1
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Bonanata J. The role of the active site lysine residue on FAD reduction by NADPH in glutathione reductase. Comput Biol Chem 2024; 110:108075. [PMID: 38678729 DOI: 10.1016/j.compbiolchem.2024.108075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 04/01/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024]
Abstract
Glutathione reductase (GR) is a two dinucleotide binding domain flavoprotein (tDBDF) that catalyzes the reduction of glutathione disulfide to glutathione coupled to the oxidation of NADPH to NADP+. An interesting feature of GR and other tDBDFs is the presence of a lysine residue (Lys-66 in human GR) at the active site, which interacts with the flavin group, but has an unknown function. To better understand the role of this residue, the dynamics of GR was studied using molecular dynamics simulations, and the reaction mechanism of FAD reduction by NADPH was studied using QM/MM molecular modeling. The two possible protonation states of Lys-66 were considered: neutral and protonated. Molecular dynamics results suggest that the active site is more structured for neutral Lys-66 than for protonated Lys-66. QM/MM modeling results suggest that Lys-66 should be in its neutral state for a thermodynamically favorable reduction of FAD by NADPH. Since the reaction is unfavorable with protonated Lys-66, the reverse reaction (the reduction of NADP+ by FADH-) is expected to take place. A phylogenetic analysis of various tDBDFs was performed, finding that an active site lysine is present in different the tDBDFs enzymes, suggesting that it has a conserved biological role. Overall, these results suggest that the protonation state of the active site lysine determines the energetics of the reaction, controlling its reversibility.
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Affiliation(s)
- Jenner Bonanata
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Uruguay; Centro de Investigaciones Biomédicas, Universidad de la República, Uruguay.
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2
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Sahrawat AS, Polidori N, Kroutil W, Gruber K. Deciphering the Unconventional Reduction of C=N Bonds by Old Yellow Enzymes Using QM/MM. ACS Catal 2024; 14:1257-1266. [PMID: 38327643 PMCID: PMC10845114 DOI: 10.1021/acscatal.3c04362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/01/2023] [Accepted: 12/20/2023] [Indexed: 02/09/2024]
Abstract
The reduction of C=X (X = N, O) bonds is a cornerstone in both synthetic organic chemistry and biocatalysis. Conventional reduction mechanisms usually involve a hydride ion targeting the less electronegative carbon atom. In a departure from this paradigm, our investigation into Old Yellow Enzymes (OYEs) reveals a mechanism involving transfer of hydride to the formally more electronegative nitrogen atom within a C=N bond. Beyond their known ability to reduce electronically activated C=C double bonds, e.g., in α, β-unsaturated ketones, these enzymes have recently been shown to reduce α-oximo-β-ketoesters to the corresponding amines. It has been proposed that this transformation involves two successive reduction steps and proceeds via imine intermediates formed by the reductive dehydration of the oxime moieties. We employ advanced quantum mechanics/molecular mechanics (QM/MM) simulations, enriched by a two-tiered approach incorporating QM/MM (UB3LYP-6-31G*/OPLS2005) geometry optimization, QM/MM (B3LYP-6-31G*/amberff19sb) steered molecular dynamics simulations, and detailed natural-bond-orbital analyses to decipher the unconventional hydride transfer to nitrogen in both reduction steps and to delineate the role of active site residues as well as of substituents present in the substrates. Our computational results confirm the proposed mechanism and agree well with experimental mutagenesis and enzyme kinetics data. According to our model, the catalysis of OYE involves hydride transfer from the flavin cofactor to the nitrogen atom in oximoketoesters as well as iminoketoesters followed by protonation at the adjacent oxygen or carbon atoms by conserved tyrosine residues and active site water molecules. Two histidine residues play a key role in the polarization and activation of the C=N bond, and conformational changes of the substrate observed along the reaction coordinate underline the crucial importance of dynamic electron delocalization for efficient catalysis.
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Affiliation(s)
| | - Nakia Polidori
- Institute
of Molecular Biosciences, University of
Graz, Graz 8010, Austria
| | - Wolfgang Kroutil
- Institute
of Chemistry, University of Graz, Graz 8010, Austria
- Field
of Excellence BioHealth, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, Graz 8010, Austria
| | - Karl Gruber
- Institute
of Molecular Biosciences, University of
Graz, Graz 8010, Austria
- Field
of Excellence BioHealth, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, Graz 8010, Austria
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3
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Curtolo F, Arantes GM. Dissecting Reaction Mechanisms and Catalytic Contributions in Flavoprotein Fumarate Reductases. J Chem Inf Model 2023. [PMID: 37196341 DOI: 10.1021/acs.jcim.3c00292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The interconversion between fumarate and succinate is fundamental to the energy metabolism of nearly all organisms. This redox reaction is catalyzed by a large family of enzymes, fumarate reductases and succinate dehydrogenases, using hydride and proton transfers from a flavin cofactor and a conserved Arg side-chain. These flavoenzymes also have substantial biomedical and biotechnological importance. Therefore, a detailed understanding of their catalytic mechanisms is valuable. Here, calibrated electronic structure calculations in a cluster model of the active site of the Fcc3 fumarate reductase were employed to investigate various reaction pathways and possible intermediates in the enzymatic environment and to dissect interactions that contribute to catalysis of fumarate reduction. Carbanion, covalent adduct, carbocation, and radical intermediates were examined. Significantly lower barriers were obtained for mechanisms via carbanion intermediates, with similar activation energies for hydride and proton transfers. Interestingly, the carbanion bound to the active site is best described as an enolate. Hydride transfer is stabilized by a preorganized charge dipole in the active site and by the restriction of the C1-C2 bond in a twisted conformation of the otherwise planar fumarate dianion. But, protonation of a fumarate carboxylate and quantum tunneling effects are not critical for catalysis of the hydride transfer. Calculations also suggest that the driving force for enzyme turnover is provided by regeneration of the catalytic Arg, either coupled with flavin reduction and decomposition of a proposed transient state or directly from the solvent. The detailed mechanistic description of enzymatic reduction of fumarate provided here clarifies previous contradictory views and provides new insights into catalysis by essential flavoenzyme reductases and dehydrogenases.
