1
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Beach A, Adhikari P, Singh G, Song M, DeGroot N, Lu Y. Structural Effects on the Temperature Dependence of Hydride Kinetic Isotope Effects of the NADH/NAD + Model Reactions in Acetonitrile: Charge-Transfer Complex Tightness Is a Key. J Org Chem 2024; 89:3184-3193. [PMID: 38364859 PMCID: PMC10913049 DOI: 10.1021/acs.joc.3c02562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024]
Abstract
It has recently frequently been found that the kinetic isotope effect (KIE) is independent of temperature (T) in H-tunneling reactions in enzymes but becomes dependent on T in their mutants. Many enzymologists found that the trend is related to different donor-acceptor distances (DADs) at tunneling-ready states (TRSs), which could be sampled by protein dynamics. That is, a more rigid system of densely populated short DADs gives rise to a weaker T dependence of KIEs. Theoreticians have attempted to develop H-tunneling theories to explain the observations, but none have been universally accepted. It is reasonable to assume that the DAD sampling concept, if it exists, applies to the H-transfer reactions in solution, as well. In this work, we designed NADH/NAD+ model reactions to investigate their structural effects on the T dependence of hydride KIEs in acetonitrile. Hammett correlations together with N-CH3/CD3 secondary KIEs were used to provide the electronic structure of the TRSs and thus the rigidity of their charge-transfer complexation vibrations. In all three pairs of reactions, a weaker T dependence of KIEs always corresponds to a steeper Hammett slope on the substituted hydride acceptors. It was found that a tighter/rigid charge-transfer complexation system corresponds with a weaker T dependence of KIEs, consistent with the observations in enzymes.
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Affiliation(s)
- Amanda Beach
- Department of Chemistry, Southern
Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Pratichhya Adhikari
- Department of Chemistry, Southern
Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Grishma Singh
- Department of Chemistry, Southern
Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Meimei Song
- Department of Chemistry, Southern
Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Nicholas DeGroot
- Department of Chemistry, Southern
Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Yun Lu
- Department of Chemistry, Southern
Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
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2
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Bai M, Pratap R, Salarvand S, Lu Y. Correlation of temperature dependence of hydride kinetic isotope effects with donor-acceptor distances in two solvents of different polarities. Org Biomol Chem 2023; 21:5090-5097. [PMID: 37278324 PMCID: PMC10339711 DOI: 10.1039/d3ob00718a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recently observed nearly temperature (T)-independent kinetic isotope effects (KIEs) in wild-type enzymes and T-dependent KIEs in variants were used to suggest that H-tunneling in enzymes is assisted by the fast protein vibrations that help sample short donor-acceptor distances (DADs). This supports the recently proposed role of protein vibrations in DAD sampling catalysis. However, use of T-dependence of KIEs to suggest DAD sampling associated with protein vibrations is debated. We have formulated a hypothesis regarding the correlation and designed experiments in solution to investigate it. The hypothesis is, a more rigid system with shorter DADTRS's at the tunneling ready states (TRSs) gives rise to a weaker T-dependence of KIEs, i.e., a smaller ΔEa (= EaD - EaH). In a former work, the solvent effects of acetonitrile versus chloroform on the ΔEa of NADH/NAD+ model reactions were determined, and the DADPRC's of the productive reactant complexes (PRCs) were computed to substitute the DADTRS for the DADTRS-ΔEa correlation study. A smaller ΔEa was found in the more polar acetonitrile where the positively charged PRC is better solvated and has a shorter DADPRC, indirectly supporting the hypothesis. In this work, the TRS structures of different DADTRS's for the hydride tunneling reaction from 1,3-dimethyl-2-phenylimidazoline to 10-methylacridinium were computed. The N-CH3/CD3 secondary KIEs on both reactants were calculated and fitted to the observed values to find the DADTRS order in both solutions. It was found that the equilibrium DADTRS is shorter in acetonitrile than in chloroform. Results directly support the DADTRS-ΔEa correlation hypothesis as well as the explanation that links T-dependence of KIEs to DAD sampling catalysis in enzymes.
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Affiliation(s)
- Mingxuan Bai
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, USA.
| | - Rijal Pratap
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, USA.
| | - Sanaz Salarvand
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, USA.
| | - Yun Lu
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, USA.
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3
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Adhikari P, Song M, Bai M, Rijal P, DeGroot N, Lu Y. Solvent Effects on the Temperature Dependence of Hydride Kinetic Isotope Effects: Correlation to the Donor-Acceptor Distances. J Phys Chem A 2022; 126:7675-7686. [PMID: 36228057 DOI: 10.1021/acs.jpca.2c06065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein structural effects on the temperature (T) dependence of kinetic isotope effects (KIEs) in H-tunneling reactions have recently been used to discuss about the role of enzyme thermal motions in catalysis. Frequently observed nearly T-independent KIEs in the wild-type enzymes and T-dependent KIEs in variants suggest that H-tunneling in the former is assisted by the naturally evolved protein constructive vibrations that help sample short donor-acceptor distances (DADs) needed. This explanation that correlates the T-dependence of KIEs with DAD sampling has been highly debated as simulations following other H-tunneling models sometimes gave alternative explanations. In this paper, solvent effects on the T-dependence of KIEs of two hydride tunneling reactions of NADH/NAD+ analogues (represented by ΔEa = EaD - EaH) were determined in attempts to replicate the observations in enzymes and test the protein vibration-assisted DAD sampling concept. Effects of selected aprotic solvents on the DADPRC's of the productive reactant complexes (PRCs) and the DADTRS's of the activated tunneling ready states (TRSs) were obtained through computations and analyses of the kinetic data, including 2° KIEs, respectively. A weaker T-dependence of KIEs (i.e., smaller ΔEa) was found in a more polar aprotic solvent in which the system has a shorter average DADPRC and DADTRS. Further results show that a charge-transfer (CT) complexation made of a stronger donor/acceptor gives rise to a smaller ΔEa. Overall, the shorter and less broadly distributed DADs resulting from the stronger CT complexation vibrations give rise to a smaller ΔEa. Our results appear to support the explanation that links the T-dependence of KIEs to the donor-acceptor rigidity in enzymes.
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Affiliation(s)
- Pratichhya Adhikari
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Meimei Song
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Mingxuan Bai
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Pratap Rijal
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Nicholas DeGroot
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Yun Lu
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
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4
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The catalytic mechanism of the mitochondrial methylenetetrahydrofolate dehydrogenase/cyclohydrolase (MTHFD2). PLoS Comput Biol 2022; 18:e1010140. [PMID: 35613161 PMCID: PMC9173628 DOI: 10.1371/journal.pcbi.1010140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/07/2022] [Accepted: 04/26/2022] [Indexed: 11/19/2022] Open
Abstract
Methylenetetrahydrofolate dehydrogenase/cyclohydrolase (MTHFD2) is a new drug target that is expressed in cancer cells but not in normal adult cells, which provides an Achilles heel to selectively kill cancer cells. Despite the availability of crystal structures of MTHFD2 in the inhibitor- and cofactor-bound forms, key information is missing due to technical limitations, including (a) the location of absolutely required Mg2+ ion, and (b) the substrate-bound form of MTHFD2. Using computational modeling and simulations, we propose that two magnesium ions are present at the active site whereby (i) Arg233, Asp225, and two water molecules coordinate MgA2+, while MgA2+ together with Arg233 stabilize the inorganic phosphate (Pi); (ii) Asp168 and three water molecules coordinate MgB2+, and MgB2+ further stabilizes Pi by forming a hydrogen bond with two oxygens of Pi; (iii) Arg201 directly coordinates the Pi; and (iv) through three water-mediated interactions, Asp168 contributes to the positioning and stabilization of MgA2+, MgB2+ and Pi. Our computational study at the empirical valence bond level allowed us also to elucidate the detailed reaction mechanisms. We found that the dehydrogenase activity features a proton-coupled electron transfer with charge redistribution connected to the reorganization of the surrounding water molecules which further facilitates the subsequent cyclohydrolase activity. The cyclohydrolase activity then drives the hydration of the imidazoline ring and the ring opening in a concerted way. Furthermore, we have uncovered that two key residues, Ser197/Arg233, are important factors in determining the cofactor (NADP+/NAD+) preference of the dehydrogenase activity. Our work sheds new light on the structural and kinetic framework of MTHFD2, which will be helpful to design small molecule inhibitors that can be used for cancer treatment.
