1
|
Shirazi J, Jafari S, Ryde U, Irani M. Catalytic Reaction Mechanism of Glyoxalase II: A Quantum Mechanics/Molecular Mechanics Study. J Phys Chem B 2023; 127:4480-4495. [PMID: 37191640 DOI: 10.1021/acs.jpcb.3c01495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Methylglyoxal (MG) is a reactive and toxic compound produced in carbohydrate, lipid, and amino acid metabolism. The glyoxalase system is the main detoxifying route for MG and consists of two enzymes, glyoxalase I (GlxI) and glyoxalase II (GlxII). GlxI catalyzes the formation of S-d-lactoylglutathione from hemithioacetal, and GlxII converts this intermediate to d-lactate. A relationship between the glyoxalase system and some diseases like diabetes has been shown, and inhibiting enzymes of this system may be an effective means of controlling certain diseases. A detailed understanding of the reaction mechanism of an enzyme is essential to the rational design of competitive inhibitors. In this work, we use quantum mechanics/molecular mechanics (QM/MM) calculations and energy refinement utilizing the big-QM and QM/MM thermodynamic cycle perturbation methods to propose a mechanism for the GlxII reaction that starts with a nucleophilic attack of the bridging OH- group on the substrate. The coordination of the substrate to the Zn ions places its electrophilic center close to the hydroxide group, enabling the reaction to proceed. Our estimated reaction energies are in excellent agreement with experimental data, thus demonstrating the reliability of our approach and the proposed mechanism. Additionally, we examined alternative protonation states of Asp-29, Asp-58, Asp-134, and the bridging hydroxide ion in the catalytic process. However, these give less favorable reactions, a poorer reproduction of the crystal structure geometry of the active site, and higher root-mean-squared deviations of the active site residues in molecular dynamics simulations.
Collapse
Affiliation(s)
- Javad Shirazi
- Department of Chemistry, University of Kurdistan, P.O. Box 66175-416, 66177-15177 Sanandaj, Iran
| | - Sonia Jafari
- Department of Chemistry, University of Kurdistan, P.O. Box 66175-416, 66177-15177 Sanandaj, Iran
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Mehdi Irani
- Department of Chemistry, University of Kurdistan, P.O. Box 66175-416, 66177-15177 Sanandaj, Iran
| |
Collapse
|
2
|
Jafari S, Tavares Santos YA, Bergmann J, Irani M, Ryde U. Benchmark Study of Redox Potential Calculations for Iron-Sulfur Clusters in Proteins. Inorg Chem 2022; 61:5991-6007. [PMID: 35403427 PMCID: PMC9044450 DOI: 10.1021/acs.inorgchem.1c03422] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Redox potentials
have been calculated for 12 different iron–sulfur
sites of 6 different types with 1–4 iron ions. Structures were
optimized with combined quantum mechanical and molecular mechanical
(QM/MM) methods, and the redox potentials were calculated using the
QM/MM energies, single-point QM methods in a continuum solvent or
by QM/MM thermodynamic cycle perturbations. We show that the best
results are obtained with a large QM system (∼300 atoms, but
a smaller QM system, ∼150 atoms, can be used for the QM/MM
geometry optimization) and a large value of the dielectric constant
(80). For absolute redox potentials, the B3LYP density functional
method gives better results than TPSS, and the results are improved
with a larger basis set. However, for relative redox potentials, the
opposite is true. The results are insensitive to the force field (charges
of the surroundings) used for the QM/MM calculations or whether the
protein and solvent outside the QM system are relaxed or kept fixed
at the crystal structure. With the best approach for relative potentials,
mean absolute and maximum deviations of 0.17 and 0.44 V, respectively,
are obtained after removing a systematic error of −0.55 V.
Such an approach can be used to identify the correct oxidation states
involved in a certain redox reaction. We
have studied redox potentials of 12 iron−sulfur
sites of 6 types with 1−4 iron ions. Structures were optimized
with combined quantum mechanical and molecular mechanical (QM/MM)
methods, and the redox potentials were calculated with QM/MM, QM calculations
in a continuum solvent or by QM/MM thermodynamic cycle perturbations.
The best results are obtained with the second approach using ∼300
atoms in the QM model and a large dielectric constant.