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Affiliation(s)
- Felipe Curtolo
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, São Paulo, Brazil
| | - Guilherme M Arantes
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, São Paulo, Brazil
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4
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Suenaga S, Takano Y, Saito T. Unraveling Binding Mechanism and Stability of Urease Inhibitors: A QM/MM MD Study. Molecules 2023; 28:molecules28062697. [PMID: 36985670 PMCID: PMC10051795 DOI: 10.3390/molecules28062697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023] Open
Abstract
Soil bacteria can produce urease, which catalyzes the hydrolysis of urea to ammonia (NH3) and carbamate. A variety of urease inhibitors have been proposed to reduce NH3 volatilization by interfering with the urease activity. We report a quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) study on the mechanism employed for the inhibition of urease by three representative competitive inhibitors; namely, acetohydroxamic acid (AHA), hydroxyurea (HU), and N-(n-butyl)phosphorictriamide (NBPTO). The possible connections between the structural and thermodynamical properties and the experimentally observed inhibition efficiency were evaluated and characterized. We demonstrate that the binding affinity decreases in the order NBPTO >> AHA > HU in terms of the computed activation and reaction free energies. This trend also indicates that NBPTO shows the highest inhibitory activity and the lowest IC50 value of 2.1 nM, followed by AHA (42 μM) and HU (100 μM). It was also found that the X=O moiety (X = carbon or phosphorous) plays a crucial role in the inhibitor binding process. These findings not only elucidate why the potent urease inhibitors are effective but also have implications for the design of new inhibitors.
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Affiliation(s)
- Shunya Suenaga
- Faculty of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan
| | - Yu Takano
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan
| | - Toru Saito
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan
- Correspondence: ; Tel.: +81-82-830-1617
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5
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Conformational transitions induced by NADH binding promote reduction half-reaction in 2-hydroxybiphenyl-3-monooxygenase catalytic cycle. Biochem Biophys Res Commun 2023; 639:77-83. [PMID: 36470075 DOI: 10.1016/j.bbrc.2022.11.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/15/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
2-Hydroxybiphenyl-3-monoxygenase from Pseudomonas azelaica is an effective catalyst of the regiospecific conversions of various aromatic compounds. A comprehensive understanding of the complete catalytic cycle, including the as yet unclear details of NADH binding, NADH/FAD interaction as well as related conformational changes could facilitate the rational design of improved enzyme variants for practical applications. Induced fit formation of a specific pocket for the nicotinamide ring at NADH binding has been revealed using advanced molecular simulation methods including metadynamics and QM/MM modeling. The resulting triple stacking interaction of the nicotinamide as well as isoalloxazine rings and evolutionarily correlated amino acid residues of the active site greatly contributes to the stabilization of the charge-transfer complex and determines the Pro-S stereospecificity of the hydride transfer and the low energy barrier 11 kcal/mol. Then the resulting FADH- anion undergoes the consequent conformational transition of the FAD isoalloxazine ring from the open out to the closed in position which is followed by the binding of an oxygen molecule what is crucial for the next step of substrate oxidation and the completion of the catalytic cycle.
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6
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Adhikari P, Song M, Bai M, Rijal P, DeGroot N, Lu Y. Solvent Effects on the Temperature Dependence of Hydride Kinetic Isotope Effects: Correlation to the Donor-Acceptor Distances. J Phys Chem A 2022; 126:7675-7686. [PMID: 36228057 DOI: 10.1021/acs.jpca.2c06065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein structural effects on the temperature (T) dependence of kinetic isotope effects (KIEs) in H-tunneling reactions have recently been used to discuss about the role of enzyme thermal motions in catalysis. Frequently observed nearly T-independent KIEs in the wild-type enzymes and T-dependent KIEs in variants suggest that H-tunneling in the former is assisted by the naturally evolved protein constructive vibrations that help sample short donor-acceptor distances (DADs) needed. This explanation that correlates the T-dependence of KIEs with DAD sampling has been highly debated as simulations following other H-tunneling models sometimes gave alternative explanations. In this paper, solvent effects on the T-dependence of KIEs of two hydride tunneling reactions of NADH/NAD+ analogues (represented by ΔEa = EaD - EaH) were determined in attempts to replicate the observations in enzymes and test the protein vibration-assisted DAD sampling concept. Effects of selected aprotic solvents on the DADPRC's of the productive reactant complexes (PRCs) and the DADTRS's of the activated tunneling ready states (TRSs) were obtained through computations and analyses of the kinetic data, including 2° KIEs, respectively. A weaker T-dependence of KIEs (i.e., smaller ΔEa) was found in a more polar aprotic solvent in which the system has a shorter average DADPRC and DADTRS. Further results show that a charge-transfer (CT) complexation made of a stronger donor/acceptor gives rise to a smaller ΔEa. Overall, the shorter and less broadly distributed DADs resulting from the stronger CT complexation vibrations give rise to a smaller ΔEa. Our results appear to support the explanation that links the T-dependence of KIEs to the donor-acceptor rigidity in enzymes.
