Emergence of preferred structures in a simple model of protein folding - PubMed

Emergence of preferred structures in a simple model of protein folding

H Li et al. Science. 1996.

Abstract

Protein structures in nature often exhibit a high degree of regularity (for example, secondary structure and tertiary symmetries) that is absent from random compact conformations. With the use of a simple lattice model of protein folding, it was demonstrated that structural regularities are related to high "designability" and evolutionary stability. The designability of each compact structure is measured by the number of sequences that can design the structure-that is, sequences that possess the structure as their nondegenerate ground state. Compact structures differ markedly in terms of their designability; highly designable structures emerge with a number of associated sequences much larger than the average. These highly designable structures possess "proteinlike" secondary structure and even tertiary symmetries. In addition, they are thermodynamically more stable than other structures. These results suggest that protein structures are selected in nature because they are readily designed and stable against mutations, and that such a selection simultaneously leads to thermodynamic stability.

Comment in

• Which came first, protein sequence or structure?

  Karkar M. Karkar M. Science. 1996 Aug 2;273(5275):610. doi: 10.1126/science.273.5275.610. Science. 1996. PMID: 8701315 No abstract available.

Similar articles

• The designability of protein structures.

  Helling R, Li H, Mélin R, Miller J, Wingreen N, Zeng C, Tang C. Helling R, et al. J Mol Graph Model. 2001;19(1):157-67. doi: 10.1016/s1093-3263(00)00137-6. J Mol Graph Model. 2001. PMID: 11381527

• Emergence of highly designable protein-backbone conformations in an off-lattice model.

  Miller J, Zeng C, Wingreen NS, Tang C. Miller J, et al. Proteins. 2002 Jun 1;47(4):506-12. doi: 10.1002/prot.10107. Proteins. 2002. PMID: 12001229

• Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix.

  Li H, Tang C, Wingreen NS. Li H, et al. Proteins. 2002 Nov 15;49(3):403-12. doi: 10.1002/prot.10239. Proteins. 2002. PMID: 12360530

• Principles of protein folding--a perspective from simple exact models.

  Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, Thomas PD, Chan HS. Dill KA, et al. Protein Sci. 1995 Apr;4(4):561-602. doi: 10.1002/pro.5560040401. Protein Sci. 1995. PMID: 7613459 Free PMC article. Review.

• Is protein folding hierarchic? II. Folding intermediates and transition states.

  Baldwin RL, Rose GD. Baldwin RL, et al. Trends Biochem Sci. 1999 Feb;24(2):77-83. doi: 10.1016/s0968-0004(98)01345-0. Trends Biochem Sci. 1999. PMID: 10098403 Review.

Cited by

• Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models.

  Jacquin H, Gilson A, Shakhnovich E, Cocco S, Monasson R. Jacquin H, et al. PLoS Comput Biol. 2016 May 13;12(5):e1004889. doi: 10.1371/journal.pcbi.1004889. eCollection 2016 May. PLoS Comput Biol. 2016. PMID: 27177270 Free PMC article.

• A generic framework for hierarchical de novo protein design.

  Harteveld Z, Bonet J, Rosset S, Yang C, Sesterhenn F, Correia BE. Harteveld Z, et al. Proc Natl Acad Sci U S A. 2022 Oct 25;119(43):e2206111119. doi: 10.1073/pnas.2206111119. Epub 2022 Oct 17. Proc Natl Acad Sci U S A. 2022. PMID: 36252041 Free PMC article.

• Divergent evolution of a structural proteome: phenomenological models.

  Roland CB, Shakhnovich EI. Roland CB, et al. Biophys J. 2007 Feb 1;92(3):701-16. doi: 10.1529/biophysj.106.081265. Epub 2006 Oct 27. Biophys J. 2007. PMID: 17071665 Free PMC article.

• An impedance-based integrated biosensor for suspended DNA characterization.

  Ma H, Wallbank RW, Chaji R, Li J, Suzuki Y, Jiggins C, Nathan A. Ma H, et al. Sci Rep. 2013;3:2730. doi: 10.1038/srep02730. Sci Rep. 2013. PMID: 24060937 Free PMC article.

• Protein robustness promotes evolutionary innovations on large evolutionary time-scales.

  Ferrada E, Wagner A. Ferrada E, et al. Proc Biol Sci. 2008 Jul 22;275(1643):1595-602. doi: 10.1098/rspb.2007.1617. Proc Biol Sci. 2008. PMID: 18430649 Free PMC article.

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Atypon
  • Ovid Technologies, Inc.

• Other Literature Sources

  • The Lens - Patent Citations Database