1
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Smith N, Horswill AR, Wilson MA. X-ray-driven chemistry and conformational heterogeneity in atomic resolution crystal structures of bacterial dihydrofolate reductases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.566054. [PMID: 37986818 PMCID: PMC10659368 DOI: 10.1101/2023.11.07.566054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Dihydrofolate reductase (DHFR) catalyzes the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate. Bacterial DHFRs are targets of several important antibiotics as well as model enzymes for the role of protein conformational dynamics in enzyme catalysis. We collected 0.93 Å resolution X-ray diffraction data from both Bacillus subtilis (Bs) and E. coli (Ec) DHFRs bound to folate and NADP+. These oxidized ternary complexes should not be able to perform chemistry, however electron density maps suggest hydride transfer is occurring in both enzymes. Comparison of low- and high-dose EcDHFR datasets show that X-rays drive partial production of tetrahydrofolate. Hydride transfer causes the nicotinamide moiety of NADP+ to move towards the folate as well as correlated shifts in nearby residues. Higher radiation dose also changes the conformational heterogeneity of Met20 in EcDHFR, supporting a solvent gating role during catalysis. BsDHFR has a different pattern of conformational heterogeneity and an unexpected disulfide bond, illustrating important differences between bacterial DHFRs. This work demonstrates that X-rays can drive hydride transfer similar to the native DHFR reaction and that X-ray photoreduction can be used to interrogate catalytically relevant enzyme dynamics in favorable cases.
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Affiliation(s)
- Nathan Smith
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588
| | - Alexander R. Horswill
- Department of Immunology & Microbiology, University of Colorado Anschutz School of Medicine, Aurora, CO 80045
| | - Mark A. Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588
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2
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Andrews BA, Dyer RB. Comparison of the Role of Protein Dynamics in Catalysis by Dihydrofolate Reductase from E. coli and H. sapiens. J Phys Chem B 2022; 126:7126-7134. [PMID: 36069763 DOI: 10.1021/acs.jpcb.2c05112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dihydrofolate reductase (DHFR) is a well-studied, clinically relevant enzyme known for being highly dynamic over the course of its catalytic cycle. However, the role dynamic motions play in the explicit hydride transfer from the nicotinamide cofactor to the dihydrofolate substrate remains unclear because reaction initiation and direct spectroscopic examination on the appropriate time scale for such femtosecond to picosecond motions is challenging. Here, we employ pre-steady-state kinetics to observe the hydride transfer as directly as possible in two different species of DHFR: Escherichia coli and Homo sapiens. While the hydride transfer has been well-characterized in DHFR from E. coli, improvements in time resolution now allow for sub-millisecond dead times for stopped-flow spectroscopy, which reveals that the maximum rate is indeed faster than previously recorded. The rate in the human enzyme, previously only estimated, is also able to be directly observed using cutting-edge stopped-flow instrumentation. In addition to the pH dependence of the hydride transfer rates for both enzymes, we examine the primary H/D kinetic isotope effect to reveal a temperature dependence in the human enzyme that is absent from the E. coli counterpart. This dependence, which appears above a temperature of 15 °C is a shared feature among other hydride transfer enzymes and is also consistent with computational work suggesting the presence of a fast promoting-vibration that provides donor-acceptor compression on the time scale of catalysis to facilitate the chemistry step.
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Affiliation(s)
- Brooke A Andrews
- Chemistry Department, Emory University, Atlanta, Georgia 30322, United States
| | - R Brian Dyer
- Chemistry Department, Emory University, Atlanta, Georgia 30322, United States
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3
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Adesina AS, Świderek K, Luk LYP, Moliner V, Allemann RK. Electric Field Measurements Reveal the Pivotal Role of Cofactor-Substrate Interaction in Dihydrofolate Reductase Catalysis. ACS Catal 2020; 10:7907-7914. [PMID: 32905264 PMCID: PMC7467645 DOI: 10.1021/acscatal.0c01856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/18/2020] [Indexed: 12/31/2022]
Abstract
![]()
The
contribution of ligand–ligand electrostatic interaction
to transition state formation during enzyme catalysis has remained
unexplored, even though electrostatic forces are known to play a major
role in protein functions and have been investigated by the vibrational
Stark effect (VSE). To monitor electrostatic changes along important
steps during catalysis, we used a nitrile probe (T46C-CN) inserted
proximal to the reaction center of three dihydrofolate reductases
(DHFRs) with different biophysical properties, Escherichia
coli DHFR (EcDHFR), its conformationally impaired variant
(EcDHFR-S148P), and Geobacillus stearothermophilus DHFR (BsDHFR). Our combined experimental and computational approach
revealed that the electric field projected by the substrate toward
the probe negates those exerted by the cofactor when both are bound
within the enzymes. This indicates that compared to previous models
that focus exclusively on subdomain reorganization and protein–ligand
contacts, ligand–ligand interactions are the key driving force
to generate electrostatic environments conducive for catalysis.