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Affiliation(s)
- Pratichhya Adhikari
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Meimei Song
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Mingxuan Bai
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Pratap Rijal
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Nicholas DeGroot
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
| | - Yun Lu
- Department of Chemistry, Southern Illinois University, Edwardsville, Edwardsville, Illinois 62026, United States
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7
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Machado TFG, Purg M, Åqvist J, da Silva RG. Transition States for Psychrophilic and Mesophilic ( R)-3-Hydroxybutyrate Dehydrogenase-Catalyzed Hydride Transfer at Sub-zero Temperatures. Biochemistry 2021; 60:2186-2194. [PMID: 34190541 DOI: 10.1021/acs.biochem.1c00322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
(R)-3-Hydroxybutyrate dehydrogenase (HBDH) catalyzes the NADH-dependent reduction of 3-oxocarboxylates to (R)-3-hydroxycarboxylates. The active sites of a pair of cold- and warm-adapted HBDHs are identical except for a single residue, yet kinetics evaluated at -5, 0, and 5 °C show a much higher steady-state rate constant (kcat) for the cold-adapted than for the warm-adapted HBDH. Intriguingly, single-turnover rate constants (kSTO) are strikingly similar between the two orthologues. Psychrophilic HBDH primary deuterium kinetic isotope effects on kcat (Dkcat) and kSTO (DkSTO) decrease at lower temperatures, suggesting more efficient hydride transfer relative to other steps as the temperature decreases. However, mesophilic HBDH Dkcat and DkSTO are generally temperature-independent. The DkSTO data allowed calculation of intrinsic primary deuterium kinetic isotope effects. Intrinsic isotope effects of 4.2 and 3.9 for cold- and warm-adapted HBDH, respectively, at 5 °C, supported by quantum mechanics/molecular mechanics calculations, point to a late transition state for both orthologues. Conversely, intrinsic isotope effects of 5.7 and 3.1 for cold- and warm-adapted HBDH, respectively, at -5 °C indicate the transition state becomes nearly symmetric for the psychrophilic enzyme, but more asymmetric for the mesophilic enzyme. His-to-Asn and Asn-to-His mutations in the psychrophilic and mesophilic HBDH active sites, respectively, swap the single active-site position where these orthologues diverge. At 5 °C, the His-to-Asn mutation in psychrophilic HBDH decreases Dkcat to 3.1, suggesting a decrease in transition-state symmetry, while the His-to-Asn mutation in mesophilic HBDH increases Dkcat to 4.4, indicating an increase in transition-state symmetry. Hence, temperature adaptation and a single divergent active-site residue may influence transition-state geometry in HBDHs.
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Affiliation(s)
- Teresa F G Machado
- School of Chemistry, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Miha Purg
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Rafael G da Silva
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
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8
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Miller MD, Phillips GN. Moving beyond static snapshots: Protein dynamics and the Protein Data Bank. J Biol Chem 2021; 296:100749. [PMID: 33961840 PMCID: PMC8164045 DOI: 10.1016/j.jbc.2021.100749] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 01/02/2023] Open
Abstract
Proteins are the molecular machines of living systems. Their dynamics are an intrinsic part of their evolutionary selection in carrying out their biological functions. Although the dynamics are more difficult to observe than a static, average structure, we are beginning to observe these dynamics and form sound mechanistic connections between structure, dynamics, and function. This progress is highlighted in case studies from myoglobin and adenylate kinase to the ribosome and molecular motors where these molecules are being probed with a multitude of techniques across many timescales. New approaches to time-resolved crystallography are allowing simple “movies” to be taken of proteins in action, and new methods of mapping the variations in cryo-electron microscopy are emerging to reveal a more complete description of life’s machines. The results of these new methods are aided in their dissemination by continual improvements in curation and distribution by the Protein Data Bank and their partners around the world.
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Affiliation(s)
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas, USA; Department of Chemistry, Rice University, Houston, Texas, USA.
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9
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Santi N, Morrill LC, Swiderek K, Moliner V, Luk LYP. Transfer hydrogenations catalyzed by streptavidin-hosted secondary amine organocatalysts. Chem Commun (Camb) 2021; 57:1919-1922. [PMID: 33496282 PMCID: PMC8330412 DOI: 10.1039/d0cc08142f] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/14/2021] [Indexed: 12/19/2022]
Abstract
Here, the streptavidin-biotin technology was applied to enable organocatalytic transfer hydrogenation. By introducing a biotin-tethered pyrrolidine (1) to the tetrameric streptavidin (T-Sav), the resulting hybrid catalyst was able to mediate hydride transfer from dihydro-benzylnicotinamide (BNAH) to α,β-unsaturated aldehydes. Hydrogenation of cinnamaldehyde and some of its aryl-substituted analogues was found to be nearly quantitative. Kinetic measurements revealed that the T-Sav:1 assembly possesses enzyme-like behavior, whereas isotope effect analysis, performed by QM/MM simulations, illustrated that the step of hydride transfer is at least partially rate-limiting. These results have proven the concept that T-Sav can be used to host secondary amine-catalyzed transfer hydrogenations.
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Affiliation(s)
- Nicolò Santi
- School of Chemistry, Main Building, Cardiff University, Cardiff CF10 3AT, UK.
| | - Louis C Morrill
- School of Chemistry, Main Building, Cardiff University, Cardiff CF10 3AT, UK. and Cardiff Catalysis Institute, School of Chemistry, Main Building, Cardiff University, Cardiff CF10 3AT, UK
| | - Katarzyna Swiderek
- Departament de Química Física i Analítica, Universitat Jaume I, Castelló 12071, Spain
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, Castelló 12071, Spain
| | - Louis Y P Luk
- School of Chemistry, Main Building, Cardiff University, Cardiff CF10 3AT, UK. and Cardiff Catalysis Institute, School of Chemistry, Main Building, Cardiff University, Cardiff CF10 3AT, UK
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10
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Abstract
This review examines low-frequency vibrational modes of proteins and their coupling to enzyme catalytic sites. That protein motions are critical to enzyme function is clear, but the kinds of motions present in proteins and how they are involved in function remain unclear. Several models of enzyme-catalyzed reaction suggest that protein dynamics may be involved in the chemical step of the catalyzed reaction, but the evidence in support of such models is indirect. Spectroscopic studies of low-frequency protein vibrations consistently show that there are underdamped modes of the protein with frequencies in the tens of wavenumbers where overdamped behavior would be expected. Recent studies even show that such underdamped vibrations modulate enzyme active sites. These observations suggest that increasingly sophisticated spectroscopic methods will be able to unravel the link between low-frequency protein vibrations and enzyme function.
