The non-native conformations of cytochrome c in sodium dodecyl sulfate and their modulation by ATP

European Biophysics Journal

Volumn 40, Issue 3, 2011, Pages 259-271

  Ahluwalia, Unnati ^a   Nayeem, Shahid M ^a   Deep, Shashank ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY DELHI   (India)

Author keywords

ATP; Cytochrome c; Docking; GTP; Non native conformation; Sodium dodecyl sulfate

Indexed keywords

EQUIDAE;

ADENOSINE TRIPHOSPHATE; CYTOCHROME C; CYTOCHROME C''; DODECYL SULFATE SODIUM; GUANOSINE TRIPHOSPHATE;

ANIMAL; ARTICLE; CHEMISTRY; CIRCULAR DICHROISM; HORSE; KINETICS; METABOLISM; METHODOLOGY; MICELLE; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; SPECTROFLUOROMETRY;

ADENOSINE TRIPHOSPHATE; ANIMALS; CIRCULAR DICHROISM; CYTOCHROME C GROUP; CYTOCHROMES C; GUANOSINE TRIPHOSPHATE; HORSES; KINETICS; MICELLES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SODIUM DODECYL SULFATE; SPECTROMETRY, FLUORESCENCE;

EID: 79958721281     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-010-0643-6     Document Type: Article

References (51)

