[Enzymes: Conformational Dynamics and Catalytic Power]

By

Acknowledgement

I would take this opportunity to thank my research supervisor, family and friends for their support and guidance without which this research would not have been possible.

DECLARATION

I, [type your full first names and surname here], declare that the contents of this dissertation/thesis represent my own unaided work, and that the dissertation/thesis has not previously been submitted for academic examination towards any qualification. Furthermore, it represents my own opinions and not necessarily those of the University.

Signed __________________ Date _________________

Table of Contents

ACKNOWLEDGEMENTII

DECLARATIONIII

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

Protein Conformation8

CHAPTER 3: TIME-SCALE OF DYNAMICS IN PROTEINS12

Model potential energy functions12

Comparison with motions in other dense materials12

Fast motions13

Single group motions14

Rapid Motions15

Mechanistic Roles Of Enzymeconformational Dynamics17

A Mechanistic Model for Lid Dynamics17

Collective Contributions To Local Motions19

Side Chain Rotation22

CHAPTER 4: CONFORMATIONAL DYNAMICS LOWER ACTIVATION ENERGY24

REFERENCES29

APPENDICES38

Chapter 1: Introduction

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 ...