Collapse
Affiliation(s)
- Sonia Jafari
- Department of Chemistry, University of Kurdistan, 66175-416 Sanandaj, Iran.,Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Yakini A Tavares Santos
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Justin Bergmann
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Mehdi Irani
- Department of Chemistry, University of Kurdistan, 66175-416 Sanandaj, Iran
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| |
Collapse
|
3
|
Bhattacharjee S, Isegawa M, Garcia-Ratés M, Neese F, Pantazis DA. Ionization Energies and Redox Potentials of Hydrated Transition Metal Ions: Evaluation of Domain-Based Local Pair Natural Orbital Coupled Cluster Approaches. J Chem Theory Comput 2022; 18:1619-1632. [PMID: 35191695 PMCID: PMC8908766 DOI: 10.1021/acs.jctc.1c01267] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
Hydrated transition
metal ions are prototypical systems that can
be used to model properties of transition metals in complex chemical
environments. These seemingly simple systems present challenges for
computational chemistry and are thus crucial in evaluations of quantum
chemical methods for spin-state and redox energetics. In this work,
we explore the applicability of the domain-based pair natural orbital
implementation of coupled cluster (DLPNO-CC) theory to the calculation
of ionization energies and redox potentials for hydrated ions of all
first transition row (3d) metals in the 2+/3+ oxidation states, in
connection with various solvation approaches. In terms of model definition,
we investigate the construction of a minimally explicitly hydrated
quantum cluster with a first and second hydration layer. We report
on the convergence with respect to the coupled cluster expansion and
the PNO space, as well as on the role of perturbative triple excitations.
A recent implementation of the conductor-like polarizable continuum
model (CPCM) for the DLPNO-CC approach is employed to determine self-consistent
redox potentials at the coupled cluster level. Our results establish
conditions for the convergence of DLPNO-CCSD(T) energetics and stress
the absolute necessity to explicitly consider the second solvation
sphere even when CPCM is used. The achievable accuracy for redox potentials
of a practical DLPNO-based approach is, on average, 0.13 V. Furthermore,
multilayer approaches that combine a higher-level DLPNO-CCSD(T) description
of the first solvation sphere with a lower-level description of the
second solvation layer are investigated. The present work establishes
optimal and transferable methodological choices for employing DLPNO-based
coupled cluster theory, the associated CPCM implementation, and cost-efficient
multilayer derivatives of the approach for open-shell transition metal
systems in complex environments.
Collapse
Affiliation(s)
- Sinjini Bhattacharjee
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Miho Isegawa
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Miquel Garcia-Ratés
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
4
|
Oszajca M, Drabik G, Radoń M, Franke A, van Eldik R, Stochel G. Experimental and Computational Insight into the Mechanism of NO Binding to Ferric Microperoxidase. The Likely Role of Tautomerization to Account for the pH Dependence. Inorg Chem 2021; 60:15948-15967. [PMID: 34476946 DOI: 10.1021/acs.inorgchem.1c00933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
According to the current paradigm, the metal-hydroxo bond in a six-coordinate porphyrin complex is believed to be significantly less reactive in ligand substitution than the analogous metal-aqua bond, due to a much higher strength of the former bond. Here, we report kinetic studies for nitric oxide (NO) binding to a heme-protein model, acetylated microperoxidase-11 (AcMP-11), that challenge this paradigm. In the studied pH range 7.4-12.6, ferric AcMP-11 exists in three acid-base forms, assigned in the literature as [(AcMP-11)FeIII(H2O)(HisH)] (1), [(AcMP-11)FeIII(OH)(HisH)] (2), and [(AcMP-11)FeIII(OH)(His-)] (3). From the pH dependence of the second-order rate constant for NO binding (kon), we determined individual rate constants characterizing forms 1-3, revealing only a ca. 10-fold decrease in the NO binding rate on going from 1 (kon(1) = 3.8 × 106 M-1 s-1) to 2 (kon(2) = 4.0 × 105 M-1 s-1) and the inertness of 3. These findings lead to the abandonment of the dissociatively activated mechanism, in which the reaction rate can be directly correlated with the Fe-OH bond energy, as the mechanistic explanation for the process with regard to 2. The reactivity of 2 is accounted for through the existence of a tautomeric equilibrium between the major [(AcMP-11)FeIII(OH)(HisH)] (2a) and minor [(AcMP-11)FeIII(H2O)(His-)] (2b) species, of which the second one is assigned as the NO binding target due to its labile Fe-OH2 bond. The proposed mechanism is further substantiated by quantum-chemical calculations, which confirmed both the significant labilization of the Fe-OH2 bond in the [(AcMP-11)FeIII(H2O)(His-)] tautomer and the feasibility of the tautomer formation, especially after introducing empirical corrections to the computed relative acidities of the H2O and HisH ligands based on the experimental pKa values. It is shown that the "effective lability" of the axial ligand (OH-/H2O) in 2 may be comparable to the lability of the H2O ligand in 1.
Collapse
Affiliation(s)
- Maria Oszajca
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Gabriela Drabik
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Mariusz Radoń
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Alicja Franke
- Department of Chemistry, Ludwigs-Maximilians University, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Rudi van Eldik
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Egerlandstr. 1, 91058 Erlangen, Germany
- Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Grażyna Stochel
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| |
Collapse
|
5
|
Schröder GC, Meilleur F. Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography. Acta Crystallogr D Struct Biol 2021; 77:1251-1269. [PMID: 34605429 PMCID: PMC8489226 DOI: 10.1107/s2059798321009025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/31/2021] [Indexed: 11/11/2022] Open
Abstract
Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.