1. Antalik M, Bagel'ova J (1995) Effect of nucleotides on thermal stability of ferricytochrome C. Gen Physiol Biophys 14:19-37
2. Babul J, Stellwagen E (1971) The existence of heme-protein coordinate-covalent bonds in denaturing solvents. Biopolymers 10:2359-2361
3. Bai Y, Sosnick TR, Mayne L, Englander SW (1995) Protein folding intermediates: native-state hydrogen exchange. Science 269:192-197
4. Bertini I, Turano P, Vasos PR, Bondon A, Chevance S, Simonneaux G (2004) Cytochrome c and SDS: a molten globule protein with altered axial ligation. J Mol Biol 336:489-496 (Pubitemid 38147642)
5. Bhuyan AK (2010) On the mechanism of SDS-induced protein denaturation. Biopolymers 93:186-199
6. Bushnell GW, Louie GV, Brayer GD (1990) High-resolution three-dimensional structure of horse heart cytochrome c. J Mol Biol 214:585-595 (Pubitemid 20261984)
7. Chattopadhyay K, Mazumdar S (2003) Stabilization of partially folded states of cytochrome c in aqueous surfactant: effects of ionic and hydrophobic interactions. Biochemistry 42:14606-14613 (Pubitemid 37532007)
8. Chen E, Van Vranken V, Kliger DS (2008) The folding kinetics of the SDS-induced molten globule form of reduced cytochrome c. Biochemistry 47:5450-5459 (Pubitemid 351656989)
9. Colon W, Wakem LP, Sherman F, Roder H (1997) Identification of the predominant non-native histidine ligand in unfolded cytochrome c. Biochemistry 36:12535-12541 (Pubitemid 27446677)
10. Cortese JD, Voglino AL, Hackenbrock CR (1998) Multiple conformations of physiological membrane-bound cytochrome c. Biochemistry 37:6402-6409 (Pubitemid 28213660)
11. Craig DB, Wallace CJ (1991) The specificity and Kd at physiological ionic strength of an ATP-binding site on cytochrome c suit it to a regulatory role. Biochem J 279(Pt 3):781-786
12. Das TK, Mazumdar S, Mitra S (1998) Characterization of a partially unfolded structure of cytochrome c induced by sodium dodecyl sulphate and the kinetics of its refolding. Eur J Biochem 254:662-670 (Pubitemid 28308120)
13. Davis-Searles PR, Morar AS, Saunders AJ, Erie DA, Pielak GJ (1998) Sugar-induced molten-globule model. Biochemistry 37:17048-17053 (Pubitemid 28566784)
14. Fedurco M, Augustynski J, Indiani C, Smulevich G, Antalik M, Bano M, Sedlak E, Glascock MC, Dawson JH (2004) The heme iron coordination of unfolded ferric and ferrous cytochrome c in neutral and acidic urea solutions. Spectroscopic and electrochemical studies. Biochim Biophys Acta 1703:31-41 (Pubitemid 39575071)
15. Godoy LC, Munoz-Pinedo C, Castro L, Cardaci S, Schonhoff CM, King M, Tortora V, Marin M, Miao Q, Jiang JF, Kapralov A, Jemmerson R, Silkstone GG, Patel JN, Evans JE, Wilson MT, Green DR, Kagan VE, Radi R, Mannick JB (2009) Disruption of the M80-Fe ligation stimulates the translocation of cytochrome c to the cytoplasm and nucleus in nonapoptotic cells. Proc Natl Acad Sci USA 106:2653-2658
16. Goto Y, Calciano LJ, Fink AL (1990) Acid-induced folding of proteins. Proc Natl Acad Sci USA 87:573-577
17. Green DR, Reed JC (1998) Mitochondria and apoptosis. Science 281:1309-1312 (Pubitemid 28406816)
18. Hamada D, Hoshino M, Kataoka M, Fink AL, Goto Y (1993) Intermediate conformational states of apocytochrome c. Biochemistry 32:10351-10358 (Pubitemid 23320158)
19. Jemmerson R, Liu J, Hausauer D, Lam KP, Mondino A, Nelson RD (1999) A conformational change in cytochrome c of apoptotic and necrotic cells is detected by monoclonal antibody binding and mimicked by association of the native antigen with synthetic phospholipid vesicles. Biochemistry 38:3599-3609
20. Jeng MF, Englander SW, Elove GA, Wand AJ, Roder H (1990) Structural description of acid-denatured cytochrome c by hydrogen exchange and 2D NMR. Biochemistry 29:10433-10437
21. Jordan T, Eads JC, Spiro TG (1995) Secondary and tertiary structure of the A-state of cytochrome c from resonance Raman spectroscopy. Protein Sci 4:716-728
22. Kluck RM, Ellerby LM, Ellerby HM, Naiem S, Yaffe MP, Margoliash E, Bredesen D, Mauk AG, Sherman F, Newmeyer DD (2000) Determinants of cytochrome c pro-apoptotic activity. The role of lysine 72 trimethylation. J Biol Chem 275:16127-16133 (Pubitemid 30366922)
23. Li P, Nijhawan D, Budihardjo I, Srinivasula SM, Ahmad M, Alnemri ES, Wang X (1997) Cytochrome c and dATP-dependent formation of Apaf-1/caspase-9 complex initiates an apoptotic protease cascade. Cell 91:479-489 (Pubitemid 27508237)
24. Liu X, Kim CN, Yang J, Jemmerson R, Wang X (1996) Induction of apoptotic program in cell-free extracts: requirement for dATP and cytochrome c. Cell 86:147-157 (Pubitemid 26256586)
25. Maity H, Maity M, Krishna MM, Mayne L, Englander SW (2005) Protein folding: the stepwise assembly of foldon units. Proc Natl Acad Sci USA 102:4741-4746 (Pubitemid 40471524)
26. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19:1639-1662 (Pubitemid 128590223)
