title: Entropic mechanism of allosteric communication in conformational transitions of dihydrofolate reductase.
abstract: The mechanism of allosteric conformational transitions of Escherichia coli dihydrofolate reductase (DHFR) is investigated theoretically by applying a newly developed coarse-grained model. Functional forms of interaction potentials in the model depend on the local structural environments around those interactions to represent the many-residue effects due to atomic packing in each local region, and hence, this model is called "the chameleon model". The chameleon model consistently describes the free-energy landscape of two conformational transitions in the catalytic cycle of DHFR, which we call conformational transition 1 (CT1) and conformational transition 2 (CT2); CT1 is accompanied by the hydride transfer reaction, and CT2 is accompanied by the product ligand release. The transition state of CT1 is entropically stabilized by the disordering of loops at the peripheral regions of the protein, which enhances the positively correlated fluctuations at the center part of the protein, showing that the allosteric communication between distant regions through the central region is intrinsically associated with the entropic stabilization of the transition state. The transition state of CT2 is entropically stabilized through the mechanism that enhances the breathing motion of two domains, showing that the difference in the distribution of interactions brings about the difference in the transition mechanism between CT1 and CT2. The chameleon model opens a way to consistently describe the dynamical energy landscape of enzymatic reactions.
authors.affiliation: Department of Computational Science and Engineering and ‡Department of Applied Physics, Nagoya University , Nagoya 464-8603, Japan.
authors.forename: Tomoki P
authors.initials: TP
authors.lastname: Terada
authors.forename: Toru
authors.initials: T
authors.lastname: Kimura
authors.forename: Masaki
authors.initials: M
authors.lastname: Sasai
mesh_terms: D000494:Allosteric Regulation; D019277:Entropy; D004926:Escherichia coli / Q000201:enzymology; D008958:Models, Molecular; D009249:NADP / Q000737:chemistry / Q000378:metabolism; D017434:Protein Structure, Tertiary; D013762:Tetrahydrofolate Dehydrogenase / Q000737:chemistry* / Q000378:metabolism
chemical_list: D009249:NADP; D013762:Tetrahydrofolate Dehydrogenase