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5
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Zhao LN, Kaldis P. Pairing structural reconstruction with catalytic competence to evaluate the mechanisms of key enzymes in the folate-mediated one-carbon pathway. FEBS J 2022; 290:2279-2291. [PMID: 35303396 DOI: 10.1111/febs.16439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/05/2022] [Accepted: 03/16/2022] [Indexed: 02/01/2023]
Abstract
Mammalian metabolism comprises a series of interlinking pathways that include two major cycles: the folate and methionine cycles. The folate-mediated metabolic cycle uses several oxidation states of tetrahydrofolate to carry activated one-carbon units to be readily used and interconverted within the cell. They are required for nucleotide synthesis, methylation and metabolism, and particularly for proliferation of cancer cells. Based on the latest progress in genome-wide CRISPR loss-of-function viability screening of 789 cell lines, we focus on the most cancer-dependent enzymes in this pathway, especially those that are hyperactivated in cancer, to provide new insight into the chemical basis for cancer drug development. Since the complete 3D structure of several of these enzymes of the one-carbon pathway in their active form are not available, we used homology modelling integrated with the interpretation of the reaction mechanism. In addition, have reconstructed the most likely scenario for the reactions taking place paired with their catalytic competence that provides a testable framework for this pathway.
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Affiliation(s)
- Li Na Zhao
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Philipp Kaldis
- Department of Clinical Sciences, Lund University, Malmö, Sweden
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6
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Singh P, Vandemeulebroucke A, Li J, Schulenburg C, Fortunato G, Kohen A, Hilvert D, Cheatum CM. Evolution of the Chemical Step in Enzyme Catalysis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00442] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Priyanka Singh
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | | | - Jiayue Li
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Cindy Schulenburg
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Gabriel Fortunato
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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7
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Mhashal AR, Major DT. Temperature-Dependent Kinetic Isotope Effects in R67 Dihydrofolate Reductase from Path-Integral Simulations. J Phys Chem B 2021; 125:1369-1377. [PMID: 33522797 PMCID: PMC7883348 DOI: 10.1021/acs.jpcb.0c10318] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/05/2021] [Indexed: 11/28/2022]
Abstract
Calculation of temperature-dependent kinetic isotope effects (KIE) in enzymes presents a significant theoretical challenge. Additionally, it is not trivial to identify enzymes with available experimental accurate intrinsic KIEs in a range of temperatures. In the current work, we present a theoretical study of KIEs in the primitive R67 dihydrofolate reductase (DHFR) enzyme and compare with experimental work. The advantage of R67 DHFR is its significantly lower kinetic complexity compared to more evolved DHFR isoforms. We employ mass-perturbation-based path-integral simulations in conjunction with umbrella sampling and a hybrid quantum mechanics-molecular mechanics Hamiltonian. We obtain temperature-dependent KIEs in good agreement with experiments and ascribe the temperature-dependent KIEs primarily to zero-point energy effects. The active site in the primitive enzyme is found to be poorly preorganized, which allows excessive water access to the active site and results in loosely bound reacting ligands.
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Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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8
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Maness P, Koirala S, Adhikari P, Salimraftar N, Lu Y. Substituent Effects on Temperature Dependence of Kinetic Isotope Effects in Hydride-Transfer Reactions of NADH/NAD + Analogues in Solution: Reaction Center Rigidity Is the Key. Org Lett 2020; 22:5963-5967. [PMID: 32662653 DOI: 10.1021/acs.orglett.0c02049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Substituent effects on the temperature dependence of primary kinetic isotope effects, characterized by ΔEa = EaD - EaH, for two series of the title reactions in acetonitrile were studied. The change from ΔEa ≈ 0 for a highly rigid system to ΔEa > 0 for systems with reduced rigidities was observed. The rigidities were controlled by the electronic and steric effects. This work replicates the observations in enzymes and opens a new research direction that studies structure-ΔEa relationship.
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Affiliation(s)
- Peter Maness
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Shailendra Koirala
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Pratichhya Adhikari
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Nasim Salimraftar
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Yun Lu
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
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9
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Prah A, Ogrin P, Mavri J, Stare J. Nuclear quantum effects in enzymatic reactions: simulation of the kinetic isotope effect of phenylethylamine oxidation catalyzed by monoamine oxidase A. Phys Chem Chem Phys 2020; 22:6838-6847. [DOI: 10.1039/d0cp00131g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By using computational techniques for quantizing nuclear motion one can accurately reproduce kinetic isotope effect of enzymatic reactions, as demonstrated for phenylethylamine oxidation catalyzed by the monoamine oxidase A enzyme.
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Affiliation(s)
- Alja Prah
- Theory Department
- National Institute of Chemistry
- Ljubljana
- Slovenia
- University of Ljubljana
| | - Peter Ogrin
- Theory Department
- National Institute of Chemistry
- Ljubljana
- Slovenia
- University of Ljubljana
| | - Janez Mavri
- Theory Department
- National Institute of Chemistry
- Ljubljana
- Slovenia
| | - Jernej Stare
- Theory Department
- National Institute of Chemistry
- Ljubljana
- Slovenia
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10
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Lu Y, Wilhelm S, Bai M, Maness P, Ma L. Replication of the Enzymatic Temperature Dependency of the Primary Hydride Kinetic Isotope Effects in Solution: Caused by the Protein-Controlled Rigidity of the Donor-Acceptor Centers? Biochemistry 2019; 58:4035-4046. [PMID: 31478638 DOI: 10.1021/acs.biochem.9b00574] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The change from the temperature independence of the primary (1°) H/D kinetic isotope effects (KIEs) in wild-type enzyme-catalyzed H-transfer reactions (ΔEa = EaD - EaH ∼ 0) to a strong temperature dependence with the mutated enzymes (ΔEa ≫ 0) has recently been frequently observed. This has prompted some enzymologists to develop new H-tunneling models to correlate ΔEa with the donor-acceptor distance (DAD) at the tunneling-ready state (TRS) as well as the protein thermal motions/dynamics that sample the short DADTRS's for H-tunneling to occur. While extensive evidence supporting or disproving the thermally activated DAD sampling concept has emerged, a comparable study of the simpler bimolecular H-tunneling reactions in solution has not been carried out. In particular, small ΔEa's (∼0) have not been found. In this paper, we report a study of the hydride-transfer reactions from four NADH models to the same hydride acceptor in acetonitrile. The ΔEa's were determined: 0.37 (small), 0.60, 0.99, and 1.53 kcal/mol (large). The α-secondary (2°) KIEs on the acceptor that serve as a ruler for the rigidity of reaction centers were previously reported or determined. All possible productive reactant complex (PRC) configurations were computed to provide insight into the structures of the TRS's. Relationships among structures, 2° KIEs, DADPRC's, and ΔEa's were discussed. The more rigid system with more suppressed 2° C-H vibrations at the TRS and more narrowly distributed DADPRC's in PRCs gave a smaller ΔEa. The results replicated the trend observed in enzymes versus mutated enzymes and appeared to support the concepts of different thermally activated DADTRS sampling processes in response to the rigid versus flexible donor-acceptor centers.
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Affiliation(s)
- Yun Lu
- Department of Chemistry , Southern Illinois University Edwardsville , Edwardsville , Illinois 62026 , United States
| | - Samantha Wilhelm
- Department of Chemistry , Southern Illinois University Edwardsville , Edwardsville , Illinois 62026 , United States
| | - Mingxuan Bai
- Department of Chemistry , Southern Illinois University Edwardsville , Edwardsville , Illinois 62026 , United States
| | - Peter Maness
- Department of Chemistry , Southern Illinois University Edwardsville , Edwardsville , Illinois 62026 , United States
| | - Li Ma
- Department of Chemistry , Southern Illinois University Edwardsville , Edwardsville , Illinois 62026 , United States
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11
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Kulkarni Y, Kamerlin SCL. Computational physical organic chemistry using the empirical valence bond approach. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2019. [DOI: 10.1016/bs.apoc.2019.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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12
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Mhashal AR, Pshetitsky Y, Cheatum CM, Kohen A, Major DT. Evolutionary Effects on Bound Substrate pKa in Dihydrofolate Reductase. J Am Chem Soc 2018; 140:16650-16660. [DOI: 10.1021/jacs.8b09089] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Yaron Pshetitsky
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | | | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Dan Thomas Major
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
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13
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Hong NS, Petrović D, Lee R, Gryn'ova G, Purg M, Saunders J, Bauer P, Carr PD, Lin CY, Mabbitt PD, Zhang W, Altamore T, Easton C, Coote ML, Kamerlin SCL, Jackson CJ. The evolution of multiple active site configurations in a designed enzyme. Nat Commun 2018; 9:3900. [PMID: 30254369 PMCID: PMC6156567 DOI: 10.1038/s41467-018-06305-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/21/2018] [Indexed: 12/11/2022] Open
Abstract
Developments in computational chemistry, bioinformatics, and laboratory evolution have facilitated the de novo design and catalytic optimization of enzymes. Besides creating useful catalysts, the generation and iterative improvement of designed enzymes can provide valuable insight into the interplay between the many phenomena that have been suggested to contribute to catalysis. In this work, we follow changes in conformational sampling, electrostatic preorganization, and quantum tunneling along the evolutionary trajectory of a designed Kemp eliminase. We observe that in the Kemp Eliminase KE07, instability of the designed active site leads to the emergence of two additional active site configurations. Evolutionary conformational selection then gradually stabilizes the most efficient configuration, leading to an improved enzyme. This work exemplifies the link between conformational plasticity and evolvability and demonstrates that residues remote from the active sites of enzymes play crucial roles in controlling and shaping the active site for efficient catalysis.
