Loops in proteins can be modeled as worm-like chains

Journal of Physical Chemistry B

Volumn 105, Issue 29, 2001, Pages 6763-6766

  Zhou, Huan Xiang ^a  

^a DREXEL UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SECONDARY STRUCTURE ELEMENTS (SSE);

CORRELATION METHODS; ENTROPY; MOLECULAR STRUCTURE; PROBABILITY DENSITY FUNCTION;

PROTEINS;

EID: 0035954950     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp011355n     Document Type: Article

References (22)

1. Kratky, O.; Porod, G. Rec. Trap. Chim. 1949, 68, 1106.
2. Gobush, W.; Yamawaka, H.; Stockmayer, W.H.; Magee, W.S. J. Chem. Phys. 1972, 57, 2839. Yamawaka, H.; Stockmayer, W.H. J. Chem. Phys. 1972, 57, 2843.
3. Gobush, W.; Yamawaka, H.; Stockmayer, W.H.; Magee, W.S. J. Chem. Phys. 1972, 57, 2839. Yamawaka, H.; Stockmayer, W.H. J. Chem. Phys. 1972, 57, 2843.
4. Wilhelm, J.; Frey, E. Phys. Rev. Lett. 1996, 77, 2581.
5. Nagi, A.D.; Regan, L. Folding Design 1997, 2, 67.
6. Holm, L.; Sander, C. Nucl. Acids Res. 1997, 25, 3389.
7. Berman, H.M.; Westhrook, J.; Feng, Z.; Gillíland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, N.; Bourne, P.E. Nucl. Acids Res. 2000, 28, 235.
8. Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577.
9. Zhou, H.-X. Biophys. J. 1995, 69, 2298.
10. Jacobson, H.; Stockmayer, W.H. J. Chem. Phys. 1950, 18, 1600.
11. Pace, C.N.; Grimsley, G.R.; Thomson, J.A.; Barnett, B.J. J. Biol. Chem. 1988, 263, 11820.
12. Banner, W.; Kokkinidis, M.; Tsernoglou, D. J. Mol. Biol. 1987, 196, 657.
13. 4 what is measured is the free-energy difference between the homodimer and the two unfolded subunits.
14. Chan H.S.; Dill, K.A. J. Chem. Phys. 1989, 90, 492.
15. Rief, M.M.; Gautel, F.; Oesterhelt, F.; Fernandez, J.M.; Gaub, H.E. Science 1997, 276, 1109.
16. Oberhauser, A.F.; Marszalek, P.E.; Erickson, H.P.; Fernandez, J.M. Nature 1998, 393, 181.
17. Rief, M.; Pascual, J.; Saraste, M.; Gaub, H.E. J. Mol. Biol. 1999, 286, 553.
18. Yang, G.; Cecconi, C.; Baase, W.A.; Vetter, I.R.; Breyer, W.A.; Haack, J.A.; Matthews, B.W.; Dahlquist, F.W.; Bustamante, C. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 139.
19. Doi, M.; Edwards, S.F. The Theory of Polymer Dynamics; Clarendon Press: Oxford, 1986.
20. The secondary structure elements (to which the two ends of the loop are attached) may have some influence on the persistence length. It is thus possible that the persistence length of 3.04 Å obtained on the loops collected from the protein structures may indeed be somewhat smaller than what would be obtained if the proteins are unfolded.
21. Ladurner, A.G.; Fersht, A.R. J. Mol. Biol. 1997, 273, 330.
22. Lapidus, L.J.; Eaton, W.A.; Hofrichter, J. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 7220.