1
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Zheng J, Tang J, Jin S, Hu H, Jiang ZJ, Chen J, Bai JF, Gao Z. Site-Selective Deuteration of α-Amino Esters with 2-Hydroxynicotinaldehyde as a Catalyst. ACS OMEGA 2024; 9:26963-26972. [PMID: 38947810 PMCID: PMC11209932 DOI: 10.1021/acsomega.3c09974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/27/2024] [Accepted: 05/31/2024] [Indexed: 07/02/2024]
Abstract
An efficient method has been developed for the synthesis of α-deuterated α-amino esters via hydrogen isotope exchange of α-amino esters in D2O with 2-hydroxynicotinaldehyde as a catalyst under mild conditions. This methodology exhibits a wide range of substrate scopes, remarkable functional group tolerance, and affording the desired products in good yields with excellent deuterium incorporation. Notably, the ortho-hydroxyl group and the pyridine ring of the catalyst play a crucial role in the catalytic activity, which not only stabilizes the carbon-anion intermediates but also enhances the acidity of the amino esters' α-C-H bond.
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Affiliation(s)
- Jinfeng Zheng
- NingboTech-Cuiying
Joint Laboratory of Stable Isotope Technology, School of Biological
and Chemical Engineering, NingboTech University, Ningbo 315100, People’s Republic of China
- School
of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, People’s
Republic of China
| | - Jianbo Tang
- NingboTech-Cuiying
Joint Laboratory of Stable Isotope Technology, School of Biological
and Chemical Engineering, NingboTech University, Ningbo 315100, People’s Republic of China
- State
Key Laboratory of Applied Organic Chemistry, College of Chemistry
and Chemical Engineering, Lanzhou University, Lanzhou 730000, People’s Republic of China
| | - Shenhao Jin
- NingboTech-Cuiying
Joint Laboratory of Stable Isotope Technology, School of Biological
and Chemical Engineering, NingboTech University, Ningbo 315100, People’s Republic of China
| | - Hao Hu
- NingboTech-Cuiying
Joint Laboratory of Stable Isotope Technology, School of Biological
and Chemical Engineering, NingboTech University, Ningbo 315100, People’s Republic of China
| | - Zhi-Jiang Jiang
- NingboTech-Cuiying
Joint Laboratory of Stable Isotope Technology, School of Biological
and Chemical Engineering, NingboTech University, Ningbo 315100, People’s Republic of China
| | - Jia Chen
- NingboTech-Cuiying
Joint Laboratory of Stable Isotope Technology, School of Biological
and Chemical Engineering, NingboTech University, Ningbo 315100, People’s Republic of China
| | - Jian-Fei Bai
- NingboTech-Cuiying
Joint Laboratory of Stable Isotope Technology, School of Biological
and Chemical Engineering, NingboTech University, Ningbo 315100, People’s Republic of China
| | - Zhanghua Gao
- NingboTech-Cuiying
Joint Laboratory of Stable Isotope Technology, School of Biological
and Chemical Engineering, NingboTech University, Ningbo 315100, People’s Republic of China
- Ningbo
Cuiying Chemical Technology Co. Ltd., Ningbo 315100, People’s Republic of China
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2
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Drago VN, Devos JM, Blakeley MP, Forsyth VT, Parks JM, Kovalevsky A, Mueser TC. Neutron diffraction from a microgravity-grown crystal reveals the active site hydrogens of the internal aldimine form of tryptophan synthase. CELL REPORTS. PHYSICAL SCIENCE 2024; 5:101827. [PMID: 38645802 PMCID: PMC11027755 DOI: 10.1016/j.xcrp.2024.101827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Pyridoxal 5'-phosphate (PLP), the biologically active form of vitamin B6, is an essential cofactor in many biosynthetic pathways. The emergence of PLP-dependent enzymes as drug targets and biocatalysts, such as tryptophan synthase (TS), has underlined the demand to understand PLP-dependent catalysis and reaction specificity. The ability of neutron diffraction to resolve the positions of hydrogen atoms makes it an ideal technique to understand how the electrostatic environment and selective protonation of PLP regulates PLP-dependent activities. Facilitated by microgravity crystallization of TS with the Toledo Crystallization Box, we report the 2.1 Å joint X-ray/neutron (XN) structure of TS with PLP in the internal aldimine form. Positions of hydrogens were directly determined in both the α- and β-active sites, including PLP cofactor. The joint XN structure thus provides insight into the selective protonation of the internal aldimine and the electrostatic environment of TS necessary to understand the overall catalytic mechanism.
