[Enzymes: Conformational Dynamics and Catalytic Power]
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Table of Contents
CHAPTER 1: INTRODUCTION1
Enzyme Dynamics During Catalysis2
Linkage Between Dynamics and Catalysis in a Thermophilic-Mesophilic Enzyme Pair2
Instrinsic Motions Along an Enzymatic Reaction Trajectory3
A Perspective on Enzyme Catalysis4
Enzyme millisecond conformational dynamics4
CHAPTER 2: STRUCTURAL CONFORMERS AND THE ORIGIN OF PROTEIN DYNAMICS7
Conformational Dynamics Of Proteins7
CHAPTER 3: TIME-SCALE OF DYNAMICS IN PROTEINS12
Model potential energy functions12
Comparison with motions in other dense materials12
Single group motions14
Mechanistic Roles Of Enzymeconformational Dynamics17
Enzymes play a key role in almost all biological processes, accelerating a variety of metabolic reactions as well as controlling energy transduction, transcription and translation of genetic information, and signaling. (Berkowitz 2003 : 120) They possess the remarkable capacity to accelerate reactions by many orders of magnitude compared to their uncatalyzed counterparts, making feasible crucial processes that would otherwise not occur on biologically relevant timescales. Thus, there is broad interest in understanding the catalytic power of enzymes on a molecular level. Several proposals have been put forward to try to explain this phenomenon, and one that has rapidly gained momentum in recent years is the idea that enzyme dynamics somehow contributes to catalysis. (Mc Cammon 2006 : 29)
Enzymes play fundamental roles in almost all life processes. They accelerate a great variety of metabolic reactions and they control signaling, energy transduction, and the transcription and translation of genetic information. Their ability to catalyze reactions by many orders of magnitude allows cells to carry out reactions that otherwise would not occur on biologically useful timescales. There is, therefore, broad interest in understanding the origin of this catalytic power on a molecular level. (Levy 2002b : 88)
Although many proposals have been put forward to rationalize the catalytic power of enzymes and some have accounted for the observed catalytic effects, we do not yet have a consensus about the relative importance of different factors. One of the most intriguing proposals is associated with the idea that dynamical effects contribute to enzyme catalysis. (Careri 2009 : 154)
The general idea that dynamical effects play a major role in enzyme catalysis dates back at least 25 years. It has gained momentum since the mid-nineties and continues to attract considerable attention. Although this idea has been challenged, it clearly has major appeal as is seen from its frequent appearance in high impact journals. (Carrell 2007: 134-138)The situation in the field is still in a state of flux, where, in some cases, the dynamical proposal is stated more ...