Skip to main content

Monte-Carlo Simulated Annealing in Protein Folding

  • Reference work entry
Encyclopedia of Optimization
  • 395 Accesses

Article Outline

Keywords

Introduction

Energy Functions of Protein Systems

Methods

Results

Conclusions

See also

References

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 2,500.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 2,499.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Achari A, Hale SP, Howard AJ, Clore GM, Gronenborn AM, Hardman KD, Whitlow M (1992) 1.67- Å X-ray structure of the B2 immunoglobulin-binding domain of streptococcal protein G and comparison to the NMR structure of the B1 domain. Biochemistry 31:10449–10457

    Article  Google Scholar 

  2. Bacon D, Anderson WF (1988) A fast algorithm for rendering space-filling molecular pictures. J Mol Graphics 6:219–220

    Article  Google Scholar 

  3. Berg BA, Neuhaus T (1991) Multicanonical algorithms for first order phase transitions. Phys Lett B267:249–253

    Google Scholar 

  4. Brooks III CL (1998) Simulations of protein folding and unfolding. Curr Opin Struct Biol 8:222–226

    Article  Google Scholar 

  5. Brünger AT (1988) Crystallographic refinement by simulated annealing: Application to a 2.8 Å resolution structure of aspartate aminotransferase. J Mol Biol 203:803–816

    Article  Google Scholar 

  6. Chakrabartty A, Kortemme T, Baldwin RL (1994) Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci 3:843–852

    Google Scholar 

  7. Chandler D, Andersen HC (1972) Optimized cluster expansions for classical fluids. Theory of molecular liquids. J Chem Phys 57:1930–1937

    Article  Google Scholar 

  8. Chou PY, Fasman GD (1974) Prediction of protein conformation. Biochemistry 13:222–245

    Article  Google Scholar 

  9. Daggett V, Kollman PA, Kuntz ID (1991) Molecular dynamics simulations of small peptides: dependence on dielectric model and pH. Biopolymers 31:285–304

    Article  Google Scholar 

  10. Deisenhofer J, Steigemann W (1975) Crystallographic refinement of the structure of bovine pancreatic trypsin inhibitor at 1.5 Å resolution. Acta Crystallogr B31:238–250

    Google Scholar 

  11. Dill K (1990) The meaning of hydrophobicity. Science 250:297–297

    Article  Google Scholar 

  12. Epstain CJ, Goldberger RF, Anfinsen CB (1963) The genetic control of tertiary protein structure: studies with model systems. Cold Spring Harbor Symp Quant Biol 28: 439–449

    Google Scholar 

  13. Graham WH, Carter ES, II, Hicks RP (1992) Conformational analysis of Met-enkephalin in both aqueous solution and in the presence of sodium dodecyl sulfate micelles using multidimensional NMR and molecular modeling. Biopolymers 32:1755–1764

    Article  Google Scholar 

  14. Gronenborn AM, Filpula DR, Essig NZ, Achari A, Whitlow M, Wingfield PT, Clore GM (1991) A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G. Science 253:657–661

    Article  Google Scholar 

  15. Hansmann UHE, Okamoto Y (1993) Prediction of peptide conformation by multicanonical algorithm: new approach to the multiple-minima problem. J Comput Chem 14:1333–1338

    Article  Google Scholar 

  16. Hansmann UHE, Okamoto Y (1994) Comparative study of multicanonical and simulated annealing algorithms in the protein folding problem. Phys A 212:415–437

    Article  Google Scholar 

  17. Hansmann UHE, Okamoto Y (1994) Sampling ground-state configurations of a peptide by multicanonical annealing. J Phys Soc Japan 63:3945–3949

    Article  Google Scholar 

  18. Hansmann UHE, Okamoto Y (1998) Tertiary structure prediction of C-peptide of ribonuclease A by multicanonical algorithm. J Phys Chem B 102:653–656

    Article  Google Scholar 

  19. Hansmann UHE, Okamoto Y (1999) Effects of side-chain charges on α-helix stability in C-peptide of ribonuclease A studied by multicanonical algorithm. J Phys Chem B 103:1595–1604

    Article  Google Scholar 

  20. Hingerty BE, Ritchie RH, Ferrell T, Turner JE (1985) Dielectric effects in biopolymers: the theory of ionic saturation revisited. Biopolymers 24:427–439

