- Physical Review Journals
All JournalsPhysics Magazine
Access Provided by Xinjiang University

Reviews of Modern Physics

Export citation

Export citation

Choose format for download:

Download Citation
  • Access by Xinjiang University

Colloquium: Geometrical approach to protein folding: a tube picture

Jayanth R. Banavar and Amos Maritan

Jayanth R. Banavar

  • Department of Physics, 104 Davey Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802

Amos Maritan

  • International School for Advanced Studies (S.I.S.S.A.), Via Beirut 2-4, 34014 Trieste,
  • INFM and the Abdus Salam International Center for Theoretical Physics, Trieste, Italy

PDF

Rev. Mod. Phys. 75, 23 – Published 6 January, 2003

DOI: https://doi.org/10.1103/RevModPhys.75.23

Abstract

A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed characteristics of protein structures. The authors show here that proteins may be regarded as tubes of nonzero thickness. This approach allows one to bridge the conventional compact polymer phase with a novel phase employed by Nature to house biomolecular structures. The continuum description of a tube (or a sheet) of arbitrary thickness entails using appropriately chosen many-body interactions rather than two-body interactions. The authors suggest that the structures of folded proteins are selected based on geometrical considerations and are poised at the edge of compaction, thus accounting for their versatility and flexibility. This approach also offers an explanation for why helices and sheets are the building blocks of protein structures.

View figure in article

References (49)