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Affiliation(s)
- Victoria N. Drago
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Juliette M. Devos
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 38000 Grenoble, France
| | - Matthew P. Blakeley
- Large Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - V. Trevor Forsyth
- Faculty of Medicine, Lund University, and LINXS Institute for Advanced Neutron and X-ray Science, Lund, Sweden
| | - Jerry M. Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy C. Mueser
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
- Lead contact
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3
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Han SW, Shin JS. Aromatic L-amino acid decarboxylases: mechanistic features and microbial applications. Appl Microbiol Biotechnol 2022; 106:4445-4458. [DOI: 10.1007/s00253-022-12028-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/04/2022] [Accepted: 06/10/2022] [Indexed: 11/02/2022]
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4
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Yang Y, Zhang Y, Yang J, Xue Y. Computational Insight into the Mechanism of Mannich Reaction between Glycinate and Aryl
N
‐Diphenylphosphinyl Imine Catalyzed by N‐Quaternized Pyridoxal. ChemistrySelect 2020. [DOI: 10.1002/slct.202001606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yongsheng Yang
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of EducationSichuan University Chengdu 610064 People's Republic of China
| | - Yan Zhang
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of EducationSichuan University Chengdu 610064 People's Republic of China
| | - Junxia Yang
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of EducationSichuan University Chengdu 610064 People's Republic of China
| | - Ying Xue
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of EducationSichuan University Chengdu 610064 People's Republic of China
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5
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Structural insights into the mechanism of internal aldimine formation and catalytic loop dynamics in an archaeal Group II decarboxylase. J Struct Biol 2019; 208:137-151. [PMID: 31445086 DOI: 10.1016/j.jsb.2019.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 01/01/2023]
Abstract
Formation of the internal aldimine (LLP) is the first regulatory step that activates pyridoxal 5'-phosphate (PLP) dependent enzymes. The process involves a nucleophilic attack on PLP by an active site Lys residue, followed by proton transfers resulting in a carbinolamine (CBA) intermediate that undergoes dehydration to form the aldimine. Despite a general understanding of the pathway, the structural basis of the mechanistic roles of specific residues in each of these steps is unclear. Here we determined the crystal structure of the LLP form (holo-form) of a Group II PLP-dependent decarboxylase from Methanocaldococcus jannaschii (MjDC) at 1.7 Å resolution. By comparing the crystal structure of MjDC in the LLP form with that of the pyridoxal-P (non-covalently bound aldehyde) form, we demonstrate structural evidence for a water-mediated mechanism of LLP formation. A conserved extended hydrogen-bonding network around PLP coupled to the pyridinyl nitrogen influences activation and catalysis by affecting the electronic configuration of PLP. Furthermore, the two cofactor bound forms revealed open and closed conformations of the catalytic loop (CL) in the absence of a ligand, supporting a hypothesis for a regulatory link between LLP formation and CL dynamics. The evidence suggests that activation of Group II decarboxylases involves a complex interplay of interactions between the electronic states of PLP, the active site micro-environment and CL dynamics.
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6
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7
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Fesko K, Suplatov D, Švedas V. Bioinformatic analysis of the fold type I PLP-dependent enzymes reveals determinants of reaction specificity in l-threonine aldolase from Aeromonas jandaei. FEBS Open Bio 2018; 8:1013-1028. [PMID: 29928580 PMCID: PMC5986058 DOI: 10.1002/2211-5463.12441] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 04/27/2018] [Indexed: 01/19/2023] Open
Abstract
Understanding the role of specific amino acid residues in the molecular mechanism of a protein's function is one of the most challenging problems in modern biology. A systematic bioinformatic analysis of protein families and superfamilies can help in the study of structure–function relationships and in the design of improved variants of enzymes/proteins, but represents a methodological challenge. The pyridoxal‐5′‐phosphate (PLP)‐dependent enzymes are catalytically diverse and include the aspartate aminotransferase superfamily which implements a common structural framework known as type fold I. In this work, the recently developed bioinformatic online methods Mustguseal and Zebra were used to collect and study a large representative set of the aspartate aminotransferase superfamily with high structural, but low sequence similarity to l‐threonine aldolase from Aeromonas jandaei (LTAaj), in order to identify conserved positions that provide general properties in the superfamily, and to reveal family‐specific positions (FSPs) responsible for functional diversity. The roles of the identified residues in the catalytic mechanism and reaction specificity of LTAaj were then studied by experimental site‐directed mutagenesis and molecular modelling. It was shown that FSPs determine reaction specificity by coordinating the PLP cofactor in the enzyme's active centre, thus influencing its activation and the tautomeric equilibrium of the intermediates, which can be used as hotspots to modulate the protein's functional properties. Mutagenesis at the selected FSPs in LTAaj led to a reduction in a native catalytic activity and increased the rate of promiscuous reactions. The results provide insight into the structural basis of catalytic promiscuity of the PLP‐dependent enzymes and demonstrate the potential of bioinformatic analysis in studying structure–function relationship in protein superfamilies.