Collapse
Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| |
Collapse
|
6
|
Direct detection of coupled proton and electron transfers in human manganese superoxide dismutase. Nat Commun 2021; 12:2079. [PMID: 33824320 PMCID: PMC8024262 DOI: 10.1038/s41467-021-22290-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 02/26/2021] [Indexed: 11/30/2022] Open
Abstract
Human manganese superoxide dismutase is a critical oxidoreductase found in the mitochondrial matrix. Concerted proton and electron transfers are used by the enzyme to rid the mitochondria of O2•−. The mechanisms of concerted transfer enzymes are typically unknown due to the difficulties in detecting the protonation states of specific residues and solvent molecules at particular redox states. Here, neutron diffraction of two redox-controlled manganese superoxide dismutase crystals reveal the all-atom structures of Mn3+ and Mn2+ enzyme forms. The structures deliver direct data on protonation changes between oxidation states of the metal. Observations include glutamine deprotonation, the involvement of tyrosine and histidine with altered pKas, and four unusual strong-short hydrogen bonds, including a low barrier hydrogen bond. We report a concerted proton and electron transfer mechanism for human manganese superoxide dismutase from the direct visualization of active site protons in Mn3+ and Mn2+ redox states. Human manganese superoxide dismutase (MnSOD) is an oxidoreductase that uses concerted proton and electron transfers to reduce the levels of superoxide radicals in mitochondria, but mechanistic insights into this process are limited. Here, the authors report neutron crystal structures of Mn3+SOD and Mn2+SOD, revealing changes in the protonation states of key residues in the enzyme active site during the redox cycle.
Collapse
|
7
|
Jafari S, Ryde U, Irani M. QM/MM Study of the Catalytic Reaction of Myrosinase; Importance of Assigning Proper Protonation States of Active-Site Residues. J Chem Theory Comput 2021; 17:1822-1841. [PMID: 33543623 PMCID: PMC8023669 DOI: 10.1021/acs.jctc.0c01121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Myrosinase from Sinapis alba hydrolyzes glycosidic
bonds of β-d-S-glucosides. The enzyme
shows an enhanced activity in the presence of l-ascorbic
acid. In this work, we employed combined quantum mechanical and molecular
mechanical (QM/MM) calculations and molecular dynamics simulations
to study the catalytic reaction of wild-type myrosinase and its E464A,
Q187A, and Q187E mutants. Test calculations show that a proper QM
region to study the myrosinase reaction must contain the whole substrate,
models of Gln-187, Glu-409, Gln-39, His-141, Asn-186, Tyr-330, Glu-464,
Arg-259, and a water molecule. Furthermore, to make the deglycosylation
step possible, Arg-259 must be charged, Glu-464 must be protonated
on OE2, and His-141 must be protonated on the NE2 atom. The results
indicate that assigning proper protonation states of the residues
is more important than the size of the model QM system. Our model
reproduces the anomeric retaining characteristic of myrosinase and
also reproduces the experimental fact that ascorbate increases the
rate of the reaction. A water molecule in the active site, positioned
by Gln-187, helps the aglycon moiety of the substrate to stabilize
the buildup of negative charge during the glycosylation reaction and
this in turn makes the moiety a better leaving group. The water molecule
also lowers the glycosylation barrier by ∼9 kcal/mol. The results
indicate that the Q187E and E464A mutants but not the Q187A mutant
can perform the glycosylation step. However, the energy profiles for
the deglycosylation step of the mutants are not similar to that of
the wild-type enzyme. The Glu-464 residue lowers the barriers of the
glycosylation and deglycosylation steps. The ascorbate ion can act
as a general base in the reaction of the wild-type enzyme only if
the Glu-464 and His-141 residues are properly protonated.
