1
|
Cummins PL, Kannappan B, Gready JE. Revised mechanism of carboxylation of ribulose-1,5-biphosphate by rubisco from large scale quantum chemical calculations. J Comput Chem 2018; 39:1656-1665. [PMID: 29756365 DOI: 10.1002/jcc.25343] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 01/06/2023]
Abstract
Here, we describe a computational approach for studying enzymes that catalyze complex multi-step reactions and apply it to Ribulose 1,5-bisphosphate carboxylase-oxygenase (Rubisco), the enzyme that fixes atmospheric carbon dioxide within photosynthesis. In the 5-step carboxylase reaction, the substrate Ribulose-1,5-bisphosphate (RuBP) first binds Rubisco and undergoes enolization before binding the second substrate, CO2 . Hydration of the RuBP.CO2 complex is followed by CC bond scission and stereospecific protonation. However, details of the roles and protonation states of active-site residues, and sources of protons and water, remain highly speculative. Large-scale computations on active-site models provide a means to better understand this complex chemical mechanism. The computational protocol comprises a combination of hybrid semi-empirical quantum mechanics and molecular mechanics within constrained molecular dynamics simulations, together with constrained gradient minimization calculations using density functional theory. Alternative pathways for hydration of the RuBP.CO2 complex and associated active-site protonation networks and proton and water sources were investigated. The main findings from analysis of the resulting energetics advocate major revision to existing mechanisms such that: hydration takes place anti to the CO2 ; both hydration and CC bond scission require early protonation of CO2 in the RuBP.CO2 complex; CC bond scission and stereospecific protonation reactions are concerted and, effectively, there is only one stable intermediate, the C3-gemdiolate complex. Our main conclusions for interpreting enzyme kinetic results are that the gemdiolate may represent the elusive Michaelis-Menten-like complex corresponding to the empirical Km (=Kc ) with turnover to product via bond scission concerted with stereospecific protonation consistent with the observed catalytic rate. © 2018 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Peter L Cummins
- John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, 0200, Australia
| | - Babu Kannappan
- John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, 0200, Australia
| | - Jill E Gready
- John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, 0200, Australia
| |
Collapse
|
2
|
Koyano Y, Takenaka N, Nakagawa Y, Nagaoka M. An optimum strategy for solution chemistry using semiempirical molecular orbital method. II. Primary importance of reproducing electrostatic interaction in the QM/MM framework. J Comput Chem 2010; 31:2628-41. [DOI: 10.1002/jcc.21558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
3
|
Wang SC, Beal PA, Tantillo DJ. Covalent hydration energies for purine analogs by quantum chemical methods. J Comput Chem 2010; 31:721-5. [PMID: 19569207 DOI: 10.1002/jcc.21364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In this work, covalent hydration energies for a variety of azanaphthalenes and purine analogs have been calculated using a variety of quantum chemical methods. On the basis of these results, we recommend the CPCM(UA0)-B3LYP/6-31+G(d,p) level for rapid prediction of covalent hydration energies. However, we caution the use of this methodology for computing covalent hydration energies for fluorine-containing compounds.
Collapse
Affiliation(s)
- Selina C Wang
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
| | | | | |
Collapse
|
4
|
Alonso H, Cummins PL, Gready JE. Methyltetrahydrofolate:corrinoid/iron−sulfur Protein Methyltransferase (MeTr): Protonation State of the Ligand and Active-Site Residues. J Phys Chem B 2009; 113:14787-96. [DOI: 10.1021/jp900181g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hernán Alonso
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Peter L. Cummins
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Jill E. Gready
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| |
Collapse
|
5
|
Vener MV, Tovmash AV, Rostov IV, Basilevsky MV. Molecular simulations of outersphere reorganization energies in polar and quadrupolar solvents. The case of intramolecular electron and hole transfer. J Phys Chem B 2007; 110:14950-5. [PMID: 16869609 DOI: 10.1021/jp061069h] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Outersphere reorganization energies (lambda) for intramolecular electron and hole transfer are studied in anion- and cation-radical forms of complex organic substrates (p-phenylphenyl-spacer-naphthyl) in polar (water, 1,2-dichloroethane, tetrahydrofuran) and quadrupolar (supercritical CO2) solvents. Structure and charge distributions of solute molecules are obtained at the HF/6-31G(d,p) level. Standard Lennard-Jones parameters for solutes and the nonpolarizable simple site-based models of solvents are used in molecular dynamics (MD) simulations. Calculation of lambda is done by means of the original procedure, which treats electrostatic polarization of a solvent in terms of a usual nonpolarizable MD scheme supplemented by scaling of reorganization energies at the final stage. This approach provides a physically relevant background for separating inertial and inertialless polarization responses by means of a single parameter epsilon(infinity), optical dielectric permittivity of the solvent. Absolute lambda values for hole transfer in 1,2-dichloroethane agree with results of previous computations in terms of the different technique (MD/FRCM, Leontyev, I. V.; et al. Chem. Phys. 2005, 319, 4). Computed lambda values for electron transfer in tetrahydrofuran are larger than the experimental values by ca. 2.5 kcal/mol; for the case of hole transfer in 1,2-dichloroethane the discrepancy is of similar magnitude provided the experimental data are properly corrected. The MD approach gives nonzero lambda values for charge-transfer reaction in supercritical CO2, being able to provide a uniform treatment of nonequilibrium solvation phenomena in both quadrupolar and polar solvents.
