QM/MM Calculations on Solvated Molecules and Enzyme Reaction Mechanisms


An understanding of the mechanisms by which protein and solvent environments influence the stability of reactants, products and transition states in biologically significant reactions is important and has a number of applications, for example, in the rational design of enzyme inhibitors as possible drugs. Combined quantum mechanical and molecular mechanical (QM/MM) methods are required for the theoretical study of enzymic reaction mechanisms. Since enzymes are solvated systems, we adopt models for the interaction of the reaction centre (QM) with both the surrounding protein and solvent medium (MM). Given access to "state of the art" computers, we can use molecular dynamics (MD) simulation techniques to obtain local free energy minima (reactant and product states) and transition states with respect to a suitably chosen set of reaction coordinates. This project focuses on assessing the utility of such free energy calculations, and the development of computationally efficient strategies together with our computer code, Molecular Orbital Programs for Simulations (MOPS), for examining the free energy changes along reaction pathways.


Principal Investigator

Peter Cummins
Biochemistry & Molecular Biology
JCSMR
ANU

Project

u51, d52

Facilities Used

VPP, PC, SC

Co-Investigators

Jill Gready
Stephen Titmuss
Biochemistry & Molecular Biology
JCSMR
ANU

Alistair Rendell
Computer Science
Faculty of Science
ANU

Ivan Rostov
ANU Supercomputer Facility
ANU

Kritsana Sagarik
School of Chemistry
Institute of Science
Suranaree University of Technology, Thailand

RFCD Codes

250601, 250602, 270108


Significant Achievements, Anticipated Outcomes and Future Work

One reaction mechanism of interest is the hydride-ion transfer in dihydrofolate reductase (DHFR). Initial free-energy gradient calculations on the hydride-ion transfer in DHFR have proved very encouraging with the characterisation of both reactant and product free-energy minima and the transition state. We have already carried out quantum chemical studies of the relative stabilities of different protonation sites of the substrates and acidic side chains in the active site of DHFR. Considerable progress has now been made in identifying protonation states in the enzyme active site, and in simulating the hydride-ion transfer step using semiempirical QM/MM methods. In addition, our recent results have shown the need to perform calculations using the more accurate ab initio or DFT methods on systems of up to 200 atoms, and possibly larger. This may also involve the use of ab initio or DFT QM/MM calculation such as Morokuma's ONIOM method implemented in the Gaussian 98 program. Future protocol development may focus on the use of multiple MD trajectories for speeding up the calculation of reaction free energies, allowing for a larger number of reaction pathways to be investigated using QM/MM methods.

Complementary to this work, we have been using ab initio quantum chemical and linear-scaling semiempirical (using the MOZYME program of J.J.P. Stewart) methods for the validation of certain aspects of the QM/MM methodology for biomolecular systems. This has led to the investigation of new approaches for improving the quality of QM/MM force-fields for simulating enzyme catalysed reactions within the semiempirical QM approximation. This has the potential to be a significant step forward in terms of both computational efficiency and reliability of the methodology, as it may allow us to perform MD simulations with ab initio QM quality force fields for the cost of semiempirical QM calculations.

 

Computational Techniques Used

The study of chemical reactions in solvated systems of biochemical interest requires large allocations of computer time. Our QM/MM computer (Fortran) code, Molecular Orbital Programs for Simulations (MOPS), is being continually developed and improved in both capability and performance. The computationally intensive terms arising from interaction between the QM and MM atoms, and between MM and MM atoms, have now been fully parallelized under the Message Passing Interface (MPI) standard. This will effectively render the QM-only part of the calculations the rate limiting step in the calculation of an MD trajectory. Work is in progress to test the effectiveness of running multiple trajectories under MPI in order to improve the efficiency of free energy calculations. These reductions should become greater for systems that are larger compared with the ones we have treated to date. The implications of such reductions in computation time are significant. We will be able to treat larger systems more accurately by both extending the cutoff for the neglect of electrostatic interactions in the MM region and increasing the numbers of water molecules that solvate the protein. The APAC National Facility represents a major advance for these types of computations. The parallel computations that we have started have reduced by at least one order of magnitude the time taken to complete the calculations of the QM/MM and MM/MM non-bonded interactions.

 

Publications, Awards and External Funding

P.L. Cummins, J.E. Gready, Combined quantum and molecular mechanics (QM/MM) study of the ionization state of 8-methylpterin substrate bound to dihydrofolate reductase. J. Phys. Chem. B, 104, 2000, 4503-4510 .

P.L. Cummins, J.E. Gready, QM/MM and SCRF Studies of the ionization state of 8-methylpterin substrate bound to dihydrofolate reductase: existence of a low-barrier hydrogen bond and implications for the catalytic mechanism. J. Mol. Graph. Mod., 18, 2000, 42-49.

S.J. Titmuss, P.L. Cummins, A.A. Bliznyuk, A.P. Rendell, J.E. Gready, Comparison of linear scaling semiempirical methods and combined quantum mechanical/ molecular mechanical methods applied to enzyme reactions. Chem. Phys. Lett., 320, 2000, 169-176.

P.L. Cummins, J.E. Gready, Energetically most likely substrate and active-site protonation sites and pathways in the catalytic mechanism of dihydrofolate reductase. J. Am. Chem. Soc., 123, 2001, 3418-3428.

P.L. Cummins, S.J. Titmuss, D. Jayatilaka, A.A. Bliznyuk, A.P. Rendell, J.E. Gready, Comparison of semiempirical and ab initio QM decomposition analyses for the interaction energy between molecules. Chem. Phys. Lett., 352, 2002, 245-251.

Titmuss, P.L. Cummins, A.P. Rendell, A.A. Bliznyuk, J.E. Gready, Comparison of linear scaling semiempirical methods and combined quantum mechanical/ molecular mechanical methods for enzymic enzyme reactions II: an energy decomposition analysis. J. Comput. Chem. , in press.

P.L. Cummins, S.P. Greatbanks, A.P. Rendell, J.E. Gready, Mechanism of the hydride transfer step in the catalytic mechanism of dihydrofolate reductase I role of conserved water and protein interactions. J. Am. Chem. Soc., submitted.