27. Moza B, Qureshi SH, Islam A, Singh R, Anjum F, Moosavi-Movahedi AA, Ahmad F (2006) A unique molten globule state occurs during unfolding of cytochrome c by LiClO4 near physiological pH and temperature: structural and thermodynamic characterization. Biochemistry 45:4695-4702
28. Myer YP (1968) Far ultraviolet circular dichroism spectra of cytochrome c. Biochim Biophys Acta 154:84-90
29. Oellerich S, Wackerbarth H, Hildebrandt P (2002) Spectroscopic characterization of nonnative conformational states of cytochrome c. J Phys Chem B 106:6566-6580 (Pubitemid 35289249)
30. Oellerich S, Wackerbarth H, Hildebrandt P (2003) Conformational equilibria and dynamics of cytochrome c induced by binding of sodium dodecyl sulfate monomers and micelles. Eur Biophys J 32:599-613 (Pubitemid 37413244)
31. Patriarca A, Eliseo T, Sinibaldi F, Piro MC, Melis R, Paci M, Cicero DO, Polticelli F, Santucci R, Fiorucci L (2009) ATP acts as a regulatory effector in modulating structural transitions of cytochrome c: implications for apoptotic activity. Biochemistry 48:3279-3287
32. Pinheiro TJ, Watts A (1994) Lipid specificity in the interaction of cytochrome c with anionic phospholipid bilayers revealed by solid-state 31P NMR. Biochemistry 33:2451-2458 (Pubitemid 24099650)
33. Pinheiro TJ, Elove GA, Watts A, Roder H (1997) Structural and kinetic description of cytochrome c unfolding induced by the interaction with lipid vesicles. Biochemistry 36:13122-13132 (Pubitemid 27465428)
34. Rytomaa M, Kinnunen PK (1994) Evidence for two distinct acidic phospholipid-binding sites in cytochrome c. J Biol Chem 269:1770-1774 (Pubitemid 24035373)
35. Rytomaa M, Kinnunen PK (1995) Reversibility of the binding of cytochrome c to liposomes. Implications for lipid-protein interactions. J Biol Chem 270:3197-3202
36. Saini K, Deep S (2010) Relationship between the wavelength maximum of a protein and the temperature dependence of its intrinsic tryptophan fluorescence intensity. Eur Biophys J 39:1445-1451
37. Sanghera N, Pinheiro TJ (2000) Unfolding and refolding of cytochrome c driven by the interaction with lipid micelles. Protein Sci 9:1194-1202 (Pubitemid 30419153)
38. Sedlak E, Antalik M (1999) Molten globule-like state of cytochrome c induced by polyanion poly(vinylsulfate) in slightly acidic pH. Biochim Biophys Acta 1434:347-355 (Pubitemid 29486756)
39. Sinibaldi F, Piro MC, Howes BD, Smulevich G, Ascoli F, Santucci R (2003) Rupture of the hydrogen bond linking two Omega-loops induces the molten globule state at neutral pH in cytochrome c. Biochemistry 42:7604-7610 (Pubitemid 36735838)
40. Sinibaldi F, Mei G, Polticelli F, Piro MC, Howes BD, Smulevich G, Santucci R, Ascoli F, Fiorucci L (2005) ATP specifically drives refolding of non-native conformations of cytochrome c. Protein Sci 14:1049-1058 (Pubitemid 40389375)
41. Sinibaldi F, Howes BD, Piro MC, Caroppi P, Mei G, Ascoli F, Smulevich G, Santucci R (2006) Insights into the role of the histidines in the structure and stability of cytochrome c. J Biol Inorg Chem 11:52-62 (Pubitemid 43018080)
42. Sinibaldi F, Fiorucci L, Patriarca A, Lauceri R, Ferri T, Coletta M, Santucci R (2008) Insights into cytochrome c-cardiolipin interaction. Role played by ionic strength. Biochemistry 47:6928-6935
43. Spooner PJ, Watts A (1991a) Reversible unfolding of cytochrome c upon interaction with cardiolipin bilayers. 1. Evidence from deuterium NMR measurements. Biochemistry 30:3871-3879
44. Spooner PJ, Watts A (1991b) Reversible unfolding of cytochrome c upon interaction with cardiolipin bilayers. 2. Evidence from phosphorus-31 NMR measurements. Biochemistry 30:3880-3885
45. Spooner PJ, Watts A (1992) Cytochrome c interactions with cardiolipin in bilayers: a multinuclear magic-angle spinning NMR study. Biochemistry 31:10129-10138
46. Tsong TY (1975) An acid induced conformational transition of denatured cytochrome c in urea and guanidine hydrochloride solutions. Biochemistry 14:1542-1547
47. Umlong IM, Ismail K (2007) Micellization behaviour of sodium dodecyl sulfate in different electrolyte media. Colloids Surf A Physicochem Eng Asp 299:8-14 (Pubitemid 46441813)
48. Vincent JS, Levin IW (1986) Interaction of Ferricytochrome-C with Cardiolipin Multilayers - a Resonance Raman-Study. J Am Chem Soc 108:3551-3554
49. Vincent JS, Kon H, Levin IW (1987) Low-temperature electron paramagnetic resonance study of the ferricytochrome c-cardiolipin complex. Biochemistry 26:2312-2314 (Pubitemid 17080976)
50. Xu Q, Keiderling TA (2004) Effect of sodium dodecyl sulfate on folding and thermal stability of acid-denatured cytochrome c: a spectroscopic approach. Protein Sci 13:2949-2959 (Pubitemid 39431257)
51. Xu Q, Keiderling TA (2006) Stop-flow kinetics studies of the interaction of surfactant, sodium dodecyl sulfate, with acid-denatured cytochrome c. Proteins 63:571-580