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Affiliation(s)
- Nan-Sook Hong
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Dušan Petrović
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden
| | - Richmond Lee
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Ganna Gryn'ova
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.,Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Miha Purg
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden
| | - Jake Saunders
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Paul Bauer
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden
| | - Paul D Carr
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Ching-Yeh Lin
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Peter D Mabbitt
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - William Zhang
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Timothy Altamore
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Chris Easton
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Michelle L Coote
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Shina C L Kamerlin
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden.
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
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14
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Mhashal AR, Pshetitsky Y, Eitan R, Cheatum CM, Kohen A, Major DT. Effect of Asp122 Mutation on the Hydride Transfer in E. coli DHFR Demonstrates the Goldilocks of Enzyme Flexibility. J Phys Chem B 2018; 122:8006-8017. [PMID: 30040418 DOI: 10.1021/acs.jpcb.8b05556] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Dihydrofolate reductase (DHFR) catalyzes the reduction of dihydrofolate (DHF) to tetrahydrofolate (THF) in the presence of NADPH. The key hydride transfer step in the reaction is facilitated by a combination of enzyme active site preorganization and correlated protein motions in the Michaelis-Menten (E:NADPH:DHF) complex. The present theoretical study employs mutagenesis to examine the relation between structural and functional properties of the enzyme. We mutate Asp122 in Escherichia coli DHFR, which is a conserved amino acid in the DHFR family. The consequent effect of the mutation on enzyme catalysis is examined from an energetic, structural and short-time dynamic perspective. Our investigations suggest that the structural and short-time dynamic perturbations caused by Asp122X mutations (X = Asn, Ser, Ala) are along the reaction coordinate and lower the rate of hydride transfer. Importantly, analysis of the correlated and principle component motions in the enzyme suggest that the mutation alters the coupled motions that are present in the wild-type enzyme. In the case of D122N and D122S, the mutations inhibit coupled motion, whereas in the case of D122A, the mutation enhances coupled motion, although all mutations result in similar rate reduction. These results emphasize a Goldilocks principle of enzyme flexibility, that is, enzymes should neither be too rigid nor too flexible.
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Affiliation(s)
- Anil R Mhashal
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Yaron Pshetitsky
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Reuven Eitan
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Christopher M Cheatum
- Department of Chemistry , University of Iowa , Iowa City , Iowa 52242 , United States
| | - Amnon Kohen
- Department of Chemistry , University of Iowa , Iowa City , Iowa 52242 , United States
| | - Dan Thomas Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
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15
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Xu Y, Song K, Shi Q. Mixed quantum-classical simulation of the hydride transfer reaction catalyzed by dihydrofolate reductase based on a mapped system-harmonic bath model. J Chem Phys 2018; 148:102322. [DOI: 10.1063/1.4990515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yang Xu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Song
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
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16
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Cooperativity and flexibility in enzyme evolution. Curr Opin Struct Biol 2018; 48:83-92. [DOI: 10.1016/j.sbi.2017.10.020] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/24/2017] [Indexed: 11/23/2022]
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17
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Roy S, Schopf P, Warshel A. Origin of the Non-Arrhenius Behavior of the Rates of Enzymatic Reactions. J Phys Chem B 2017; 121:6520-6526. [PMID: 28613876 DOI: 10.1021/acs.jpcb.7b03698] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The origin of the non-Arrhenius behavior of the rate constant for hydride transfer enzymatic reactions has been a puzzling problem since its initial observation. This effect has been used originally to support the idea that enzymes work by dynamical effects and more recently to suggest an entropy funnel model. Our analysis, however, has advanced the idea that the reason for the non-Arrhenius trend reflects the temperature dependence of the rearrangements of the protein polar groups in response to the change in the charge distribution of the reacting system during the transition from the ground state (GS) to the transition state (TS). Here we examine the validity of our early proposal by simulating the catalytic reaction of alcohol dehydrogenase (ADH) and determine the microscopic origin of the entropic and enthalpic contributions to the activation barrier. The corresponding analysis establishes the origin of the non-Arrhenius behaviors and quantifies our original suggestion that the classical effect is due to the entropic contributions of the environment. We also find that the quantum effects reflect in part the temperature dependence of the donor-acceptor distance.
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Affiliation(s)
- Subhendu Roy
- Department of Chemistry, University of Southern California , 3620 McClintock Avenue, Los Angeles, California 90089, United States
| | - Patrick Schopf
- Astex Pharmaceuticals , Cambridge CB4 0QA, United Kingdom
| | - Arieh Warshel
- Department of Chemistry, University of Southern California , 3620 McClintock Avenue, Los Angeles, California 90089, United States
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18
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Warshel A, Bora RP. Perspective: Defining and quantifying the role of dynamics in enzyme catalysis. J Chem Phys 2017; 144:180901. [PMID: 27179464 DOI: 10.1063/1.4947037] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Enzymes control chemical reactions that are key to life processes, and allow them to take place on the time scale needed for synchronization between the relevant reaction cycles. In addition to general interest in their biological roles, these proteins present a fundamental scientific puzzle, since the origin of their tremendous catalytic power is still unclear. While many different hypotheses have been put forward to rationalize this, one of the proposals that has become particularly popular in recent years is the idea that dynamical effects contribute to catalysis. Here, we present a critical review of the dynamical idea, considering all reasonable definitions of what does and does not qualify as a dynamical effect. We demonstrate that no dynamical effect (according to these definitions) has ever been experimentally shown to contribute to catalysis. Furthermore, the existence of non-negligible dynamical contributions to catalysis is not supported by consistent theoretical studies. Our review is aimed, in part, at readers with a background in chemical physics and biophysics, and illustrates that despite a substantial body of experimental effort, there has not yet been any study that consistently established a connection between an enzyme's conformational dynamics and a significant increase in the catalytic contribution of the chemical step. We also make the point that the dynamical proposal is not a semantic issue but a well-defined scientific hypothesis with well-defined conclusions.
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Affiliation(s)
- Arieh Warshel
- Department of Chemistry, University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, USA
| | - Ram Prasad Bora
- Department of Chemistry, University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, USA
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19
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On the indirect relationship between protein dynamics and enzyme activity. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 125:52-60. [PMID: 28163054 DOI: 10.1016/j.pbiomolbio.2017.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 02/01/2017] [Indexed: 11/22/2022]
Abstract
The behaviors of simple thermal systems have been well studied in physical chemistry and the principles obtained from such studies have been applied to complex thermal systems, such as proteins and enzymes. But the simple application of such principles is questionable and may lead to mistakes under some circumstances. In enzymology, the transition state theory of chemical reactions has been accepted as a fundamental theory, but the role of protein dynamics in enzyme catalysis is controversial in the context of transition state theory. By studying behaviors of complex thermal systems, we have revised the Arrhenius equation and transition state theory and our model is validated in enzymology. Formally speaking, the revised Arrhenius equation is apparently similar to a conventional Arrhenius equation, but the physical meanings of its parameters differ from that of traditional forms in principle. Within this model, the role of protein dynamics in enzyme catalysis is well defined and quantified.