  1. Allain, F. H. T., M. Yen, J. E. Masse, P. Schultze, T. Dieckmann, R. C. Johnson, and J. Feigon, 1999, “Solution structure of the HMG protein NHP6A and its interaction with DNA reveals the structural determinants for non sequence specific binding,” EMBO J. 18, 2563–2579.
  2. Anfinsen, C., 1973, “Principles that govern the folding of protein chains,” Science 181, 223–230.
  3. Baker, D., 2000, “A surprising simplicity to protein folding,” Nature (London) 405, 39–42.
  4. Baldwin, R. L., and G. D. Rose, 1999, “Is protein folding hierarchic? I. Local structure and peptide folding,” Trends Biochem. Sci. 24, 26–33.
  5. Banavar, J. R., A. Flammini, D. Marenduzzo, A. Maritan, and A. Trovato, 2003, “Geometry of compact tubes and protein structures,” ComPlexUs 1, 4–13.
  6. Banavar, J. R., O. Gonzalez, J. H. Maddocks, and A. Maritan, 2003, “Self-interactions of strands and sheets,” J. Stat. Phys. 110, 35–50.
  7. Banavar, J. R., and A. Maritan, 2001, “Computational approach to the protein folding problem,” Proteins 42, 433–435.
  8. Banavar, J. R., A. Maritan, C. Micheletti, and A. Trovato, 2002, “Geometry and physics of proteins,” Proteins 47, 315–322.
  9. Banavar, J. R., A. Maritan, and F. Seno, 2002, “Anisotropic Effective Interactions in a Coarse-Grained Tube Picture of Proteins,” Proteins 49, 246–254.
  10. Baumann, U., S. Wu, K. M. Flaherty, and D. B. Mckay, 1993, “Three-dimensional structure of the alkalyne protease of pseudomonas aeruginosa: a two-domain protein with a calcium binding parallel beta roll motif,” EMBO J. 12, 3357–3364.
  11. Bernal, J. D., 1939, “Structure of proteins,” Nature (London) 143, 663–667.
  12. Branden, C., and J. Tooze, 1999, Introduction to Protein Structure, 2nd ed. (Garland, New York).
  13. Bryngelson, J. D., J. N. Onuchic, N. D. Socci, and P. G. Wolynes, 1995, “Funnels, pathways and the energy landscape of protein folding: A synthesis,” Proteins 21, 167–195.
  14. Bryngelson, J. D., and P. G. Wolynes, 1987, “Spin glasses and the statistical-mechanics of protein folding,” Proc. Natl. Acad. Sci. U.S.A. 84, 7524–7528.
  15. Chaikin, P. M., and T. C. Lubensky, 1995, Principles of Condensed Matter Physics (Cambridge University Press, Cambridge, England).
  16. Chang, K. Y., and I. Tinoco, 1997, “The Structure of an RNA ‘kissing’ hairpin complex of the HIV tar hairpin loop and its complement,” J. Mol. Biol. 269, 52–66.
  17. Chothia, C., 1984, “Principles that determine the structure of proteins,” Annu. Rev. Biochem. 53, 537–572.
  18. Chothia, C., 1992, “One thousand families for the molecular biologist,” Nature (London) 357, 543–544.
  19. Creighton, T. E., 1993, Proteins, Structure and Molecular Properties, 2nd ed. (Freeman, New York).
  20. Denton, M., and C. Marshall, 2001, “Laws of form revisited,” Nature (London) 410, 417–417.
  21. Dill, K. A., and H. S. Chan, 1997, “From Levinthal to pathways to funnels,” Nat. Struct. Biol. 4, 10–19.
  22. Dobson, C. M., 1999, “Protein misfolding, evolution and disease,” Trends Biochem. Sci. 24, 329–332.
  23. Dobson, C. M., 2002, “Protein-misfolding diseases: Getting out of shape,” Nature (London) 418, 729–730.
  24. Doi, M., and S. F. Edwards, 1993, The Theory of Polymer Dynamics (Clarendon Press, New York).
  25. Fersht, A. R., 1998, Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding (Freeman, New York).
  26. Flory, P. J., 1969, Statistical Mechanics of Chain Molecules (Wiley, New York).
  27. Gonzalez, O., and J. H. Maddocks, 1999, “Global curvature, thickness and the ideal shapes of knots,” Proc. Natl. Acad. Sci. U.S.A. 96, 4769–4773.
  28. Holm, L., and C. Sander, 1997, “An evolutionary treasure: unification of a broad set of amidohydrolases related to urease,” Proteins 28, 72–82.
  29. Hunt, N. G., L. M. Gregoret, and F. E. Cohen, 1994, “The origins of protein secondary structure,” J. Mol. Biol. 241, 214–225.
  30. Jacobs, D. J., A. J. Rader, L. A. Kuhn, and M. F. Thorpe, 2001, “Protein flexibility predictions using graph theory,” Proteins 44, 150–165.
  31. Kamtekar, S., J. M. Schiffer, H. Y. Xiong, J. M. Babik, and M. H. Hecht, 1993, “Protein design by binary patterning of polar and non-polar amino acids,” Science 262, 1680–1685.
  32. Katritch, V., J. Bednar, D. Michoud, R. G. Scharein, J. Dubochet, and A. Stasiak, 1996, “Geometry and physics of knots,” Nature (London) 384, 142–145.
  33. Lesk, A. M., and C. Chothia, 1980, “How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of globins,” J. Mol. Biol. 136, 225–270.
  34. Levitt, M., and C. Chothia, 1976, “Structural patterns in globular proteins,” Nature (London) 261, 552–558.
  35. Maritan, A., C. Micheletti, and J. R. Banavar, 2000, “Role of secondary motifs in fast folding polymers: a dynamical variational principle,” Phys. Rev. Lett. 84, 3009–3012.
  36. Maritan, A., C. Micheletti, A. Trovato, and J. R. Banavar, 2000, “Optimal shapes of compact strings,” Nature (London) 406, 287–290.
  37. Micheletti, C., J. R. Banavar, A. Maritan, and F. Seno, 1999, “Protein structures and optimal folding from a geometrical variational principle,” Phys. Rev. Lett. 82, 3372–3375.
  38. Pauling, L., and R. B. Corey, 1951, “Conformations of polypeptide chains with favored orientations around single bonds: two new pleated sheets,” Proc. Natl. Acad. Sci. U.S.A. 37, 729–740.
  39. Pauling, L., R. B. Corey, and H. R. Branson, 1951, “The structure of proteins: two hydrogen-bonded helical conformations of the polypeptide chain,” Proc. Natl. Acad. Sci. U.S.A. 37, 205–211.
  40. Ramachandran, G. N., and V. Sasisekharan, 1968, “Conforma-tions of polypeptides and proteins,” Adv. Protein Chem. 23, 283–438.
  41. Richardson, J. S., 1997, “β-sheet topology and the relatedness of proteins,” Nature (London) 268, 495–500.
  42. Rose, G. D., 1996, “No assembly required,” Sciences (N.Y.) 36, 26–31.
  43. Sander, C., and R. Schneider, 1991, “Database of homology-derived protein structures and the structural meaning of sequence alignment,” Proteins 9, 56–68.
  44. Stanley, H. E., 1999, “Scaling, universality and renormalization: three pillars of modern critical phenomena,” Rev. Mod. Phys. 71, S358–S366.
  45. Stasiak, A., and J. H. Maddocks, 2000, “Mathematics—Best packing in proteins and DNA,” Nature (London) 406, 251–253.
  46. Tinkham, M., 1996, Introduction to Superconductivity (McGraw-Hill, New York).
  47. Yee, D. P., H. S. Chan, T. F. Havel, and K. A. Dill, 1994, “Does compactness induce secondary structure in proteins?,” J. Mol. Biol. 241, 557–573.
  48. Watson, J. D., and F. H. C. Crick, 1953, “A structure for deoxyribose nucleic acid,” Nature (London) 171, 737.
  49. West, M. W., et al., 1999, “De novo amyloid proteins from designed combinatorial libraries,” Proc. Natl. Acad. Sci. U.S.A. 96, 11 211–11 216.

Outline

Information

Rev. Mod. Phys. 75, 23– Published 6 January, 2003

    © 2003 American Physical Society

    Sign In to Your Journals Account

    Filter

    Filter

    Article Lookup

    Enter a citation