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Affiliation(s)
- Kateryna Fesko
- Institute of Organic Chemistry Graz University of Technology Austria
| | - Dmitry Suplatov
- Belozersky Institute of Physicochemical Biology Lomonosov Moscow State University Russia
| | - Vytas Švedas
- Belozersky Institute of Physicochemical Biology Lomonosov Moscow State University Russia
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8
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Kirca BK. The crystal structure of ( E)-4-(3-ethoxy-2-hydroxybenzylideneamino)benzoic acid, C 16H 15NO 4. Z KRIST-NEW CRYST ST 2018. [DOI: 10.1515/ncrs-2017-0276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
C16H15NO4, triclinic, P1̅ (no. 2), a = 4.9960(4) Å, b = 6.9139(5) Å, c = 20.7650(15) Å, α = 83.718(6)°, β = 84.805(6)°, γ = 78.648(6)°, V = 697.25(9) Å3, Z = 2, R
gt(F) = 0.0480, wR
ref(F
2) = 0.0988, T = 296 K.
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Affiliation(s)
- Başak Koşar Kirca
- Department of Mathematics and Science Education, Sinop University , TR-57100, Sinop , Turkey
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9
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Direct visualization of critical hydrogen atoms in a pyridoxal 5'-phosphate enzyme. Nat Commun 2017; 8:955. [PMID: 29038582 PMCID: PMC5643538 DOI: 10.1038/s41467-017-01060-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/15/2017] [Indexed: 11/13/2022] Open
Abstract
Enzymes dependent on pyridoxal 5′-phosphate (PLP, the active form of vitamin B6) perform a myriad of diverse chemical transformations. They promote various reactions by modulating the electronic states of PLP through weak interactions in the active site. Neutron crystallography has the unique ability of visualizing the nuclear positions of hydrogen atoms in macromolecules. Here we present a room-temperature neutron structure of a homodimeric PLP-dependent enzyme, aspartate aminotransferase, which was reacted in situ with α-methylaspartate. In one monomer, the PLP remained as an internal aldimine with a deprotonated Schiff base. In the second monomer, the external aldimine formed with the substrate analog. We observe a deuterium equidistant between the Schiff base and the C-terminal carboxylate of the substrate, a position indicative of a low-barrier hydrogen bond. Quantum chemical calculations and a low-pH room-temperature X-ray structure provide insight into the physical phenomena that control the electronic modulation in aspartate aminotransferase. Pyridoxal 5’-phosphate (PLP) is a ubiquitous co factor for diverse enzymes, among them aspartate aminotransferase. Here the authors use neutron crystallography, which allows the visualization of the positions of hydrogen atoms, and computation to characterize the catalytic mechanism of the enzyme.
