1469-896X/asset/olbannerleft.gif?v=1&s=d218899ae53b2862ab119790ed504b8d72122fb3)
1469-896X/asset/olbannerright.gif?v=1&s=59470eb9a1d9b7b13b1be75e9445e6c46ee2214f)
Article
You have full text access to this OnlineOpen article
Predicting repeat protein folding kinetics from an experimentally determined folding energy landscape
Article first published online: 2 DEC 2008
DOI: 10.1002/pro.9
Copyright © 2008 The Protein Society
Additional Information
How to Cite
Street, T. O. and Barrick, D. (2009), Predicting repeat protein folding kinetics from an experimentally determined folding energy landscape. Protein Science, 18: 58–68. doi: 10.1002/pro.9
Publication History
- Issue published online: 16 DEC 2008
- Article first published online: 2 DEC 2008
- Manuscript Accepted: 13 OCT 2008
- Manuscript Revised: 30 SEP 2008
- Manuscript Received: 25 AUG 2008
Funded by
- Burroughs Welcome Predoctoral Fellowship
- NIH. Grant Number: 1RO1 GM068462
References
- 1( 1998) How do small single-domain proteins fold? Fold Des 3: R81–R91.
- 2, , , ( 2000) Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics. Biochemistry 39: 11177–11183.
- 3, , ( 2004) Critical nucleation size in the folding of small apparently two-state proteins. Prot Sci 13: 1173–1181.Direct Link:
- 4, , , ( 1989) Mapping the transition state and pathway of protein folding by protein engineering. Nature 340: 122–126.
- 5, ( 2007) Intermediates: ubiquitous species on folding energy landscapes? Curr Opin Struct Biol 17: 30–37.
- 6, , ( 2007) Protein folding and misfolding: mechanism and principles. Q Rev Biophys 40: 287–326.
- 7, ( 1995) Kinetics of protein folding: nucleation mechanism, time scales, and pathways. Biopolymers 36: 83–102.Direct Link:
- 8, , , ( 1995) Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins 21: 167–195.Direct Link:
- 9, ( 1997) From Levinthal to pathways to funnels. Nat Struct Biol 4: 10–19.
- 10, ( 2005) The experimental survey of protein-folding energy landscapes. Q Rev Biophys 38: 245–288.
- 11, ( 1989) Residual structure in large fragments of staphylococcal nuclease: effects of amino acid substitutions. Biochemistry 28: 936–944.
- 12, , , , , ( 2003) Chain length dependence of apomyoglobin folding: structural evolution from misfolded sheets to native helices. Biochemistry 42: 7090–7099.
- 13, , ( 2008) Repeat-protein folding: new insights into origins of cooperativity, stability, and topology. Arch Biochem Biophys 469: 83–99.
- 14, ( 2004) An experimentally determined protein folding energy landscape. Proc Natl Acad Sci USA 101: 14102–14107.
- 15, , , ( 2005) Local and long-range stability in tandemly arrayed tetratricopeptide repeats. Proc Natl Acad Sci USA 102: 5721–5726.
- 16, , , , , , , , , , , , ( 2007) Asparaginyl hydroxylation of the notch ankyrin repeat domain by factor inhibiting hypoxia-inducible factor. J Biol Chem 282: 24027–24038.
- 17, , , , , ( 2007) Dissection of protein–protein interaction and CDK4 inhibition in the oncogenic versus tumor suppressing functions of gankyrin and P16. J Mol Biol 373: 990–1005.
- 18, , , ( 2008) Transfer of flexibility between ankyrin repeats in IkappaB* upon formation of the NF-kappaB complex. J Mol Biol 380: 917–931.
- 19, , , , ( 2008) Folding and unfolding mechanism of highly stable full-consensus ankyrin repeat proteins. J Mol Biol 376: 241–257.
- 20, , , ( 2003) Structure and stability of the ankyrin domain of the Drosophila notch receptor. Protein Sci 12: 2622–2632.Direct Link:
- 21, , , , ( 2005) A new folding paradigm for repeat proteins. J Am Chem Soc 127: 10188–10190.