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Affiliation(s)
- Aduragbemi S. Adesina
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Louis Y. P. Luk
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Rudolf K. Allemann
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
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4
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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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5
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Evolutionarily Related Dihydrofolate Reductases Perform Coequal Functions Yet Show Divergence in Their Trajectories. Protein J 2018; 37:301-310. [PMID: 30019321 DOI: 10.1007/s10930-018-9784-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The enzyme dihydrofolate reductase (DHFR) catalyzes NADPH dependent reduction of dihydrofolate to tetrahydrofolate. It plays a crucial role in the DNA synthesis. The investigation of evolution of DHFR generates immense curiosity. It aids in predicting how the enzyme has adapted to the surroundings of various cell types. In spite of great similarity in the structure of E. coli DHFR and human DHFR, their primary sequences are divergent to a great extent, which is evident in variations in the kinetics mechanism of their catalysis. In presence of physiological levels of ligands, they possess distinct kinetics and different rate limiting steps. We have reviewed the process of their unfolding and refolding, their behaviour in denaturing conditions and in presence of various chaperones. Although there is structural similarity between these two homologous enzymes yet they have established distinct mechanisms to accomplish the coequal functions.
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6
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Loveridge EJ, Hroch L, Hughes RL, Williams T, Davies RL, Angelastro A, Luk LYP, Maglia G, Allemann RK. Reduction of Folate by Dihydrofolate Reductase from Thermotoga maritima. Biochemistry 2017; 56:1879-1886. [PMID: 28319664 DOI: 10.1021/acs.biochem.6b01268] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mammalian dihydrofolate reductases (DHFRs) catalyze the reduction of folate more efficiently than the equivalent bacterial enzymes do, despite typically having similar efficiencies for the reduction of their natural substrate, dihydrofolate. In contrast, we show here that DHFR from the hyperthermophilic bacterium Thermotoga maritima can catalyze reduction of folate to tetrahydrofolate with an efficiency similar to that of reduction of dihydrofolate under saturating conditions. Nuclear magnetic resonance and mass spectrometry experiments showed no evidence of the production of free dihydrofolate during either the EcDHFR- or TmDHFR-catalyzed reductions of folate, suggesting that both enzymes perform the two reduction steps without release of the partially reduced substrate. Our results imply that the reaction proceeds more efficiently in TmDHFR than in EcDHFR because the more open active site of TmDHFR facilitates protonation of folate. Because T. maritima lives under extreme conditions where tetrahydrofolate is particularly prone to oxidation, this ability to salvage folate may impart an advantage to the bacterium by minimizing the squandering of a valuable cofactor.
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Affiliation(s)
- E Joel Loveridge
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K.,Department of Chemistry, Swansea University , Singleton Park, Swansea SA2 8PP, U.K
| | - Lukas Hroch
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K.,Department of Pharmaceutical Chemistry and Drug Control, Faculty of Pharmacy in Hradec Kralove, Charles University in Prague , Akademika Heyrovskeho 1203, 500 05 Hradec Kralove, Czech Republic
| | - Robert L Hughes
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Thomas Williams
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Rhidian L Davies
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Antonio Angelastro
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Louis Y P Luk
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Giovanni Maglia
- School of Chemical Sciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, U.K
| | - Rudolf K Allemann
- School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, U.K.,School of Chemical Sciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, U.K
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7
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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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8
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Rabelo VW, Sampaio TF, Duarte LD, Lopes DHB, Abreu PA. Structure–activity relationship of a series of 1,2-dihydroquinoline analogues and binding mode with Vibrio cholerae dihydrofolate reductase. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1583-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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9
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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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10
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Mao H, Wu W, She D, Sun G, Lv P, Xu J. Microfluidic surface-enhanced Raman scattering sensors based on nanopillar forests realized by an oxygen-plasma-stripping-of-photoresist technique. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:127-134. [PMID: 23606301 DOI: 10.1002/smll.201300036] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 01/29/2013] [Indexed: 06/02/2023]
Abstract
A novel surface-enhanced Raman scattering (SERS) sensor is developed for real-time and highly repeatable detection of trace chemical and biological indicators. The sensor consists of a polydimethylsiloxane (PDMS) microchannel cap and a nanopillar forest-based open SERS-active substrate. The nanopillar forests are fabricated based on a new oxygen-plasma-stripping-of-photoresist technique. The enhancement factor (EF) of the SERS-active substrate reaches 6.06 × 10(6) , and the EF of the SERS sensor is about 4 times lower due to the influence of the PDMS cap. However, the sensor shows much higher measurement repeatability than the open substrate, and it reduces the sample preparation time from several hours to a few minutes, which makes the device more reliable and facile for trace chemical and biological analysis.
