Global and local motions in ribonuclease A: A molecular dynamics study

Biopolymers

Volumn 65, Issue 4, 2002, Pages 274-283

  Merlino, Antonello ^a   Vitagliano, Luigi ^b   Ceruso, Marc Antoine ^c   Di Nola, Alfredo ^d   Mazzarella, Lelio ^a,b  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b CNR   (Italy)

^c MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^d SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

Essential dynamics; Molecular dynamics; Protein dynamics; Protein structure function; Ribonucleases

Indexed keywords

ENZYMES; SOLVENTS; X RAYS;

LIGANDS;

BIOPOLYMERS;

ASPARAGINE; ASPARTIC ACID; HISTIDINE; LIGAND; LYSINE; RIBONUCLEASE A; SOLVENT; THREONINE; WATER;

ALPHA HELIX; ARTICLE; BETA SHEET; CRYSTALLOGRAPHY; ENZYME ACTIVE SITE; ENZYME SUBSTRATE; ENZYME SUBSTRATE COMPLEX; MOLECULAR DYNAMICS; NONHUMAN; PROTEIN FUNCTION; PROTEIN STRUCTURE;

ANIMALS; CATALYTIC DOMAIN; CATTLE; ENZYME STABILITY; MODELS, MOLECULAR; MOTION; PROTEIN CONFORMATION; RIBONUCLEASE, PANCREATIC; THERMODYNAMICS;

EID: 0037111516     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/bip.10225     Document Type: Article

References (60)

