Sequence-specific solvent accessibilities of protein residues in unfolded protein ensembles

Biophysical Journal

Volumn 91, Issue 12, 2006, Pages 4536-4543

  Bernadó, Pau ^a,b   Blackledge, Martin ^a   Sancho, Javier ^c  

^a INSTITUT DE BIOLOGIE STRUCTURALE   (France)

^b INSTITUTE FOR RESEARCH IN BIOMEDICINE   (Spain)

^c UNIVERSITY OF ZARAGOZA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN DERIVATIVE; SOLVENT; TRIPEPTIDE DERIVATIVE;

ACCURACY; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ARTICLE; CALCULATION; FEASIBILITY STUDY; MUTATIONAL ANALYSIS; PROTEIN ANALYSIS; PROTEIN DENATURATION; PROTEIN FOLDING; SEQUENCE HOMOLOGY;

EID: 33845408125     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.087528     Document Type: Article

References (51)

1. Shortle, D. 1996. The denatured state (the other half of the folding equation) and its role in protein stability. FASEB J. 10:27-34.
2. Funahashi, J., Y. Sugita, A. Kitao, and K. Yutani. 2003. How can free energy component analysis explain the difference in protein stability caused by amino acid substitutions? Effect of three hydrophobic mutations at the 56th residue on the stability of human lysozyme. Protein Eng. Des. Sel. 16:665-671.
3. Lazaridis, T., and M. Karplus. 2003. Thermodynamics of protein folding: a microscopic view. Biophys. Chem. 100:367-395.
4. Myers, J. K., and C. N. Pace. 1996. Hydrogen bonding stabilizes globular proteins. Biophys. J. 71:2033-2039.
5. Campos, L. A., S. Cuesta-Lopez, J. Lopez-Llano, F. Falo, and J. Sancho. 2005. A double-deletion method to quantifying incremental binding energies in proteins from experiment: example of a destabilizing hydrogen bonding pair. Biophys. J. 88:1311-1321.
6. Kono, H., M. Saito, and A. Sarai. 2000. Stability analysis for the cavity-filling mutations of the Myb DNA- binding domain utilizing free-energy calculations. Proteins. 38:197-209.
7. Gatchell, D. W., S. Dennis, and S. Vajda. 2000. Discrimination of near-native protein structures from misfolded models by empirical free energy functions. Proteins. 41:518-534.
8. Baldwin, R. L. 1986. Temperature dependence of the hydrophobic interaction in protein folding. Proc. Natl. Acad. Sci. USA. 83:8069-8072.
9. Kauzmann, W. 1959. Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14:1-63.
10. Privalov, P. L. 1979. Stability of proteins: small globular proteins. Adv. Protein Chem. 33:167-241.
11. Dill, K. A. 1990. Dominant forces in protein folding. Biochemistry. 29:7133-7155.
12. Miller, S., J. Janin, A. M. Lesk, and C. Chothia. 1987. Interior and surface of monomeric proteins. J. Mol. Biol.196:641-656.
13. Shrake, A., and J. A. Rupley. 1973. Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J. Mol. Biol. 79:351-371.
14. Rose, G. D., A. R. Geselowitz, G. J. Lesser, R. H. Lee, and M. H. Zehfus. 1985. Hydrophobicity of amino acid residues in globular proteins. Science. 229:834-838.
15. Zielenkiewicz, P., and W. Saenger. 1992. Residue solvent accessibilities in the unfolded polypeptide chain. Biophys. J. 63:1483-1486.
16. Creamer, T. P., R. Srinivasan, and G. D. Rose. 1995. Modeling unfolded states of peptides and proteins. Biochemistry. 34:16245-16250.
17. Creamer, T. P., R. Srinivasan, and G. D. Rose. 1997. Modeling unfolded states of proteins and peptides. II. Backbone solvent accessibility. Biochemistry. 36:2832-2835.
18. Pappu, R. V., R. Srinivasan, and G. D. Rose. 2000. The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding. Proc. Natl. Acad. Sci. USA. 101:12565-12570.
19. Goldenberg, D. P. 2003. Computational simulation of the statistical properties of unfolded proteins. J. Mol. Biol. 326:1615-1633.
20. Fersht, A. R., A. Matouschek, and L. Serrano. 1992. The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. J. Mol. Biol. 224:771-782.
21. Freire, E. 1993. Structural thermodynamics: prediction of protein stability and protein binding affinities. Arch. Biochem. Biophys. 303:181-184.
22. Shortle, D., and M. S. Ackerman. 2001. Persistence of native-like topology in a denatured protein in 8 M urea. Science. 293:487-489.
23. Ohnishi, S., A. L. Lee, M. H. Edgell, and D. Shortle. 2004. Direct demonstration of structural similarity between native and denatured eglin C. Biochemistry. 43:4064-4070.
24. Tran, H. T., X. Wang, and R. V. Pappu. 2005. Reconciling observations of sequence-specific conformational propensities with the generic polymeric behavior of denatured proteins. Biochemistry. 44:11369-11380.
25. Shi, Z., K. Chen, Z. Liu, and N. R. Kallenbach. 2006. Conformation of the backbone in unfolded proteins. Chem. Rev. 106:1877-1897.
26. Tjandra, N., and A. Bax. 1997. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science. 278:1111-1114.