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Affiliation(s)
- Haiyang Mao
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication, Institute of Microelectronics, Peking University, Beijing, 100871, PR China; Key Laboratory of Microelectronics Devices & Integrated Technology, Institute of Microelectronics, Chinese Academy of Sciences, Beijing 100029, PR China; Smart Sensor Engineering Center, Jiangsu R&D Center for Internet of Things, Wuxi 214135, PR China
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11
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Doron D, Kohen A, Major DT. Collective Reaction Coordinate for Hybrid Quantum and Molecular Mechanics Simulations: A Case Study of the Hydride Transfer in Dihydrofolate Reductase. J Chem Theory Comput 2012; 8:2484-96. [PMID: 26588977 DOI: 10.1021/ct300235k] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The optimal description of the reaction coordinate in chemical systems is of great importance in simulating condensed phase reactions. In the current work, we present a collective reaction coordinate which is composed of several geometric coordinates which represent structural progress during the course of a hydride transfer reaction: the antisymmetric reactive stretch coordinate, the donor-acceptor distance (DAD) coordinate, and an orbital rehybridization coordinate. In this approach, the former coordinate serves as a distinguished reaction coordinate, while the latter two serve as environmental, Marcus-type inner-sphere reorganization coordinates. The classical free energy surface is obtained from multidimensional quantum mechanics-molecular mechanics (QM/MM) potential of mean force (PMF) simulations in conjunction with a general and efficient multidimensional weighted histogram method implementation. The minimum free energy path, or the collective reaction coordinate, connecting the dividing hypersurface to reactants and products, is obtained using an iterative scheme. In this approach, the string method is used to find the minimum free energy path. This path guides the multidimensional sampling, while the path is adaptively refined until convergence is achieved. As a model system, we choose the hydride transfer reaction in Escherichia coli dihydrofolate reductase (ecDHFR) using a recently developed accurate semiempirical potential energy surface. To estimate the advantages of the collective reaction coordinate, we perform activated dynamics simulations to obtain the reaction transmission coefficient. The results show that the combination of a distinguished reaction coordinate and an inner-sphere reorganization coordinate considerably reduces the dividing surface recrossing.
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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 52900, Israel
| | - 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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12
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Engel H, Doron D, Kohen A, Major DT. Momentum Distribution as a Fingerprint of Quantum Delocalization in Enzymatic Reactions: Open-Chain Path-Integral Simulations of Model Systems and the Hydride Transfer in Dihydrofolate Reductase. J Chem Theory Comput 2012; 8:1223-34. [DOI: 10.1021/ct200874q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hamutal Engel
- Department of Chemistry and
the Lise Meitner−Minerva Center of Computational Quantum Chemistry,
Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dvir Doron
- Department of Chemistry and
the Lise Meitner−Minerva Center of Computational Quantum Chemistry,
Bar-Ilan University, Ramat-Gan 52900, Israel
| | - 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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13
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Doron D, Major DT, Kohen A, Thiel W, Wu X. Hybrid Quantum and Classical Simulations of the Dihydrofolate Reductase Catalyzed Hydride Transfer Reaction on an Accurate Semi-Empirical Potential Energy Surface. J Chem Theory Comput 2011; 7:3420-37. [PMID: 26598171 DOI: 10.1021/ct2004808] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydrofolate reductase (DHFR) catalyzes the reduction of 7,8-dihydrofolate by nicotinamide adenine dinucleotide phosphate hydride (NADPH) to form 5,6,7,8-tetrahydrofolate and oxidized nicotinamide. DHFR is a small, flexible, monomeric protein with no metals or SS bonds and serves as one of the enzymes commonly used to examine basic aspects in enzymology. In the current work, we present extensive benchmark calculations for several model reactions in the gas phase that are relevant to the DHFR catalyzed hydride transfer. To this end, we employ G4MP2 and CBS-QB3 ab initio calculations as well as numerous density functional theory methods. Using these results, we develop two specific reaction parameter (SRP) Hamiltonians based on the semiempirical AM1 method. The first generation SRP Hamiltonian does not account for dispersion, while the second generation SRP accounts for dispersion implicitly via the AM1 core-repulsion functions. These SRP semiempirical Hamiltonians are subsequently used in hybrid quantum mechanics/molecular mechanics simulations of the DHFR catalyzed reaction. Finally, kinetic isotope effects are computed using a mass-perturbation-based path-integral approach.