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11
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Chen J, Ma Q, Li M, Wu W, Huang L, Liu L, Fang Y, Dong S. Coenzyme-dependent nanozymes playing dual roles in oxidase and reductase mimics with enhanced electron transport. NANOSCALE 2020; 12:23578-23585. [PMID: 33225340 DOI: 10.1039/d0nr06605b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Although nanozymes overcome a series of shortcomings of natural enzymes, their wide applications are hampered due to their limited varieties. In this work, we propose a coenzyme-dependent nanozyme, a synergistic composite comprising zeolitic imidazolate frameworks encapsulated with polyethylenimine (PEI) and functionalized with a flavin mononucleotide (PEI/ZIF-FMN). The flavin mononucleotide (FMN) plays the role of a prosthetic group, and the positively charged NH2 groups in PEI readily provide the binding affinity to nicotinamide adenine dinucleotide (NADH), which facilitates the electron transfer from NADH to FMN and terminal electron acceptors (such as O2) with a greatly enhanced (80 times) catalytic performance. The integrated nanoparticle-coenzyme composite works as an NADH oxidase mimic and couples with dehydrogenases for the tandem enzymatic reaction. PEI/ZIF-FMN also mediated the electron transfer from NADH to cytochrome c (Cyt c), thereby exhibiting Cyt c reductase-like activity.
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Affiliation(s)
- Jinxing Chen
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China.
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12
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Curtolo F, Arantes GM. Mechanisms for Flavin-Mediated Oxidation: Hydride or Hydrogen-Atom Transfer? J Chem Inf Model 2020; 60:6282-6287. [DOI: 10.1021/acs.jcim.0c00945] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Felipe Curtolo
- Department of Biochemistry, Instituto de Quı́mica, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
| | - Guilherme M. Arantes
- Department of Biochemistry, Instituto de Quı́mica, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
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13
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14
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Chen X, Schwartz SD. Multiple Reaction Pathways in the Morphinone Reductase-Catalyzed Hydride Transfer Reaction. ACS OMEGA 2020; 5:23468-23480. [PMID: 32954200 PMCID: PMC7496013 DOI: 10.1021/acsomega.0c03472] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
Morphinone reductase (MR) is an important model system for studying the contribution of protein motions to H-transfer reactions. In this research, we used quantum mechanical/molecular mechanics (QM/MM) simulation together with transition path sampling (TPS) simulation to study two important topics of current research on MR: the existence of multiple catalytic reaction pathways and the involvement of fast protein motions in the catalytic process. We have discovered two reaction pathways for the wild type and three reaction pathways for the N189A mutant. With the committor distribution analysis method, we found reaction coordinates for all five reaction pathways. Only one wild-type reaction pathway has a rate-promoting vibration from His186, while all of the other four pathways do not involve any protein motions in their catalytic process through the transition state. The rate-promoting vibration in the wild-type MR, which comes from a direction perpendicular to the donor-acceptor axis, functions to decrease the donor-acceptor distance by causing a subtle "out-of-plane" motion of a donor atom. By comparing reaction pathways between the two enzymes, we concluded that the major effect of the N189A point mutation is to increase the active site volume by altering the active site backbone and eliminating the Asn189 side chain. This effect causes a different NADH geometry at the reactant state, which very well explains the different reaction mechanisms between the two enzymes, as well as the disappearance of the His186 rate-promoting vibrations in the N189A mutant. The unfavorable geometry of the NADH pyridine ring induced by the N189A point mutation is the potential cause of multiple reaction pathways in N189A mutants.
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15
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Kiss DJ, Ferenczy GG. A detailed mechanism of the oxidative half-reaction of d-amino acid oxidase: another route for flavin oxidation. Org Biomol Chem 2020; 17:7973-7984. [PMID: 31407761 DOI: 10.1039/c9ob00975b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
d-Amino acid oxidase (DAAO) is a flavoenzyme whose inhibition is expected to have therapeutic potential in schizophrenia. DAAO catalyses hydride transfer from the substrate to the flavin in the reductive half-reaction, and the flavin is reoxidized by O2 in the oxidative half-reaction. Quantum mechanical/molecular mechanical calculations were performed and their results together with available experimental information were used to elucidate the detailed mechanism of the oxidative half-reaction. The reaction starts with a single electron transfer from FAD to O2, followed by triplet-singlet transition. FAD oxidation is completed by a proton coupled electron transfer to the oxygen species and the reaction terminates with H2O2 formation by proton transfer from the oxidized substrate to the oxygen species via a chain of water molecules. The substrate plays a double role by facilitating the first electron transfer and by providing a proton in the last step. The mechanism differs from the oxidative half-reaction of other oxidases.
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Affiliation(s)
- Dóra Judit Kiss
- Doctoral School of Chemistry, Eötvös Loránd University, Pázmány s 1/A, H-1117, Budapest, Hungary. and Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt 2, H-1117, Budapest, Hungary.
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt 2, H-1117, Budapest, Hungary.
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16
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Soler J, González-Lafont À, Lluch JM. A protocol to obtain multidimensional quantum tunneling corrections derived from QM(DFT)/MM calculations for an enzyme reaction. Phys Chem Chem Phys 2020; 22:27385-27393. [DOI: 10.1039/d0cp05265e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The multidimensional small-curvature tunneling (SCT) method with Electrostatic Embedding calculations is a compromise between an accessible computational cost and the attainment of an accurate enough estimation of tunneling for an enzyme reaction.