    Article  Google Scholar 

  21. Hirata F, Rossky PJ (1981) An extended RISM equation for molecular polar fluids. Chem Phys Lett 83:329–334

    Article  Google Scholar 

  22. Kawai H, Kikuchi T, Okamoto Y (1989) A prediction of tertiary structures of peptide by the Monte Carlo simulated annealing method. Protein Eng 3:85–94

    Article  Google Scholar 

  23. Kawai H, Okamoto Y, Fukugita M, Nakazawa T, Kikuchi T (1991) Prediction of α-helix folding of isolated C-peptide of ribonuclease A by Monte Carlo simulated annealing. Chem Lett:213–216

    Google Scholar 

  24. Kinoshita M, Okamoto Y, Hirata F (1997) Calculation of hydration free energy for a solute with many atomic sites using the RISM theory: robust and efficient algorithm. J Comput Chem 18:1320–1326

    Article  Google Scholar 

  25. Kinoshita M, Okamoto Y, Hirata F (1997) Solvation structure and stability of peptides in aqueous solutions analyzed by the reference interaction site model theory. J Chem Phys 107:1586–1599

    Article  Google Scholar 

  26. Kinoshita M, Okamoto Y, Hirata F (1998) First-principle determination of peptide conformations in solvents: combination of Monte Carlo simulated annealing and RISM theory. J Amer Chem Soc 120:1855–1863

    Article  Google Scholar 

  27. Kirkpatrick S, Gelatt, CD Jr, Vecchi MP (1983) Optimization by simulated annealing. Science 220:671–680

    Article  MathSciNet  Google Scholar 

  28. Klaus W, Dieckmann T, Wray V, Schomburg D, Wingender E, Mayer H (1991) Investigation of the solution structure of the human parathyroid hormone fragment (1–34) by 1H NMR spectroscopy, distance geometry, and molecular dynamics calculations. Biochemistry 30:6936–6942

    Article  Google Scholar 

  29. Kraulis PJ (1991) MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24:946–950

    Article  Google Scholar 

  30. Levinthal C (1968) Are there pathways for protein folding? J Chem Phys 65:44–45

    Google Scholar 

  31. Li Z, Scheraga HA (1987) Monte Carlo-minimzation approach to the multiple-minima problem in protein folding. Proc Natl Acad Sci USA 84:6611–6615

    Article  MathSciNet  Google Scholar 

  32. Marx UT, Austermann S, Bayer P, Adermann K, Ejchart A, Sticht H, Walter S, Schmid F-X, Jaenicke R, Forssmann W-G, Rösch P (1995) Structure of human parathyroid hormone 1–37 in solution. J Biol Chem 270:15194–15202

    Article  Google Scholar 

  33. Masuya M, Okamoto Y, in preparation

    Google Scholar 

  34. Masuya M, Okamoto Y, in preparation

    Google Scholar 

  35. Merritt EA, Murphy MEP (1994) Raster3D version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr D50:869–873

    Google Scholar 

  36. Metropolis N, Rosenbluth A, Rosenbluth M, Teller A, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 21:1087–1092

    Article  Google Scholar 

  37. Momany FA, McGuire RF, Burgess AW, Scheraga HA (1975) 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. J Phys Chem 79:2361–2381

    Article  Google Scholar 

  38. Nakazawa T, Kawai H, Okamoto Y, Fukugita M (1992) β-sheet folding of bovine pancreatic trypsin inhibitor fragment (16–36) as predicted by Monte Carlo simulated annealing. Protein Eng 5:495–503

    Article  Google Scholar 

  39. Nakazawa T, Okamoto Y (1999) Electrostatic effects on the α-helix and β-strand folding of BPTI(16–36) as predicted by Monte Carlo simulated annealing. J Peptide Res 54:230–236

    Article  Google Scholar 

  40. Nakazawa T, Okamoto Y, Kobayashi Y, Kyogoku Y, Aimoto S, in preparation

    Google Scholar 

  41. Némethy G, Pottle MS, Scheraga HA (1983) Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids. J Phys Chem 87:1883–1887

    Article  Google Scholar 

  42. Nilges M, Clore GM, Gronenborn AM (1988) Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Lett 229:317–324

    Article  Google Scholar 

  43. Okamoto Y (1994) Dependence on the dielectric model and pH in a synthetic helical peptide studied by Monte Carlo simulated annealing. Biopolymers 34:529–539

    Article  Google Scholar 

  44. Okamoto Y (1994) Helix-forming tendencies of nonpolar amino acids predicted by Monte Carlo simulated annealing. PROTEINS: Struct Funct Genet 19:14–23

