Protein unfolding at interfaces: Slow dynamics of α-helix to β-sheet transition

Proteins: Structure, Function and Genetics

Volumn 56, Issue 4, 2004, Pages 669-678

  Sethuraman, Ananthakrishnan ^a   Vedantham, Ganesh ^b,d   Imoto, Taiji ^c   Przybycien, Todd ^b   Belfort, Georges ^a  

^a RENSSELAER POLYTECHNIC INSTITUTE   (United States)

^b CARNEGIE MELLON UNIVERSITY   (United States)

^c KYUSHU UNIVERSITY   (Japan)

^d AMGEN INC   (United States)

Author keywords

Protein folding; Protein substrate interactions; Secondary structure

Indexed keywords

ALKANE; HEN EGG LYSOZYME; LYSOZYME; PROTEIN; THIOL DERIVATIVE; UNCLASSIFIED DRUG;

ADSORPTION; ALGORITHM; ALPHA HELIX; ARTICLE; ATTENUATED TOTAL REFLECTION FOURIER TRANSFORM INFRARED SPECTROSCOPY; BETA SHEET; CONCENTRATION (PARAMETERS); CONFORMATIONAL TRANSITION; CONTACT ANGLE; INFRARED SPECTROSCOPY; MOLECULAR DYNAMICS; MOLECULAR MODEL; OPTIMIZATION ALGORITHM; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; PROTEIN SUBSTRATE INTERACTION; PROTEIN UNFOLDING; SURFACE PROPERTY; TIME TO ADSORPTION; WETTABILITY;

BIOPOLYMERS; KINETICS; MURAMIDASE; POLYMERS; POLYTETRAFLUOROETHYLENE; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; SUBSTRATE SPECIFICITY; WETTABILITY;

EID: 4043104043     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20183     Document Type: Article

References (61)

