Molecular dynamics simulations of human glutathione transferase P1-1: Analysis of the induced-fit mechanism by GSH binding

Proteins: Structure, Function and Genetics

Volumn 37, Issue 1, 1999, Pages 1-9

  Stella, Lorenzo ^a   Nicotra, Maria ^a   Ricci, Giorgio ^a   Rosato, Nicola ^a,c   Di Iorio, Ernesto E ^b  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

^b ETH ZURICH   (Switzerland)

^c IRCCS ISTITUTO CENTRO SAN GIOVANNI DI DIO FATEBENEFRATELLI   (Italy)

Author keywords

Detoxification; Fluctuations; Protein dynamics; Structure; Sulfhydryl reactivity

Indexed keywords

5,5' DITHIOBIS(2 NITROBENZOIC ACID); APOPROTEIN; CYSTEINE; GLUTATHIONE; GLUTATHIONE TRANSFERASE; SOLVENT; THIOL DERIVATIVE;

ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; CRYSTALLOGRAPHY; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME SUBSTRATE; HUMAN; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN TERTIARY STRUCTURE; SIMULATION;

BINDING SITES; COMPUTER SIMULATION; CYSTEINE; GLUTATHIONE; GLUTATHIONE S-TRANSFERASE PI; GLUTATHIONE TRANSFERASE; HUMANS; ISOENZYMES; MODELS, CHEMICAL; MODELS, MOLECULAR; MOTION; PROTEIN BINDING; PROTEIN CONFORMATION; SPECTROMETRY, FLUORESCENCE; TRYPTOPHAN;

GOES;

EID: 0033215104     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19991001)37:1<1::AID-PROT1>3.0.CO;2-B     Document Type: Article

References (44)

