OneG: A computational tool for predicting cryptic intermediates in the unfolding kinetics of proteins under native conditions

PLoS ONE

Volumn 7, Issue 3, 2012, Pages

  Richa, Tambi ^a   Sivaraman, Thirunavukkarasu ^a  

^a SASTRA UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

APOCYTOCHROME B562; CARDIOTOXIN; CARDIOTOXIN III; COBROTOXIN; CYTOCHROME; CYTOCHROME C; UNCLASSIFIED DRUG; AMIDE; PROLINE; PROTEIN;

ARTICLE; AUTOMATION; COMPUTER PREDICTION; COMPUTER PROGRAM; CONTROLLED STUDY; PROTEIN STRUCTURE; PROTEIN UNFOLDING; VALIDATION PROCESS; ALGORITHM; CHEMISTRY; ISOMERISM; KINETICS; MOLECULAR DYNAMICS; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING;

ALGORITHMS; AMIDES; ISOMERISM; KINETICS; MOLECULAR DYNAMICS SIMULATION; PROLINE; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEINS; SOFTWARE;

EID: 84857862992     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0032465     Document Type: Article

References (66)

1. Dobson CM, Karplus M, (1999) The fundamentals of protein folding, bringing together theory and experiment. Curr Opin Struct Biol 9: 99-101.
2. Dagget V, Fersht A, (2003) The present view of the mechanism of protein folding. Nat Rev Mol Cell Biol 4 (5): 497-502.
3. Pace CN, Scholtz CM, (1997) Measuring the conformational stability of a protein. In: Creighton TE, editors. Protein Structure- A Practical Approach New York Oxford University Press Inc pp. 300-321.
4. Plaxco KW, Dobson CM, (1996) Time-resolved biophysical methods in the study of protein folding. Curr Opin Struct Biol 6: 630-636.
5. Woodward CK, (1994) Hydrogen exchange rates and protein folding. Curr Opin Struct Biol 4: 112-116.
6. Hvidt A, Nielsen SO, (1966) Hydrogen exchange in proteins. Adv Protein Chem 21: 287-366.
7. Bai Y, Milne JS, Mayne L, Englander SW, (1993) Primary structure effects hydrogen exchange on peptide group. Proteins 17: 75-86.
8. Huyghues-Despointes BMP, Pace CN, Englander SW, Scholtz JM, (2001) Measuring the conformational stability of a protein by hydrogen exchange. In: Murphy KM, editors. Protein Structure, stability and folding New Jersy Humana Press Inc pp. 69-92.
9. Huyghues-Despointes BMP, Scholtz JM, Pace CN, (1999) Protein conformational stabilities can be determined from hydrogen exchange rates. Nat Struct Biol 6: 910-912.
10. Yadav S, Ahmad F, (2000) A new method for determination of stability parameters of proteins from their heat-induced denaturation curves. Arch Biochem Biophys 283: 207-213.
11. Mayne L, Englander SW, (2000) Two-state vs multistate protein unfolding studied by optical melting and hydrogen exchange. Protein Sci 9: 1873-1877.
12. Clarke J, Fresht A, (1996) An evaluation of the use of hydrogen exchange at equilibrium to probe intermediates on the protein folding pathway. Fold Des 1: 243-254.
13. Arrington CB, Teesch LM, Robertson AD, (1999) Defining protein ensembles with native-state NH exchange: kinetics of interconversion and cooperative units from combined NMR and MS analysis. J Mol Biol 285: 1265-1275.
14. Zhang Y, (1995) Protein and peptide structure and interactions studied by hydrogen exchange and NMR. Ph.D. Thesis. University of Pennsylvania, Structural Biology and Molecular Biophysics.
15. Tartaglia GG, Cavalli A, Vendruscolo M, (2007) Prediction of local Structural stabilities of sroteins from their amino acid sequences. Structure 15: 139-143.
16. Dovidchenko NV, Lobanov MY, Garbuzynskiy SO, Galzitskaya OV, (1999) Prediction of amino acid residues protected from hydrogen-deuterium exchange in a protein chain. Biochemistry (Mosc) 74: 888-897.
17. Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG, (1995) Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins 21: 167-195.
