Simple Energy Landscape Model for the Kinetics of Functional Transitions in Proteins Export

@article{citeulike:802619, abstract = {PMID: 16851180 It is evident that protein conformational transitions play important roles in biological machinery; however, detailed pictures of these transition processes capable of making kinetic prediction are not yet available. For a full description of these transitions, we first need to describe kinematically movements between stable states. Then, more importantly, a free energy profile associated with the conformational change needs to be obtained. Recently, a new model to describe the energy landscape of protein conformational changes was applied to the conformational transition of adenylate kinase [Miyashita, O.; Onuchic, J. N.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 1257012575]. In this model, the conformational change coupled to the ligand binding is described as a switching between two energy surfaces that correspond to ligand bound and unbound states. The nonlinearity of the protein conformational changes is described through an iterative usage of normal mode calculations. In addition, another kind of nonlinearity enters the dynamics of the conformational transitions due to cracking, or partial unfolding, which may occur during the conformational transitions. The consequences of this theoretical model are explored in greater detail. An improved model for the cracking that includes the cooperativity of the partial unfolding in analogy to nucleation is introduced.}, author = {Miyashita, Osamu and Wolynes, Peter G. and Onuchic, Jose N.}, citeulike-article-id = {802619}, citeulike-linkout-0 = {http://dx.doi.org/10.1021/jp046736q}, citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/jp046736q}, day = {1}, doi = {10.1021/jp046736q}, journal = {The Journal of Physical Chemistry B}, keywords = {activation, active-state, conformational\_changes, dynamics, energy\_landscape, kinetics, pathways}, month = {February}, number = {5}, pages = {1959--1969}, posted-at = {2009-10-28 12:45:14}, priority = {2}, title = {Simple Energy Landscape Model for the Kinetics of Functional Transitions in Proteins}, url = {http://dx.doi.org/10.1021/jp046736q}, volume = {109}, year = {2005} }

TY - JOUR ID - citeulike:802619 L3 - citeulike-article-id:802619 N2 - PMID: 16851180 It is evident that protein conformational transitions play important roles in biological machinery; however, detailed pictures of these transition processes capable of making kinetic prediction are not yet available. For a full description of these transitions, we first need to describe kinematically movements between stable states. Then, more importantly, a free energy profile associated with the conformational change needs to be obtained. Recently, a new model to describe the energy landscape of protein conformational changes was applied to the conformational transition of adenylate kinase [Miyashita, O.; Onuchic, J. N.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 1257012575]. In this model, the conformational change coupled to the ligand binding is described as a switching between two energy surfaces that correspond to ligand bound and unbound states. The nonlinearity of the protein conformational changes is described through an iterative usage of normal mode calculations. In addition, another kind of nonlinearity enters the dynamics of the conformational transitions due to cracking, or partial unfolding, which may occur during the conformational transitions. The consequences of this theoretical model are explored in greater detail. An improved model for the cracking that includes the cooperativity of the partial unfolding in analogy to nucleation is introduced. IS - 5 JF - The Journal of Physical Chemistry B EP - 1969 TI - Simple Energy Landscape Model for the Kinetics of Functional Transitions in Proteins VL - 109 SP - 1959 KW - activation KW - active-state KW - conformational_changes KW - dynamics KW - energy_landscape KW - kinetics KW - pathways AU - Miyashita, Osamu AU - Wolynes, Peter AU - Onuchic, Jose PY - 2005/02/01/ UR - http://dx.doi.org/10.1021/jp046736q ER -