Reconciling Mediating and Slaving Roles of Water in Protein Conformational Dynamics

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Zhao, Li ^a   Li, Wenzhao ^a   Tian, Pu ^a  

^a JILIN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BARSTAR; WATER;

ARTICLE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CORRELATION COEFFICIENT; ENERGY; MOLECULAR DYNAMICS; POTENTIAL ENERGY SURFACE ROUGHNESS; PROBABILITY; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN SELF ENERGY; PROTEIN WATER INTERACTION ENERGY; STATISTICAL ANALYSIS; STRUCTURE ANALYSIS; SURFACE PROPERTY; TIME SERIES ANALYSIS; VALIDATION PROCESS;

BACTERIAL PROTEINS; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; TIME FACTORS; WATER;

EID: 84876154922     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0060553     Document Type: Article

References (37)

1. Karplus M, Kuriyan J, (2005) Molecular dynamics and protein function. Proceedings of the National Academy of Sciences of the United States of America 102: 6679-85.
2. Agarwal PK, (2005) Role of protein dynamics in reaction rate enhancement by enzymes. Journal of the American Chemical Society 127: 15248-56.
3. Henzler-Wildman K, Kern D, (2007) dynamic personalities of proteins. Nature 450: 964-972.
4. Borreguero JM, He J, Meilleur F, Weiss KL, Brown CM, et al. (2011) Redox-promoting protein motions in rubredoxin. The journal of physical chemistry B 115: 8925-36.
5. Tokuriki N, Tawfik DS, (2009) Protein dynamism and evolvability. Science (New York, NY) 324: 203-7.
6. Frauenfelder H, Sligar S, Wolynes P, (1991) The energy landscapes and motions of proteins. Science 254: 1598-1603.
7. Chang CW, He TF, Guo L, Stevens JA, Li T, et al. (2010) Mapping solvation dynamics at the function site of avodoxin in three redox states. Journal of the American Chemical Society 132: 12741-7.
8. Jha A, Ishii K, Udgaonkar JB, Tahara T, Krishnamoorthy G (2010) Exploration of the Correlation between Solvation Dynamics and Internal Dynamics of a Protein. Biochemistry: 397-408.
9. Kwon OH, Yoo TH, Othon CM, Van Deventer JA, Tirrell DA, et al. (2010) Hydration dynamics at fluorinated protein surfaces. Proceedings of the National Academy of Sciences of the United States of America 107: 17101-6.
10. Scorciapino MA, Robertazzi A, Casu M, Ruggerone P, Ceccarelli M, (2010) Heme proteins: the role of solvent in the dynamics of gates and portals. Journal of the American Chemical Society 132: 5156-63.
11. Zhang L, Yang Y, Kao YT, Wang L, Zhong D, (2009) Protein hydration dynamics and molecular mechanism of coupled water-protein uctuations. Journal of the American Chemical Society 131: 10677-91.
12. Zhang L, Wang L, Kao YT, Qiu W, Yang Y, et al. (2007) Mapping hydration dynamics around a protein surface. Proceedings of the National Academy of Sciences of the United States of America 104: 18461-6.
13. Mattos C, (2002) Protein-water interactions in a dynamic world. Trends in biochemical sciences 27: 203-8.
14. Ansari A, Jones CM, Henry ER, Hofrichter J, Eaton WA, (1992) The role of solvent viscosity in the dynamics of protein conformational changes. Science (New York, NY) 256: 1796-8.
15. Barron LD, Hecht L, Wilson G, (1997) New Concepts in Biochemistry The Lubricant of Life: A Proposal That Solvent Water Promotes Extremely Fast Conformational Fluctuations in Mobile Heteropolypeptide Structure. October 36: 0-4.
16. Fenimore PW, Frauenfelder H, McMahon BH, Parak FG, (2002) Slaving: solvent uctuations dominate protein dynamics and functions. Proceedings of the National Academy of Sciences of the United States of America 99: 16047-51.
17. Frauenfelder H, Fenimore PW, Chen G, McMahon BH, (2006) Protein folding is slaved to solvent motions. Proceedings of the National Academy of Sciences of the United States of America 103: 15469-72.