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Affiliation(s)
- Jordi Soler
- Departament de Química Universitat Autònoma de Barcelona
- Bellaterra
- Spain
| | - Àngels González-Lafont
- Departament de Química Universitat Autònoma de Barcelona
- Bellaterra
- Spain
- Institut de Biotecnologia i de Biomedicina (IBB)
- Universitat Autònoma de Barcelona
| | - José M. Lluch
- Departament de Química Universitat Autònoma de Barcelona
- Bellaterra
- Spain
- Institut de Biotecnologia i de Biomedicina (IBB)
- Universitat Autònoma de Barcelona
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17
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Johannissen LO, Iorgu AI, Scrutton NS, Hay S. What are the signatures of tunnelling in enzyme-catalysed reactions? Faraday Discuss 2020; 221:367-378. [DOI: 10.1039/c9fd00044e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computed tunnelling contributions and correlations between apparent activation enthalpy and entropy are explored for the interpretation of enzyme-catalysed H-transfer reactions.
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Affiliation(s)
- Linus O. Johannissen
- Manchester Institute of Biotechnology (MIB)
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Andreea I. Iorgu
- Manchester Institute of Biotechnology (MIB)
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology (MIB)
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Sam Hay
- Manchester Institute of Biotechnology (MIB)
- School of Chemistry
- University of Manchester
- Manchester
- UK
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18
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Lu Y, Wilhelm S, Bai M, Maness P, Ma L. Replication of the Enzymatic Temperature Dependency of the Primary Hydride Kinetic Isotope Effects in Solution: Caused by the Protein-Controlled Rigidity of the Donor-Acceptor Centers? Biochemistry 2019; 58:4035-4046. [PMID: 31478638 DOI: 10.1021/acs.biochem.9b00574] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The change from the temperature independence of the primary (1°) H/D kinetic isotope effects (KIEs) in wild-type enzyme-catalyzed H-transfer reactions (ΔEa = EaD - EaH ∼ 0) to a strong temperature dependence with the mutated enzymes (ΔEa ≫ 0) has recently been frequently observed. This has prompted some enzymologists to develop new H-tunneling models to correlate ΔEa with the donor-acceptor distance (DAD) at the tunneling-ready state (TRS) as well as the protein thermal motions/dynamics that sample the short DADTRS's for H-tunneling to occur. While extensive evidence supporting or disproving the thermally activated DAD sampling concept has emerged, a comparable study of the simpler bimolecular H-tunneling reactions in solution has not been carried out. In particular, small ΔEa's (∼0) have not been found. In this paper, we report a study of the hydride-transfer reactions from four NADH models to the same hydride acceptor in acetonitrile. The ΔEa's were determined: 0.37 (small), 0.60, 0.99, and 1.53 kcal/mol (large). The α-secondary (2°) KIEs on the acceptor that serve as a ruler for the rigidity of reaction centers were previously reported or determined. All possible productive reactant complex (PRC) configurations were computed to provide insight into the structures of the TRS's. Relationships among structures, 2° KIEs, DADPRC's, and ΔEa's were discussed. The more rigid system with more suppressed 2° C-H vibrations at the TRS and more narrowly distributed DADPRC's in PRCs gave a smaller ΔEa. The results replicated the trend observed in enzymes versus mutated enzymes and appeared to support the concepts of different thermally activated DADTRS sampling processes in response to the rigid versus flexible donor-acceptor centers.
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Affiliation(s)
- Yun Lu
- Department of Chemistry , Southern Illinois University Edwardsville , Edwardsville , Illinois 62026 , United States
| | - Samantha Wilhelm
- Department of Chemistry , Southern Illinois University Edwardsville , Edwardsville , Illinois 62026 , United States
| | - Mingxuan Bai
- Department of Chemistry , Southern Illinois University Edwardsville , Edwardsville , Illinois 62026 , United States
| | - Peter Maness
- Department of Chemistry , Southern Illinois University Edwardsville , Edwardsville , Illinois 62026 , United States
| | - Li Ma
- Department of Chemistry , Southern Illinois University Edwardsville , Edwardsville , Illinois 62026 , United States
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19
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Iorgu AI, Hedison TM, Hay S, Scrutton NS. Selectivity through discriminatory induced fit enables switching of NAD(P)H coenzyme specificity in Old Yellow Enzyme ene-reductases. FEBS J 2019; 286:3117-3128. [PMID: 31033202 PMCID: PMC6767020 DOI: 10.1111/febs.14862] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/22/2019] [Accepted: 04/24/2019] [Indexed: 11/30/2022]
Abstract
Most ene‐reductases belong to the Old Yellow Enzyme (OYE) family of flavin‐dependent oxidoreductases. OYEs use nicotinamide coenzymes as hydride donors to catalyze the reduction of alkenes that contain an electron‐withdrawing group. There have been many investigations of the structures and catalytic mechanisms of OYEs. However, the origin of coenzyme specificity in the OYE family is unknown. Structural NMR and X‐ray crystallographic data were used to rationally design variants of two OYEs, pentaerythritol tetranitrate reductase (PETNR) and morphinone reductase (MR), to discover the basis of coenzyme selectivity. PETNR has dual‐specificity and reacts with NADH and NADPH; MR accepts only NADH as hydride donor. Variants of a β‐hairpin motif in an active site loop of both these enzymes were studied using stopped‐flow spectroscopy. Specific attention was placed on the potential role of arginine residues within the β‐hairpin motif. Mutagenesis demonstrated that Arg130 governs the preference of PETNR for NADPH, and that Arg142 interacts with the coenzyme pyrophosphate group. These observations were used to switch coenzyme specificity in MR by replacing either Glu134 or Leu146 with arginine residues. These variants had increased (~15‐fold) affinity for NADH. Mutagenesis enabled MR to accept NADPH as a hydride donor, with E134R MR showing a significant (55‐fold) increase in efficiency in the reductive half‐reaction, when compared to the essentially unreactive wild‐type enzyme. Insight into the question of coenzyme selectivity in OYEs has therefore been addressed through rational redesign. This should enable coenzyme selectivity to be improved and switched in other OYEs.