18. Panchenko AR, Luthey-Schulten Z, Wolynes PG, (1996) Foldons, protein structural modules and exons. Proc Natl Acad Sci U S A 93: 2008-2013.
19. Fischer KF, Marqusee S, (2000) A rapid test for identification of autonomous folding units in proteins. J Mol Biol 302: 701-712.
20. Hilser VJ, B. Garcia-Moreno E, Oas TG, Kapp G, Whitten ST, (2006) A statistical thermodynamic model of the protein ensemble. Chem Rev 106: 1545-1558.
21. Molday RS, Englander SW, Kallen RG, (1977) Primary structure effects on peptide group hydrogen exchange. Biochemistry 11: 150-158.
22. Bhattacharyya R, Pal D, Chakrabarti P, (2004) Disulfide bonds, their stereospecific environment and conservation in protein structures. Protein Eng Des Sel 17 (11): 795-808.
23. DeLano WL, (2002) The PyMOL Molecular Graphics System San Carlos, CA, USA DeLano Scientific.
24. Reimer U, Scherer G, Drewello M, Kruber S, Schutkowski M, et al. (1998) Side-chain effects on peptidyl-prolyl cis/trans isomerisation. J Mol Biol 279: 449-460.
25. Fisher G, (2000) Chemical aspects of peptide and isomerisation. Chem Soc Rev 29: 119-127.
26. Swint-Kruseand L, Robertson AD, (1995) Temperature and pH dependences of hydrogen exchange and global stability for ovomucoid third domain. Biochemistry 35: 171-180.
27. Takei J, Chu R, Bai Y, (2000) Absence of stable intermediates on the folding pathway of barnase. Proc Natl Acad Sci U S A 97: 10796-10801.
28. Itzhaki LS, Neira JL, Fersht AR, (1997) Hydrogen exchange in chymotrypsin inhibitor-2 probed by denaturants and temperature. J Mol Biol 270: 89-98.
29. Padmanabhan S, Jimenez MA, Gonzalez C, Sanz JM, Gimenez-Gallego, et al. (1997) Three-dimensional solution structure and stability of phage 434 Cro protein. Biochemistry 36: 6424-6436.
30. Radford SE, Buck M, Topping KD, Dobson CM, Evans PA, (1992) Hydrogen exchange in Native and Denatured states of Hen Egg-White lysozyme. Proteins 14: 234-248.
31. Bhuyan AK, Udgaonkar JB, (1998) Two structural sub-domains of barstar detected by rapid mixing NMR measurement of amide hydrogen exchange. Proteins 30: 295-308.
32. Grantcharova VP, Baker D, (1997) Folding dynamics of the src SH3 domain. Biochemistry 36: 15685-15692.
33. Sivaraman T, Kumar TKS, Hung KW, Yu C, (2000) Comparison of the structural stability of two homologous toxins isolated from the Taiwan cobra Naja naja atra venom. Biochemistry 39: 8705-8710.
34. Llinas M, Gillespie B, Dahlquist FW, Marquesee S, (1999) The energetics of T4 lysozyme reveals a hierarchy of conformations. Nat Struct Biol 6: 1072-1078.
35. Fuentes EJ, Wand AJ, (1998) Local dynamics and stability of apocytochrome b562 examined by hydrogen exchange. Biochemistry 37: 3687-3698.
36. Yi Q, Scalley ML, Simons KT, Galdwin ST, Baker D, (1997) Characterization of free energy spectrum of peptostreptococcal protein L. Fold Des 2: 271-278.
37. Lin LN, Brandts JF, (1983) Determination of cis-trans proline isomerization by trypsin proteolysis. Application to a model pentapeptide and to oxidized ribonuclease A. Biochemistry 22: 553-559.
38. Pace CN, (1986) Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods Enzymol 131: 266-280.
39. Pace CN, (1990) Measuring and increasing protein stability. Trends Biotechnol 8: 93-98.
40. Santoro MM, Bolen DW, (1988) Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl alpha-chymotrypsin using different denaturants. Biochemistry 27: 8063-8068.
41. Sivaraman T, Arrington CB, Robertson AD, (2001) Kinetics of unfolding and folding from amide hydrogen exchange in native ubiquitin. Nat Struct Biol 8 (4): 331-333.
42. Robertson AD, Murphy KP, (1997) Protein structure and the energetics of protein stability. Chem Rev 97: 1251-67.