- 22, ( 2006) The notch ankyrin domain folds via a discrete, centralized pathway. Structure 14: 1303–1312.
- 23, ( 2002) Limits of cooperativity in a structurally modular protein: response of the notch ankyrin domain to analogous alanine substitutions in each repeat. J Mol Biol 324: 373–386.
- 24, ( 2005) Effect of multiple prolyl isomerization reactions on the stability and folding kinetics of the notch ankyrin domain: experiment and theory. J Mol Biol 352: 253–265.
- 25, , , ( 2005) Experimental characterization of the folding kinetics of the notch ankyrin domain. J Mol Biol 352: 266–281.
- 26, ( 1974) Urea and guanidine hydrochloride denaturation of ribonuclease, lysozyme, alpha-chymotrypsin, and beta-lactoglobulin. J Biol Chem 249: 5388–5393.
- 27
- 28, ( 1988) Unfolding free energy changes determined by the linear extrapolation method, Part 1: Unfolding of phenylmethanesulfonyl alpha-chymotrypsin using different denaturants. Biochemistry 27: 8063–8068.
- 29, , , ( 1999) Structural changes in the transition state of protein folding: alternative interpretations of curved chevron plots. Biochemistry 38: 6499–6511.
- 30, , ( 2000) Absence of stable intermediates on the folding pathway of barnase. Proc Natl Acad Sci USA 97: 10796–10801.
- 31, ( 2003) Non-linear rate-equilibrium free energy relationships and Hammond behavior in protein folding. Biophys Chem 100: 397–407.
- 32, , , , ( 2007) The folding pathway of T4 lysozyme: an on-pathway hidden folding intermediate. J Mol Biol 365: 881–891.
- 33, ( 1987) Structure and thermal stability of phage T4 lysozyme. Methods Enzymol 154: 511–533.
- 34, , ( 2005) An improved experimental system for determining small folding entropy changes resulting from proline to alanine substitutions. Protein Sci 14: 2429–2435.Direct Link:
- 35, ( 2007) Enhancing the stability and folding rate of a repeat protein through the addition of consensus repeats. J Mol Biol 365: 1187–1200.
- 36, ( 2008) Rerouting the folding pathway of the notch ankyrin domain by reshaping the energy landscape. J Am Chem Soc 130: 5681–5688.
- 37, ( 1994) Protein folding dynamics: the diffusion-collision model and experimental data. Prot Sci 3: 650–668.Direct Link:
- 38, , ( 1998) Protein folding dynamics: quantitative comparison between theory and experiment. Biochemistry 37: 5337–5343.
- 39, ( 1999) Reinterpretation of GCN4-p1 folding kinetics: partial helix formation precedes dimerization in coiled coil folding. J Mol Biol 289: 205–209.
- 40, ( 2001) Preorganized secondary structure as an important determinant of fast protein folding. Nat Struct Biol 8: 552–558.
- 41, , ( 2002) Application of the diffusion-collision model to the folding of three-helix bundle proteins. J Mol Biol 318: 199–215.
- 42, , ( 1998) Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 277: 985–994.
- 43, , , ( 2005) The energy landscape of modular repeat proteins: topology determines folding mechanism in the ankyrin family. J Mol Biol 354: 679–692.
- 44, , ( 2002) Consensus-derived structural determinants of the ankyrin repeat motif. Proc Natl Acad Sci USA 99: 16029–16034.
- 45, ( 2001) Studies of the ankyrin repeats of the Drosophila melanogaster notch receptor, Part 1: Solution conformational and hydrodynamic properties. Biochemistry 40: 14344–14356.
- 46, , ( 2007) Predicting coupling limits from an experimentally determined energy landscape. Proc Natl Acad Sci USA 104: 4907–4912.
- 47, , ( 2007) Anatomy of energetic changes accompanying urea-induced protein denaturation. Proc Natl Acad Sci USA 104: 15317–15322.
- 48( 1976) A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J Comput Phys 22: 403–434.
- 49( 1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81: 2340–2361.