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Affiliation(s)
- Andreea I Iorgu
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, UK
| | - Tobias M Hedison
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, UK
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20
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Wei W, Ma J, Xie D, Zhou Y. Linking inhibitor motions to proteolytic stability of sunflower trypsin inhibitor-1. RSC Adv 2019; 9:13776-13786. [PMID: 35519558 PMCID: PMC9063939 DOI: 10.1039/c9ra02114k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 04/25/2019] [Indexed: 12/20/2022] Open
Abstract
The remarkable capability of an enzyme isn't only determined by its active site but also controlled by the environment. To unravel the environment role in catalysis, the dynamic motions as well as the static mechanism need to be studied. In this work, QM/MM MD simulations were employed to study the proteolysis process of SFTI-1 and BiKF, which revealed that a combination of static non-bonded interactions and dynamic motions along the reaction coordinate can account for the different hydrolysis rates between them. A comparison among SFTI-1 and three analogs with similar non-bonded interactions further revealed a positive correlation between the mobility of inhibitors and the hydrolysis rates. Apart from the cyclic backbone and disulfide bond, intramolecular hydrogen bonds also increase the rigidity of the backbone of inhibitors, and therefore hinder inhibitor motions to resist proteolysis. These new detailed mechanistic insights suggest the need to consider inhibitor motions in the rational design of peptide inhibitors. Besides the non-bonded interactions, inhibitor motions especially rotation of the scissile bond also influence proteolytic stability.![]()
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Affiliation(s)
- Wanqing Wei
- Institute of Theoretical and Computational Chemistry, Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Jing Ma
- Institute of Theoretical and Computational Chemistry, Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Daiqian Xie
- Institute of Theoretical and Computational Chemistry, Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Yanzi Zhou
- Institute of Theoretical and Computational Chemistry, Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
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21
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Wapeesittipan P, Mey ASJS, Walkinshaw MD, Michel J. Allosteric effects in cyclophilin mutants may be explained by changes in nano-microsecond time scale motions. Commun Chem 2019. [DOI: 10.1038/s42004-019-0136-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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22
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Marion A, Gokcan H, Monard G. Semi-Empirical Born-Oppenheimer Molecular Dynamics (SEBOMD) within the Amber Biomolecular Package. J Chem Inf Model 2019; 59:206-214. [PMID: 30433776 DOI: 10.1021/acs.jcim.8b00605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Semi-empirical quantum methods from the neglect of differential diatomic overlap (NDDO) family such as MNDO, AM1, or PM3 are fast albeit approximate quantum methods. By combining them with linear scaling methods like the divide & conquer (D&C) method, it is possible to quickly evaluate the energy of systems containing hundreds to thousands of atoms. We here present our implementation in the Amber biomolecular package of a SEBOMD module that provides a way to run semi-empirical Born-Oppenheimer molecular dynamics. At each step of a SEBOMD, a fully converged self-consistent field (SCF) calculation is performed to obtain the semiempirical quantum potential energy of a molecular system encaged or not in periodic boundary conditions. We describe the implementation and the features of our SEBOMD implementation. We show the requirements to conserve the total energy in NVE simulations, and how to accelerate SCF convergence through density matrix extrapolation. Specific ways of handling periodic boundary conditions using mechanical embedding or electrostatic embedding through a tailored quantum Ewald summation is developed. The parallel performance of SEBOMD simulations using the D&C scheme are presented for liquid water systems of various sizes, and a comparison between the traditional full diagonalization scheme and the D&C approach for the reproduction of the structure of liquid water illustrates the potentiality of SEBOMD to simulate molecular systems containing several hundreds of atoms for hundreds of picoseconds with a quantum mechanical potential in a reasonable amount of CPU time.
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Affiliation(s)
- Antoine Marion
- Université de Lorraine, CNRS, LPCT , F-54000 Nancy , France.,Department of Chemistry , Middle East Technical University , 06800 , Ankara , Turkey
| | - Hatice Gokcan
- Université de Lorraine, CNRS, LPCT , F-54000 Nancy , France.,Department of Chemistry , University of North Texas , Denton , Texas 76201 , United States
| | - Gerald Monard
- Université de Lorraine, CNRS, LPCT , F-54000 Nancy , France
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23
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Pu Z, Zhao M, Zhang Y, Sun W, Bao Y. Dynamic Description of the Catalytic Cycle of Malate Enzyme: Stereoselective Recognition of Substrate, Chemical Reaction, and Ligand Release. J Phys Chem B 2018; 122:12241-12250. [PMID: 30500201 DOI: 10.1021/acs.jpcb.8b05135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In protein engineering, investigations of catalytic cycle facilitate rational design of enzymes. In the present work, deeper analysis on the catalytic cycle of malate enzyme (EC 1.1.1.40), an enzyme involved in cancer metabolic and fatty acid synthesis, was performed. In substrate binding, stereoselective recognition of a substrate originates from distance and angle difference between two chiral substrates and Mn2+ as well as monodentate or coplanar ion reaction with Arg165. In catalytic transformation, the activation barrier for the hydride transfer of d-malate is 20.28 kcal/mol higher than that for l-malate. The activation barrier for β-decarboxylation of oxaloacetate is about 4.59 kcal/mol higher than the activation barrier for the hydride transfer of l-malate. The effective activation barrier is 16.44 kcal/mol, which is in close agreement with the value derived from the application of transition-state theory and the Eyring equation to kcat. In ligand release, l/d-malate needs to overcome a higher barrier than pyruvate to break all bonds in parallel and then to escape from the binding pocket. Leu167 and Asn421 comprise a swinging gate to control the product release. The more open gate is possibly required in the direction of pyruvate to l-malate. Our studies are focused on extending structural knowledge regarding the malate enzyme and provided a powerful strategy for future experimental investigations.