Collapse
Affiliation(s)
- Sonia Jafari
- Department of Chemistry, University of Kurdistan, 66175-416 Sanandaj, Iran
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Mehdi Irani
- Department of Chemistry, University of Kurdistan, 66175-416 Sanandaj, Iran
| |
Collapse
|
8
|
Jafari S, Ryde U, Irani M. Two-Substrate Glyoxalase I Mechanism: A Quantum Mechanics/Molecular Mechanics Study. Inorg Chem 2021; 60:303-314. [PMID: 33315368 DOI: 10.1021/acs.inorgchem.0c02957] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Glyoxalase I (GlxI) is an important enzyme that catalyzes the detoxification of methylglyoxal (MG) with the help of glutathione (H-SG). It is currently unclear whether MG and H-SG are substrates of GlxI or whether the enzyme processes hemithioacetal (HTA), which is nonenzymatically formed from MG and H-SG. Most previous studies have concentrated on the latter mechanism. Here, we study the two-substrate reaction mechanism of GlxI from humans (HuGlxI) and corn (ZmGlxI), which are Zn(II)-active and -inactive, respectively. Hybrid quantum mechanics/molecular mechanics calculations were used to obtain geometrical structures of the stationary points along reaction paths, and big quantum mechanical systems with more than 1000 atoms and free-energy perturbations were used to improve the quality of the calculated energies. We studied, on an equal footing, all reasonable reaction paths to the S- and R-enantiomers of HTA from MG and H-SG (the latter was considered in two different binding modes). The results indicate that the MG and H-SG reaction in both enzymes can follow the same path to reach S-HTA. However, the respective overall barriers and reaction energies are different for the two enzymes (6.1 and -9.8 kcal/mol for HuGlxI and 15.7 and -2.2 kcal/mol for ZmGlxI). The first reaction step to produce S-HTA is facilitated by a crystal water molecule that forms hydrogen bonds with a Glu and a Thr residue in the active site. The two enzymes also follow similar paths to R-HTA. However, the reactions reach a deprotonated and protonated R-HTA in the human and corn enzymes, respectively. The production of deprotonated R-HTA in HuGlxI is consistent with other theoretical and experimental works. However, our calculations show a different behavior for ZmGlxI (both S- and R-HTA can be formed in the enzyme with the alcoholic proton on HTA). This implies that Glu-144 of corn GlxI is not basic enough to keep the alcoholic proton. In HuGlxI, the two binding modes of H-SG that lead to S- and R-HTA are degenerate, but the barrier leading to R-HTA is lower than the barrier to S-HTA. On the other hand, ZmGlxI prefers the binding mode, which produces S-HTA; this observation is consistent with experiments. Based on the results, we present a modification for a previously proposed two-substrate reaction mechanism for ZmGlxI.
Collapse
Affiliation(s)
- Sonia Jafari
- Department of Chemistry, University of Kurdistan, P.O. Box 66175-416, Sanandaj, Iran.,Department of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Mehdi Irani
- Department of Chemistry, University of Kurdistan, P.O. Box 66175-416, Sanandaj, Iran
| |
Collapse
|
9
|
Jafari S, Ryde U, Fouda AEA, Alavi FS, Dong G, Irani M. Quantum Mechanics/Molecular Mechanics Study of the Reaction Mechanism of Glyoxalase I. Inorg Chem 2020; 59:2594-2603. [PMID: 32011880 DOI: 10.1021/acs.inorgchem.9b03621] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Glyoxalase I (GlxI) is a member of the glyoxalase system, which is important in cell detoxification and converts hemithioacetals of methylglyoxal (a cytotoxic byproduct of sugar metabolism that may react with DNA or proteins and introduce nucleic acid strand breaks, elevated mutation frequencies, and structural or functional changes of the proteins) and glutathione into d-lactate. GlxI accepts both the S and R enantiomers of hemithioacetal, but converts them to only the S-d enantiomer of lactoylglutathione. Interestingly, the enzyme shows this unusual specificity with a rather symmetric active site (a Zn ion coordinated to two glutamate residues; Glu-99 and Glu-172), making the investigation of its reaction mechanism challenging. Herein, we have performed a series of combined quantum mechanics and molecular mechanics calculations to study the reaction mechanism of GlxI. The substrate can bind to the enzyme in two different modes, depending on the direction of its alcoholic proton (H2; toward Glu-99 or Glu-172). Our results show that the S substrate can react only if H2 is directed toward Glu-99 and the R substrate only if H2 is directed toward Glu-172. In both cases, the reactions lead to the experimentally observed S-d enantiomer of the product. In addition, the results do not show any low-energy paths to the wrong enantiomer of the product from neither the S nor the R substrate. Previous studies have presented several opposing mechanisms for the conversion of R and S enantiomers of the substrate to the correct enantiomer of the product. Our results confirm one of them for the S substrate, but propose a new one for the R substrate.