43. Prakash V, Loucheux C, Scheufele S, Gorbunoff MJ, Timasheff SN, (1981) Interactions of proteins with solvent components in 8 M urea. Arch Biochem Biophys 210: 455-464.
44. Bai Y, Sasnick TR, Mayne L, Englander SW, (1995) Protein folding intermediates: Native state hydrogen exchange. Science 269: 192-197.
45. Chamberlain AK, Handel TM, Marqusee S, (1996) Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH. Nat Struct Biol 3 (9): 782-787.
46. Arrington CB, Robertson AD, (1997) Microsecond protein folding kinetics from native-state hydrogen exchange. Biochemistry 36: 8686-8691.
47. Ferraro DM, Robertson AD, (2004) EX1 hydrogen exchange and protein folding. Biochemistry 43 (3): 587-594.
48. Englander SW, (2000) Protein folding intermediates and pathways studied by hydrogen exchange. Annu Rev Biophys Biomol Struct 29: 213-38.
49. Parker MJ, Marqusee S, (2000) A statistical appraisal of native state hydrogen exchange data: Evidence for a burst phase continuum? J Mol Biol 300 (5): 1361-1375.
50. Bai Y, (2007) Protein folding pathways studied by pulsed- and native state hydrogen exchange. Chem Rev 106: 1757-1768.
51. Bhaskaran R, Huang CC, Chang DK, Yu C, (1994) Cardiotoxin III from the Taiwan cobra (Naja naja atra). Determination of structure in solution and comparison with short neurotoxins. J Mol Biol 235 (4): 1291-1301.
52. Sivaraman T, Kumar TKS, Yu C, (1999) Investigation of the structural stability of cardiotoxin analogue III from the Taiwan cobra by hydrogen-deuterium exchange kinetics. Biochemistry 38: 9899-9905.
53. Sivaraman T, Kumar TKS, Chang DK, Lin WY, Yu C, (1998) Events in the kinetic folding pathway of a small all β-sheet protein. J Biol Chem 273: 10181-10189.
54. Sivaraman T, Kumar TKS, Jayaraman G, Han CC, Yu C, (1997) Characterization of partially structured state in an all β-sheet protein. Biochem J 321: 457-464.
55. Kumar TKS, Jayaraman G, Lee CS, Sivaraman T, Lin WY, et al. (1995) Identification of molten globule-like state in an all β-sheet protein. Biochem Biophys Res Commun 207: 536-543.
56. Yu C, Bhaskaran R, Chuang LC, Yang CC, (1993) Solution conformation of cobrotoxin: A nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing study. Biochemistry 32 (9): 2131-2136.
57. Kumar TKS, Sivaraman T, Samuel D, Srisailam S, Ganesh G, et al. (2000) Protein folding and β-sheet proteins. J Chin Chem Soc 47 (5): 1009-42.
58. Sivaraman T, Kumar TKS, Tu YT, Peng HJ, Yu C, (1999) Structurally homologous toxins isolated from the Taiwan cobra (Naja naja atra) differ significantly in their structural stability. Arch Biochem Biophys 363 (1): 107-15.
59. Hsieh HC, Kumar TKS, Sivaraman T, Yu C, (2006) Refolding of a small all β-sheet protein proceeds with accumulation of kinetic intermediates. Arch Biochem Biophys 447 (2): 147-54.
60. Sivaraman T, Kumar TKS, Tu YT, Wang W, Lin WY, et al. (1999) Secondary structure formation is the earliest structural events in refolding of an all β-sheet protein. Biochem Biophys Res Commun 260: 284-288.
61. Arrington CB, Robertson AD, (2000) Correlated motions in native proteins from MS analysis of NH exchange: evidence for a manifold of unfolding reactions in ovomucoid third domain. J Mol Biol 300: 221-232.
62. Ivankov DN, Bogatyreva NS, Lobanov MY, Gazitskaya OV, (2009) Coupling between properties of the protein shape and the rate of protein folding. PLoS ONE 4 (8): e6476.
63. Gromiha MM, Selvaraj S, (2001) Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding rate prediction. J Mol Biol 301: 27-32.
64. Wall L, Christiansen T, Orwant J, (2000) Programming Perl Sebastopol O'Reilly Media, Inc.
65. Wuthrich K, (1986) NMR of proteins and nucleic acids New York John Wiley & Sons.
66. Stickle DF, Presta LG, Dill KA, Rose GD, (1992) Hydrogen bonding in globular proteins. J Mol Biol 226: 1143-1159.