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10
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Dajnowicz S, Parks JM, Hu X, Gesler K, Kovalevsky AY, Mueser TC. Direct evidence that an extended hydrogen-bonding network influences activation of pyridoxal 5'-phosphate in aspartate aminotransferase. J Biol Chem 2017; 292:5970-5980. [PMID: 28232482 DOI: 10.1074/jbc.m116.774588] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/07/2017] [Indexed: 11/06/2022] Open
Abstract
Pyridoxal 5'-phosphate (PLP) is a fundamental, multifunctional enzyme cofactor used to catalyze a wide variety of chemical reactions involved in amino acid metabolism. PLP-dependent enzymes optimize specific chemical reactions by modulating the electronic states of PLP through distinct active site environments. In aspartate aminotransferase (AAT), an extended hydrogen bond network is coupled to the pyridinyl nitrogen of the PLP, influencing the electrophilicity of the cofactor. This network, which involves residues Asp-222, His-143, Thr-139, His-189, and structural waters, is located at the edge of PLP opposite the reactive Schiff base. We demonstrate that this hydrogen bond network directly influences the protonation state of the pyridine nitrogen of PLP, which affects the rates of catalysis. We analyzed perturbations caused by single- and double-mutant variants using steady-state kinetics, high resolution X-ray crystallography, and quantum chemical calculations. Protonation of the pyridinyl nitrogen to form a pyridinium cation induces electronic delocalization in the PLP, which correlates with the enhancement in catalytic rate in AAT. Thus, PLP activation is controlled by the proximity of the pyridinyl nitrogen to the hydrogen bond microenvironment. Quantum chemical calculations indicate that Asp-222, which is directly coupled to the pyridinyl nitrogen, increases the pKa of the pyridine nitrogen and stabilizes the pyridinium cation. His-143 and His-189 also increase the pKa of the pyridine nitrogen but, more significantly, influence the position of the proton that resides between Asp-222 and the pyridinyl nitrogen. These findings indicate that the second shell residues directly enhance the rate of catalysis in AAT.
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Affiliation(s)
- Steven Dajnowicz
- From the Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606.,the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, and
| | - Jerry M Parks
- the University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Xiche Hu
- From the Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606
| | - Korie Gesler
- From the Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606
| | - Andrey Y Kovalevsky
- the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, and
| | - Timothy C Mueser
- From the Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606,
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11
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Caulkins BG, Young RP, Kudla RA, Yang C, Bittbauer T, Bastin B, Hilario E, Fan L, Marsella MJ, Dunn MF, Mueller LJ. NMR Crystallography of a Carbanionic Intermediate in Tryptophan Synthase: Chemical Structure, Tautomerization, and Reaction Specificity. J Am Chem Soc 2016; 138:15214-15226. [PMID: 27779384 PMCID: PMC5129030 DOI: 10.1021/jacs.6b08937] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Indexed: 12/22/2022]
Abstract
Carbanionic intermediates play a central role in the catalytic transformations of amino acids performed by pyridoxal-5'-phosphate (PLP)-dependent enzymes. Here, we make use of NMR crystallography-the synergistic combination of solid-state nuclear magnetic resonance, X-ray crystallography, and computational chemistry-to interrogate a carbanionic/quinonoid intermediate analogue in the β-subunit active site of the PLP-requiring enzyme tryptophan synthase. The solid-state NMR chemical shifts of the PLP pyridine ring nitrogen and additional sites, coupled with first-principles computational models, allow a detailed model of protonation states for ionizable groups on the cofactor, substrates, and nearby catalytic residues to be established. Most significantly, we find that a deprotonated pyridine nitrogen on PLP precludes formation of a true quinonoid species and that there is an equilibrium between the phenolic and protonated Schiff base tautomeric forms of this intermediate. Natural bond orbital analysis indicates that the latter builds up negative charge at the substrate Cα and positive charge at C4' of the cofactor, consistent with its role as the catalytic tautomer. These findings support the hypothesis that the specificity for β-elimination/replacement versus transamination is dictated in part by the protonation states of ionizable groups on PLP and the reacting substrates and underscore the essential role that NMR crystallography can play in characterizing both chemical structure and dynamics within functioning enzyme active sites.
