- Post Doctoral
MIT Unit Affiliation:
- Chemical Engineering
Post Doc Sponsor / Advisor:
Date PhD Completed:
Top 3 Areas of Expertise:
Expected End Date of Post Doctoral Position:
I am interested in how a combination of quantum mechanics and classical physics can enhance our understanding of catalysis and specifically how enzymes, nature's catalysts, can produce such high catalytic rate enhancement. I want to further understand the mechanistic features of complex catalysts and to facilitate and develop tools for the computationally driven design of new catalysts.
In addition to employing new, accelerated quantum-mechanical atomistic simulations tools to enable predictive study and design of catalysts, I am also interested in understanding how electronic structure properties of enzymes inform their function.
There exists a concerted and continual effort to simulate systems of genuine biological interest to greater accuracy with methods of increasing transferability. More accurate descriptions of these systems at a truly atomistic and electronic level are irrevocably changing our understanding of biochemical processes. Broadly, classical techniques do not employ enough rigour, while conventional quantum mechanical approaches are too com- putationally expensive for systems of the requisite size. Linear-scaling density-functional theory (DFT) is an accurate method that can apply the predictive power of quantum mechanics to the system sizes required to study problems in enzymology. This dissertation presents methodological developments and protocols, including best practice, for accurate preparation and optimisation, combined with proof-of-principle calculations demonstrating reliable results for a range of small molecule and large biomolecular systems. Previous authors have shown that DFT calculations yield an unphysical, negligible energy gap between the highest occupied and lowest unoccupied molecular orbitals for proteins and large water clusters, a characteristic reproduced in this dissertation. However, whilst others use this phenomenon to question the applicability of Kohn-Sham DFT to large systems, it is shown within this dissertation that the vanishing gap is, in fact, an electro- static artefact of the method used to prepare the system. Furthermore, practical solutions are demonstrated for ensuring a physical gap is maintained upon increasing system size. Harnessing these advances, the first application using linear-scaling DFT to optimise sta- tionary points in the reaction pathway for the Bacillus subtilis chorismate mutase (CM) enzyme is made. Averaged energies of activation and reaction are presented for the rear- rangement of chorismate to prephenate in CM and in water, for system sizes comprising up to 2000 atoms. Compared to the uncatalysed reaction, the calculated activation barrier is lowered by 10.5 kcal/mol in the presence of CM, in good agreement with experiment. In addition, a detailed analysis of the interactions between individual active-site residues and the bound substrate is performed, predicting the significance of individual enzyme sidechains in CM catalysis. These proof-of-principle applications of powerful large-scale DFT methods to enzyme catalysis will provide new insight into enzymatic principles from an atomistic and electronic perspective.
5 Recent Papers:
"Large-scale density functional theory transition state searching in enzymes", G. Lever, D. J. Cole, R. Lonsdale, K. E. Ranaghan, D. J. Wales, A. J. Mulholland, C. -K. Skylaris and M. C. Payne, Submitted to J. Phys. Chem. Lett. (2014).
"Electrostatic considerations affecting the calculated HOMO-LUMO gap in protein molecules", G. Lever, D. J. Cole, N. D. M. Hine, P. D. Haynes, and M. C. Payne - J. Phys.: Condens. Matter, 25, 152101, (2013) (Fast Track Communication). Chosen for inclusion in IOPselect collection. Labtalk article also available. 6 citations
"Model system for controlling strain in silicon at the atomic scale", P. Studer, S.R. Schofield, G. Lever, D.R. Bowler, C.F. Hirjibehedin and N.J. Curson - Phys. Rev. B, 84, 041306, (2011). 4 citations
"A Uniformly Derived Catalogue of Exoplanets from Radial Velocities", M.D.J. Hollis, S.T. Balan, G. Lever and O. Lahav - Mon. Not. R. Astron. Soc., 423, 2800 (2012). 1 citation
"Uniformly Derived Orbital Parameters of Exo-Planets using EXOFIT", S.T. Balan, G. Lever and O. Lahav -Astronomical Society of the Pacific Conference Series, 430, 122, (2010).