    Article  Google Scholar 

  45. Okamoto Y (1998) Protein folding problem as studied by new simulation algorithms. Recent Res Developm Pure Appl Chem 2:1–23

    Google Scholar 

  46. Okamoto Y, Fukugita M, Nakazawa T, Kawai H (1991) α-helix folding by Monte Carlo simulated annealing in isolated C-peptide of ribonuclease A. Protein Eng 4:639–647

    Article  Google Scholar 

  47. Okamoto Y, Hansmann UHE (1995) Thermodynamics of helix-coil transitions studied by multicanonical algorithms. J Phys Chem 99:11276–11287

    Article  Google Scholar 

  48. Okamoto Y, Hansmann UHE, Nakazawa T (1995) α-Helix propensities of amino acids studied by multicanonical algorithm. Chem Lett 391–392

    Google Scholar 

  49. Okamoto Y, Kikuchi T, Kawai H (1992) Prediction of low-energy structures of Met-enkephalin by Monte Carlo simulated annealing. Chem Lett 1275–1278

    Google Scholar 

  50. Okamoto Y, Kikuchi T, Nakazawa T, Kawai H (1993) α-Helix structure of parathyroid hormone fragment (1–34) predicted by Monte Carlo simulated annealing. Internat J Peptide Protein Res 42:300–303

    Google Scholar 

  51. Okamoto Y, Masuya M, Nabeshima M, Nakazawa T (1999) β-Sheet formation in BPTI(16–36) by Monte Carlo simulated annealing. Chem Phys Lett 299:17–24

    Article  Google Scholar 

  52. Ooi T, Oobatake M, Némethy G, Scheraga HA (1987) Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc Natl Acad Sci USA 84:3086–3090

    Article  Google Scholar 

  53. Osterhout JJ, Baldwin RL, York EJ, Stewart JM, Dyson HJ, Wright PE (1989) 1H NMR studies of the solution conformations of an analogue of the C-peptide of ribonuclease A. Biochemistry 28:7059–7064

    Article  Google Scholar 

  54. Ramstein J, Lavery R (1988) Energetic coupling between DNA bending and base pair opening. Proc Natl Acad Sci USA 85:7231–7235

    Article  Google Scholar 

  55. Sayle RA, Milner-White EJ (1995) RasMol: biomolecular graphics for all. TIBS 20:374–376

    Google Scholar 

  56. Shoemaker KR, Kim PS, Brems DN, Marqusee S, York EJ, Chaiken IM, Stewart JM, Baldwin RL (1985) Nature of the charged-group effect on the stability of the C-peptide helix. Proc Natl Acad Sci USA 82:2349–2353

    Article  Google Scholar 

  57. Sippl MJ, Némethy G, Scheraga HA (1984) Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H ⋯O = C hydrogen bonds from packing configurations. J Phys Chem 88:6231–6233

    Article  Google Scholar 

  58. Tilton RF Jr, Dewan JC, Petsko GA (1992) Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K. Biochemistry 31:2469–2481

    Article  Google Scholar 

  59. Wesson L, Eisenberg D (1992) Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci 1:227–235

    Google Scholar 

  60. Wetlaufer DB (1973) Nucleation, rapid folding, and globular intrachain regions in proteins. Proc Natl Acad Sci USA 70:697–701

    Article  Google Scholar 

  61. Wilson C, Doniach S (1989) A computer model to dynamically simulate protein folding: studies with crambin. PROTEINS: Struct Funct Genet 6:193–209

    Article  Google Scholar 

  62. Wilson SR, Cui W (1994) Conformation searching using simulated annealing. In: The Protein Folding Problem and Tertiary Structure Prediction. In: Lecture Notes. Birkhäuser, Basel, pp 43–70

    Google Scholar 

  63. Wilson SR, Cui W, Moskowitz JW, Schmidt KE (1988) Conformational analysis of flexible molecules: location of the global minimum energy conformation by the simulated annealing method. Tetrahedron Lett 29:4373–4376

    Article  Google Scholar 

  64. Wychoff HW, Tsernoglou D, Hanson AW, Knox JR, Lee B, Richards FM (1970) The three-dimensional structure of ribonuclease-S. J Biol Chem 245:305–328

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Springer-Verlag

About this entry

Cite this entry

Okamoto, Y. (2008). Monte-Carlo Simulated Annealing in Protein Folding . In: Floudas, C., Pardalos, P. (eds) Encyclopedia of Optimization. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-74759-0_403

Download citation

Publish with us

Policies and ethics