Collapse
Affiliation(s)
- Sonia Jafari
- Department of Chemistry , University of Kurdistan , P.O. Box 66175-416, Sanandaj 66177-15177 , Iran.,Department of Theoretical Chemistry , Lund University , P.O. Box 124, SE-22100 Lund , Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry , Lund University , P.O. Box 124, SE-22100 Lund , Sweden
| | - Adam Emad Ahmed Fouda
- Department of Theoretical Chemistry , Lund University , P.O. Box 124, SE-22100 Lund , Sweden
| | - Fatemeh Sadat Alavi
- Department of Theoretical Chemistry , Lund University , P.O. Box 124, SE-22100 Lund , Sweden
| | - Geng Dong
- Department of Theoretical Chemistry , Lund University , P.O. Box 124, SE-22100 Lund , Sweden
| | - Mehdi Irani
- Department of Chemistry , University of Kurdistan , P.O. Box 66175-416, Sanandaj 66177-15177 , Iran
| |
Collapse
|
10
|
QM/MM study of the stereospecific proton exchange of glutathiohydroxyacetone by glyoxalase I. RESULTS IN CHEMISTRY 2019. [DOI: 10.1016/j.rechem.2019.100011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
|
11
|
Dong G, Phung QM, Pierloot K, Ryde U. Reaction Mechanism of [NiFe] Hydrogenase Studied by Computational Methods. Inorg Chem 2018; 57:15289-15298. [PMID: 30500163 DOI: 10.1021/acs.inorgchem.8b02590] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
[NiFe] hydrogenases catalyze the reversible conversion of molecular hydrogen to protons and electrons. This seemingly simple reaction has attracted much attention because of the prospective use of H2 as a clean fuel. In this paper, we have studied the full reaction mechanism of this enzyme with various computational methods. Geometries were obtained with combined quantum mechanical and molecular mechanics (QM/MM) calculations. To get more accurate energies and obtain a detailed account of the surroundings, we performed big-QM calculations with 819 atoms in the QM region. Moreover, QM/MM thermodynamic cycle perturbation calculations were performed to obtain free energies. Finally, density matrix renormalisation group complete active space self-consistent field calculations were carried out to study the electronic structures of the various states in the reaction mechanism. Our calculations indicate that the Ni-L state is not involved in the reaction mechanism. Instead, the Ni-C state is reduced by one electron and then the bridging hydride ion is transferred to the sulfur atom of Cys546 as a proton and the two electrons transfer to the Ni ion. This step turned out to be rate-determining with an energy barrier of 58 kJ/mol, which is consistent with the experimental rate of 750 ± 90 s-1 (corresponding to ∼52 kJ/mol). The cleavage of the H-H bond is facile with an energy barrier of 33 kJ/mol, according to our calculations. We also find that the reaction energies are sensitive to the size of the QM system, the basis set, and the density functional theory method, in agreement with previous studies.
Collapse
Affiliation(s)
- Geng Dong
- Department of Theoretical Chemistry, Chemical Centre , Lund University , P.O. Box 124, SE-221 00 Lund , Sweden
- Department of Biochemistry and Molecular Biology , Shantou University Medical College , Shantou 514041 , Guangdong , PR China
| | - Quan Manh Phung
- Department of Chemistry , KU Leuven , Celestijnenlaan 200F , B-3001 Leuven , Belgium
| | - Kristine Pierloot
- Department of Chemistry , KU Leuven , Celestijnenlaan 200F , B-3001 Leuven , Belgium
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical Centre , Lund University , P.O. Box 124, SE-221 00 Lund , Sweden
| |
Collapse
|
12
|
Azadmanesh J, Lutz WE, Weiss KL, Coates L, Borgstahl GEO. Redox manipulation of the manganese metal in human manganese superoxide dismutase for neutron diffraction. Acta Crystallogr F Struct Biol Commun 2018; 74:677-687. [PMID: 30279321 PMCID: PMC6168772 DOI: 10.1107/s2053230x18011299] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/07/2018] [Indexed: 11/17/2022] Open
Abstract
Human manganese superoxide dismutase (MnSOD) is one of the most significant enzymes in preventing mitochondrial dysfunction and related diseases by combating reactive oxygen species (ROS) in the mitochondrial matrix. Mitochondria are the source of up to 90% of cellular ROS generation, and MnSOD performs its necessary bioprotective role by converting superoxide into oxygen and hydrogen peroxide. This vital catalytic function is conducted via cyclic redox reactions between the substrate and the active-site manganese using proton-coupled electron transfers. Owing to protons being difficult to detect experimentally, the series of proton transfers that compose the catalytic mechanism of MnSOD are unknown. Here, methods are described to discern the proton-based mechanism using chemical treatments to control the redox state of large perdeuterated MnSOD crystals and subsequent neutron diffraction. These methods could be applicable to other crystal systems in which proton information on the molecule in question in specific chemical states is desired.
Collapse
Affiliation(s)
- Jahaun Azadmanesh
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA
- Department of Biochemistry and Molecular Biology, 985870 Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - William E. Lutz
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA
| | - Kevin L. Weiss
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Leighton Coates
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Gloria E. O. Borgstahl
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA
| |
Collapse
|
13
|
Shen L, Zeng X, Hu H, Hu X, Yang W. Accurate Quantum Mechanical/Molecular Mechanical Calculations of Reduction Potentials in Azurin Variants. J Chem Theory Comput 2018; 14:4948-4957. [PMID: 30040901 DOI: 10.1021/acs.jctc.8b00403] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Understanding the regulation mechanism and molecular determinants of the reduction potential of metalloprotein is a major challenge. An ab initio quantum mechanical/molecular mechanical (QM/MM) method combining the minimum free energy path (MFEP) and fractional number of electron (FNE) approaches has been developed in our group to simulate the redox processes of large systems. The FNE scheme provides an efficient unique description for the redox process, while the MFEP method provides improved conformational sampling on complex environments such as protein in the QM/MM calculations. The reduction potentials of wild-type and seven mutants of azurin, a type 1 copper metalloprotein, were simulated with the QM/MM-MFEP+FNE approach in this paper. A range of 350 mV for the variations of the reduction potentials of these azurin proteins was reproduced faithfully with relative errors around 20 mV. The correlation between structural interactions and reduction potentials observed in simulations provides in-depth insight into the regulation of reduction potentials, which potentially can also be very useful to the engineering of metalloprotein-based electrocatalysts in artificial photosynthesis. The excellent accuracy and efficiency of the QM/MM-MFEP+FNE approach demonstrate the potential for simulations of many electron transfer processes in condensed phases and biochemical systems.