Collapse
Affiliation(s)
- M V Vener
- Karpov Institute of Physical Chemistry, ul. Vorontsovo Pole 10, Moscow 105064, Russia
| | | | | | | |
Collapse
|
6
|
Cummins PL, Rostov IV, Gready JE. Calculation of a Complete Enzymic Reaction Surface: Reaction and Activation Free Energies for Hydride-Ion Transfer in Dihydrofolate Reductase. J Chem Theory Comput 2007; 3:1203-11. [DOI: 10.1021/ct600313b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter L. Cummins
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Ivan V. Rostov
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Jill E. Gready
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| |
Collapse
|
7
|
Nagaoka M, Nagae Y, Koyano Y, Oishi Y. Transition-State Characterization of the Ammonia Ionization Process in Aqueous Solution via the Free-Energy Gradient Method. J Phys Chem A 2006; 110:4555-63. [PMID: 16571063 DOI: 10.1021/jp056115c] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For the ionization process of ammonia in aqueous solution, the transition-state (TS) structure was fully optimized for the first time on the free-energy surface (FES) by applying the free-energy gradient (FEG) method combined with a hybrid quantum mechanical and molecular mechanical molecular dynamics (QM/MM-MD) method. In aqueous solution, the ionization process was found to proceed by way of a clear TS (R(N1-H5) = 1.512 A), which does not exist in the gas phase. The free-energy (FE) of activation for ionization obtained was 14.7 kcal/mol, within the classical approximation, via the QM/MM-MD FEG method, and is found to be in good agreement with 9.57 kcal/mol estimated from the TS theory using the experimental value of the rate constant. Apart from the dynamic correction, it is indicated that the theoretical value would be improved to be 10.28 kcal/mol if the electronic-state calculation could be executed at the B3LYP/6-31G(d) level of theory.
Collapse
Affiliation(s)
- Masataka Nagaoka
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
| | | | | | | |
Collapse
|
8
|
Cummins PL, Gready JE. Computational methods for the study of enzymic reaction mechanisms III: A perturbation plus QM/MM approach for calculating relative free energies of protonation. J Comput Chem 2005; 26:561-8. [PMID: 15726569 DOI: 10.1002/jcc.20192] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We describe a coupling parameter, that is, perturbation, approach to effectively create and annihilate atoms in the quantum mechanical Hamiltonian within the closed shell restricted Hartree-Fock formalism. This perturbed quantum mechanical atom (PQA) method is combined with molecular mechanics (MM) methods (PQA/MM) within a molecular dynamics simulation, to model the protein environment (MM region) effects that also make a contribution to the overall free energy change. Using the semiempirical PM3 method to model the QM region, the application of this PQA/MM method is illustrated by calculation of the relative protonation free energy of the conserved OD2 (Asp27) and the N5 (dihydrofolate) proton acceptor sites in the active site of Escherichia coli dihydrofolate reductase (DHFR) with the bound nicotinamide adenine dinucleotide phosphate (NADPH) cofactor. For a number of choices for the QM region, the relative protonation free energy was calculated as the sum of contributions from the QM region and the interaction between the QM and MM regions via the thermodynamic integration (TI) method. The results demonstrate the importance of including the whole substrate molecule in the QM region, and the overall protein (MM) environment in determining the relative stabilities of protonation sites in the enzyme active site. The PQA/MM free energies obtained by TI were also compared with those estimated by a less computationally demanding nonperturbative method based on the linear response approximation (LRA). For some choices of QM region, the total free energies calculated using the LRA method were in very close agreement with the PQA/MM values. However, the QM and QM/MM component free energies were found to differ significantly between the two methods.