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20
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Luk LYP, Loveridge EJ, Allemann RK. Protein motions and dynamic effects in enzyme catalysis. Phys Chem Chem Phys 2016; 17:30817-27. [PMID: 25854702 DOI: 10.1039/c5cp00794a] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The role of protein motions in promoting the chemical step of enzyme catalysed reactions remains a subject of considerable debate. Here, a unified view of the role of protein dynamics in dihydrofolate reductase catalysis is described. Recently the role of such motions has been investigated by characterising the biophysical properties of isotopically substituted enzymes through a combination of experimental and computational analyses. Together with previous work, these results suggest that dynamic coupling to the chemical coordinate is detrimental to catalysis and may have been selected against during DHFR evolution. The full catalytic power of Nature's catalysts appears to depend on finely tuning protein motions in each step of the catalytic cycle.
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Affiliation(s)
- Louis Y P Luk
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
| | - E Joel Loveridge
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
| | - Rudolf K Allemann
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
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21
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Vianello R, Domene C, Mavri J. The Use of Multiscale Molecular Simulations in Understanding a Relationship between the Structure and Function of Biological Systems of the Brain: The Application to Monoamine Oxidase Enzymes. Front Neurosci 2016; 10:327. [PMID: 27471444 PMCID: PMC4945635 DOI: 10.3389/fnins.2016.00327] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 06/28/2016] [Indexed: 01/17/2023] Open
Abstract
HIGHLIGHTS Computational techniques provide accurate descriptions of the structure and dynamics of biological systems, contributing to their understanding at an atomic level.Classical MD simulations are a precious computational tool for the processes where no chemical reactions take place.QM calculations provide valuable information about the enzyme activity, being able to distinguish among several mechanistic pathways, provided a carefully selected cluster model of the enzyme is considered.Multiscale QM/MM simulation is the method of choice for the computational treatment of enzyme reactions offering quantitative agreement with experimentally determined reaction parameters.Molecular simulation provide insight into the mechanism of both the catalytic activity and inhibition of monoamine oxidases, thus aiding in the rational design of their inhibitors that are all employed and antidepressants and antiparkinsonian drugs. Aging society and therewith associated neurodegenerative and neuropsychiatric diseases, including depression, Alzheimer's disease, obsessive disorders, and Parkinson's disease, urgently require novel drug candidates. Targets include monoamine oxidases A and B (MAOs), acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and various receptors and transporters. For rational drug design it is particularly important to combine experimental synthetic, kinetic, toxicological, and pharmacological information with structural and computational work. This paper describes the application of various modern computational biochemistry methods in order to improve the understanding of a relationship between the structure and function of large biological systems including ion channels, transporters, receptors, and metabolic enzymes. The methods covered stem from classical molecular dynamics simulations to understand the physical basis and the time evolution of the structures, to combined QM, and QM/MM approaches to probe the chemical mechanisms of enzymatic activities and their inhibition. As an illustrative example, the later will focus on the monoamine oxidase family of enzymes, which catalyze the degradation of amine neurotransmitters in various parts of the brain, the imbalance of which is associated with the development and progression of a range of neurodegenerative disorders. Inhibitors that act mainly on MAO A are used in the treatment of depression, due to their ability to raise serotonin concentrations, while MAO B inhibitors decrease dopamine degradation and improve motor control in patients with Parkinson disease. Our results give strong support that both MAO isoforms, A and B, operate through the hydride transfer mechanism. Relevance of MAO catalyzed reactions and MAO inhibition in the context of neurodegeneration will be discussed.
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Affiliation(s)
- Robert Vianello
- Computational Organic Chemistry and Biochemistry Group, Ruđer Bošković InstituteZagreb, Croatia
| | - Carmen Domene
- Department of Chemistry, King's College LondonLondon, UK
- Chemistry Research Laboratory, University of OxfordOxford, UK
| | - Janez Mavri
- Department of Computational Biochemistry and Drug Design, National Institute of ChemistryLjubljana, Slovenia
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22
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Abstract
Advances in computational and experimental methods in enzymology have aided comprehension of enzyme-catalyzed chemical reactions. The main difficulty in comparing computational findings to rate measurements is that the first examines a single energy barrier, while the second frequently reflects a combination of many microscopic barriers. We present here intrinsic kinetic isotope effects and their temperature dependence as a useful experimental probe of a single chemical step in a complex kinetic cascade. Computational predictions are tested by this method for two model enzymes: dihydrofolate reductase and thymidylate synthase. The description highlights the significance of collaboration between experimentalists and theoreticians to develop a better understanding of enzyme-catalyzed chemical conversions.
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Affiliation(s)
- P Singh
- University of Iowa, Iowa City, IA, United States
| | - Z Islam
- University of Iowa, Iowa City, IA, United States
| | - A Kohen
- University of Iowa, Iowa City, IA, United States.
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23
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Derakhshani-Molayousefi M, Kashefolgheta S, Eilers JE, Lu Y. Computational Replication of the Primary Isotope Dependence of Secondary Kinetic Isotope Effects in Solution Hydride-Transfer Reactions: Supporting the Isotopically Different Tunneling Ready State Conformations. J Phys Chem A 2016; 120:4277-84. [DOI: 10.1021/acs.jpca.6b03571] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Sadra Kashefolgheta
- Department
of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
- Department of Theory & Bio-systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - James E. Eilers
- Department
of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Yun Lu
- Department
of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
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24
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Ruiz-Pernía JJ, Behiry E, Luk LYP, Loveridge EJ, Tuñón I, Moliner V, Allemann RK. Minimization of dynamic effects in the evolution of dihydrofolate reductase. Chem Sci 2016; 7:3248-3255. [PMID: 29997817 PMCID: PMC6006479 DOI: 10.1039/c5sc04209g] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/02/2016] [Indexed: 11/22/2022] Open
Abstract
Protein isotope labeling is a powerful technique to probe functionally important motions in enzyme catalysis and can be applied to investigate the conformational dynamics of proteins. Previous investigations have indicated that dynamic coupling is detrimental to catalysis by dihydrofolate reductase (DHFR) from the mesophile Escherichia coli (EcDHFR). Comparison of DHFRs from organisms adapted to survive at a wide range of temperatures suggests that dynamic coupling in DHFR catalysis has been minimized during evolution; it arises from reorganizational motions needed to facilitate charge transfer events. Contrary to the behaviour observed for the DHFR from the moderate thermophile Geobacillus stearothermophilus (BsDHFR), the chemical transformation catalyzed by the cold-adapted bacterium Moritella profunda (MpDHFR) is only weakly affected by protein isotope substitutions at low temperatures, but the isotopically substituted enzyme is a substantially inferior catalyst at higher, non-physiological temperatures. QM/MM studies revealed that this behaviour is caused by the enzyme's structural sensitivity to temperature changes, which enhances unfavorable dynamic coupling at higher temperatures by promoting additional recrossing trajectories on the transition state dividing surface. We postulate that these motions are minimized by fine-tuning DHFR flexibility through optimization of the free energy surface of the reaction, such that a nearly static reaction-ready configuration with optimal electrostatic properties is maintained under physiological conditions.
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Affiliation(s)
- J Javier Ruiz-Pernía
- Departament de Química Física i Analítica , Universitat Jaume I , 12071 Castelló , Spain .
| | - Enas Behiry
- School of Chemistry & Cardiff Catalysis Institute , Cardiff University , Park Place , Cardiff , CF10 3AT , UK .
| | - Louis Y P Luk
- School of Chemistry & Cardiff Catalysis Institute , Cardiff University , Park Place , Cardiff , CF10 3AT , UK .
| | - E Joel Loveridge
- School of Chemistry & Cardiff Catalysis Institute , Cardiff University , Park Place , Cardiff , CF10 3AT , UK .
| | - Iñaki Tuñón
- Departament de Química Física , Universitat de València , 46100 Burjassot , Spain .
| | - Vicent Moliner
- Departament de Química Física i Analítica , Universitat Jaume I , 12071 Castelló , Spain .
| | - Rudolf K Allemann
- School of Chemistry & Cardiff Catalysis Institute , Cardiff University , Park Place , Cardiff , CF10 3AT , UK .
