Modeling Protein–Protein and Protein–Nucleic Acid Interactions: Structure, Thermodynamics, and Kinetics
作者： Huan-Xiang Zhou , Sanbo Qin , Harianto Tjong
DOI: 10.1016/S1574-1400(08)00004-2
关键词:
摘要: Abstract We review recent progress in modeling the structures, binding affinities, and rates of protein–protein protein–nucleic acid complexes. Limitations promises a wide range computational approaches are presented.
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Michael J Law, Michael E Linde, Eric J Chambers, Chris Oubridge, Phinikoula S Katsamba, Lennart Nilsson, Ian S Haworth, Ite A Laird-Offringa, The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA Nucleic Acids Research. ,vol. 34, pp. 275- 285 ,(2006) , 10.1093/NAR/GKJ436
Federico Fogolari, Raffaella Ugolini, Henriette Molinari, Paolo Viglino, Gennaro Esposito, Simulation of electrostatic effects in Fab-antigen complex formation. FEBS Journal. ,vol. 267, pp. 4861- 4869 ,(2000) , 10.1046/J.1432-1327.2000.01542.X
Gideon Schreiber, Tzvia Selzer, Shira Albeck, Rational design of faster associating and tighter binding protein complexes Nature Structural & Molecular Biology. ,vol. 7, pp. 537- 541 ,(2000) , 10.1038/76744
Jaya Bhatnagar, Jack H. Freed, Brian R. Crane, Rigid body refinement of protein complexes with long-range distance restraints from pulsed dipolar ESR. Methods in Enzymology. ,vol. 423, pp. 117- 133 ,(2007) , 10.1016/S0076-6879(07)23004-6
Huan Xiang. Zhou, Kinetics of diffusion-influenced reactions studied by Brownian dynamics The Journal of Physical Chemistry. ,vol. 94, pp. 8794- 8800 ,(1990) , 10.1021/J100388A010
Ryan J. Darling, Uma Kuchibhotla, Wolfgang Glaesner, Radmila Micanovic, Derrick R. Witcher, John M. Beals, Glycosylation of erythropoietin affects receptor binding kinetics: role of electrostatic interactions. Biochemistry. ,vol. 41, pp. 14524- 14531 ,(2002) , 10.1021/BI0265022
Jessica M. J. Swanson, John Mongan, J. Andrew McCammon, Limitations of atom-centered dielectric functions in implicit solvent models. Journal of Physical Chemistry B. ,vol. 109, pp. 14769- 14772 ,(2005) , 10.1021/JP052883S
Alexander Spaar, Christian Dammer, Razif R. Gabdoulline, Rebecca C. Wade, Volkhard Helms, Diffusional encounter of barnase and barstar. Biophysical Journal. ,vol. 90, pp. 1913- 1924 ,(2006) , 10.1529/BIOPHYSJ.105.075507
Jessica M. J. Swanson, Jason A. Wagoner, Nathan A. Baker, J. A. McCammon, Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies: Lessons Learned with Atom-Centered Dielectric Functions. Journal of Chemical Theory and Computation. ,vol. 3, pp. 170- 183 ,(2007) , 10.1021/CT600216K
Ramzi Alsallaq, Huan-Xiang Zhou, Prediction of protein-protein association rates from a transition-state theory. Structure. ,vol. 15, pp. 215- 224 ,(2007) , 10.1016/J.STR.2007.01.005