Size and sequence and the volume change of protein folding

Journal of the American Chemical Society

Volumn 133, Issue 15, 2011, Pages 6020-6027

  Rouget, Jean Baptiste ^a   Aksel, Tural ^b   Roche, Julien ^a,c   Saldana, Jean Louis ^a   Garcia, Angel E ^c   Barrick, Doug ^b   Royer, Catherine A ^a  

^a CENTRE DE BIOCHIMIE STRUCTURALE   (France)

^b JOHNS HOPKINS UNIVERSITY   (United States)

^c Research Rensselaer Polytechnic Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

3D STRUCTURE; ANKYRIN-REPEAT DOMAIN; CONTRIBUTING FACTOR; COOPERATIVITY; DELETION VARIANTS; DISTRIBUTED EFFECTS; FOLDED STATE; LE CHATELIER'S PRINCIPLES; MODEL SYSTEM; MOLAR VOLUMES; NOTCH RECEPTOR; PACKING DEFECT; PROTEIN SIZE; PROTEIN STABILITY; PROTEIN STRUCTURES; PROTEIN UNFOLDING; SURFACE AREA; VOLUME CHANGE; VOLUMETRIC PROPERTIES;

HYDROSTATIC PRESSURE; PRESSURE EFFECTS; PROTEIN FOLDING; VOLUMETRIC ANALYSIS;

SURFACE DEFECTS;

ANKYRIN; NOTCH RECEPTOR;

AMINO ACID SEQUENCE; ARTICLE; ATMOSPHERIC PRESSURE; HYDRATION; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN LOCALIZATION; PROTEIN STABILITY; PROTEIN STRUCTURE; SURFACE PROPERTY; TEMPERATURE SENSITIVITY; THREE DIMENSIONAL IMAGING;

AMINO ACID SEQUENCE; ANKYRIN REPEAT; BACTERIAL PROTEINS; HALORHODOSPIRA HALOPHILA; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN DENATURATION; PROTEIN FOLDING; RECEPTORS, NOTCH; THERMODYNAMICS;

EID: 79954549743     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja200228w     Document Type: Article

References (47)

