Protein loop dynamics are complex and depend on the motions of the whole protein

Entropy

Volumn 14, Issue 4, 2012, Pages 687-700

  Zimmermann, Michael T ^a   Jernigan, Robert L ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

Correlated motions; Elastic network models; Molecular dynamics; Protein dynamics; Protein loops

Indexed keywords

EID: 84860688588     PISSN: None     EISSN: 10994300     Source Type: Journal    
DOI: 10.3390/e14040687     Document Type: Article

References (27)

1. Jacobson, H.; Stockmayer, W.H. Intramolecular reaction in polycondensations. I. The theory of linear systems. J. Chem. Phys. 1950, 18, 1600-1606.
2. Flory, P.J.; Semlyen, J.A. Macrocyclization equilibrium constants and the statistical configuration of poly (dimethylsiloxane) chains. J. Am. Chem. Soc. 1966, 88, 3209-3212.
3. Hu, X.; Stebbins, C.E. Dynamics of the WPD loop of the Yersinia protein tyrosine phosphatase. Biophys. J. 2006, 91, 948-956.
4. Chirikjian, G.S. Modeling loop entropy. Methods Enzymol. 2011, 487, 99-132.
5. Zhou, H. Loops, linkages, rings, catenanes, cages, and crowders: Entropy-based strategies for stabilising proteins. Acc. Chem. Res. 2004, 37, 123-130.
6. Baron, R.; McCammon, J.A. (Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding. Chemphyschem 2008, 9, 983-988.
7. Srinivasan, J.; Miller, J.; Kollman, P.A.; Case, D.A. Continuum solvent studies of the stability of RNA hairpin loops and helices. J. Biomol. Struct. Dyn. 1998, 16, 671-682.
8. Mihailescu, M.; Meirovitch, H. Entropy and free energy of a mobile loop based on the crystal structures of the free and bound proteins. Entropy 2010, 12, 1946-1974.
9. General, I.J.; Meirovitch, H. Relative stability of the open and closed conformations of the active site loop of streptavidin. J. Chem. Phys. 2011, 134, 025104.
10. General, I.J.; Dragomirova, R.; Meirovitch, H. New method for calculating the absolute free energy of binding: The effect of a mobile loop on the avidin/biotin complex. J. Phys. Chem. B 2011, 115, 168-175.
11. Skliros, A.; Zimmermann, M.T.; Chakraborty, D.; Saraswathi, S.; Katebi, A.R.; Leelananda, S.P.; Kloczkowski, A.; Jernigan, R.L. The importance of slow motions for protein functional loops. Phys. Biol. 2012, 9, 014001.
12. Atilgan, A.R.; Durell, S.R.; Jernigan, R.L.; Demirel, M.C.; Keskin, O.; Bahar, I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 2001, 80, 505-515.
13. Meyer, T.; D'Abramo, M.; Hospital, A.; Rueda, M.; Ferrer-Costa, C.; Perez, A.; Carrillo, O.; Camps, J.; Fenollosa, C.; Repchevsky, D.; et al. MoDEL (Molecular Dynamics Extended Library): A database of atomistic molecular dynamics trajectories. Structure 2010, 18, 1399-1409.
14. Kabsch, W.; Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22, 2577-2637.
15. Zimmermann, M.T.; Leelananda, S.P.; Gniewek, P.; Feng, Y.; Jernigan, R.L.; Kloczkowski, A. Free energies of coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models. J. Struct. Funct. Genomics 2011, 12, 137-147.
16. Zimmermann, M.T.; Leelananda, S.P.; Kloczkowski, A.; Jernigan, R.L. Combining statistical potentials with dynamics based entropies improves selection from protein decoys and docking poses. J. Phys. Chem. 2012, in press.
17. Zimmermann, M.T.; Kloczkowski, A.; Jernigan, R.L. MAVENs: Motion analysis and visualization of elastic networks and structural ensembles. BMC Bioinformatics 2011, 12, 264.
18. Tirion, M.M. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 1996, 77, 1905-1908.
19. Jolliffe, I.T. Principal Component Analysis; Springer-Verlag: New York, NY, USA, 2002.
20. Hayward, S.; de Groot, B.L. Normal modes and essential dynamics. In Molecular Modeling of Proteins; Humana Press: Totowa, NJ, USA, 2008; p. 89-106.
21. Case, D.A.; Cheatham, T.E., III; Darden, T.; Gohlke, H.; Luo, R.; Merz, K.M., Jr.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R.J. The Amber biomolecular simulation programs. J. Comput. Chem. 2005, 26, 1668-1688.
22. Ichiye, T.; Karplus, M. Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins 1991, 11, 205-217.
23. Leo-Macias, A.; Lopez-Romero, P.; Lupyan, D.; Zerbino, D.; Ortiz, A.R. An analysis of core deformations in protein superfamilies. Biophys. J. 2005, 88, 1291-1299.
24. MacKerell, A.D., Jr.; Banavali, N.; Foloppe, N. Development and current status of the CHARMM force field for nucleic acids. Biopolymers 2000, 56, 257-265.
25. MacKerell, A.D. Jr.; Feig, M.; Brooks, C.L., III Improved treatment of the protein backbone in empirical force fields. J. Am. Chem. Soc. 2004, 126, 698-699.
26. Cerutti, D.S.; Freddolino, P.L.; Duke, R.E., Jr.; Case, D.A. Simulations of a protein crystal with a high resolution X-ray structure: Evaluation of force fields and water models. J. Phys. Chem. B 2010, 114, 12811-12824.
27. Rueda, M.; Ferrer-Costa, C.; Meyer, T.; Perez, A.; Camps, J.; Hospital, A.; Gelpi, J.L.; Orozco, M. A consensus view of protein dynamics. Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 796-801.