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Affiliation(s)
- Dvir Doron
- Department of Chemistry, The Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University , Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry, The Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University , Ramat-Gan 52900, Israel
| | - Amnon Kohen
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Xin Wu
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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14
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Qian C, Ni C, Yu W, Wu W, Mao H, Wang Y, Xu J. Highly-ordered, 3D petal-like array for surface-enhanced Raman scattering. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:1800-1806. [PMID: 21608122 DOI: 10.1002/smll.201002026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 03/14/2011] [Indexed: 05/30/2023]
Abstract
Despite the great potential of the application of surface-enhanced Raman scattering (SERS), the difficulty in fabricating suitable SERS substrates is still a problem. Based on the self-assembly of silica nanoparticles, a simple method is here proposed to fabricate a highly-ordered, 3D, petal-like arrayed structure (3D PLAS) that serves as a promising SERS substrate for both its high reproducibility and enormous SERS enhancement. Such a novel structure is easily achieved by anisotropically etching a self-assembly bilayer of silica nanoparticles, followed by metal deposition. The SERS performance of the 3D PLAS and its relationship with the main parameters, including the etching time, the diameter of silica nanoparticles, and the deposited metal film, are characterized using 632.8 nm incident light. With Rhodamine 6G as a probe molecule, the spatially averaged SERS enhancement factor is on the order of 5 × 10(7) and the local enhancement factor is much higher, both of which can be improved further by optimizing the parameters.
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Affiliation(s)
- Chuang Qian
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication, Institute of Microelectronics, Peking University, Beijing, 100871, P.R. China
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15
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Loveridge EJ, Allemann RK. Effect of pH on hydride transfer by Escherichia coli dihydrofolate reductase. Chembiochem 2011; 12:1258-62. [PMID: 21506230 DOI: 10.1002/cbic.201000794] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Indexed: 11/07/2022]
Abstract
The kinetic isotope effect (KIE) on hydride transfer in the reaction catalysed by dihydrofolate reductase from Escherichia coli (EcDHFR) is known to be temperature dependent at pH 7, but essentially independent of temperature at elevated pH. Here, we show that the transition from the temperature-dependent regime to the temperature-independent regime occurs sharply between pH 7.5 and 8. The activation energy for hydride transfer is independent of pH. The mechanism leading to the change in behaviour of the KIEs is not clear, but probably involves a conformational change in the enzyme brought about by deprotonation of a key residue (or residues) at high pH. The KIE on hydride transfer at low pH suggests that the rate constant for the reaction is not limited by a conformational change to the enzyme under these conditions. The effect of pH on the temperature dependence of the rate constants and KIEs for hydride transfer catalysed by EcDHFR suggests that enzyme motions and conformational changes do not directly influence the chemistry, but that the reaction conditions affect the conformational ensemble of the enzyme prior to reaction and control the reaction though this route.
