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Proc Natl Acad Sci U S A. 1996 April 16; 93(8): 3341–3345. | PMCID: PMC39609 |
Why are some proteins structures so common? S Govindarajan and R A Goldstein Department of Chemistry, University of Michigan, Ann Arbor 48109-1055, USA. Abstract Many biological proteins are observed to fold into one of a limited number of structural motifs. By considering the requirements imposed on proteins by their need to fold rapidly, and the ease with which such requirements can be fulfilled as a function of the native structure, we can explain why certain structures are repeatedly observed among proteins with negligible sequence similarity. This work has implications for the understanding of protein sequence structure relationships as well as protein evolution. Full text Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (904K), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References. These references are in PubMed. This may not be the complete list of references from this article. - Davidson AR, Sauer RT. Folded proteins occur frequently in libraries of random amino acid sequences. Proc Natl Acad Sci U S A. 1994 Mar 15;91(6):2146–2150. [PubMed]
- Orengo CA, Jones DT, Thornton JM. Protein superfamilies and domain superfolds. Nature. 1994 Dec 15;372(6507):631–634. [PubMed]
- Finkelstein AV, Ptitsyn OB. Why do globular proteins fit the limited set of folding patterns? Prog Biophys Mol Biol. 1987;50(3):171–190. [PubMed]
- Finkelstein AV, Gutun AM, Badretdinov AYa Why are the same protein folds used to perform different functions? FEBS Lett. 1993 Jun 28;325(1-2):23–28. [PubMed]
- Finkelstein AV, Gutin AM, Badretdinov AYa Boltzmann-like statistics of protein architectures. Origins and consequences. Subcell Biochem. 1995;24:1–26. [PubMed]
- Bryngelson JD, Wolynes PG. Spin glasses and the statistical mechanics of protein folding. Proc Natl Acad Sci U S A. 1987 Nov;84(21):7524–7528. [PubMed]
- Honeycutt JD, Thirumalai D. Metastability of the folded states of globular proteins. Proc Natl Acad Sci U S A. 1990 May;87(9):3526–3529. [PubMed]
- Goldstein RA, Luthey-Schulten ZA, Wolynes PG. Optimal protein-folding codes from spin-glass theory. Proc Natl Acad Sci U S A. 1992 Jun 1;89(11):4918–4922. [PubMed]
- Fukugita M, Lancaster D, Mitchard MG. Kinematics and thermodynamics of a folding heteropolymer. Proc Natl Acad Sci U S A. 1993 Jul 1;90(13):6365–6368. [PubMed]
- Shakhnovich EI. Proteins with selected sequences fold into unique native conformation. Phys Rev Lett. 1994 Jun 13;72(24):3907–3910. [PubMed]
- Sali A, Shakhnovich E, Karplus M. Kinetics of protein folding. A lattice model study of the requirements for folding to the native state. J Mol Biol. 1994 Feb 4;235(5):1614–1636. [PubMed]
- Sali A, Shakhnovich E, Karplus M. How does a protein fold? Nature. 1994 May 19;369(6477):248–251. [PubMed]
- Yue K, Dill KA. Inverse protein folding problem: designing polymer sequences. Proc Natl Acad Sci U S A. 1992 May 1;89(9):4163–4167. [PubMed]
- Goldstein RA, Luthey-Schulten ZA, Wolynes PG. Protein tertiary structure recognition using optimized Hamiltonians with local interactions. Proc Natl Acad Sci U S A. 1992 Oct 1;89(19):9029–9033. [PubMed]
- Schuster P, Fontana W, Stadler PF, Hofacker IL. From sequences to shapes and back: a case study in RNA secondary structures. Proc Biol Sci. 1994 Mar 22;255(1344):279–284. [PubMed]
- Zuker M, Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981 Jan 10;9(1):133–148. [PubMed]
- Onuchic JN, Wolynes PG, Luthey-Schulten Z, Socci ND. Toward an outline of the topography of a realistic protein-folding funnel. Proc Natl Acad Sci U S A. 1995 Apr 11;92(8):3626–3630. [PubMed]
- Wetlaufer DB. Nucleation, rapid folding, and globular intrachain regions in proteins. Proc Natl Acad Sci U S A. 1973 Mar;70(3):697–701. [PubMed]
- Zwanzig R, Szabo A, Bagchi B. Levinthal's paradox. Proc Natl Acad Sci U S A. 1992 Jan 1;89(1):20–22. [PubMed]
- Dill KA, Fiebig KM, Chan HS. Cooperativity in protein-folding kinetics. Proc Natl Acad Sci U S A. 1993 Mar 1;90(5):1942–1946. [PubMed]
- Srinivasan R, Rose GD. LINUS: a hierarchic procedure to predict the fold of a protein. Proteins. 1995 Jun;22(2):81–99. [PubMed]
- Govindarajan S, Goldstein RA. Optimal local propensities for model proteins. Proteins. 1995 Aug;22(4):413–418. [PubMed]
- Abkevich VI, Gutin AM, Shakhnovich EI. Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. J Mol Biol. 1995 Sep 29;252(4):460–471. [PubMed]
- Leopold PE, Montal M, Onuchic JN. Protein folding funnels: a kinetic approach to the sequence-structure relationship. Proc Natl Acad Sci U S A. 1992 Sep 15;89(18):8721–8725. [PubMed]
- Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins. 1995 Mar;21(3):167–195. [PubMed]
- Frauenfelder H, Sligar SG, Wolynes PG. The energy landscapes and motions of proteins. Science. 1991 Dec 13;254(5038):1598–1603. [PubMed]
- Subramaniam V, Bergenhem NC, Gafni A, Steel DG. Phosphorescence reveals a continued slow annealing of the protein core following reactivation of Escherichia coli alkaline phosphatase. Biochemistry. 1995 Jan 31;34(4):1133–1136. [PubMed]
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