1. Bridgman, P. W. J. Biol. Chem. 1914, 19, 511-512
2. Brandts, J. F.; Oliveira, R. J.; Westort, C. Biochemistry 1970, 9 (4) 1038-1047
3. Hawley, S. A. Biochemistry 1971, 10 (13) 2436-2442
4. Smeller, L.; Meersman, F.; Heremans, K. Biochim. Biophys. Acta 2006, 1764 (3) 497-505
5. Zipp, A.; Kauzmann, W. Biochemistry 1973, 12 (21) 4217-4228
6. Royer, C. A. Biochim. Biophys. Acta 2002, 1595 (1-2) 201-209
7. Chalikian, T. V.; Macgregor, R. B., Jr. J. Mol. Biol. 2009, 394 (5) 834-842
8. Ando, N.; Barstow, B.; Baase, W. A.; Fields, A.; Matthews, B. W.; Gruner, S. M. Biochemistry 2008, 47 (42) 11097-11109
9. Collins, M. D.; Hummer, G.; Quillin, M. L.; Matthews, B. W.; Gruner, S. M. Proc. Natl. Acad. Sci. U.S.A. 2005, 102 (46) 16668-16671
10. Frye, K. J.; Royer, C. A. Protein Sci. 1998, 7 (10) 2217-2222
11. Lassalle, M. W.; Yamada, H.; Morii, H.; Ogata, K.; Sarai, A.; Akasaka, K. Proteins 2001, 45 (1) 96-101
12. Brun, L.; Isom, D. G.; Velu, P.; Garcia-Moreno, B.; Royer, C. A. Biochemistry 2006, 45 (11) 3473-3480
13. Herberhold, H.; Winter, R. Biochemistry 2002, 41 (7) 2396-2401
14. Jacob, M. H.; Saudan, C.; Holtermann, G.; Martin, A.; Perl, D.; Merbach, A. E.; Schmid, F. X. J. Mol. Biol. 2002, 318 (3) 837-845
15. Kitahara, R.; Royer, C.; Yamada, H.; Boyer, M.; Saldana, J. L.; Akasaka, K.; Roumestand, C. J. Mol. Biol. 2002, 320 (3) 609-628
16. Mei, G.; Di, V. A.; Campeggi, F. M.; Gilardi, G.; Rosato, N.; De, M. F.; Finazzi-Agro, A. Eur. J. Biochem. 1999, 265 (2) 619-626
17. Mohana-Borges, R.; Silva, J. L.; Ruiz-Sanz, J.; de Prat-Gay, G. Proc. Natl. Acad. Sci. U.S.A. 1999, 96 (14) 7888-7893
18. Sasahara, K.; Nitta, K. Protein Sci. 1999, 8 (7) 1469-1474
19. Myers, J. K.; Pace, C. N.; Scholtz, J. M. Protein Sci. 1995, 4 (10) 2138-2148
20. Damjanovic, A.; Garcia-Moreno, B.; Lattman, E. E.; Garcia, A. E. Proteins 2005, 60 (3) 433-449
21. Zweifel, M. E.; Leahy, D. J.; Hughson, F. M.; Barrick, D. Protein Sci. 2003, 12 (11) 2622-2632
22. Mello, C. C.; Barrick, D. Proc. Natl. Acad. Sci. U.S.A. 2004, 101 (39) 14102-14107
23. Rouget, J. B.; Schroer, M. A.; Jeworrek, C.; Puhse, M.; Saldana, J. L.; Bessin, Y.; Tolan, M.; Barrick, D.; Winter, R.; Royer, C. A. Biophys. J. 2010, 98 (11) 2712-2721
24. van der Spoel, S.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A.; Berendsen, H. J. Comput. Chem. 2005, 98, 2712-2721
25. Kaminski, G.; Friesner, R.; Tirado-Rives, J.; Jorgensen, W. J. Phys. Chem. B 2011, 105, 6474-6487
26. Gnanakaran, S.; Garcia, A. E. Proteins 2005, 59 (4) 773-782
27. Sgourakis, N. G.; Yan, Y.; McCallum, S. A.; Wang, C.; Garcia, A. E. J. Mol. Biol. 2007, 368 (5) 1448-1457
28. Fiser, A.; Sali, A. Methods Enzymol. 2003, 374, 461-491
29. Berendsen, H.; Grigera, J.; Straatsma, T. J. Phys. Chem. 1987, 91, 6269-6271
30. Hess, B., Bekker, H., Berendsen, H., and Fraaije, J. J. Comput. Chem. 1997, 18, 1463-1472
31. Miyamoto, S.; Kollman, P. J. Comput. Chem. 1992, 13, 952-962
32. Essmann, U.; Perera, L.; Berkowitz, M.; Darden, T.; Lee, H.; Pedersen, L. J. Chem. Phys. 1995, 103, 8577-8593
33. Hoover, W. Phys. Rev. 1985, 31, 1695-1697
34. Nosé, S. Mol. Phys. 1984, 52, 255-268
35. Nosé, S.; Klein, M. Mol. Phys. 1983, 50, 1055-1076
36. Parrinello, M.; Rahman, A. J. Appl. Phys. 1981, 52, 7182-7190
37. Till, M. S.; Ullmann, G. M. J. Mol. Model. 2010, 16 (3) 419-429
38. Ahmad, S.; Gromiha, M.; Fawareh, H.; Sarai, A. BMC Bioinform. 2004, 5, 51
39. Mello, C. C.; Bradley, C. M.; Tripp, K. W.; Barrick, D. J. Mol. Biol. 2005, 352 (2) 266-281
40. Pappenberger, G.; Saudan, C.; Becker, M.; Merbach, A. E.; Kiefhaber, T. Proc. Natl. Acad. Sci. U.S.A. 2000, 97 (1) 17-22
41. Bradley, C. M.; Barrick, D. Structure 2006, 14 (8) 1303-1312
42. Bradley, C. M.; Barrick, D. J. Mol. Biol. 2002, 324 (2) 373-386
43. Lin, L. N.; Brandts, J. F.; Brandts, J. M.; Plotnikov, V. Anal. Biochem. 2002, 302 (1) 144-160
44. Mitra, L.; Smolin, N.; Ravindra, R.; Royer, C.; Winter, R. Phys. Chem. Chem. Phys. 2006, 8 (11) 1249-1265
45. Mitra, L.; Rouget, J. B.; Garcia-Moreno, B.; Royer, C. A.; Winter, R. Chemphyschem 2008, 9 (18) 2715-2721
46. Chowdury, P. D.; Gruebele, M. J. Phys. Chem. 2009, 113, 13139-13143
47. Baldwin, R. L.; Frieden, C.; Rose, G. D. Proteins 2010, 78, 2725-2737