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Affiliation(s)
- Bethany G. Caulkins
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Robert P. Young
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Ryan A. Kudla
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Chen Yang
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Thomas
J. Bittbauer
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Baback Bastin
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Eduardo Hilario
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Li Fan
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Michael J. Marsella
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Michael F. Dunn
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Leonard J. Mueller
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
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12
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Gökcan H, Monard G, Sungur Konuklar FA. Molecular dynamics simulations of apo, holo, and inactivator bound GABA-at reveal the role of active site residues in PLP dependent enzymes. Proteins 2016; 84:875-91. [PMID: 26800298 DOI: 10.1002/prot.24991] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 12/24/2015] [Accepted: 12/29/2015] [Indexed: 11/08/2022]
Abstract
The pyridoxal 5-phosphate (PLP) cofactor is a significant organic molecule in medicinal chemistry. It is often found covalently bound to lysine residues in proteins to form PLP dependent enzymes. An example of this family of PLP dependent enzymes is γ-aminobutyric acid aminotransferase (GABA-AT) which is responsible for the degradation of the neurotransmitter GABA. Its inhibition or inactivation can be used to prevent the reduction of GABA concentration in brain which is the source of several neurological disorders. As a test case for PLP dependent enzymes, we have performed molecular dynamics simulations of GABA-AT to reveal the roles of the protein residues and its cofactor. Three different states have been considered: the apoenzyme, the holoenzyme, and the inactive state obtained after the suicide inhibition by vigabatrin. Different protonation states have also been considered for PLP and two key active site residues: Asp298 and His190. Together, 24 independent molecular dynamics trajectories have been simulated for a cumulative total of 2.88 µs. Our results indicate that, unlike in aqueous solution, the PLP pyridine moiety is protonated in GABA-AT. This is a consequence of a pKa shift triggered by a strong charge-charge interaction with an ionic "diad" formed by Asp298 and His190 that would help the activation of the first half-reaction of the catalytic mechanism in GABA-AT: the conversion of PLP to free pyridoxamine phosphate (PMP). In addition, our MD simulations exhibit additional strong hydrogen bond networks between the protein and PLP: the phosphate group is held in place by the donation of at least three hydrogen bonds while the carbonyl oxygen of the pyridine ring interacts with Gln301; Phe181 forms a π-π stacking interaction with the pyridine ring and works as a gate keeper with the assistance of Val300. All these interactions are hypothesized to help maintain free PMP in place inside the protein active site to facilitate the second half-reaction in GABA-AT: the regeneration of PLP-bound GABA-AT (i.e., the holoenzyme). Proteins 2016; 84:875-891. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Hatice Gökcan
- Universite De Lorraine, UMR 7565 SRSMC, Boulevard Des Aiguillettes B.P. 70239, Vandoeuvre-les-Nancy, 54506, France.,CNRS, UMR 7565 SRSMC, Boulevard Des Aiguillettes B.P. 70239, Vandoeuvre-les-Nancy, 54506, France.,Computational Science and Engineering Division, Informatics Institute, Ayazağa Campus, Maslak, Istanbul, 34496, Turkey
| | - Gerald Monard
- Universite De Lorraine, UMR 7565 SRSMC, Boulevard Des Aiguillettes B.P. 70239, Vandoeuvre-les-Nancy, 54506, France.,CNRS, UMR 7565 SRSMC, Boulevard Des Aiguillettes B.P. 70239, Vandoeuvre-les-Nancy, 54506, France
| | - F Aylin Sungur Konuklar
- Computational Science and Engineering Division, Informatics Institute, Ayazağa Campus, Maslak, Istanbul, 34496, Turkey
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13
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Huang YMM, You W, Caulkins BG, Dunn MF, Mueller LJ, Chang CEA. Protonation states and catalysis: Molecular dynamics studies of intermediates in tryptophan synthase. Protein Sci 2015; 25:166-83. [PMID: 26013176 DOI: 10.1002/pro.2709] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/13/2015] [Accepted: 05/14/2015] [Indexed: 12/13/2022]
Abstract
The importance of protonation states and proton transfer in pyridoxal 5'-phosphate (PLP)-chemistry can hardly be overstated. Although experimental approaches to investigate pKa values can provide general guidance for assigning proton locations, only static pictures of the chemical species are available. To obtain the overall protein dynamics for the interpretation of detailed enzyme catalysis in this study, guided by information from solid-state NMR, we performed molecular dynamics (MD) simulations for the PLP-dependent enzyme tryptophan synthase (TRPS), whose catalytic mechanism features multiple quasi-stable intermediates. The primary objective of this work is to elucidate how the position of a single proton on the reacting substrate affects local and global protein dynamics during the catalytic cycle. In general, proteins create a chemical environment and an ensemble of conformational motions to recognize different substrates with different protonations. The study of these interactions in TRPS shows that functional groups on the reacting substrate, such as the phosphoryl group, pyridine nitrogen, phenolic oxygen and carboxyl group, of each PLP-bound intermediate play a crucial role in constructing an appropriate molecular interface with TRPS. In particular, the protonation states of the ionizable groups on the PLP cofactor may enhance or weaken the attractions between the enzyme and substrate. In addition, remodulation of the charge distribution for the intermediates may help generate a suitable environment for chemical reactions. The results of our study enhance knowledge of protonation states for several PLP intermediates and help to elucidate their effects on protein dynamics in the function of TRPS and other PLP-dependent enzymes.