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Affiliation(s)
- Zhongji Pu
- School of Life Science and Biotechnology , Dalian University of Technology , Dalian 116024 , China
| | - Mengdi Zhao
- Department of Nanoenergy Engineering , Pusan National University , Busan 46241 , Republic of Korea
| | - Yue Zhang
- School of Life Science and Biotechnology , Dalian University of Technology , Dalian 116024 , China
| | - Wenhui Sun
- School of Life Science and Biotechnology , Dalian University of Technology , Dalian 116024 , China
| | - Yongming Bao
- School of Life Science and Biotechnology , Dalian University of Technology , Dalian 116024 , China.,School of Food and Environment Science and Engineering , Dalian University of Technology , Panjin 124221 , China
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24
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Iorgu AI, Baxter NJ, Cliff MJ, Levy C, Waltho JP, Hay S, Scrutton NS. Nonequivalence of Second Sphere "Noncatalytic" Residues in Pentaerythritol Tetranitrate Reductase in Relation to Local Dynamics Linked to H-Transfer in Reactions with NADH and NADPH Coenzymes. ACS Catal 2018; 8:11589-11599. [PMID: 31119061 PMCID: PMC6516726 DOI: 10.1021/acscatal.8b02810] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/23/2018] [Indexed: 11/28/2022]
Abstract
![]()
Many enzymes that
catalyze hydride transfer reactions work via
a mechanism dominated by quantum mechanical tunneling. The involvement
of fast vibrational modes of the reactive complex is often inferred
in these reactions, as in the case of the NAD(P)H-dependent pentaerythritol
tetranitrate reductase (PETNR). Herein, we interrogated the H-transfer
mechanism in PETNR by designing conservative (L25I and I107L) and
side chain shortening (L25A and I107A) PETNR variants and using a
combination of experimental approaches (stopped-flow rapid kinetics,
X-ray crystallography, isotope/temperature dependence studies of H-transfer
and NMR spectroscopy). X-ray data show subtle changes in the local
environment of the targeted side chains but no major structural perturbation
caused by mutagenesis of these two second sphere active site residues.
However, temperature dependence studies of H-transfer revealed a coenzyme-specific
and complex thermodynamic equilibrium between different reactive configurations
in PETNR–coenzyme complexes. We find that mutagenesis of these
second sphere “noncatalytic” residues affects differently
the reactivity of PETNR with NADPH and NADH coenzymes. We attribute
this to subtle, dynamic structural changes in the PETNR active site,
the effects of which impact differently in the nonequivalent reactive
geometries of PETNR−NADH and PETNR−NADPH complexes.
This inference is confirmed through changes observed in the NMR chemical
shift data for PETNR complexes with unreactive 1,4,5,6-tetrahydro-NAD(P)
analogues. We show that H-transfer rates can (to some extent) be buffered
through entropy–enthalpy compensation, but that use of integrated
experimental tools reveals hidden complexities that implicate a role
for dynamics in this relatively simple H-transfer reaction. Similar
approaches are likely to be informative in other enzymes to understand
the relative importance of (distal) hydrophobic side chains and dynamics
in controlling the rates of enzymatic H-transfer.
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Affiliation(s)
- Andreea I. Iorgu
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nicola J. Baxter
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Colin Levy
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jonathan P. Waltho
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Sam Hay
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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25
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Roca M, Ruiz-Pernía JJ, Castillo R, Oliva M, Moliner V. Temperature dependence of dynamic, tunnelling and kinetic isotope effects in formate dehydrogenase. Phys Chem Chem Phys 2018; 20:25722-25737. [PMID: 30280169 DOI: 10.1039/c8cp04244f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The origin of the catalytic power of enzymes has been a question of debate for a long time. In this regard, the possible contribution of protein dynamics in enzymatic catalysis has become one of the most controversial topics. In the present work, the hydride transfer step in the formate dehydrogenase (FDH EC 1.2.1.2) enzyme is studied by means of molecular dynamic (MD) simulations with quantum mechanics/molecular mechanics (QM/MM) potentials in order to explore any correlation between dynamics, tunnelling effects and the rate constant. The temperature dependence of the kinetic isotope effects (KIEs), which is one of the few tests that can be studied by experiments and simulations to shed light on this debate, has been computed and the results have been compared with previous experimental data. The classical mechanical free energy barrier and the number of recrossing trajectories seem to be temperature-independent while the quantum vibrational corrections and the tunnelling effects are slightly temperature-dependent over the interval of 5-45 °C. The computed primary KIEs are in very good agreement with previous experimental data, being almost temperature-independent within the standard deviations. The modest dependence on the temperature is due to just the quantum vibrational correction contribution. These results, together with the analysis of the evolution of the collective variables such as the electrostatic potential or the electric field created by the protein on the key atoms involved in the reaction, confirm that while the protein is well preorganised, some changes take place along the reaction that favour the hydride transfer and the product release. Coordinates defining these movements are, in fact, part of the real reaction coordinate.