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Affiliation(s)
- E Joel Loveridge
- School of Chemistry, Cardiff University, Park Place, Cardiff, UK
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16
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Grubbs J, Rahmanian S, DeLuca A, Padmashali C, Jackson M, Duff MR, Howell EE. Thermodynamics and solvent effects on substrate and cofactor binding in Escherichia coli chromosomal dihydrofolate reductase. Biochemistry 2011; 50:3673-85. [PMID: 21462996 DOI: 10.1021/bi2002373] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Chromosomal dihydrofolate reductase from Escherichia coli catalyzes the reduction of dihydrofolate to tetrahydrofolate using NADPH as a cofactor. The thermodynamics of ligand binding were examined using an isothermal titration calorimetry approach. Using buffers with different heats of ionization, zero to a small, fractional proton release was observed for dihydrofolate binding, while a proton was released upon NADP(+) binding. The role of water in binding was additionally monitored using a number of different osmolytes. Binding of NADP(+) is accompanied by the net release of ∼5-24 water molecules, with a dependence on the identity of the osmolyte. In contrast, binding of dihydrofolate is weakened in the presence of osmolytes, consistent with "water uptake". Different effects are observed depending on the identity of the osmolyte. The net uptake of water upon dihydrofolate binding was previously observed in the nonhomologous R67-encoded dihydrofolate reductase (dfrB or type II enzyme) [Chopra, S., et al. (2008) J. Biol. Chem. 283, 4690-4698]. As R67 dihydrofolate reductase possesses a nonhomologous sequence and forms a tetrameric structure with a single active site pore, the observation of weaker DHF binding in the presence of osmolytes in both enzymes implicates cosolvent effects on free dihydrofolate. Consistent with this analysis, stopped flow experiments find betaine mostly affects DHF binding via changes in k(on), while betaine mostly affects NADPH binding via changes in k(off). Finally, nonadditive enthalpy terms when binary and ternary cofactor binding events are compared suggest the presence of long-lived conformational transitions that are not included in a simple thermodynamic cycle.
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Affiliation(s)
- Jordan Grubbs
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, USA
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17
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Loveridge EJ, Maglia G, Allemann RK. The role of arginine 28 in catalysis by dihydrofolate reductase from the hyperthermophile Thermotoga maritima. Chembiochem 2010; 10:2624-7. [PMID: 19816891 DOI: 10.1002/cbic.200900465] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- E Joel Loveridge
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK
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18
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Loveridge EJ, Behiry EM, Swanwick RS, Allemann RK. Different Reaction Mechanisms for Mesophilic and Thermophilic Dihydrofolate Reductases. J Am Chem Soc 2009; 131:6926-7. [DOI: 10.1021/ja901441k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- E. Joel Loveridge
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, U.K
| | - Enas M. Behiry
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, U.K
| | - Richard S. Swanwick
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, U.K
| | - Rudolf K. Allemann
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, U.K
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19
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Choi D, Kang T, Cho H, Choi Y, Lee LP. Additional amplifications of SERS via an optofluidic CD-based platform. LAB ON A CHIP 2009; 9:239-43. [PMID: 19107279 DOI: 10.1039/b812067f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In this paper, signal amplifications of surface-enhanced Raman scattering (SERS) are realized by an optofluidic compact disc (CD)-based preconcentration method for effective label-free environmental and biomolecular detections. The preconcentration of target molecules is accomplished through the accumulation of adsorbed molecules on SERS-active sites by repeating a 'filling-drying' cycle of the assay solution in the optofluidic CD platform. After 30 cycles, the clear and high SERS signal of rhodamine 6G of 1 nM is readily detected. In addition to the preconcentration-based signal amplification by the optofluidic SERS system on the CD platform, we introduce a controlled precipitation of gold nanoparticles by CuSO4 for SERS substrates. This method provides high-throughput, high-sensitive and large-area uniform SERS substrates on the optofluidic CD platform. The uniform SERS signals from different positions in spots of 3 mm2 on the different CDs gives us confidence in the reliability and stability of our SERS substrates.
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Affiliation(s)
- Dukhyun Choi
- Biomolecular Nanotechnology Center, Berkeley Sensor & Actuator Center, Department of Bioengineering, University of California at Berkeley, Berkeley, California 94720, USA
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20
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Khavrutskii IV, Price DJ, Lee J, Brooks CL. Conformational change of the methionine 20 loop of Escherichia coli dihydrofolate reductase modulates pKa of the bound dihydrofolate. Protein Sci 2007; 16:1087-100. [PMID: 17473015 PMCID: PMC2206655 DOI: 10.1110/ps.062724307] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Revised: 03/05/2007] [Accepted: 03/06/2007] [Indexed: 10/23/2022]
Abstract
We evaluate the pK(a) of dihydrofolate (H(2)F) at the N(5) position in three ternary complexes with Escherichia coli dihydrofolate reductase (ecDHFR), namely ecDHFR(NADP(+):H(2)F) in the closed form (1), and the Michaelis complexes ecDHFR(NADPH:H(2)F) in the closed (2) and occluded (3) forms, by performing free energy perturbation with molecular dynamics simulations (FEP/MD). Our simulations suggest that in the Michaelis complex the pK(a) is modulated by the Met20 loop fluctuations, providing the largest pK(a) shift in substates with a "tightly closed" loop conformation; in the "partially closed/open" substates, the pK(a) is similar to that in the occluded complex. Conducive to the protonation, tightly closing the Met20 loop enhances the interactions of the cofactor and the substrate with the Met20 side chain and aligns the nicotinamide ring of the cofactor coplanar with the pterin ring of the substrate. Overall, the present study favors the hypothesis that N(5) is protonated directly from solution and provides further insights into the mechanism of the substrate protonation.