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25
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Meisner J, Kästner J. Atom Tunneling in Chemistry. Angew Chem Int Ed Engl 2016; 55:5400-13. [DOI: 10.1002/anie.201511028] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/08/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Jan Meisner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Johannes Kästner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
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26
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Affiliation(s)
- Jan Meisner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Deutschland
| | - Johannes Kästner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Deutschland
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27
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Lameira J, Kupchencko I, Warshel A. Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions. J Phys Chem B 2016; 120:2155-64. [PMID: 26866994 PMCID: PMC5380004 DOI: 10.1021/acs.jpcb.5b11966] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite the enormous increase in computer power, it is still extremely challenging to obtain computationally converging sampling of ab initio QM/MM (QM(ai)/MM) free energy surfaces in condensed phases. The sampling problem can be significantly reduced by the use of the reference potential paradynamics (PD) approach, but even this approach still requires major computer time in studies of enzymatic reactions. To further reduce the sampling problem we developed here a new PD version where we use an empirical valence bond reference potential that has a minimum rather than a maximum at the transition state region of the target potential (this is accomplished conveniently by shifting the EVB of the product state). Hence, we can map the TS region in a more efficient way. Here, we introduce and validate the inverted EVB PD approach. The validation involves the study of the S(N)2 step of the reaction catalyzed by haloakene dehalogenase (DhlA) and the GTP hydrolysis in the RasGAP system. In addition, we have also studied the corresponding reaction in water for each of the systems described here and the reaction involving trimethylsulfonium and dimethylamine in solution. The results are encouraging and the new strategy appears to provide a powerful way of evaluating QM(ai)/MM activation free energies.
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Affiliation(s)
- Jerônimo Lameira
- Department of Chemistry (SGM418), University of Southern California , 3620 McClintock Avenue, Los Angeles, California 90089, United States
- Faculdade de Biotecnologia e Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará , 66075-110, Belém, Pará, Brazil
| | - Ilya Kupchencko
- Department of Chemistry (SGM418), University of Southern California , 3620 McClintock Avenue, Los Angeles, California 90089, United States
| | - Arieh Warshel
- Department of Chemistry (SGM418), University of Southern California , 3620 McClintock Avenue, Los Angeles, California 90089, United States
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28
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Francis K, Sapienza PJ, Lee AL, Kohen A. The Effect of Protein Mass Modulation on Human Dihydrofolate Reductase. Biochemistry 2016; 55:1100-6. [PMID: 26813442 DOI: 10.1021/acs.biochem.5b00945] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydrofolate reductase (DHFR) from Escherichia coli has long served as a model enzyme with which to elucidate possible links between protein dynamics and the catalyzed reaction. Such physical properties of its human counterpart have not been rigorously studied so far, but recent computer-based simulations suggest that these two DHFRs differ significantly in how closely coupled the protein dynamics and the catalyzed C-H → C hydride transfer step are. To test this prediction, two contemporary probes for studying the effect of protein dynamics on catalysis were combined here: temperature dependence of intrinsic kinetic isotope effects (KIEs), which are sensitive to the physical nature of the chemical step, and protein mass modulation, which slows down fast dynamics (femto- to picosecond time scale) throughout the protein. The intrinsic H/T KIEs of human DHFR, like those of E. coli DHFR, are shown to be temperature-independent in the range from 5 to 45 °C, indicating fast sampling of donor and acceptor distances (DADs) at the reaction's transition state (or tunneling ready state, TRS). Mass modulation of these enzymes through isotopic labeling with (13)C, (15)N, and (2)H at nonexchangeable hydrogens yields an 11% heavier enzyme. The additional mass has no effect on the intrinsic KIEs of the human enzyme. This finding indicates that the mass modulation of the human DHFR affects neither DAD distribution nor the DAD's conformational sampling dynamics. Furthermore, reduction in the enzymatic turnover number and the dissociation rate constant for the product indicate that the isotopic substitution affects kinetic steps that are not the catalyzed C-H → C hydride transfer. The findings are discussed in terms of fast dynamics and their role in catalysis, the comparison of calculations and experiments, and the interpretation of isotopically modulated heavy enzymes in general.
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Affiliation(s)
- Kevin Francis
- The Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Paul J Sapienza
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Andrew L Lee
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Amnon Kohen
- The Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
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29
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Dixit M, Das S, Mhashal A, Eitan R, Major D. Practical Aspects of Multiscale Classical and Quantum Simulations of Enzyme Reactions. Methods Enzymol 2016; 577:251-86. [DOI: 10.1016/bs.mie.2016.05.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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30
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Šebesta F, Burda JV. Reduction Process of Tetraplatin in the Presence of Deoxyguanosine Monophosphate (dGMP): A Computational DFT Study. Chemistry 2015; 22:1037-47. [PMID: 26663432 DOI: 10.1002/chem.201503555] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 10/15/2015] [Indexed: 01/01/2023]
Abstract
The reduction mechanism of [Pt(IV) (dach)Cl4 ] (dach=diaminocyclohexyl) in the presence of dGMP was studied. The first step is substitution of a chloro ligand by dGMP, followed by nucleophilic attack of a phosphate or sugar oxygen atom to the C8-position of guanine. Subsequent reduction forms the [Pt(II) (dach)Cl2 ] complex. The whole process is completed by a hydrolysis. Two different pathways for the substitution reaction were examined: a direct associative and a Basolo-Pearson autocatalytic mechanism. All the explored structures were optimized at the B3LYP-D3/6-31G(d) level and by using the COSMO solvation model with Klamt's radii. Single-point energetics was determined at the B3LYP-GD3BJ/6-311++G(2df,2pd)/PCM/scaled-UAKS level. Activation barriers were used for an estimation of the rate constants and these were compared with experimental values. It was found that the rate-determining step is the nucleophilic attack with a slightly faster performance in the 3'-dGMP branch than in the case of 5'-dGMP with activation barriers of 21.1 and 20.4 kcal mol(-1) (experimental: 23.8 and 23.2 kcal mol(-1) ). The reduction reaction is connected with an electron flow from guanine. The product of the reduction reaction is a chelate structure, which dissociates within the last reaction step, that is, a hydrolysis reaction. The whole redox process (substitution, reduction, and hydrolysis) is exergonic by 34 and 28 kcal mol(-1) for 5'-dGMP and 3'-dGMP, respectively.
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Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague 2, Czech Republic
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague 2, Czech Republic.
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31
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Vardi-Kilshtain A, Nitoker N, Major DT. Nuclear quantum effects and kinetic isotope effects in enzyme reactions. Arch Biochem Biophys 2015; 582:18-27. [DOI: 10.1016/j.abb.2015.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/02/2015] [Accepted: 03/03/2015] [Indexed: 11/28/2022]
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32
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Hoeven R, Heyes DJ, Hay S, Scrutton NS. Does the pressure dependence of kinetic isotope effects report usefully on dynamics in enzyme H-transfer reactions? FEBS J 2015; 282:3243-55. [PMID: 25581554 PMCID: PMC4949571 DOI: 10.1111/febs.13193] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/15/2014] [Accepted: 01/08/2015] [Indexed: 11/30/2022]
Abstract
The temperature dependence of kinetic isotope effects (KIEs) has emerged as the main experimental probe of enzymatic H-transfer by quantum tunnelling. Implicit in the interpretation is a presumed role for dynamic coupling of H-transfer chemistry to the protein environment, the so-called 'promoting motions/vibrations hypothesis'. This idea remains contentious, and others have questioned the importance and/or existence of promoting motions/vibrations. New experimental methods of addressing this problem are emerging, including use of mass-modulated enzymes and time-resolved spectroscopy. The pressure dependence of KIEs has been considered as a potential probe of quantum tunnelling reactions, because semi-classical KIEs, which are defined by differences in zero-point vibrational energy, are relatively insensitive to kbar changes in pressure. Reported combined pressure and temperature (p-T) dependence studies of H-transfer reactions are, however, limited. Here, we extend and review the available p-T studies that have utilized well-defined experimental systems in which quantum mechanical tunnelling is established. These include flavoproteins, quinoproteins, light-activated enzymes and chemical model systems. We show that there is no clear general trend between the p-T dependencies of the KIEs in these systems. Given the complex nature of p-T studies, we conclude that computational simulations using determined (e.g. X-ray) structures are also needed alongside experimental measurements of reaction rates/KIEs to guide the interpretation of p-T effects. In providing new insight into H-transfer/environmental coupling, combined approaches that unite both atomistic understanding with experimental rate measurements will require careful evaluation on a case-by-case basis. Although individually informative, we conclude that p-T studies do not provide the more generalized insight that has come from studies of the temperature dependence of KIEs.
