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ACS chemical biology, ISSN 1554-8929, 01/2013, Volume 8, Issue 1, pp. 71 - 81
Enzymes achieve their transition states by dynamic conformational searches on the femtosecond to picosecond time scale... 
Life Sciences & Biomedicine | Biochemistry & Molecular Biology | Science & Technology | Enzymes - chemistry | HIV Protease Inhibitors - pharmacology | HIV Protease - drug effects | Models, Biological | Drug Design | Indinavir - pharmacology | Models, Molecular | HIV Protease Inhibitors - chemistry | HIV Protease - chemistry | Kinetics | Indinavir - chemistry | Index Medicus | Transition state analysis—the process of measuring intrinsic kinetic isotope effects at sufficient atomic positions to permit reconstruction of a transition state wave function by computational matching of all isotope effects to a quantum chemistry-derived transition state | Dynamic barrier crossing—reactants aligned in the catalytic site by the slow conformational change are subjected to local, fast interactions with catalytic site groups moving on the fsec time scale. When the interactions are optimized by simultaneous chance motion, the barrier to the reaction falls, the transition state is reached and barrier crossing (chemical reaction) can occur | Transition state—the traditional description is a one-dimensional energetic description: the point on the reaction coordinate profile of highest energy relative to substrate | Intrinsic kinetic isotope effects—kinetic isotope effects directly from the chemical step with all obscuring effects removed. Intrinsic kinetic isotope effects report on the bond vibrational status of the labeled reactant atom at the transition state | Transition state analogue—a chemically stable molecule with features of bond lengths, angles and electron density at the van der Waals surface to resemble the actual transition state more closely than it does the reactant. Faithful mimics of enzymatic transition states bind more tightly than substrates by orders of magnitude | Heavy enzyme—enzyme with isotopically substituted atoms to increase the protein mass and thereby decrease the bond vibrational frequency of the protein. Substitution with 2H, 13C and 15N alters mass but not electrostatics according to the Born-Oppenheimer approximation | Transition state structure—a static chemical model of the bond lengths, angles and electron density at the van der Waals surface of the reactant at the instant of the transition state. The transition state structure has a lifetime on the fsec timescale and has equal probability of partitioning to reactant or product | Kinetic isotope effects—the experimentally observed change in reaction rate caused by a specific isotopic substitution in a reactant substrate of the enzyme. Kinetic isotope effects are largest for atoms near the bonds being broken at the transition state but can be partly or fully hidden by kinetic effects obscuring the chemical step | Slow protein conformational changes—enzymes undergo loop, flap and domain motions to bind reactants and release products. These slow conformational changes are necessary steps in an enzymatic catalytic cycle but are too slow to couple to transition state formation
Journal Article
Journal Article
Proceedings of the National Academy of Sciences - PNAS, ISSN 1091-6490, 12/2009, Volume 107, Issue 2, pp. 715 - 720
Journal Article
Journal of the American Chemical Society, ISSN 0002-7863, 12/2012, Volume 134, Issue 49, pp. 19953 - 19956
.... Conformational transitions in RNA molecules offer an important way to regulate their biological functions... 
Nucleic Acid Conformation | RNA - chemistry | G-Quadruplexes | Usage | Helix-loop-helix motif | RNA | Protein folding | Conformational analysis | Genetic aspects | Research | Structure | Gene expression | Index Medicus | Communication
Journal Article