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Affiliation(s)
- Ilja V Khavrutskii
- The Scripps Research Institute, Department of Molecular Biology, TPC6, La Jolla, California 92037, USA
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21
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Khandogin J, Brooks CL. Chapter 1 Molecular Simulations of pH-Mediated Biological Processes. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/s1574-1400(07)03001-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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22
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Lu Y, Liu GL, Kim J, Mejia YX, Lee LP. Nanophotonic crescent moon structures with sharp edge for ultrasensitive biomolecular detection by local electromagnetic field enhancement effect. NANO LETTERS 2005; 5:119-24. [PMID: 15792424 DOI: 10.1021/nl048232+] [Citation(s) in RCA: 206] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We present novel gold nanophotonic crescent moon structures with a sub-10 nm sharp edge, which can enhance local electromagnetic field at the edge area. The formation of unconventional nanophotonic crescent moon structure is accomplished by using a sacrificial nanosphere template and conventional thin film deposition method, which allows an effective batch nanofabrication and precise controls of nanostructure shapes. Unique multiple scattering peaks are observed in a single gold nanocrescent moon with dark-field white light illumination. A 785 nm near-infrared (NIR) diode laser was used as the excitation source to induce the amplified scattering field on the sharp edge of the single gold nanocrescent moon. The Raman scattering spectrum of Rhodamine 6G molecules adsorbed on the single gold nanocrescent moon are characterized, and the Raman enhancement factor of single gold nanocrescent moon is estimated larger than 10(10), which suggests the potential applications of gold nanocrescent moons in ultrasensitive biomolecular detection and cellular imaging using surface enhanced Raman spectroscopy.
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Affiliation(s)
- Yu Lu
- Berkeley Sensor and Actuator Center, Department of Bioengineering, University of California-Berkeley, Berkeley, California 94720, USA
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23
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Ferrer S, Silla E, Tuñón I, Martí S, Moliner V. Catalytic Mechanism of Dihydrofolate Reductase Enzyme. A Combined Quantum-Mechanical/Molecular-Mechanical Characterization of the N5 Protonation Step. J Phys Chem B 2003. [DOI: 10.1021/jp0354898] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Shrimpton P, Mullaney A, Allemann RK. Functional role for Tyr 31 in the catalytic cycle of chicken dihydrofolate reductase. Proteins 2003; 51:216-23. [PMID: 12660990 DOI: 10.1002/prot.10370] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Despite much work, many key aspects of the mechanism of the dihydrofolate reductase (DHFR) catalyzed reduction of dihydrofolate remain unresolved. In bacterial forms of DHFR both substrate and water access to the active site are controlled by the conformation of the mobile M20 loop. In vertebrate DHFRs only one conformation of the residues corresponding to the M20 loop has been observed. Access to the active site was proposed to be controlled by residue 31. MD simulations of chicken DHFR complexed with substrates and cofactor revealed a closing of the side chain of Tyr 31 over the active site on binding of dihydrofolate. This conformational change was dependent on the presence of glutamate on the para-aminobenzoylamide moiety of dihydrofolate. In its absence, the conformation remained open. Although water could enter the active site and hydrogen bond to N5 of dihydrofolate, indicating the feasibility of water as the proton donor, this was not controlled by the conformation of Tyr 31. The water accessibility of the active site was low for both conformations of Tyr 31. However, when hydride was transferred from NADPH to C6 of dihydrofolate before protonation, the average time during which water was found in hydrogen bonding distance to N5 of dihydrofolate in the active site increased almost fivefold. These results indicated that water can serve as the Broensted acid for the protonation of N5 of dihydrofolate during the DHFR catalyzed reduction.