Collapse
Affiliation(s)
- Lin Shen
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - Xiancheng Zeng
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - Hao Hu
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - Xiangqian Hu
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - Weitao Yang
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| |
Collapse
|
14
|
Abstract
Sulfite oxidase is a mononuclear molybdenum enzyme that oxidises sulfite to sulfate in many organisms, including man. Three different reaction mechanisms have been suggested, based on experimental and computational studies. Here, we study all three with combined quantum mechanical (QM) and molecular mechanical (QM/MM) methods, including calculations with large basis sets, very large QM regions (803 atoms) and QM/MM free-energy perturbations. Our results show that the enzyme is set up to follow a mechanism in which the sulfur atom of the sulfite substrate reacts directly with the equatorial oxo ligand of the Mo ion, forming a Mo-bound sulfate product, which dissociates in the second step. The first step is rate limiting, with a barrier of 39–49 kJ/mol. The low barrier is obtained by an intricate hydrogen-bond network around the substrate, which is preserved during the reaction. This network favours the deprotonated substrate and disfavours the other two reaction mechanisms. We have studied the reaction with both an oxidised and a reduced form of the molybdopterin ligand and quantum-refinement calculations indicate that it is in the normal reduced tetrahydro form in this protein.
Collapse
|
15
|
Azadmanesh J, Borgstahl GEO. A Review of the Catalytic Mechanism of Human Manganese Superoxide Dismutase. Antioxidants (Basel) 2018; 7:antiox7020025. [PMID: 29385710 PMCID: PMC5836015 DOI: 10.3390/antiox7020025] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 01/13/2018] [Accepted: 01/26/2018] [Indexed: 12/15/2022] Open
Abstract
Superoxide dismutases (SODs) are necessary antioxidant enzymes that protect cells from reactive oxygen species (ROS). Decreased levels of SODs or mutations that affect their catalytic activity have serious phenotypic consequences. SODs perform their bio-protective role by converting superoxide into oxygen and hydrogen peroxide by cyclic oxidation and reduction reactions with the active site metal. Mutations of SODs can cause cancer of the lung, colon, and lymphatic system, as well as neurodegenerative diseases such as Parkinson's disease and amyotrophic lateral sclerosis. While SODs have proven to be of significant biological importance since their discovery in 1968, the mechanistic nature of their catalytic function remains elusive. Extensive investigations with a multitude of approaches have tried to unveil the catalytic workings of SODs, but experimental limitations have impeded direct observations of the mechanism. Here, we focus on human MnSOD, the most significant enzyme in protecting against ROS in the human body. Human MnSOD resides in the mitochondrial matrix, the location of up to 90% of cellular ROS generation. We review the current knowledge of the MnSOD enzymatic mechanism and ongoing studies into solving the remaining mysteries.
Collapse
Affiliation(s)
- Jahaun Azadmanesh
- Department of Biochemistry and Molecular Biology, 985870 Nebraska Medical Center, Omaha, NE 68198-5870, USA.
| | - Gloria E O Borgstahl
- Department of Biochemistry and Molecular Biology, 985870 Nebraska Medical Center, Omaha, NE 68198-5870, USA.
- Eppley Institute for Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.