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Affiliation(s)
- Robin Hoeven
- Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, UK
| | - Derren J Heyes
- Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, UK
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33
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Luk LYP, Ruiz-Pernía JJ, Adesina AS, Loveridge EJ, Tuñón I, Moliner V, Allemann RK. Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase. Angew Chem Int Ed Engl 2015; 54:9016-20. [PMID: 26079622 PMCID: PMC4985705 DOI: 10.1002/anie.201503968] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 11/21/2022]
Abstract
Chemical ligation has been used to alter motions in specific regions of dihydrofolate reductase from E. coli and to investigate the effects of localized motional changes on enzyme catalysis. Two isotopic hybrids were prepared; one with the mobile N-terminal segment containing heavy isotopes ((2) H, (13) C, (15) N) and the remainder of the protein with natural isotopic abundance, and the other one with only the C-terminal segment isotopically labeled. Kinetic investigations indicated that isotopic substitution of the N-terminal segment affected only a physical step of catalysis, whereas the enzyme chemistry was affected by protein motions from the C-terminal segment. QM/MM studies support the idea that dynamic effects on catalysis mostly originate from the C-terminal segment. The use of isotope hybrids provides insights into the microscopic mechanism of dynamic coupling, which is difficult to obtain with other studies, and helps define the dynamic networks of intramolecular interactions central to enzyme catalysis.
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Affiliation(s)
- Louis Y P Luk
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT (UK)
| | - J Javier Ruiz-Pernía
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló (Spain)
| | | | - E Joel Loveridge
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT (UK)
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot (Spain).
| | - Vincent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló (Spain).
| | - Rudolf K Allemann
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT (UK).
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34
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Luk LYP, Ruiz-Pernía JJ, Adesina AS, Loveridge EJ, Tuñón I, Moliner V, Allemann RK. Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503968] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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Singh P, Francis K, Kohen A. Network of remote and local protein dynamics in dihydrofolate reductase catalysis. ACS Catal 2015; 5:3067-3073. [PMID: 27182453 DOI: 10.1021/acscatal.5b00331] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics calculations and bionformatic studies of dihydrofolate reductase (DHFR) have suggested a network of coupled motions across the whole protein that is correlated to the reaction coordinate. Experimental studies demonstrated that distal residues G121, M42 and F125 in E. coli DHFR participate in that network. The missing link in our understanding of DHFR catalysis is the lack of a mechanism by which such remote residues can affect the catalyzed chemistry at the active site. Here, we present a study of the temperature dependence of intrinsic kinetic isotope effects (KIEs) that indicates synergism between a remote residue in that dynamic network, G121, and the active site's residue I14. The intrinsic KIEs for the I14A-G121V double mutant showed steeper temperature dependence (ΔEa(T-H)) than expected from comparison of the wild type and two single mutants. That effect was non-additive, i.e., ΔEa(T-H)G121V +ΔEa(T-H) I14A < ΔEa(T-H) double mutant, which indicates a synergism between the two residues. This finding links the remote residues in the network under investigation to the enzyme's active site, providing a mechanism by which these residues can be coupled to the catalyzed chemistry. This experimental evidence validates calculations proposing that both remote and active site residues constitute a network of coupled promoting motions correlated to the bond activation step (C-H→C hydride transfer in this case). Additionally, the effect of I14A and G121V mutations on single turnover rates was additive rather than synergistic. Although single turnover rate measurements are more readily available and thus more popular than assessing intrinsic kinetic isotope effects, the current finding demonstrates that for these rates, which in DHFR reflect several microscopic rate constants, can fall short of revealing the nature of the C-H bond activation per se.
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Affiliation(s)
- Priyanka Singh
- The Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Kevin Francis
- The Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Amnon Kohen
- The Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
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36
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Lameira J, Ram Prasad B, Chu ZT, Warshel A. Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization. Proteins 2015; 83:318-30. [PMID: 25388538 PMCID: PMC4300294 DOI: 10.1002/prot.24717] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 10/30/2014] [Accepted: 11/03/2014] [Indexed: 11/05/2022]
Abstract
The enzyme catechol O-methyltransferase (COMT) catalyzes the transfer of a methyl group from S-adenosylmethionine to dopamine and related catechols. The search for the origin of COMT catalysis has led to different proposals and hypothesis, including the entropic, the NAC, and the compression proposals as well as the more reasonable electrostatic idea. Thus, it is important to understand the catalytic power of this enzyme and to examine the validity of different proposals and in particular the repeated recent implication of the compression idea. The corresponding analysis should be done by well-defined physically-based considerations that involve computations rather than circular interpretations of experimental results. Thus, we explore here the origin of the catalytic efficiency of COMT by using the empirical valence bond and the linear response approximation approaches. The results demonstrate that the catalytic effect of COMT is mainly due to electrostatic preorganization effects. It is also shown that the compression, NAC and entropic proposals do not account for the catalytic effect.
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Affiliation(s)
- Jeronimo Lameira
- University of Southern California, Department of Chemistry, SGM 418, 3620 McClintosk Avenue, Los Angeles, California 90089, United States
- Faculdade de Biotecnologia e Laboratório de Planejamento e Desenvolvimento de Fármacos; Universidade Federal do Pará, 66075-110, Belém, PA, Brazil
| | - B Ram Prasad
- University of Southern California, Department of Chemistry, SGM 418, 3620 McClintosk Avenue, Los Angeles, California 90089, United States
| | - Zhen T. Chu
- University of Southern California, Department of Chemistry, SGM 418, 3620 McClintosk Avenue, Los Angeles, California 90089, United States
| | - Arieh Warshel
- University of Southern California, Department of Chemistry, SGM 418, 3620 McClintosk Avenue, Los Angeles, California 90089, United States
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37
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Singh P, Abeysinghe T, Kohen A. Linking protein motion to enzyme catalysis. Molecules 2015; 20:1192-209. [PMID: 25591120 PMCID: PMC4341894 DOI: 10.3390/molecules20011192] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 01/07/2015] [Indexed: 12/01/2022] Open
Abstract
Enzyme motions on a broad range of time scales can play an important role in various intra- and intermolecular events, including substrate binding, catalysis of the chemical conversion, and product release. The relationship between protein motions and catalytic activity is of contemporary interest in enzymology. To understand the factors influencing the rates of enzyme-catalyzed reactions, the dynamics of the protein-solvent-ligand complex must be considered. The current review presents two case studies of enzymes—dihydrofolate reductase (DHFR) and thymidylate synthase (TSase)—and discusses the role of protein motions in their catalyzed reactions. Specifically, we will discuss the utility of kinetic isotope effects (KIEs) and their temperature dependence as tools in probing such phenomena.
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Affiliation(s)
- Priyanka Singh
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA.
| | - Thelma Abeysinghe
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA.
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA.
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38
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Johannissen LO, Hay S, Scrutton NS. Nuclear quantum tunnelling in enzymatic reactions – an enzymologist's perspective. Phys Chem Chem Phys 2015; 17:30775-82. [DOI: 10.1039/c5cp00614g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The roles of nuclear quantum tunnelling and dynamics in enzyme reactions are discussed in this perspective on H-transfer reactions.
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Affiliation(s)
- Linus O. Johannissen
- SYNBIOCHEM
- Manchester Institute of Biotechnology
- Faculty of Life Sciences
- The University of Manchester
- Manchester M1 7DN
| | - Sam Hay
- SYNBIOCHEM
- Manchester Institute of Biotechnology
- Faculty of Life Sciences
- The University of Manchester
- Manchester M1 7DN
| | - Nigel S. Scrutton
- SYNBIOCHEM
- Manchester Institute of Biotechnology
- Faculty of Life Sciences
- The University of Manchester
- Manchester M1 7DN
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39
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Tuszynski JA, Winter P, White D, Tseng CY, Sahu KK, Gentile F, Spasevska I, Omar SI, Nayebi N, Churchill CD, Klobukowski M, El-Magd RMA. Mathematical and computational modeling in biology at multiple scales. Theor Biol Med Model 2014; 11:52. [PMID: 25542608 PMCID: PMC4396153 DOI: 10.1186/1742-4682-11-52] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 11/25/2014] [Indexed: 01/08/2023] Open
Abstract
A variety of topics are reviewed in the area of mathematical and computational modeling in biology, covering the range of scales from populations of organisms to electrons in atoms. The use of maximum entropy as an inference tool in the fields of biology and drug discovery is discussed. Mathematical and computational methods and models in the areas of epidemiology, cell physiology and cancer are surveyed. The technique of molecular dynamics is covered, with special attention to force fields for protein simulations and methods for the calculation of solvation free energies. The utility of quantum mechanical methods in biophysical and biochemical modeling is explored. The field of computational enzymology is examined.
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Affiliation(s)
- Jack A Tuszynski
- Department of Physics and Department of Oncology, University of Alberta, Edmonton, Canada.