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Affiliation(s)
- Paul Shrimpton
- School of Chemical Sciences, University of Birmingham, Edgbaston, United Kingdom
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25
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Desamero RZB, Cheng H, Cahill S, Girvin M, Deng H, Callender R, Rath P, Variano B, Smart JE. Physical properties of compounds promoting oral delivery of macromolecular drugs. Biopolymers 2002; 67:26-40. [PMID: 11842411 DOI: 10.1002/bip.10039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The spectroscopic and solution properties of a series of amidated acids (delivery agents), which promote the gastrointestinal absorption of USP heparin and other drugs that show poor oral bioavailability, are investigated using Raman and NMR spectroscopy. The results show evidence for self-association at low concentrations of delivery agents that increases as the concentration of the delivery agent is increased. The self-associate is characterized by ring-ring stacking interactions, and the best geometrical arrangement for the stacking is the parallel-shifted arrangement of the rings. In addition, the amide group participates in the formation of intermolecular hydrogen bonds in the self-associate. Unlike the rigid ring, the tails of these delivery agents remain relatively flexible in the self-associate. It is suggested that the limited solubility of the delivery agents at physiological pH arises from a percentage of protonated carboxyls. Their presence promotes the formation of intermolecular hydrophobic and ring stacking interactions, which are otherwise weakened by an ionized carboxyl group.
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Affiliation(s)
- Ruel Z B Desamero
- Department of Physics, City College of New York, New York, New York 10031, USA
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26
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Desamero RZB, Cheng H, Cahill S, Girvin M, Deng H, Callender R, Rath P, Variano B, Smart JE. Interactions of amidated acids with heparin. Biopolymers 2002; 67:41-8. [PMID: 11842412 DOI: 10.1002/bip.10040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Raman and NMR studies are performed to characterize the solution structures of complexes between heparin and a group of amidated acids, which act as delivery agents that facilitate the gastrointestinal absorption of orally administered heparin. At concentrations typically employed for the oral drug delivery of heparin, the contact points between heparin complexed with the delivery agents include points near the OH groups of heparin. The results suggest that heparin interacts rather nonspecifically with the amidated acids as monomers and with self-associated complexes of the delivery agents. It is also found that the carboxyl groups of at least one of the bioactive delivery agents easily protonates when it forms complexes with itself or heparin. This attribute may be one reason why this class of compounds is effective in the oral delivery of heparin.
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Affiliation(s)
- Ruel Z B Desamero
- Department of Physics, City College of New York, New York, New York 10031, USA
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27
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Cummins PL, Gready JE. Energetically most likely substrate and active-site protonation sites and pathways in the catalytic mechanism of dihydrofolate reductase. J Am Chem Soc 2001; 123:3418-28. [PMID: 11472112 DOI: 10.1021/ja0038474] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite much experimental and computational study, key aspects of the mechanism of reduction of dihydrofolate (DHF) by dihydrofolate reductase (DHFR) remain unresolved, while the secondary DHFR-catalyzed reduction of folate has been little studied. Major differences between proposed DHF mechanisms are whether the carboxylate group of the conserved active-site Asp or Glu residue is protonated or ionized during the reaction, and whether there is direct protonation of N5 or a proton shuttle from an initially protonated carboxylate group via O4. We have addressed these questions for both reduction steps with a comprehensive set of ab initio quantum chemical calculations on active-site fragment complexes, including the carboxyl side chain and, progressively, all other polar active-site residue groups including conserved water molecules. Addition of two protons in two steps was considered. The polarization effects of the remainder of the enzyme system were approximated by a dielectric continuum self-consistent reaction field (SCRF) model using an effective dielectric constant (epsilon) of 2. Optimized geometries were calculated using the density functional (B3LYP) method and Onsager SCRF model with the 6-31G basis. Single-point energy calculations were then carried out at the B3LYP/6-311+G level with either the Onsager or dielectric polarizable continuum model. Additional checking calculations at MP2 and HF levels, or with other basis sets or values of epsilon, were also done. From the results, the conserved water molecule, corresponding to W206 in the E. coli DHFR complexes, that is H-bonded to both the OD2 oxygen atom of the carboxyl (Asp) side chain and O4 of the pterin/dihydropterin ring, appears critically important and may determine the protonation site for the enzyme-bound substrates. In the absence of W206, the most stable monoprotonated species are the neutral-pair 4-enol forms of substrates with the carboxyl group OD2 oxygen protonated and H-bonded to N3. If W206 is included, then the most stable forms are still the neutral-pair complexes but now for the N3-H keto forms with the protonated OD2 atom H-bonding with W206. A second proton addition to these complexes gives protonations at N8 (folate) or N5 (DHF). Calculated H-bond distances correlate well with those for the conserved W206 observed in many X-ray structures. For all structures with occluded M20 loop conformations (closed active site), OD2-N3 distances are less than OD2-NA2 distances, which is consistent with those calculated for protonated OD2 complexes. Thus, the results (B3LYP; epsilon = 2 calculations) support a mechanism for both folate and DHF reduction in which the OD2 carboxyl oxygen is first protonated, followed by a direct protonation at N8 (folate) and N5 (DHF) to obtain the active cation complexes, i.e., doubly protonated. The results do not support a proposed protonated carboxyl with DHF in the enol form for the Michaelis complex, nor an ionized carboxyl with protonated enol-DHF as a catalytic intermediate. However, as additional calculations for the monoprotonated complete complexes show a reduction in the energy differences between the neutral-pair keto and ion-pair keto (N8- or N5-protonated) forms, we are extending the treatment using combined quantum mechanics and molecular mechanics (QM/MM) and molecular dynamics simulation methods to refine the description of the protein/solvent environment and prediction of the relative stabilization free energies of the various (OD2, O4, N5, and N8) protonation sites.