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Affiliation(s)
- Yu-Ming M Huang
- Department of Chemistry, University of California, Riverside, California, 92521
| | - Wanli You
- Department of Chemistry, University of California, Riverside, California, 92521
| | - Bethany G Caulkins
- Department of Chemistry, University of California, Riverside, California, 92521
| | - Michael F Dunn
- Department of Biochemistry, University of California, Riverside, California, 92521
| | - Leonard J Mueller
- Department of Chemistry, University of California, Riverside, California, 92521
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, California, 92521
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14
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Kassem MA, Hazazi OA, Ohsaka T, Awad MI. Electroanalysis of Pyridoxine at Copper Nanoparticles Modified Polycrystalline Gold Electrode. ELECTROANAL 2015. [DOI: 10.1002/elan.201500209] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Ding YQ, Cui YZ, Li TD. New views on the reaction of primary amine and aldehyde from DFT study. J Phys Chem A 2015; 119:4252-60. [PMID: 25859816 DOI: 10.1021/acs.jpca.5b02186] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A general theoretical investigation on the reaction of primary amine with aldehyde was carried out by density functional theory. The calculation systems involve three kinds of primary amines (methylamine, vinylamine, and phenylamine) and three kinds of aldehydes (formaldehyde, acetaldehyde, and acrylaldehyde). The steric and electronic inductive effects on the reaction mechanism were studied. Results reveal that the nucleophilic attack of primary amine on aldehyde under neutral conditions leads to carbinolamines, rather than Schiff bases. The nucleophilic attack on the protonated aldehyde produces the protonated Schiff base. The steric hindrance of the aldehyde slows down the nucleophilic attack but allows enough time to abstract a H; consequently, the formation of the protonated Schiff base is preferred. During the carbinolamine protonation, the H(+) preferably locates on the amine nitrogen and then is abstracted by the hydroxyl oxygen over an energy barrier, leaving protonated Schiff base after timely water liberation. The formation of a prereaction potential energy well obviously softens the steric and electronic inductive effects on the active barrier for different reactants.
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Affiliation(s)
- Yun-qiao Ding
- Shandong Provincial Key Laboratory of Fine Chemicals, School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology, 250353, Jinan, Shandong China
| | - Yue-zhi Cui
- Shandong Provincial Key Laboratory of Fine Chemicals, School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology, 250353, Jinan, Shandong China
| | - Tian-duo Li
- Shandong Provincial Key Laboratory of Fine Chemicals, School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology, 250353, Jinan, Shandong China
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16
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Gökcan H, Konuklar FAS. Stereoelectronic explanations for the mechanistic details of transimination and HF elimination reactions. J Mol Graph Model 2014; 51:173-83. [PMID: 24929816 DOI: 10.1016/j.jmgm.2014.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 11/26/2022]
Abstract
The β-fluoroamines are commonly used as substrate analogs to determine the mechanistic details of enzymatic reactions. Presence of fluorine atom gives rise to the alterations in the electronic profile and the pKa of molecules which results in mechanistic deviations. The fluorine-substituted mechanism-based substrate analogs are widely used in the inactivation of pyridoxal 5'-phosphate (PLP)-dependent enzymes. The presence of fluorine atom also alters the sequence of reactions taking place in PLP-dependent enzymes where the HF elimination reaction appears in between the transimination and inactivation reactions. Despite the amount of the works on β-fluoroamines, the effect of stereoelectronic differences on the transimination and HF elimination reactions taking place in PLP-dependent enzymes has not been investigated yet. A density functional theory study is conducted to elucidate mechanistic details of the reactions occurring in PLP-dependent enzymes. In order to understand the mechanistic insights of different isomers and the effect of the fluorine atom, 4-amino-3-fluorobutanoic acid (3-F-GABA) enantiomers are chosen to be investigated besides 4-aminobutanoic acid (GABA), which is the natural substrate for γ-aminobutyric acid aminotransferase (GABA-AT). The investigated β-fluoroamines are the experimentally proposed potential inhibitors of PLP-dependent enzyme GABA-AT.
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Affiliation(s)
- Hatice Gökcan
- Istanbul Technical University, Informatics Institute, Computational Science and Engineering Division, Ayazağa Campus, 34496 Maslak, Istanbul, Turkey
| | - F Aylin Sungur Konuklar
- Istanbul Technical University, Informatics Institute, Computational Science and Engineering Division, Ayazağa Campus, 34496 Maslak, Istanbul, Turkey.