| |
Collapse
|
16
|
Cao L, Caldararu O, Ryde U. Protonation States of Homocitrate and Nearby Residues in Nitrogenase Studied by Computational Methods and Quantum Refinement. J Phys Chem B 2017; 121:8242-8262. [DOI: 10.1021/acs.jpcb.7b02714] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lili Cao
- Department of Theoretical
Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Octav Caldararu
- Department of Theoretical
Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical
Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| |
Collapse
|
17
|
Kremleva A, Aparicio PA, Genest A, Rösch N. Quantum chemical modeling of tri-Mn-substituted W-based Keggin polyoxoanions. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2017.02.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
18
|
Dong G, Ryde U. O2 Activation in Salicylate 1,2-Dioxygenase: A QM/MM Study Reveals the Role of His162. Inorg Chem 2016; 55:11727-11735. [DOI: 10.1021/acs.inorgchem.6b01732] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Geng Dong
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| |
Collapse
|
19
|
Protein effects in non-heme iron enzyme catalysis: insights from multiscale models. J Biol Inorg Chem 2016; 21:645-57. [DOI: 10.1007/s00775-016-1374-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/20/2016] [Indexed: 01/09/2023]
|
20
|
Jara GE, Martínez L. Anthrax Edema Factor: An Ion-Adaptive Mechanism of Catalysis with Increased Transition-State Conformational Flexibility. J Phys Chem B 2016; 120:6504-14. [DOI: 10.1021/acs.jpcb.6b02527] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gabriel E. Jara
- Institute of Chemistry, University of Campinas, Campinas, SP 13083-861, Brazil
| | - Leandro Martínez
- Institute of Chemistry, University of Campinas, Campinas, SP 13083-861, Brazil
| |
Collapse
|
21
|
Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods. J Biol Inorg Chem 2016; 21:383-94. [DOI: 10.1007/s00775-016-1348-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 02/23/2016] [Indexed: 10/22/2022]
|
22
|
Bím D, Rulíšek L, Srnec M. Accurate Prediction of One-Electron Reduction Potentials in Aqueous Solution by Variable-Temperature H-Atom Addition/Abstraction Methodology. J Phys Chem Lett 2016; 7:7-13. [PMID: 26647144 DOI: 10.1021/acs.jpclett.5b02452] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A robust and efficient theoretical approach for calculation of the reduction potentials of charged species in aqueous solution is presented. Within this approach, the reduction potential of a charged complex (with a charge |n| ≥ 2) is probed by means of the reduction potential of its neutralized (protonated/deprotonated) cognate, employing one or several H-atom addition/abstraction thermodynamic cycles. This includes a separation of one-electron reduction from protonation/deprotonation through the temperature dependence. The accuracy of the method has been assessed for the set of 15 transition-metal complexes that are considered as highly challenging systems for computational electrochemistry. Unlike the standard computational protocol(s), the presented approach yields results that are in excellent agreement with experimental electrochemical data. Last but not least, the applicability and limitations of the approach are thoroughly discussed.
Collapse
Affiliation(s)
- Daniel Bím
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic , Dolejškova 3, 182 20 Praha 8, Czech Republic
| |
Collapse
|
23
|
|
24
|
Barbault F, Maurel F. Simulation with quantum mechanics/molecular mechanics for drug discovery. Expert Opin Drug Discov 2015; 10:1047-57. [DOI: 10.1517/17460441.2015.1076389] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
25
|
Li J, Farrokhnia M, Rulíšek L, Ryde U. Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods. J Phys Chem B 2015; 119:8268-84. [DOI: 10.1021/acs.jpcb.5b02864] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Jilai Li
- Department
of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
- Institute
of Theoretical Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Maryam Farrokhnia
- Department
of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
- The
Persian Gulf Marine Biotechnology Research Center, The Persian Gulf
Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Lubomír Rulíšek
- Institute
of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research
Center, Academy of Sciences of the Czech Republic, Flemingovo
náměstí 2, 166
10 Prague 6, Czech Republic
| | - Ulf Ryde
- Department
of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| |
Collapse
|
26
|
Nechay MR, Valdez CE, Alexandrova AN. Computational Treatment of Metalloproteins. J Phys Chem B 2015; 119:5945-56. [DOI: 10.1021/acs.jpcb.5b00028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Michael R. Nechay
- Department
of Chemistry and Biochemistry and ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Crystal E. Valdez
- Department
of Chemistry and Biochemistry and ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Anastassia N. Alexandrova
- Department
of Chemistry and Biochemistry and ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| |
Collapse
|
27
|
Li J, Ryde U. Comparison of the Active-Site Design of Molybdenum Oxo-Transfer Enzymes by Quantum Mechanical Calculations. Inorg Chem 2014; 53:11913-24. [DOI: 10.1021/ic5010837] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jilai Li
- Department of Theoretical Chemistry, Chemical
Centre, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
- State Key Laboratory of Theoretical and
Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical
Centre, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| |
Collapse
|
28
|
Sun X, Sun X, Geng C, Zhao H, Li J. Benchmark study on methanol C-H and O-H bond activation by bare [Fe(IV)O](2+). J Phys Chem A 2014; 118:7146-58. [PMID: 25091205 DOI: 10.1021/jp505662x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present a high-level computational study on methanol C-H and O-H bond cleavages by bare [Fe(IV)O](2+), as well as benchmarks of various density functional theory (DFT) methods. We considered direct and concerted hydrogen transfer (DHT and CHT) pathways, respectively. The potential energy surfaces were constructed at the CCSD(T)/def2-TZVPP//B3LYP/def2-TZVP level of theory. Mechanistically, (1) the C-H bond cleavage is dominant and the O-H activation only plays minor role on the PESs; (2) the DHT from methyl should be the most practical channel; and (3) electronic structure analysis demonstrates the proton and electron transfer coupling behavior along the reaction coordinates. The solvent effect is evident and plays distinct roles in regulating the two bond activations in different mechanisms during the catalysis. The effect of optimizing the geometries using different density functionals was also studied, showing that it is not meaningful to discuss which DFT method could give the accurate prediction of the geometries, especially for transition structures. Furthermore, the gold-standard CCSD(T) method was used to benchmark 19 different density functionals with different Hartree-Fock exchange fractions. The results revealed that (i) the structural factor plays a minor role in the single point energy (SPE) calculations; (ii) reaction energy prediction is quite challenging for DFT methods; (iii) the mean absolute deviations (MADs) reflect the problematic description of the DFs when dealing with metal oxidation state change, giving a strong correlation on the HF exchange in the DFs. Knowledge from this study should be of great value for computational chemistry, especially for the de novo design of transition metal catalysts.