27. Louhivouri, M., K. Pääkkönen, K. Fredriksson, P. Permi, J. Lounila, and A. Annila. 2003. On the origin of residual dipolar couplings from denatured proteins. J. Am. Chem. Soc. 125:15647-15650.
28. Mohana-Borges, R., N. K. Goto, G. J. A. Kroon, H. J. Dyson, and P. E. Wright. 2004. Structural characterization of unfolded states of apomyoglobin using residual dipolar couplings. J. Mol. Biol. 34:1131-1142.
29. Meier, S., S. Güthe, T. Kiefhaber, and S. Grzesiek. 2004. Foldon, the natural trimerization domain of T4 fibritin, dissociates into a monomeric A-state form containing a stable β-hairpin: atomic details of trimer dissociation and local β-hairpin stability from residual dipolar couplings. J. Mol. Biol. 344:1051-1069.
30. Jha, A. K., A. Colubri, K. F. Freed, and T. R. Sosnick. 2005. Statistical coil model of the unfolded state: resolving the reconciliation problem. Proc. Natl. Acad. Sci. USA. 102:13099-13104.
31. Bernadó, P., L. Blanchard, P. Timmins, D. Marion, R. W. H. Ruigrok, and M. Blackledge. 2005. A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering. Proc. Natl. Acad. Sci. USA. 102:17002-17007.
32. Bernadó, P., C. W. Bertoncini, C. Griesinger, M. Zweckstetter, and M. Blackledge. 2005. Defining long-range oand local disorder in native α-synuclein using residual dipolar couplings. J. Am. Chem. Soc. 127:17968-17969.
33. Gillespie, J. R., and D. Shortle. 1997. Characterization of long-range structure in the denatured state of staphylococcal nuclease. I. Paramagnetic relaxation enhancement by nitroxide spin labels. J. Mol. Biol. 268:158-169.
34. Lindorff-Larsen, K., S. Kristjansdottir, K. Teilum, W. Fieber, C. M. Dobson, F. M. Poulsen, and M. Vendruscolo. 2004. Determination of an ensemble of structures representing the denatured state of the of the bovine acyl-coenzyme A binding protein. J. Am. Chem. Soc. 126:3291-3299.
35. Bertoncini, C. W., Y.-S. Jung, C. O. Fernandez, W. Hoyer, C. Griesinger, T. M. Jovin, and M. Zweckstetter. 2005. Release of long-range tertiary interactions potentiates aggregation of natively unstructured α-synuclein. Proc. Natl. Acad. Sci. USA. 102:1430-1435.
36. Dedmon, M. W., K. Lindorff-Larsen, J. Christodoulou, M. Vendruscolo, and C. M. Dobson. 2005. Mapping long-range interactions in α-synuclein using spin-label NMR and ensemble molecular dynamics simulations. J. Am. Chem. Soc. 127:476-477.
37. Doniach, S. 2001. Changes in biomolecular conformation seen by small angle x-ray scattering. Chem. Rev. 101:1763-1798.
38. Kohn, J. E., I. S. Millett, J. Jacob, B. Zagrovic, T. M. Dillon, N. Cingel, R. S. Dothager, S. Seifert, P. Thiyagarajan, T. R. Sosnick, M. Z. Hasan, V. S. Pande, I. Ruczinski, S. Doniach, and K. W. Plaxco. 2004. Random-coil behaviour and dimensions of chemically unfolded proteins. Proc. Natl. Acad. Sci. USA. 101:12491-12496.
39. Fitzkee, N. C., and G. D. Rose. 2004. Reassessing random-coil statistics in unfolded proteins. Proc. Natl. Acad. Sci. USA. 101:12497-12502.
40. Lovell, S. C., I. W. Davis, W. B. Arendall III, P. I. W. de Bakker, J. M. Word, M. G. Prisant, J. S. Richardson, and D. C. Richardson. 2003. Structure validation by Cα geometry: φ,ψ and Cβ deviation. Proteins. 50:437-450.
41. MacArthur, M. W., and J. M. Thornton. 1991. Influence of proline residues on protein conformation. J. Mol. Biol. 218:397-412.
42. Levitt, M. 1976. A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 104:59-107.
43. Eyal, E., R. Najmanovich, B. J. McConkey, M. Edelman, and V. Sobolev. 2004. Importance of solvent accessibility and contact surfaces in modeling side-chains conformations in proteins. J. Comp. Chem. 25:712-724.
44. Hubbart, S. J., and J. M. Thornton. 1993. NACCESS Computer Program. Department of Biochemistry and Molecular Biology, University College London, London, UK.
45. Chou, P. Y., and G. D. Fasman. 1974. Conformational parameters for amino acids in helical, β-sheet, and random coil regions calculated from proteins. Biochemistry. 13:211-222.
46. Robertson, A. D., and K. P. Murphy. 1997. Protein structure and the energetics of protein stability. Chem. Rev. 97:1251-1267.
47. Lazaridis, T., and M. Karplus. 1999. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J. Mol. Biol. 288:477-487.
48. Richards, F. M. 1977. Areas, volumes, packing and protein structure. Annu. Rev. Biophys. Bioeng. 6:151-176.
49. Schrake, A., and J. A. Rupley. 1973. Environment and exposure to solvent of protein atoms. J. Mol. Biol. 79:351-371.
50. Chothia, C. 1975. Structural invariants in protein folding. Nature. 254:304-308.
51. Lee, B., and Richards, F. M. 1971. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:379-400.