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Transition-state theory (TST) of solvent-assisted (SAT) and solvent-assisted (NPT) reaction mechanisms has been applied to studies of N-substituted imidazoles and 2-nitropyridines as models for activation of water by the dioxygen molecule in enzyme-catalyzed reactions. Transition-state theory has been applied to examine the nature of the transition states involved in SAT processes. Kinetic features of the transition states in reaction between mixtures of imidazole and 2-methylimidazole have been examined. The variation in calculated dissociation energies of the transition states with solvent composition is consistent with experimental observations of solvent-assisted decomposition of N-alkyl-substituted imidazoles. Similarly, for the isomerization and hydrogen-transfer reactions of 2-nitropyridine, a series of more sophisticated models of associative reactions have been developed. The transition-state theory on which the modeling is based has been validated by analysis of solvent-assisted decomposition of 5-nitroimidazole and 5-methoxyimidazole in heptane-water solvent mixtures. Copyright 2005 Elsevier Ltd.
This article reviews the available evidence regarding the existence and properties of cooperativity in the free-energy landscape of biological macromolecules. The existence of a single transition state, corresponding to the native state of macromolecules, and a single energy landscape, corresponding to the native state ensemble, has been considered to be good approximations for the free-energy landscape of macromolecules for a long time. During the past decade, however, studies of protein folding, in which changes in quenched-molecular-dynamics simulations have become possible, have caused interest to revive the question of the existence and properties of the highly cooperative transition state in the free energy landscape. Recent data from protein kinetics indicate that the transition state has four nonequivalent states, separated by high free-energy barriers. There is experimental evidence that the noncompact transition state ensembles are formed in the unfolded states of amyloid peptides. Copyright 2005 Elsevier Ltd.
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