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40
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Liu CT, Francis K, Layfield JP, Huang X, Hammes-Schiffer S, Kohen A, Benkovic SJ. Escherichia coli dihydrofolate reductase catalyzed proton and hydride transfers: temporal order and the roles of Asp27 and Tyr100. Proc Natl Acad Sci U S A 2014; 111:18231-6. [PMID: 25453098 PMCID: PMC4280594 DOI: 10.1073/pnas.1415940111] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The reaction catalyzed by Escherichia coli dihydrofolate reductase (ecDHFR) has become a model for understanding enzyme catalysis, and yet several details of its mechanism are still unresolved. Specifically, the mechanism of the chemical step, the hydride transfer reaction, is not fully resolved. We found, unexpectedly, the presence of two reactive ternary complexes [enzyme:NADPH:7,8-dihydrofolate (E:NADPH:DHF)] separated by one ionization event. Furthermore, multiple kinetic isotope effect (KIE) studies revealed a stepwise mechanism in which protonation of the DHF precedes the hydride transfer from the nicotinamide cofactor (NADPH) for both reactive ternary complexes of the WT enzyme. This mechanism was supported by the pH- and temperature-independent intrinsic KIEs for the C-H→C hydride transfer between NADPH and the preprotonated DHF. Moreover, we showed that active site residues D27 and Y100 play a synergistic role in facilitating both the proton transfer and subsequent hydride transfer steps. Although D27 appears to have a greater effect on the overall rate of conversion of DHF to tetrahydrofolate, Y100 plays an important electrostatic role in modulating the pKa of the N5 of DHF to enable the preprotonation of DHF by an active site water molecule.
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Affiliation(s)
- C Tony Liu
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
| | - Kevin Francis
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242; and
| | - Joshua P Layfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801-3364
| | - Xinyi Huang
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801-3364
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242; and
| | - Stephen J Benkovic
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802;
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41
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Doron D, Stojković V, Gakhar L, Vardi-Kilshtain A, Kohen A, Major DT. Free energy simulations of active-site mutants of dihydrofolate reductase. J Phys Chem B 2014; 119:906-16. [PMID: 25382260 DOI: 10.1021/jp5059963] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This study employs hybrid quantum mechanics-molecular mechanics (QM/MM) simulations to investigate the effect of mutations of the active-site residue I14 of E. coli dihydrofolate reductase (DHFR) on the hydride transfer. Recent kinetic measurements of the I14X mutants (X = V, A, and G) indicated slower hydride transfer rates and increasingly temperature-dependent kinetic isotope effects (KIEs) with systematic reduction of the I14 side chain. The QM/MM simulations show that when the original isoleucine residue is substituted in silico by valine, alanine, or glycine (I14V, I14A, and I14G DHFR, respectively), the free energy barrier height of the hydride transfer reaction increases relative to the wild-type enzyme. These trends are in line with the single-turnover rate measurements reported for these systems. In addition, extended dynamics simulations of the reactive Michaelis complex reveal enhanced flexibility in the mutants, and in particular for the I14G mutant, including considerable fluctuations of the donor-acceptor distance (DAD) and the active-site hydrogen bonding network compared with those detected in the native enzyme. These observations suggest that the perturbations induced by the mutations partly impair the active-site environment in the reactant state. On the other hand, the average DADs at the transition state of all DHFR variants are similar. Crystal structures of I14 mutants (V, A, and G) confirmed the trend of increased flexibility of the M20 and other loops.
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Affiliation(s)
- Dvir Doron
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University , Ramat-Gan 5290002, Israel
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42
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Carvalho ATP, Barrozo A, Doron D, Kilshtain AV, Major DT, Kamerlin SCL. Challenges in computational studies of enzyme structure, function and dynamics. J Mol Graph Model 2014; 54:62-79. [PMID: 25306098 DOI: 10.1016/j.jmgm.2014.09.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 09/13/2014] [Accepted: 09/16/2014] [Indexed: 01/23/2023]
Abstract
In this review we give an overview of the field of Computational enzymology. We start by describing the birth of the field, with emphasis on the work of the 2013 chemistry Nobel Laureates. We then present key features of the state-of-the-art in the field, showing what theory, accompanied by experiments, has taught us so far about enzymes. We also briefly describe computational methods, such as quantum mechanics-molecular mechanics approaches, reaction coordinate treatment, and free energy simulation approaches. We finalize by discussing open questions and challenges.
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Affiliation(s)
- Alexandra T P Carvalho
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Alexandre Barrozo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Dvir Doron
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Alexandra Vardi Kilshtain
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry Bar-Ilan University, Ramat-Gan 52900, Israel.
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
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43
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Luk LP, Loveridge EJ, Allemann RK. Different dynamical effects in mesophilic and hyperthermophilic dihydrofolate reductases. J Am Chem Soc 2014; 136:6862-5. [PMID: 24779446 PMCID: PMC4046772 DOI: 10.1021/ja502673h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Indexed: 01/18/2023]
Abstract
The role of protein dynamics in the reaction catalyzed by dihydrofolate reductase from the hyperthermophile Thermotoga maritima (TmDHFR) has been examined by enzyme isotope substitution ((15)N, (13)C, (2)H). In contrast to all other enzyme reactions investigated previously, including DHFR from Escherichia coli (EcDHFR), for which isotopic substitution led to decreased reactivity, the rate constant for the hydride transfer step is not affected by isotopic substitution of TmDHFR. TmDHFR therefore appears to lack the coupling of protein motions to the reaction coordinate that have been identified for EcDHFR catalysis. Clearly, dynamical coupling is not a universal phenomenon that affects the efficiency of enzyme catalysis.
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Affiliation(s)
- Louis
Y. P. Luk
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - E. Joel Loveridge
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Rudolf K. Allemann
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
- Cardiff
Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
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44
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Doron D, Kohen A, Nam K, Major DT. How Accurate Are Transition States from Simulations of Enzymatic Reactions? J Chem Theory Comput 2014; 10:1863-1871. [PMID: 24860275 PMCID: PMC4025581 DOI: 10.1021/ct5000742] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Indexed: 11/30/2022]
Abstract
The rate expression of traditional transition state theory (TST) assumes no recrossing of the transition state (TS) and thermal quasi-equilibrium between the ground state and the TS. Currently, it is not well understood to what extent these assumptions influence the nature of the activated complex obtained in traditional TST-based simulations of processes in the condensed phase in general and in enzymes in particular. Here we scrutinize these assumptions by characterizing the TSs for hydride transfer catalyzed by the enzyme Escherichia coli dihydrofolate reductase obtained using various simulation approaches. Specifically, we compare the TSs obtained with common TST-based methods and a dynamics-based method. Using a recently developed accurate hybrid quantum mechanics/molecular mechanics potential, we find that the TST-based and dynamics-based methods give considerably different TS ensembles. This discrepancy, which could be due equilibrium solvation effects and the nature of the reaction coordinate employed and its motion, raises major questions about how to interpret the TSs determined by common simulation methods. We conclude that further investigation is needed to characterize the impact of various TST assumptions on the TS phase-space ensemble and on the reaction kinetics.
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Affiliation(s)
- Dvir Doron
- Department
of Chemistry and the Lise Meitner-Minerva Center of Computational
Quantum Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Amnon Kohen
- Department
of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Kwangho Nam
- Department
of Chemistry and Computational Life Science Cluster (CLiC), Umeå University, 901 87 Umeå, Sweden
| | - Dan Thomas Major
- Department
of Chemistry and the Lise Meitner-Minerva Center of Computational
Quantum Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
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45
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Roston D, Kohen A, Doron D, Major DT. Simulations of remote mutants of dihydrofolate reductase reveal the nature of a network of residues coupled to hydride transfer. J Comput Chem 2014; 35:1411-7. [PMID: 24798860 DOI: 10.1002/jcc.23629] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/11/2014] [Accepted: 04/06/2014] [Indexed: 11/07/2022]
Abstract
Recent experimental and theoretical studies have proposed that enzymes involve networks of coupled residues throughout the protein that participate in motions accompanying chemical barrier crossing. Here, we have examined portions of a proposed network in dihydrofolate reductase (DHFR) using quantum mechanics/molecular mechanics simulations. The simulations use a hybrid quantum mechanics-molecular mechanics approach with a recently developed semiempirical AM1-SRP Hamiltonian that provides accurate results for this reaction. The simulations reproduce experimentally determined catalytic rates for the wild type and distant mutants of E. coli DHFR, underscoring the accuracy of the simulation protocol. Additionally, the simulations provide detailed insight into how residues remote from the active site affect the catalyzed chemistry, through changes in the thermally averaged properties along the reaction coordinate. The mutations do not greatly affect the structure of the transition state near the bond activation, but we observe differences somewhat removed from the point of C-H cleavage that affect the rate. The mutations have global effects on the thermally averaged structure that propagate throughout the enzyme and the current simulations highlight several interactions that appear to be particularly important.