1. Blackburn, P.; Moore, S. In The Enzymes; Boyer, P. D., Ed; Academic Press: New York, 1982; pp 317-433.
2. Raines, R.T. Chem Rev 1998, 98, 1045-1065.
3. Smyth, D.G.; Stein, W.H.; Moore, S. J Biol Chem 1963, 238, 277-234.
4. Kartha, G.; Bello, J.; Harker, D. Nature 1967, 213, 862-865.
5. D'Alessio, G.; Di Donato, A.; Mazzarella, L.; Piccoli, R. In Ribonucleases: Structures and Functions; Riordan, J. F., D'Alessio, G., Eds.; Academic Press: New York, 1997; pp 383-423.
6. Youle, R. J.; D'Alessio, G. In Ribonuclease: Structures and Functions; D'Alessio, G., Riordan, J. F., Eds.; Academic Press: New York, 1996; pp 491-514.
7. Leland, P. A.; Schultz, L. W.; Kim, B. M.; Raines, R. T. Proc Natl Acad Sci USA 1998, 95, 10407-10412.
8. Mazzarella, L.; Capasso, S.; Demasi, D.; Di Lorenzo, G.; Mattia, C. A.; Zagari, A. Acta Cryst D 1993, 49, 389-402.
9. Mazzarella, L.; Vitagliano, L.; Zagari, A. Proc Natl Acad Sci USA 1995, 92, 3799-3803.
10. Liu, Y.; Hart, P. J.; Schlunegger, M. P.; Eisenberg, D. Proc Natl Acad Sci USA 1998, 95, 3437-3442.
11. Vitagliano, L.; Adinolfi, S.; Sica, F.; Merlino, A.; Zagari, A.; Mazzarella, L. J Mol Biol 1999, 293, 569-577.
12. Liu, Y.; Gotte, G.; Libonati, M.; Eisenberg, D. Nat Struct Biol 2001, 8, 211-214.
13. Rasmussen, B. F.; Stock, A. M.; Ringe, D.; Petsko, G. A. Nature 1992, 357, 423-424.
14. Tilton, R. F. J.; Dewan, J. C.; Petsko, G. A. Biochemistry 1992, 31, 2469-2481.
15. Vitagliano, L.; Merlino, A.; Zagari, A.; Mazzarella, L. Proteins Struct Funct Genet 2002, 46,97-104.
16. Radha Kishan, K. V.; Chandra, N. R.; Sudarsanakumar, C.; Suguna, K.; Vijayan, M. Acta Cryst D 1995, 51, 703-710.
17. Sadasivan, C.; Nagendra, H. G.; Vijayan, M. Acta Cryst D 1998, 54, 1343-1352.
18. Brunger, A. T.; Brooks, C. L.; Karplus, M. Proc Natl Acad Sci USA 1985, 82, 8458-8462.
19. Seshadri, K.; Rao, V. S.; Vishveshwara, S. J Biomol Struct Dynam 1994, 12, 581-603.
20. Nadig, G.; Ratnaparkhi, G. S.; Varadarajan, R.; Vishveshwara, S. Protein Sci 1996, 5, 2104-2114.
21. Nadig, G.; Vishveshwara, S. Biopolymers 1997, 42, 505-520.
22. Doniach, S.; Eastman, P. Curr Opin Struct Biol 1999, 9, 157-163.
23. Gilliland, G. In Ribonuclease: Structures and Functions; D'Alessio, G., Riordan, J. F., Eds.; Academic Press: New York, 1997; pp 306-341
24. Wlodawer, A.; Bott, R.; Sjolin, L. J Biol Chem 1982, 257, 1325-1332.
25. van der Spoel, D.; van Druner, R.; Berendsen, H. J. C. GROningen MAchine for Chemical Simulation, Department of Biophysical Chemistry, BIOSON Research Institute, Groningen, 1994.
26. Wlodawer, A.; Svenson, L. A.; Sjolin, L.; Gilliland, G. L. Biochemistry 1988, 27, 2705-2717
27. Berisio, R.; Lamzin, V. S.; Sica, F.; Wilson, K. S.; Zagari, A.; Mazzarella, L. J Mol Biol 1999, 292, 845-854.
28. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J Comput Phys 1977, 23, 327-341.
29. Garcia, A. E. Phys Rev Lett 1992, 68, 2696-2699.
30. Amadei, A.; Linssen, A. B.; Berendsen, H. J. Proteins 1993, 17, 412-425.
31. Wong, C. F.; Zheng, C.; Shen, J, McCammon, A.; Wolynes, P. G. J Phys Chem 1993, 97, 3100-3110.
32. Chillemi, G.; Falconi, M.; Amadei, A.; Zimatore, G.; Desideri, A.; Di Nola, A. Biophys J 1997, 73, 1007-1018.
33. Ceruso, M. A.; Amadei, A.; Di Nola, A. Protein Sci 1999, 8, 147-160.
34. Amadei, A.; Ceruso, M. A.; Di Nola, A. Proteins Struct Funct Genet 1999, 36, 419-424.
35. Santoro, J.; Gonzalez, C.; Bruix, M.; Neira, J. L.; Nieto, J. L.; Herranz, J.; Rico, M. J Mol Biol 1993, 229, 722-734.
36. Wlodawer, A. In Biological Macromolecules and Assembly; Jurnak, F., McPherson, A., Eds.; Wiley: New York, 1985; pp 394-439.
37. Fedorov, A. A.; Joseph-McCarthy, D.; Fedorov, E.; Sirakova, D.; Graf, I.; Almo, S. C. Biochemistry 1996, 35, 15962-15979.
38. Vitagliano, L.; Merlino, A.; Zagari, A.; Mazzarella, L. Protein Sci 2000, 9, 1217-1225.
39. Quirk, D. J.; Park, C.; Thompson, J. E.; Raines, R. T. Biochemistry 1998, 37, 17958-17964.
40. Quirk, D. J.; Raines, R. T. Biophys J 1999, 76, 1571-1579.
41. Schultz, L. W.; Quirk, D. J.; Raines, R. T. Biochemistry 1998, 37, 8886-8898.
42. Beintema, J. J.; Schueller, C.; Irie, M.; Carsana, A. Prog Biophys Mol Biol 1988, 51, 165-192.
43. delCardayre, S. B.; Raines, R. T. J Mol Biol 1995, 252, 328-336.
44. Vitagliano, L.; Adinolfi, S.; Riccio, A.; Sica, F.; Zagari, A.; Mazzarella, L. Protein Sci 1998, 7, 1691-1699.
45. Wladkowski, B. D.; Svensson, L. A.; Sjolin, L.; Ladner, J. E.; Gilliland, G. L. J Am Chem Soc 1993, 120, 5488-5498.
46. Zegers, I.; Maes, D.; Dao-Thi, M. H.; Poortmans, F.; Palmer, R.; Wyns, L. Protein Sci 1994, 3, 2322-1339.
47. Nemethy, G.; Scheraga, H. A. Proc Natl Acad USA 1979, 76, 6050-6054.
48. Capasso, S.; Di Donato, A.; Esposito, L.; Sica, F.; Sorrentino, G.; Vitagliano, L.; Zagari, A.; Mazzarella, L. J Mol Biol 1996, 257, 492-496.
49. Xu, X.; Rothwarf, D. M.; Scheraga, H. A. Biochemistry 1996, 35, 6406-6417.
50. Orrù, S.; Vitagliano, L.; Esposito, L.; Mazzarella, L.; Marino, G.; Ruoppolo, M. Protein Sci 2000, 9, 2577-2582.
51. van Aalten, D. M.; Findlay, J. B.; Amadei, A.; Berendsen, H. J. Protein Eng 1995, 8, 1129-1135.
52. van Aalten, D. M.; Amadei, A.; Linssen, A. B.; Eijsink, V. G.; Vriend, G.; Berendsen, H. J. Proteins 1995, 22, 45-54.
53. Hayward, S. Proteins Struct Funct Genet 1999, 36, 425-435.
54. Barlow, D. J.; Thornton, J. M. J Mol Biol 1988, 201, 601-619.
55. Benedetti, E.; Di Blasio, B.; Pavone, V.; Pedone, C.; Toniolo, C.; Crisma, M. Biopolymers 1992, 32, 453-456.
56. Laity, J. H.; Montelione, G. T.; Scheraga, H. A. Biochemistry 1999, 38, 16432-16442.
57. Baker, W. R.; Kintanar, A. Arch Biochem Biophys 1996, 327, 189-199.
58. Esposito, L.; Vitagliano, L. Sica, F.; Sorrentino, G.; Zagari, A.; Mazzarella, L. J Mol Biol 2000, 297, 713-732.
59. Kumar, S. M.; Buyong, M.; Tsai, C. J.; Sinha, N.; Nussinov, R. Protein Sci 2000, 9, 10-19.
60. Newcomer, M. E. Nature Struct Biol 2001, 8, 282-284.