18. Frauenfelder H, Fenimore PW, Young RD, (2007) Protein dynamics and function: insights from the energy landscape and solvent slaving. IUBMB life 59: 506-12.
19. Samuni U, Roche CJ, Dantsker D, Friedman JM, (2007) Conformational dependence of hemoglobin reactivity under high viscosity conditions: the role of solvent slaved dynamics. Journal of the American Chemical Society 129: 12756-64.
20. Frauenfelder H, Chen G, Berendzen J, Fenimore PW, Jansson H, et al. (2009) A unified model of protein dynamics. Proceedings of the National Academy of Sciences of the United States of America 106: 5129-34.
21. Sundaralingam M, Sekharudu YC, (1989) Water-inserted alpha-helical segments implicate reverse turns as folding intermediates. Science (New York, NY) 244: 1333-7.
22. Vitkup D, Ringe D, Petsko GA, Karplus M, (2000) Solvent mobility and the protein glass transition. Nature Structural Biology 7: 1-5.
23. Tarek M, Tobias D, (2002) Role of Protein-Water Hydrogen Bond Dynamics in the Protein Dynamical Transition. Physical Review Letters 88: 1-4.
24. Papoian GA, Ulander J, Eastwood MP, Luthey-Schulten Z, Wolynes PG, (2004) Water in protein structure prediction. Proceedings of the National Academy of Sciences of the United States of America 101: 3352-7.
25. Zong C, Papoian GA, Ulander J, Wolynes PG, (2006) Role of topology, nonadditivity, and water-mediated interactions in predicting the structures of alpha/beta proteins. Journal of the American Chemical Society 128: 5168-76.
26. Wu S, Zhuravlev PI, Papoian GA, (2008) High resolution approach to the native state ensemble kinetics and thermodynamics. Biophysical journal 95: 5524-32.
27. Materese CK, Goldmon CC, Papoian GA, (2008) Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions. Proceedings of the National Academy of Sciences of the United States of America 105: 10659-64.
28. Oleinikova A, Smolin N, Brovchenko I, Geiger A, Winter R, (2005) Formation of spanning water networks on protein surfaces via 2D percolation transition. The journal of physical chemistry B 109: 1988-98.
29. Hartley RW, (1988) Barnase and barstar: Expression of its cloned inhibitor permits expression of a cloned ribonuclease. Journal of Molecular Biology 202: 913-915.
30. Nelson ED, Grishin NV, (2008) Folding domain B of protein A on a dynamically partitioned free energy landscape. Proceedings of the National Academy of Sciences of the United States of America 105: 1489-93.
31. Miller TF, Vanden-Eijnden E, Chandler D, (2007) Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain. Proceedings of the National Academy of Sciences of the United States of America 104: 14559-64.
32. Henzler-Wildman K, Lei M, Thai V, Kerns SJ, Karplus M, et al. (2007) A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. nature 450: 913-916.
33. Schinkel JE, Downer NW, Rupley JA, (1985) Hydrogen exchange of lysozyme powders. Hydration dependence of internal motions. Biochemistry 24: 352-66.
34. Pérez J, Zanotti JM, Durand D, (1999) Evolution of the internal dynamics of two globular proteins from dry powder to solution. Biophysical journal 77: 454-69.
35. Paciaroni A, Orecchini A, Cinelli S, Onori G, Lechner R, et al. (2003) Protein dynamics on the picosecond timescale as affected by the environment: a quasielastic neutron scattering study. Chemical Physics 292: 397-404.
36. Mamontov E, Chu XQ, (2012) Water-protein dynamic coupling and new opportunities for probing it at low to physiological temperatures in aqueous solutions. Physical chemistry chemical physics: PCCP 14: 11573-88.
37. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, et al. (2005) Scalable molecular dynamics with namd. Journal of Computational Chemistry 26: 1781-1802.