Collapse
Affiliation(s)
- Peter L Cummins
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | | |
Collapse
|
9
|
Vener MV, Leontyev IV, Basilevsky MV. Computations of solvation free energies for polyatomic ions in water in terms of a combined molecular–continuum approach. J Chem Phys 2003. [DOI: 10.1063/1.1605945] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
10
|
|
11
|
Computational methods for the study of enzymic reaction mechanisms. II. An overlapping mechanically embedded method for hybrid semi-empirical-QM/MM calculations. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0166-1280(03)00303-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
12
|
Vener MV, Leontyev IV, Dyakov YA, Basilevsky MV, Newton MD. Application of the Linearized MD Approach for Computing Equilibrium Solvation Free Energies of Charged and Dipolar Solutes in Polar Solvents. J Phys Chem B 2002. [DOI: 10.1021/jp021396z] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. V. Vener
- Karpov Institute of Physical Chemistry, ul. Vorontsovo Pole 10, Moscow 105064, Russia, and Department of Chemistry, P.O. Box 5000, Brookhaven National Laboratory, Upton, New York 11973
| | - I. V. Leontyev
- Karpov Institute of Physical Chemistry, ul. Vorontsovo Pole 10, Moscow 105064, Russia, and Department of Chemistry, P.O. Box 5000, Brookhaven National Laboratory, Upton, New York 11973
| | - Yu. A. Dyakov
- Karpov Institute of Physical Chemistry, ul. Vorontsovo Pole 10, Moscow 105064, Russia, and Department of Chemistry, P.O. Box 5000, Brookhaven National Laboratory, Upton, New York 11973
| | - M. V. Basilevsky
- Karpov Institute of Physical Chemistry, ul. Vorontsovo Pole 10, Moscow 105064, Russia, and Department of Chemistry, P.O. Box 5000, Brookhaven National Laboratory, Upton, New York 11973
| | - M. D. Newton
- Karpov Institute of Physical Chemistry, ul. Vorontsovo Pole 10, Moscow 105064, Russia, and Department of Chemistry, P.O. Box 5000, Brookhaven National Laboratory, Upton, New York 11973
| |
Collapse
|
13
|
Titmuss SJ, Cummins PL, Rendell AP, Bliznyuk AA, Gready JE. Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis. J Comput Chem 2002; 23:1314-22. [PMID: 12214314 DOI: 10.1002/jcc.10122] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169-176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further divided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (approximately 16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 A) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product-reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute approximately 40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies.
Collapse
Affiliation(s)
- Stephen J Titmuss
- Computational Proteomics and Therapy Design Group, Division of Biochemistry and Molecular Biology, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra, ACT 2601, Australia
| | | | | | | | | |
Collapse
|
14
|
An iterative procedure to determine Lennard-Jones parameters for their use in quantum mechanics/molecular mechanics liquid state simulations. Chem Phys 2002. [DOI: 10.1016/s0301-0104(02)00785-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
15
|
Cummins PL, Greatbanks SP, Rendell AP, Gready JE. Computational Methods for the Study of Enzymic Reaction Mechanisms. 1. Application to the Hydride Transfer Step in the Catalysis of Dihydrofolate Reductase. J Phys Chem B 2002. [DOI: 10.1021/jp021070q] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter L. Cummins
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Stephen P. Greatbanks
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Alistair P. Rendell
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Jill E. Gready
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| |
Collapse
|
16
|
Cummins PL, Titmuss SJ, Jayatilaka D, Bliznyuk AA, Rendell AP, Gready JE. Comparison of semiempirical and ab initio QM decomposition analyses for the interaction energy between molecules. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(01)01417-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
17
|
Orozco M, Luque FJ. Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems. Chem Rev 2000; 100:4187-4226. [PMID: 11749344 DOI: 10.1021/cr990052a] [Citation(s) in RCA: 454] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Modesto Orozco
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franqués 1, E-08028 Barcelona, Spain, and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda. Diagonal s/n, E-08028 Barcelona, Spain
| | | |
Collapse
|
18
|