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Affiliation(s)
- Maite Roca
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
| | | | - Raquel Castillo
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
| | - Mónica Oliva
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
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26
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Reyes AC, Amyes TL, Richard JP. Primary Deuterium Kinetic Isotope Effects: A Probe for the Origin of the Rate Acceleration for Hydride Transfer Catalyzed by Glycerol-3-Phosphate Dehydrogenase. Biochemistry 2018; 57:4338-4348. [PMID: 29927590 PMCID: PMC6091503 DOI: 10.1021/acs.biochem.8b00536] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Large
primary deuterium kinetic isotope effects (1° DKIEs)
on enzyme-catalyzed hydride transfer may be observed when the transferred
hydride tunnels through the energy barrier. The following 1°
DKIEs on kcat/Km and relative reaction driving force are reported for wild-type and
mutant glycerol-3-phosphate dehydrogenase (GPDH)-catalyzed reactions
of NADL (L = H, D): wild-type GPDH, ΔΔG⧧ = 0 kcal/mol, 1° DKIE = 1.5;
N270A, 5.6 kcal/mol, 3.1; R269A, 9.1 kcal/mol, 2.8; R269A + 1.0 M
guanidine, 2.4 kcal/mol, 2.7; R269A/N270A, 11.5 kcal/mol, 2.4. Similar
1° DKIEs were observed on kcat. The
narrow range of 1° DKIEs (2.4–3.1) observed for a 9.1
kcal/mol change in reaction driving force provides strong evidence
that these are intrinsic 1° DKIEs on rate-determining hydride
transfer. Evidence is presented that the intrinsic DKIE on wild-type
GPDH-catalyzed reduction of DHAP lies in this range. A similar range
of 1° DKIEs (2.4–2.9) on (kcat/KGA, M–1 s–1) was reported for dianion-activated hydride transfer from NADL to
glycolaldehyde (GA) [Reyes, A. C.; Amyes, T. L.; Richard, J.
P. J. Am. Chem. Soc.2016, 138, 14526–14529].
These 1° DKIEs are much smaller than those observed for enzyme-catalyzed
hydrogen transfer that occurs mainly by quantum mechanical tunneling.
These results support the conclusion that the rate acceleration for
GPDH-catalyzed reactions is due to the stabilization of the transition
state for hydride transfer by interactions with the protein catalyst.
The small 1° DKIEs reported for mutant GPDH-catalyzed and for
wild-type dianion-activated reactions are inconsistent with a model
where the dianion binding energy is utilized in the stabilization
of a tunneling ready state.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Tina L Amyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
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27
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Garcia-Borràs M, Houk KN, Jiménez-Osés G. Computational Design of Protein Function. COMPUTATIONAL TOOLS FOR CHEMICAL BIOLOGY 2017. [DOI: 10.1039/9781788010139-00087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The computational design of enzymes is a tremendous challenge for both chemistry and biochemistry. The ability to design stable and functional biocatalysts that could operate under different conditions to perform chemical reactions without precedent in nature, allowing the large-scale production of chemicals à la carte, would revolutionise both synthetic, pharmacologic and materials chemistry. Despite the great advances achieved, this highly multidisciplinary area of research is still in its infancy. This chapter describes the ‘inside-out’ protocol for computational enzyme design and both the achievements and limitations of the current technology are highlighted. Furthermore, molecular dynamics simulations have proved to be invaluable in the enzyme design process, constituting an important tool for discovering elusive catalytically relevant conformations of the engineered or designed enzyme. As a complement to the ‘inside-out’ design protocol, different examples where hybrid QM/MM approaches have been directly applied to discover beneficial mutations in rational computational enzyme design are described.
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Affiliation(s)
- Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California Los Angeles California CA 90095-1569 USA
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry, University of California Los Angeles California CA 90095-1569 USA
| | - Gonzalo Jiménez-Osés
- Departamento de Química, Centro de Investigación en Síntesis Química Universidad de La Rioja 26006 Logroño La Rioja Spain
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28
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Ranaghan KE, Morris WG, Masgrau L, Senthilkumar K, Johannissen LO, Scrutton NS, Harvey JN, Manby FR, Mulholland AJ. Ab Initio QM/MM Modeling of the Rate-Limiting Proton Transfer Step in the Deamination of Tryptamine by Aromatic Amine Dehydrogenase. J Phys Chem B 2017; 121:9785-9798. [PMID: 28930453 DOI: 10.1021/acs.jpcb.7b06892] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aromatic amine dehydrogenase (AADH) and related enzymes are at the heart of debates on the roles of quantum tunneling and protein dynamics in catalysis. The reaction of tryptamine in AADH involves significant quantum tunneling in the rate-limiting proton transfer step, shown by large H/D primary kinetic isotope effects (KIEs), with unusual temperature dependence. We apply correlated ab initio combined quantum mechanics/molecular mechanics (QM/MM) methods, at levels up to local coupled cluster theory (LCCSD(T)/(aug)-cc-pVTZ), to calculate accurate potential energy surfaces for this reaction, which are necessary for quantitative analysis of tunneling contributions and reaction dynamics. Different levels of QM/MM treatment are tested. Multiple pathways are calculated with fully flexible transition state optimization by the climbing-image nudged elastic band method at the density functional QM/MM level. The average LCCSD(T) potential energy barriers to proton transfer are 16.7 and 14.0 kcal/mol for proton transfer to the two carboxylate atoms of the catalytic base, Asp128β. The results show that two similar, but distinct pathways are energetically accessible. These two pathways have different barriers, exothermicity and curvature, and should be considered in analyses of the temperature dependence of reaction and KIEs in AADH and other enzymes. These results provide a benchmark for this prototypical enzyme reaction and will be useful for developing empirical models, and analyzing experimental data, to distinguish between different conceptual models of enzyme catalysis.
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Affiliation(s)
- Kara E Ranaghan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - William G Morris
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Laura Masgrau
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona , 08193 Bellaterra (Barcelona), Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona , 08193 Bellaterra (Barcelona), Spain
| | | | - Linus O Johannissen
- Manchester Institute of Biotechnology, University of Manchester , Manchester M13 9PL, U.K
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, University of Manchester , Manchester M13 9PL, U.K
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven , Celestijnenlaan 200F, B-3001 Heverlee, Belgium
| | - Frederick R Manby
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
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