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Affiliation(s)
- P L Cummins
- Computational Molecular Biology and Drug Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
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28
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Cummins PL, Gready JE. Combined Quantum and Molecular Mechanics (QM/MM) Study of the Ionization State of 8-Methylpterin Substrate Bound to Dihydrofolate Reductase. J Phys Chem B 2000. [DOI: 10.1021/jp993153l] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter L. Cummins
- Computational Molecular Biology and Drug Design Group, John Curtin School of Medical Research, Australian National University, P.O. BOX 334, Canberra ACT, 2601 Australia
| | - Jill E. Gready
- Computational Molecular Biology and Drug Design Group, John Curtin School of Medical Research, Australian National University, P.O. BOX 334, Canberra ACT, 2601 Australia
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29
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Castillo R, Andrés J, Moliner V. Catalytic Mechanism of Dihydrofolate Reductase Enzyme. A Combined Quantum-Mechanical/Molecular-Mechanical Characterization of Transition State Structure for the Hydride Transfer Step. J Am Chem Soc 1999. [DOI: 10.1021/ja9843019] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R. Castillo
- Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, Castelló, Spain
| | - J. Andrés
- Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, Castelló, Spain
| | - V. Moliner
- Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, Castelló, Spain
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30
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Deng H, Callender R. Raman spectroscopic studies of the structures, energetics, and bond distortions of substrates bound to enzymes. Methods Enzymol 1999; 308:176-201. [PMID: 10507005 DOI: 10.1016/s0076-6879(99)08010-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Affiliation(s)
- H Deng
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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31
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Chen YQ, Gulotta M, Cheung HTA, Callender R. Light Activates Reduction of Methotrexate by NADPH in the Ternary Complex with Escherichia coli Dihydrofolate Reductase. Photochem Photobiol 1999. [DOI: 10.1111/j.1751-1097.1999.tb05309.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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Cannon WR, Garrison BJ, Benkovic SJ. Consideration of the pH-dependent inhibition of dihydrofolate reductase by methotrexate. J Mol Biol 1997; 271:656-68. [PMID: 9281432 DOI: 10.1006/jmbi.1997.1173] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Poisson-Boltzmann calculations were used to determine the pKa of protein functional groups in the unliganded dihydrofolate reductase enzyme, and the pKa of protein and ligand groups in methotrexate-enzyme complexes. The results reported here are in conflict with two fundamental tenets of dihydrofolate reductase inhibition by methotrexate: (1) Asp27 is not expected to be protonated near pH 6.5 in the apoenzyme as previously proposed based on fitting of empirical equations to binding data, and (2) the calculated pKa for the pteridine N1 of the inhibitor while bound to the protein is significantly lower than that estimated for this group from interpretation of NMR data (>10). In fact, the electrostatic calculations and complementary quantum chemical calculations indicate that Asp27 is likely protonated when methotrexate is bound, resulting in a neutral dipole-dipole interaction rather than a salt-bridge between the enzyme and the inhibitor. Reasons for this discrepancy with the experimental data are discussed. Furthermore, His45 and Glu17 in the Escherichia coli enzyme are proposed to be in part responsible for the pH dependence of the conformational degeneracy in the inhibitor-enzyme complex.
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Affiliation(s)
- W R Cannon
- Department of Chemistry 152 Davey Laboratory, Pennsylvania State University, University Park, PA 16802, USA
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