1. Dobson CM. Protein misfolding, evolution and disease. Trends Biochem Sci 1999;24:329-332.
2. Blakeslee S. In: Folding proteins, clues to many diseases. The New York Times, Science Times May 21, 2002; Sect F;pp. F1 & F8.-
3. Anfinsen CB. Principles that govern the folding of protein chains. Science 1973;181:223-230.
4. Creighton TE. Proteins, structures and molecular properties. New York: W. H. Freeman and Company 1993.
5. Sipe JD, Cohen AS. Review: history of the amyloid fibril. J Struct Biol 2000;130:88-98.
6. Chiti F, Webster P, Taddei N, Clark A, Stefani M, Ramponi G, Dobson CM. Designing conditions for in vitro formation of amyloid protofilaments and fibrils. Proc Natl Acad Sci 1999;96:3590-3594.
7. Fandrich M, Fletcher MA, Dobson CM. Amyloid fibrils from muscle myoglobin. Nature 2001;410:165-166.
8. Sunde M, Blake CCF. From the globular to the fibrous state: protein structure and structural conversion in amyloid formation. Quart Revs Biophys 1998;31:1-39.
9. Kelly JW. The alternate conformations of amyloidogenic proteins and their multi-step assembly pathways. Curr Opin Struct Biol 1998;8:101-106.
10. Rochet J-C, Lansbury Jr PT. Amyloid fibrillogenesis: themes and variations. Curr Opin Struct Biol 2000;10:60-68.
11. Lansbury Jr. PT. Evolution of amyloid: what normal protein folding may tell us about fibrillogenesis and disease. Proc Natl Acad Sci 1999;96:3342-3344.
12. Pepys MB, Hawkins PN, Booth DR, Vigushin DM, Tennent GA, Soutar AK, Totty N, Nguyen O, Blake CC, Terry CJ, Feest TG, Zalin AM, Hsuan JJ. Human lysozyme gene mutations cause hereditary systemic amyloidosis. Nature 1993;362:553-557.
13. Booth DR, Sunde M, Bellotti V, Robinson CV, Hutchinson WL, Fraser PE, Hawkins PN, Dobson CM, Radford SE, Blake CC, Pepys MB. Instability, unfolding and aggregation of human lysozyme variants under lying amyloid fibrillogenesis. Nature 1997;385:787-793.
14. Klein-Seetharaman J, Oikawa M, Grimshaw SB, Wirmer J, Duchardt E, Ueda T, Imoto T, Smith LJ, Dobson CM, Schwalbe H. Long-range interactions within a nonnative protein. Science 2002; 295:1719-1722.
15. Zanusso G, Farinazzo A, Fiorini M, Gelati M, Castagna A, Righetti PG, Rizzuto N, Monaco S. pH-dependent prion protein conformation in classical Creutzfeldt-Jakob disease. J Biol Chem 2001;276: 40377-40380.
16. Chehin R, Iloro I, Marcos MJ, Villar E, Shnyrov VL, Arrondo JL. Thermal and pH-induced conformational changes of a β-sheet protein monitored by infrared spectroscopy. Biochemistry 1999;38: 1525-11530.
17. Blake CC, Koenig DF, Mair GA, North AC, Phillips DC, Sarma VR. Structure of hen egg-white lysozyme: A three dimensional Fourier synthesis at 2 Å resolution. Nature 1965;206:757-761.
18. Buck M, Boyd J, Redfield C, MacKenzie DA, Jeenes DJ, Archer DB, Dobson CM. Structural determinants of protein dynamics: analysis of 15N NMR relaxation measurements for main-chain and side-chain nuclei of hen egg white lysozyme. Biochemistry 1995;34:4041-4055.
19. Lee C-S, Belfort G. Changing activity of ribonuclease A during adsorption: a molecular explanation. Proc Natl Acad Sci 1989;86: 8392-8396.
20. Lenk TJ, Horbett TA, Ratner BD, Chittur KK. Infrared spectroscopy studies of time-dependent changes in fibrinogen adsorbed to polyurethanes. Langmuir 1991;7:1755-1764.
21. Chittur KK. Proteins on surfaces: Methodologies for surface preparation and engineering protein function. In: Malmsten M, editor. Biopolymers at Interfaces. New York: Dekker; 2003. p 467-496.
22. Cheng S-S, Chittur KK, Sukenik CN, Culp LA, Lewandowska K. The conformation of fibronectin on self-assembled monolayers with different surface composition: an FTIR/ATR study. J Coll InterfSci 1994;162:135-143.
23. Giacomelli, CE, Norde W. Influence of hydrophobic Teflon particles on the structure of amyloid β-peptide. Biomacromolecules 2003;4: 1719-1726.
24. 2O solutions. Anal Biochem 2000;285:33-49.
25. Saksena S, Zydney AL. Influence of protein-protein interactions on bulk mass transport during ultrafiltration. J Membrane Sci 1997;125:93-108.
26. Pieracci J, Wood DW, Crivello JV, Belfort G. UV-assisted graft polymerization of N-vinyl-2-pyrrolidinone onto poly(ether sulfone) ultrafiltration membranes: comparison of dip versus immersion modification techniques. Chem of Mat 2000;12:2123-2133.
27. Taniguchi M, Pieracci JP, Belfort G. Effect of undulations on surface energy: a quantitative assessment. Langmuir 2001;17: 4312-4315.
28. Taniguchi M, Belfort G. Correcting for surface roughness: advancing and receding contact angles. Langmuir 2002;18:6465-6467.
29. Ulbricht M, Matuschewski H, Oechel A, Hicke H-G. Photo-induced graft polymerization surface modifications for the preparation of hydrophilic and low-protein-adsorbing ultrafiltration membranes. J Mem Sci 1996;115:31-47.
30. Arai T, Norde W. The behavior of some model proteins at solid-liquid interfaces. 1. Adsorption from single protein solutions. Coll and surf 1990;51:1-15.
