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Dynamically-coupled enzyme catalysis: towards a step change in our understanding of enzyme catalysed reactions

Reference	BB/F000537/1
Principal Investigator / Supervisor	Professor Nigel Scrutton
Co-Investigators / Co-Supervisors	Dr Samuel de Visser, Professor Peter Gardner, Professor David Leys, Professor Jason Micklefield, Professor Klaus Muller-Dethlefs, Professor Michael Sutcliffe
Institution	The University of Manchester
Department	Life Sciences
Funding type	Research
Value (£)	2,402,423
Status	Completed
Type	Research Grant
Start date	01/01/2008
End date	31/10/2013
Duration	70 months

Abstract

The hallmarks of catalysis by enzymes are selectivity, specificity, and speed. However, despite their central role, the physical basis of the enormous catalytic power of enzymes is not well understood. It is generally acknowledged that dynamical processes are important, but to date detailed analysis of the role of dynamics in modulating the catalytic properties of enzymes has been difficult. Tunneling is also now recognised as a potentially important feature of enzyme catalysed reactions. Tunneling has been treated through the introduction of a tunneling correction to transition state theory. However, the examination of the temperature dependence of the kinetic isotope effects of several enzymatic hydrogen transfer reactions has led to a collapse of the semi-classical model for hydrogen tunnelling and new models are being developed to explain these observations, such as environmentally coupled tunnelling in which protein motions are proposed to drive hydrogen tunneling. It is central to our understanding of enzyme catalysis to test these models further and contrast them with potential alternatives. It is also important to understand dynamical processes at the atomic level that couple to the reaction coordinate. In this application we will use established and emerging methods to tackle these difficult problems. By uniting experiment with theory and simulation we aim to provide a complete description of catalytic processes and to provide atomic level and quantitative understanding of enzyme reactions. We seek to pull away from the semi-classical transition state theory paradigm, and to provide new types of experimental data that might (i) establish alternative models of catalysis and (ii) explicitly recognise protein motion and tunnelling as key components of enzyme chemistry. Our ultimate aim is to provide a quantitative account of biological catalysis using alternative physical frameworks supported by state-of-the-art experimental, computation and theoretical study.

Summary

The physical basis of the catalytic power of enzymes remains contentious despite sustained and intensive research efforts. Our knowledge of enzyme catalysis is predominantly descriptive gained from traditional protein crystallography and solution studies. Our ultimate goal is to introduce a step change in our understanding of catalysis by developing a complete and quantitative picture of dynamic catalytic processes in enzyme systems by adopting a synergistic and multidisciplinary approach, embracing ideas we have spearheaded from our work on quantum mechanical tunnelling effects, linked to protein dynamics, for enzyme-catalysed H-transfer reactions. The key question to be addressed is 'How do enzymes achieve high catalytic rates?' and 'What is the appropriate physical framework to model these reactions?'. Rate enhancements of up to 10 to the power 21 have been reported, but the physical basis of this catalytic power remains contentious, despite sustained and intensive research efforts. The role of protein motions in enzyme catalysis -- both in classical and quantum mechanical transfers -- is hotly debated. The very presence and identity of motions, coupled to catalysis, is currently one of the most important unanswered questions in enzyme catalysis, yet one of the most difficult to address experimentally. In recent years, we have established a multidisciplinary team, and have been at the fore of developments in this area, particularly in providing key experimental and computational evidence that supports full tunnelling models for enzyme-catalysed hydrogen transfer. Uniquely in this field, our research team has relied on a strong interplay between high resolution/time-resolved structural analysis, detailed computational simulations, chemical biology and fast reaction kinetics to develop, and provide experimental support for, new theoretical frameworks for enzyme catalysis. This application is built on these strengths and seeks to push new boundaries that will provide deeper understanding of dynamic processes/from millisecond to sub-picosecond/that drive enzyme catalysis. Hydrogen transfer -- an essential component of most biological reactions -- is a quantum problem. A crucial question of great current interest is how enzymes modulate the quantum dynamics of hydrogen transfer to achieve their outstanding catalytic properties. Despite recent progress, a detailed picture of the atomic motions accompanying the classical and quantum mechanical descriptions of chemical reactions has not been forthcoming. This is a major challenge that requires a multidisciplinary approach embracing structural biology, computational and physical methods. Thus, in this programme we will develop cutting-edge experimental and theoretical approaches to access the nature of motions coupled to catalysis. This also requires detailed understanding of all chemical aspects of the catalytic cycle. Moreover, it requires the development of new experimental approaches to investigate fast promoting motions in catalysis, which poses a major technical challenge to the field.

Committee	Closed Committee - Biomolecular Sciences (BMS)
Research Topics	Industrial Biotechnology, Structural Biology
Research Priority	X – Research Priority information not available
Research Initiative	Longer and Larger Grants (LoLas) [2007-2015]
Funding Scheme	X – not Funded via a specific Funding Scheme

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