

[67]  Lucjan Piela,et al.  Mean field theory as a tool for intramolecular conformational optimization. 3. Test on melittin , 1993 .

[68]  H. Scheraga,et al.  Theoretical determination of sterically allowed conformations of a polypeptide chain by a computer method , 1965 .

[69]  H A Scheraga,et al.  An approach to the multiple-minima problem in protein folding by relaxing dimensionality. Tests on enkephalin. , 1987, Journal of molecular biology.

[70]  G. M. Crippen,et al.  Distance geometry and conformational calculations , 1981 .

[71]  G. N. Ramachandran,et al.  Stereochemistry of polypeptide chain configurations. , 1963, Journal of molecular biology.

[72]  N Go,et al.  Combined use of proton-proton Overhauser enhancements and a distance geometry algorithm for determination of polypeptide conformations. Application to micelle-bound glucagon. , 1981, Biochimica et biophysica acta.

[73]  H. Scheraga,et al.  Statistical analysis of the physical properties of the 20 naturally occurring amino acids , 1985 .

[74]  H. Scheraga,et al.  Formation of Local Structures in Protein Folding , 1989 .

[75]  H. Scheraga,et al.  A Method for Predicting Nucleation Sites for Protein Folding Based on Hydrophobic Contacts , 1978 .

[76]  M. Woolfson,et al.  The crystal structure of a hydrated gramicidin S–urea complex , 1978, Nature.

[77]  E I Shakhnovich,et al.  Theory of cooperative transitions in protein molecules. I. Why denaturation of globular protein is a first‐order phase transition , 1989, Biopolymers.

[78]  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 .