31. Frishman D, Argos P. Knowledge based protein secondary structure assignment. Prot: Struct, Func and Gen 1995;23:566-579.
32. Norde W. Driving forces for protein adsorption at solid surfaces. In: Malmsten M, editor. Biopolymers at Interfaces. New York: Dekker; 2003. p 21-44.
33. Sigal M, Mrksich M, Whitesides GM. Effect of surface wettability on the adsorption of proteins and detergents. J Am Chem Soc 1998;120:3464-3473.
34. Cooper EA, Knutson K. Physical methods to characterize pharmaceutical proteins. Herron, JN, Jiskoot, W, Crommelin DJA, editors. New York: Crommelin, Plenum Press 1995.
35. Eaton WA, Munoz V, Hagen SJ, Jas GS, Lapidus LJ, Henry ER, Hofrichter J. Fast kinetics and mechanisms in protein folding. Annu Rev Biophys Biomol Struct 2000;29:327-359.
36. Williams S, Causgrove TP, Gilmanshin R, Fang KS, Callender RH, Woodruff WH, Dyer RB. Fast events in protein folding: helix melting and formation in a small peptide. Biochemistry 1996;35: 691-697.
37. Hummer G, Garcia AE, Garde S. Helix nucleation kinetics from molecular simulations in explicit solvent. Prot: Struct, Func and Gen 2001;42:77-84.
38. Munoz V, Thompson PA, Hofrichter J, Eaton WA. Folding dynamics and mechanism of beta-hairpin formation. Nature 1997;390: 196-199.
39. Kauffmann E, Darnton NC, Austin RH, Batt C, Gerwert K. Lifetimes of intermediates in the beta-sheet to alpha-helix transition of beta-lactoglobulin by using a diffusional IR mixer. Proc Natl Acad Sci 2001;98:6646-6649.
40. Sane SU, Cramer SM, Przybycien TM. A holistic approach to protein secondary structure characterization using amide I band raman spectroscopy. J Chrom A 1999;269:255-272.
41. Sethuraman, Han, Kane and Belfort. Submitted.
42. Denis FA, et al. Protein adsorption on model surfaces with controlled nanotopograhy and chemistry. Langmuir 2002;18:819-828.
43. Han M, Sethuraman A, Kane RS, Belfort G. Nanometer-scale roughness having little effect on the amount or structure of adsorbed protein. Langmuir 2003;19:9868-9872.
44. Matagne A, Dobson CM. The folding process of hen lysozyme: a perspective from the 'new view.' Cell Mol Life Sci 1998;54:363-371.
45. Williams MA, Thornton JM, Goodfellow JM. Modelling protein unfolding: hen egg-white lysozyme. Protein Eng 1997;10:895-903.
46. Tzannis ST, Hrushesky WJM, Wood PA, Przybycien TM. Irreversible inactivation of interleukin-2 in a pump-based delivery environment. Proc Natl Acad Sci 1996;93:5460-5465.
47. Amiel C, Sikka M, Schneider JW, Tsao YH, Tirrell M, Mays JW. Adsorption of hydrophilic-hydrophobic block co-polymers on silica from aqueous solutions. Macromol 1997;28:3125-3134.
48. Squire PG, Himmel ME. Hydrodynamics and protein hydration. Arch Biochem Biophys 1979;196:165-177.
49. Sethuraman and Belfort, Unpublished.
50. Koehler JA, Ulbricht M, Belfort G. Intermolecular forces between proteins and polymer films with relevance to filtration. Langmuir 1997;13:4162-4171.
51. Koehler JA, Ulbricht M, Belfort G. Intermolecular forces between a protein and a hydrophilic modified polysulfone film with relevance to filtration. Langmuir 2000;16:10419-10427.
52. Haggerty L, Lenhoff AM. Analysis of ordered arrays of adsorbed lysozyme by scanning tunneling microscopy. Biophys J 1993;64: 886-895.
53. Tilton RD, Blomberg E, Claesson PM. Effect of anionic surfactant on interactions between lysozyme layers adsorbed on mica. Langmuir 1993;9:2102-2108.
54. Blomberg E, Claesson PM, Fröberg JC, Tilton RD. Interaction between adsorbed layers of lysozyme studied with the surface force technique. Langmuir 1994;10:2325-2334.
55. Zurdo J, Guijarro JI, Jimenez JL, Saibil HR, Dobson CM. Dependence on solution conditions of aggregation and amyloid formation by an SH3 domain. J Mol Biol 2001;311:325-340.
56. Sokolowski F, Modler AJ, Masuch R, Zirwer D, Baier M, Lutsch G, Moss DA, Gast K, Naumann D. Formation of critical oligomers is a key event during conformational transition of recombinant syrian hamster prion protein. J Biol Chem 2003;278:40481-40492.
57. Kubelka J, Keiderling TA. Differentiation of beta-sheet-forming structures: ab initio-based simulations of IR absorption and vibrational CD for model peptide and protein beta-sheets. J Am Chem Soc 2001;123:12048-12058.
58. Ismail AA, Mantsch HH, Wong PT. Aggregation of chymotrypsinogen: portrait by infrared spectroscopy. Biochim Biophys Acta 1992;1121:183-188.
59. Dong A, Prestrelski SJ, Allison SD, Carpenter JF. Infrared spectroscopic studies of lyophilization- and temperature-induced protein aggregation. J Pharm Sci 1995;84:415-424.
60. Militello V, Casarino C, Emanuele A, Giostra A, Pullara F, Leone M. Aggregation kinetics of bovine serum albumin studied by FTIR spectroscopy and light scattering. Biophys Chem 2004;107:175-187.
61. DeMarco ML, Daggett V. From conversion to aggregation: protofibril formation of the prion protein. Proc Natl Acad Sci 2004;101: 2293-2298.