Collapse
Affiliation(s)
- Xianhui Sun
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun 130023, P.R. China
| | | | | | | | | |
Collapse
|
29
|
Pezeshki S, Lin H. Recent developments in QM/MM methods towards open-boundary multi-scale simulations. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.911870] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
30
|
de Visser SP, Quesne MG, Martin B, Comba P, Ryde U. Computational modelling of oxygenation processes in enzymes and biomimetic model complexes. Chem Commun (Camb) 2014; 50:262-82. [DOI: 10.1039/c3cc47148a] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
31
|
Hou G, Cui Q. Stabilization of different types of transition states in a single enzyme active site: QM/MM analysis of enzymes in the alkaline phosphatase superfamily. J Am Chem Soc 2013; 135:10457-69. [PMID: 23786365 PMCID: PMC3759165 DOI: 10.1021/ja403293d] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The first step for the hydrolysis of a phosphate monoester (pNPP(2-)) in enzymes of the alkaline phosphatase (AP) superfamily, R166S AP and wild-type NPP, is studied using QM/MM simulations based on an approximate density functional theory (SCC-DFTBPR) and a recently introduced QM/MM interaction Hamiltonian. The calculations suggest that similar loose transition states are involved in both enzymes, despite the fact that phosphate monoesters are the cognate substrates for AP but promiscuous substrates for NPP. The computed loose transition states are clearly different from the more synchronous ones previously calculated for diester reactions in the same AP enzymes. Therefore, our results explicitly support the proposal that AP enzymes are able to recognize and stabilize different types of transition states in a single active site. Analysis of the structural features of computed transition states indicates that the plastic nature of the bimetallic site plays a minor role in accommodating multiple types of transition states and that the high degree of solvent accessibility of the AP active site also contributes to its ability to stabilize diverse transition-state structures without the need of causing large structural distortions of the bimetallic motif. The binding mode of the leaving group in the transition state highlights that vanadate may not always be an ideal transition state analog for loose phosphoryl transfer transition states.
Collapse
Affiliation(s)
- Guanhua Hou
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| |
Collapse
|
32
|
Li JL, Mata RA, Ryde U. Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction. J Chem Theory Comput 2013; 9:1799-807. [DOI: 10.1021/ct301094r] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ji-Lai Li
- Department of Theoretical Chemistry,
Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
- State Key Laboratory of Theoretical
and Computational Chemistry, Institute of Theoretical Chemistry, Jilin
University, Changchun 130023, People’s Republic of China
| | - Ricardo A. Mata
- Institut für Physikalische
Chemie, Georg-August-Universität Göttingen, Tammannstrasse
6, D-37077, Göttingen, Germany
| | - Ulf Ryde
- Department of Theoretical Chemistry,
Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| |
Collapse
|
33
|
Rulíšek L, Ryde U. Theoretical studies of the active-site structure, spectroscopic and thermodynamic properties, and reaction mechanism of multicopper oxidases. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.04.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
34
|
Rokob TA, Srnec M, Rulíšek L. Theoretical calculations of physico-chemical and spectroscopic properties of bioinorganic systems: current limits and perspectives. Dalton Trans 2012; 41:5754-68. [DOI: 10.1039/c2dt12423h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
35
|
Hu L, Farrokhnia M, Heimdal J, Shleev S, Rulíšek L, Ryde U. Reorganization energy for internal electron transfer in multicopper oxidases. J Phys Chem B 2011; 115:13111-26. [PMID: 21955325 DOI: 10.1021/jp205897z] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We have calculated the reorganization energy for the intramolecular electron transfer between the reduced type 1 copper site and the peroxy intermediate of the trinuclear cluster in the multicopper oxidase CueO. The calculations are performed at the combined quantum mechanics and molecular mechanics (QM/MM) level, based on molecular dynamics simulations with tailored potentials for the two copper sites. We obtain a reorganization energy of 91-133 kJ/mol, depending on the theoretical treatment. The two Cu sites contribute by 12 and 22 kJ/mol to this energy, whereas the solvent contribution is 34 kJ/mol. The rest comes from the protein, involving small contributions from many residues. We have also estimated the energy difference between the two electron-transfer states and show that the reduction of the peroxy intermediate is exergonic by 43-87 kJ/mol, depending on the theoretical method. Both the solvent and the protein contribute to this energy difference, especially charged residues close to the two Cu sites. We compare these estimates with energies obtained from QM/MM optimizations and QM calculations in a vacuum and discuss differences between the results obtained at various levels of theory.
Collapse
Affiliation(s)
- Lihong Hu
- Department of Theoretical Chemistry, Lund University, Lund, Sweden
| | | | | | | | | | | |
Collapse
|