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Affiliation(s)
- Daniel Roston
- Department of Chemistry, University of Iowa, Iowa City, Iowa, 52242
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46
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Affiliation(s)
- Joshua P. Layfield
- Department of Chemistry, 600 South Mathews Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Sharon Hammes-Schiffer
- Department of Chemistry, 600 South Mathews Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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47
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Francis K, Stojković V, Kohen A. Preservation of protein dynamics in dihydrofolate reductase evolution. J Biol Chem 2013; 288:35961-8. [PMID: 24158440 PMCID: PMC3861645 DOI: 10.1074/jbc.m113.507632] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 10/09/2013] [Indexed: 11/06/2022] Open
Abstract
The hydride transfer reaction catalyzed by dihydrofolate reductase (DHFR) is a model for examining how protein dynamics contribute to enzymatic function. The relationship between functional motions and enzyme evolution has attracted significant attention. Recent studies on N23PP Escherichia coli DHFR (ecDHFR) mutant, designed to resemble parts of the human enzyme, indicated a reduced single turnover rate. NMR relaxation dispersion experiments with that enzyme showed rigidification of millisecond Met-20 loop motions (Bhabha, G., Lee, J., Ekiert, D. C., Gam, J., Wilson, I. A., Dyson, H. J., Benkovic, S. J., and Wright, P. E. (2011) Science 332, 234-238). A more recent study of this mutant, however, indicated that fast motions along the reaction coordinate are actually more dispersed than for wild-type ecDHFR (WT). Furthermore, a double mutant (N23PP/G51PEKN) that better mimics the human enzyme seems to restore both the single turnover rates and narrow distribution of fast dynamics (Liu, C. T., Hanoian, P., French, T. H., Hammes-Schiffer, S., and Benkovic, S. J. (2013) Proc. Natl. Acad. Sci. U.S.A. 110, 10159-11064). Here, we measured intrinsic kinetic isotope effects for both N23PP and N23PP/G51PEKN double mutant DHFRs over a temperature range. The findings indicate that although the C-H→C transfer and dynamics along the reaction coordinate are impaired in the altered N23PP mutant, both seem to be restored in the N23PP/G51PEKN double mutant. This indicates that the evolution of G51PEKN, although remote from the Met-20 loop, alleviated the loop rigidification that would have been caused by N23PP, enabling WT-like H-tunneling. The correlation between the calculated dynamics, the nature of C-H→C transfer, and a phylogenetic analysis of DHFR sequences are consistent with evolutionary preservation of the protein dynamics to enable H-tunneling from well reorganized active sites.
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Affiliation(s)
- Kevin Francis
- From the Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242
| | - Vanja Stojković
- From the Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242
| | - Amnon Kohen
- From the Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242
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48
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Ruiz-Pernia JJ, Luk LYP, García-Meseguer R, Martí S, Loveridge EJ, Tuñón I, Moliner V, Allemann RK. Increased dynamic effects in a catalytically compromised variant of Escherichia coli dihydrofolate reductase. J Am Chem Soc 2013; 135:18689-96. [PMID: 24252106 PMCID: PMC3949409 DOI: 10.1021/ja410519h] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Indexed: 01/19/2023]
Abstract
Isotopic substitution ((15)N, (13)C, (2)H) of a catalytically compromised variant of Escherichia coli dihydrofolate reductase, EcDHFR-N23PP/S148A, has been used to investigate the effect of these mutations on catalysis. The reduction of the rate constant of the chemical step in the EcDHFR-N23PP/S148A catalyzed reaction is essentially a consequence of an increase of the quasi-classical free energy barrier and to a minor extent of an increased number of recrossing trajectories on the transition state dividing surface. Since the variant enzyme is less well set up to catalyze the reaction, a higher degree of active site reorganization is needed to reach the TS. Although millisecond active site motions are lost in the variant, there is greater flexibility on the femtosecond time scale. The "dynamic knockout" EcDHFR-N23PP/S148A is therefore a "dynamic knock-in" at the level of the chemical step, and the increased dynamic coupling to the chemical coordinate is in fact detrimental to catalysis. This finding is most likely applicable not just to hydrogen transfer in EcDHFR but also to other enzymatic systems.
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Affiliation(s)
- J. Javier Ruiz-Pernia
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castello, Spain
| | - Louis Y. P. Luk
- School
of Chemistry & Cardiff Catalysis Institute, Cardiff University, Park Place, Cardiff, CF10
3AT, U.K.
| | | | - Sergio Martí
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castello, Spain
| | - E. Joel Loveridge
- School
of Chemistry & Cardiff Catalysis Institute, Cardiff University, Park Place, Cardiff, CF10
3AT, U.K.
| | - Iñaki Tuñón
- Departament
de Química Física, Universitat
de València, 46100 Burjassot, Spain
| | - Vicent Moliner
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castello, Spain
| | - Rudolf K. Allemann
- School
of Chemistry & Cardiff Catalysis Institute, Cardiff University, Park Place, Cardiff, CF10
3AT, U.K.
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49
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Plotnikov NV, Prasad BR, Chakrabarty S, Chu ZT, Warshel A. Quantifying the mechanism of phosphate monoester hydrolysis in aqueous solution by evaluating the relevant ab initio QM/MM free-energy surfaces. J Phys Chem B 2013; 117:12807-19. [PMID: 23601038 DOI: 10.1021/jp4020146] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Understanding the nature of the free-energy surfaces for phosphate hydrolysis is a prerequisite for understanding the corresponding key chemical reactions in biology. Here, the challenge has been to move to careful ab initio QM/MM (QM(ai)/MM) free-energy calculations, where obtaining converging results is very demanding and computationally expensive. This work describes such calculations, focusing on the free-energy surface for the hydrolysis of phosphate monoesters, paying special attention to the comparison between the one water (1W) and two water (2W) paths for the proton-transfer (PT) step. This issue has been explored before by energy minimization with implicit solvent models and by nonsystematic QM/MM energy minimization, as well as by nonsystematic free-energy mapping. However, no study has provided the needed reliable 2D (3D) surfaces that are necessary for reaching concrete conclusions. Here we report a systematic evaluation of the 2D (3D) free-energy maps for several relevant systems, comparing the results of QM(ai)/MM and QM(ai)/implicit solvent surfaces, and provide an advanced description of the relevant energetics. It is found that the 1W path for the hydrolysis of the methyl diphosphate (MDP) trianion is 6-9 kcal/mol higher than that the 2W path. This difference becomes slightly larger in the presence of the Mg(2+) ion because this ion reduces the pKa of the conjugated acid form of the phosphate oxygen that accepts the proton. Interestingly, the BLYP approach (which has been used extensively in some studies) gives a much smaller difference between the 1W and 2W activation barriers. At any rate, it is worth pointing out that the 2W transition state for the PT is not much higher that the common plateau that serves as the starting point of both the 1W and 2W PT paths. Thus, the calculated catalytic effects of proteins based on the 2W PT mechanistic model are not expected to be different from the catalytic effects predicted using the 1W PT mechanistic model, which was calibrated on the observed barrier in solution and in which the TS charge distribution was similar to the that of the plateau (as was done in all of our previous EVB studies).
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Affiliation(s)
- Nikolay V Plotnikov
- Department of Chemistry, University of Southern California , SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, United States
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Roston D, Islam Z, Kohen A. Isotope effects as probes for enzyme catalyzed hydrogen-transfer reactions. Molecules 2013; 18:5543-67. [PMID: 23673528 PMCID: PMC4342783 DOI: 10.3390/molecules18055543] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 04/30/2013] [Accepted: 05/03/2013] [Indexed: 11/16/2022] Open
Abstract
Kinetic Isotope effects (KIEs) have long served as a probe for the mechanisms of both enzymatic and solution reactions. Here, we discuss various models for the physical sources of KIEs, how experimentalists can use those models to interpret their data, and how the focus of traditional models has grown to a model that includes motion of the enzyme and quantum mechanical nuclear tunneling. We then present two case studies of enzymes, thymidylate synthase and alcohol dehydrogenase, and discuss how KIEs have shed light on the C-H bond cleavages those enzymes catalyze. We will show how the combination of both experimental and computational studies has changed our notion of how these enzymes exert their catalytic powers.
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Affiliation(s)
| | | | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
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