Luque FJ, Reuter N, Cartier A, Ruiz-López MF. Calibration of the Quantum/Classical Hamiltonian in Semiempirical QM/MM AM1 and PM3 Methods. J Phys Chem A 2000. [DOI: 10.1021/jp001974g] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- F. J. Luque
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain
| | - N. Reuter
- Unité de Recherche CNRS-UHP 7565, Laboratoire de Chimie Théorique, Université Henri Poincaré-Nancy I, BP 239, 54506 Vandoeuvre-lès-Nancy, France
| | - A. Cartier
- Unité de Recherche CNRS-UHP 7565, Laboratoire de Chimie Théorique, Université Henri Poincaré-Nancy I, BP 239, 54506 Vandoeuvre-lès-Nancy, France
| | - M. F. Ruiz-López
- Unité de Recherche CNRS-UHP 7565, Laboratoire de Chimie Théorique, Université Henri Poincaré-Nancy I, BP 239, 54506 Vandoeuvre-lès-Nancy, France
| |
Collapse
|
19
|
Chalmet S, Ruiz-López MF. New approaches to the description of short-range repulsion interactions in hybrid quantum/classical systems. Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(00)00992-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
20
|
Cummins PL, Gready JE. Combined Quantum and Molecular Mechanics (QM/MM) Study of the Ionization State of 8-Methylpterin Substrate Bound to Dihydrofolate Reductase. J Phys Chem B 2000. [DOI: 10.1021/jp993153l] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter L. Cummins
- Computational Molecular Biology and Drug Design Group, John Curtin School of Medical Research, Australian National University, P.O. BOX 334, Canberra ACT, 2601 Australia
| | - Jill E. Gready
- Computational Molecular Biology and Drug Design Group, John Curtin School of Medical Research, Australian National University, P.O. BOX 334, Canberra ACT, 2601 Australia
| |
Collapse
|
21
|
Titmuss SJ, Cummins PL, Bliznyuk AA, Rendell AP, Gready JE. Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods applied to enzyme reactions. Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(00)00215-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
22
|
Cummins PL, Gready JE. QM/MM and SCRF studies of the ionization state of 8-methylpterin substrate bound to dihydrofolate reductase: existence of a low-barrier hydrogen bond. J Mol Graph Model 2000; 18:42-9. [PMID: 10935206 DOI: 10.1016/s1093-3263(00)00034-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Using combined semiempirical quantum mechanics and molecular mechanics (QM/MM) and ab initio self-consistent reaction field (SCRF) calculations, we determined that a low-barrier hydrogen bond (LBHB) is formed when the mechanism-based substrate 8-methylpterin binds to dihydrofolate reductase (DHFR). The substrate initially was assumed bound either in the ion-pair form corresponding to N3-protonated substrate hydrogen (H) bonded to the unprotonated (carboxylate) of the conserved Glu30 residue in the active site, or in the neutral-pair form corresponding to unprotonated substrate H bonded to the neutral (carboxylic acid) from of Glu30. The free energy of interaction of these H-bonded systems with the protein/solvent surroundings was computed using a coordinate-coupled free energy perturbation (FEP) method implemented within the molecular dynamics (MD) simulation scheme and using a semiempirical (PM3) QM/MM force field. The free energy obtained from the QM/MM force-field simulations corresponds most closely with the corresponding free energy component obtained from HF/6-31G* SCRF calculations using a value of 2 for the dielectric constant (epsilon) for the solvated protein. Calculations were performed at levels ranging from HF/6-31G to MP2/6-31G* to B3LYP/6-31 + G**, with varying dielectric constants. The energy-minimized path for motion of the proton in the H bond along a one-dimensional reaction coordinate was calculated at HF/6-31G, HF/6-31G* (epsilon = 1) and B3LYP/6-31G* (epsilon = 2) levels. These calculations identified a second neutral-pair complex, involving the 2-amino group of substrate, which also interacts with Glu30, which is lower in energy than the ion-pair form. A harmonic vibrational analysis shows that the first vibrational state appears to lie near or above the TS connecting potential energy minima corresponding to the two neutral-pair configurations, thus indicating an LBHB. Consequently, the H-bonded system will have a significant probability of being found in the ion-pair form, in agreement with experimental spectral studies indicating an enzyme-bound cation and suggesting that the LBHB would activate substrate towards hydride-ion transfer from NADPH.
Collapse
Affiliation(s)
- P L Cummins
- Computational Molecular Biology and Drug Design Group, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | | |
Collapse
|