1. Berzofsky JA. Intrinsic and extrinsic factors in protein antigenic structure. Science 1985;229:932-940.
2. van Aalten DMF, Findlay JBC, Amadei A, Berendsen HJC. Essential dynamics of the cellular retinol-binding protein -Evidence for ligand-induced conformational changes. Protein Eng 1995;8:1129-1135.
3. Lim K, Herron N. Molecular dynamics of the anti-fluorescein 4-4-20 antigen-binding fragment computer simulations. Biochemistry 1995;34:6962-6974.
4. Armstrong RN. Structure, catalytic mechanism, and evolution of the glutathione transferases. Chem Res Toxicol 1997;10:2-18.
5. Sinning I, Kleywegt GJ, Cowan SW, Reinemer P, Dirr HW, Huber R, Gilliland GL, Armstrong RN, Ji X, Board PG, Olin B, Mannervik B, Jones TA. Structure determination and refinement of human alpha class glutathione transferase A1-1, and comparison with the Mu and Pi class enzymes. J Mol Biol 1993;232:192-212.
6. Cameron AD, Sinning I, L'Ermite G, Olin B, Board PG, Mannervik B, Jones TA. Structural analysis of human alpha class glutathione transferase A1-1 in the apo-form and in complexes with ethacrynic acid and its glutathione conjugate. Structure 1995;5:717-727.
7. McTigue MA, Williams DR, Tainer JA. Crystal structures of a schistosomal drug and vaccine target: glutathione-S-transferase from Schistosoma Japonica and its complex with the leading antischistosomal drug Praziquantel. J Mol Biol 1995;246:21-27.
8. Vander Jagt DL, Wilson SP, Heidrich JE. Purification and bilirubin binding properties of glutathione S-transferase from human placenta. FEBS Lett 1981;136:319-321.
9. Del Boccio G, Pennelli A, Whitehead EP, Lo Bello M, Petruzzelli R, Federici G, Ricci G. Interaction of glutathione transferase from horse erythrocytes with 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole. J Biol Chem 1991;266:13777-13782.
10. Lo Bello M, Petruzzelli R, Reale L, Ricci G, Barra D, Federici G. Chemical modification of human placental glutathione transferase by pyridoxal-5′-phosphate. Biochim Biophys Acta 1992;1121: 167-172.
11. Lo Bello M, Pastore A, Petruzzelli R, Parker MW, Wilce MCJ, Federici G, Ricci G. Conformational states of human placental glutathione transferase as probed by limited proteolysis. Biochem Biophys Res Commun 1993;194:804-810.
12. Ricci G, Del Boccio G, Pennelli A, Lo Bello M, Petruzzelli R, Caccuri AM, Barra D, Federici G. Redox forms of human placenta glutathione transferase. J Biol Chem 1991;266:21409-21415.
13. Ricci G, Caccuri AM, Lo Bello M, Rosato N, Mei G, Nicotra M, Chiessi E, Mazzetti AP, Federici G. Structural flexibility modulates the activity of human glutathione transferase P-1-1: role of helix 2 flexibility in the catalytic mechanism. J Biol Chem 1996;271:16187-16192.
14. Caccuri AM, Lo Bello M, Nuccetelli M, Nicotra M, Rossi P, Antonini G, Federici G, Ricci G. Proton release upon GSH binding to glutathione transferase P1-1: kinetic analysis of a multistep GSH binding process. Biochemistry 1998;37:3028-3034.
15. Nicotra M, Paci M, Sette M, Oakley AJ, Parker MW, Lo Bello M, Caccuri AM, Federici G, Ricci G. Solution structure of glutathione bound to glutathione transferase P1-1: comparison of NMR measurements with the crystal structure. Biochemistry 1998;37:3020-3027.
16. Reinemer P, Dirr HW, Ladenstein R, Huber R, Lo Bello M, Federici G, Parker MW. Three-dimensional structure of class p glutathione S-transferase from human placenta in complex with S-hexylglutathione at 2.8 Å resolution. J Mol Biol 1991;227:214-226.
17. Oakley AJ, Lo Bello M, Battistoni A, Ricci G, Rossjohn J, Villar HO, Parker MW. The structures of human glutathione transferase P1-1 in complex with glutathione and various inhibitors at high resolution. J Mol Biol 1997;274:84-100.
18. Neuefeind T, Huber R, Dasenbrock H, Prade L, Bieseler B. Crystal structure of the herbicide-detoxifying maize glutathione S-transferase-I in complex with lactoylglutathione: evidence for an induced-fit mechanism. J Mol Biol 1997;274:446-453.
19. Oakley AJ, Lo Bello M, Ricci G, Federici G, Parker MW. Evidence for an induced-fit mechanism operating in Pi class glutathione transferases. Biochemistry 1998;37:9912-9917.
20. Caccuri AM, Ascenzi P, Antonini G, Parker AJ, Oakley AJ, Chiessi E, Nuccetelli M, Battistoni A, Bellizia A, Ricci G. Structural flexibility modulates the activity of human glutathione transferase P-1-1: influence of a poor co-substrate on dynamics and kinetics of human glutathione transferase. J Biol Chem 1996;271: 16193-16198.
21. Stella L, Di Iorio EE, Nicotra M, Ricci G. Molecular dynamics simulations of human glutathione transferase P1-1. Conformational fluctuations of the apo-structure. Proteins 1999;37:10-19.
22. Berendsen HJC, Grigera JR, Straatsma TP. The missing term in effective pair potentials. J Phys Chem 1987;91:6269-6271.
23. van Gunsteren WF, Berendsen HJC. Groningen molecular simulation (GROMOS) library manual. Biomos, Nijenborg 16, 9747 AG Groningen, The Nederlands, 1987.
24. Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23:327-341.
25. Berendsen HJC. Treatment of long-range forces in molecular dynamics. In: Hermans J, editor. Molecular Dynamics and protein structure. Western Springs, IL: Polycrystal Book Service; 1985. p 123-125.
26. Berendsen HJC, Postma JPM, van Gusteren WF, Di Nola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
27. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
28. Koradi R, Billeter M, Wuthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 1996;14:51-55.
29. Lo Bello M, Battistoni A, Mazzetti AP, Board PG, Muramatsu M, Federici G, Ricci G. Site-directed mutagenesis of human glutathione transferase P1-1: spectral, kinetic and structural properties of Cys-47 and Lys-54 mutants. J Biol Chem 1995;270:1247-1253.
30. Stella L, Caccuri AM, Rosato N, Nicotra M, Lo Bello M, De Matteis F, Mazzetti AP, Federici G, Ricci G. Flexibility of helix 2 in the human glutathione transferase P1-1: time-resolved fluorescence spectroscopy. J Biol Chem 1998;273:23267-23273.
31. Aceto A, Caccuri AM, Sacchetta P, Bucciarelli T, Dragani B, Rosato N, Federici G, Di Ilio C. Dissociation and unfolding of Pi-class glutathione transferase. Evidence for a monomeric inactive intermediate. Biochem J 1992;285:241-245.
32. Bruccoleri RE, Karplus M. Conformational sampling using high temperature molecular dynamics. Biopolymers 1990;29:1847-1862.
33. Daggett V, Kollman PA, Kuntz ID. A molecular dynamics simulation of polyalanine: An analysis of equilibrium motions and helix-coil transitions. Biopolymers 1991;31:1115-1134.
34. Philippopoulos M, Xiang Y, Lim C. Identifying the mechanism of protein loop closure: a molecular dynamics simulation of the Bacillus stearothermophilus LDH loop in solution. Protein Eng 1995;8:565-573.
35. Daggett V , Levitt M. Realistic simulations of native-protein dynamics in solution and beyond. Annu Rev Biophys Biomol Struct 1993;22:353-380.
36. Daggett V, Levitt M. Protein unfolding pathways explored through molecular dynamics simulations. J Mol Biol 1993;232:600-619.
37. Eaton WA, Thompson PA, Chan CK, Hage SJ, Hofrichter J. Fast events in protein folding. Structure 1996;4:1133-1139.
38. Ricci G, Lo Bello M, Caccuri AM, Pastore A, Nuccetelli M, Parker MW, Federici G. Site-directed mutagenesis of human glutathione transferase P 1-1: mutation of Cys-47 induces a positive cooperativity in glutathione transferase P1-1. J Biol Chem 1995;270:1243-1248.
39. Wilce MCJ, Parker MW. Structure and function of glutathione S-transferases. Biochim Biophys Acta 1994;1205:1-18.
40. Lo Bello M, Parker MW, Desideri A, Polticelli F, Falconi M, Del Boccio G, Pennelli A, Federici G, Ricci G. Peculiar spectroscopic and kinetic properties of Cys-47 in human placental glutathione transferase. J Biol Chem 1993;268:19033-19038.
41. Ricci G, Del Boccio G, Pennelli A, Aceto A, Whitehead EP, Federici G. Nonequivalence of the two subunits of horse erythrocyte glutathione transferase in their reaction with sulfhydryl reagents. J Biol Chem 1989;264:5462-5467.
42. Weber G. Fluorescence in biophysics: accomplishments and deficiencies. Methods Enzymol. 1997;278:1-15.
43. Callis PR, Burgess BK. Tryptophan fluorescence shifts in proteins from hybrid simulations: an electrostatic approach. J Phys Chem B 1997;101:9429-9432.
44. Caflisch A, Karplus M. Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores and secondary structure of barnase. Proc Natl Acad Sci USA 1994;91:1746-1750.