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17
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Toney MD. Aspartate aminotransferase: an old dog teaches new tricks. Arch Biochem Biophys 2013; 544:119-27. [PMID: 24121043 DOI: 10.1016/j.abb.2013.10.002] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 09/28/2013] [Accepted: 10/01/2013] [Indexed: 11/29/2022]
Abstract
Aspartate aminotransferase (AAT) is a prototypical pyridoxal 5'-phosphate (PLP) dependent enzyme that catalyzes the reversible interconversion of l-aspartate and α-ketoglutarate with oxalacetate and l-glutamate via a ping-pong catalytic cycle in which the pyridoxamine 5'-phosphate enzyme form is an intermediate. There is a bountiful literature on AAT that spans approximately 60years, and much fundamental mechanistic information on PLP dependent reactions has been gained from its study. Here, we review our recent work on AAT, where we again used it as a test bed for fundamental concepts in PLP chemistry. First, we discuss the role that coenzyme protonation state plays in controlling reaction specificity, then ground state destabilization via hyperconjugation in the external aldimine intermediate is examined. The third topic is light enhancement of catalysis of Cα-H deprotonation by PLP in solution and in AAT, which occurs through a triplet state of the external aldimine intermediate. Lastly, we consider recent advances in our analyses of enzyme multiple sequence alignments for the purpose of predicting mutations that are required to interconvert structurally similar but catalytically distinct enzymes, and the application of our program JANUS to the conversion of AAT into tyrosine aminotransferase.
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Affiliation(s)
- Michael D Toney
- Department of Chemistry, University of California, Davis, Davis, CA 95616, USA.
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18
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Srivastava M, Rani P, Singh NP, Yadav RA. Experimental and theoretical studies of vibrational spectrum and molecular structure and related properties of pyridoxine (vitamin B6). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 120:274-286. [PMID: 24184922 DOI: 10.1016/j.saa.2013.09.133] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 09/12/2013] [Accepted: 09/29/2013] [Indexed: 06/02/2023]
Abstract
Vibrational spectrum of pyridoxine has been investigated using experimental IR and Raman spectroscopic and density functional theory (DFT) methods. Vibrational assignments of the observed IR and Raman bands have been proposed in light of the results obtained from computations. In order to assign the observed IR and Raman frequencies the potential energy distributions (PEDs) have also been computed. Optimized geometrical parameters suggest that if the OH groups of the two methyl groups are replaced by H atoms the resulting molecule has Cs point group symmetry. To investigate molecular stability and bond strength we have used natural bond orbital analysis (NBO). Charge transfer occurs in the molecule have been shown by the calculated highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energies. The mapping of electron density iso-surface with electrostatic potential (ESP), has been carried out to get the information about the size, shape, charge density distribution and site of chemical reactivity of the molecule.
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Affiliation(s)
- Mayuri Srivastava
- Department of Physics, UP (PG) Autonomous College, Varanasi 221002, India
| | - P Rani
- Lasers and Spectroscopy Laboratory, Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - N P Singh
- Department of Physics, UP (PG) Autonomous College, Varanasi 221002, India
| | - R A Yadav
- Lasers and Spectroscopy Laboratory, Department of Physics, Banaras Hindu University, Varanasi 221005, India.
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19
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C–H Activation in Pyridoxal-5′-phosphate and Pyridoxamine-5′-phosphate Schiff Bases: Effect of Metal Chelation. A Computational Study. J Phys Chem B 2013; 117:2339-47. [DOI: 10.1021/jp311861p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Özdemir N, Dayan S, Dayan O, Dinçer M, Kalaycıoğlu NÖ. Experimental and molecular modeling investigation of (E)-N-{2-[(2-hydroxybenzylidene)amino]phenyl}benzenesulfonamide. Mol Phys 2012. [DOI: 10.1080/00268976.2012.742209] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Namık Özdemir
- a Department of Physics , Faculty of Arts and Sciences, Ondokuz Mayıs University , 55139, Samsun , Turkey
| | - Serkan Dayan
- b Department of Chemistry , Faculty of Science, Erciyes University , 38039, Kayseri , Turkey
| | - Osman Dayan
- c Laboratory of Inorganic Synthesis and Molecular Catalysis , Çanakkale Onsekiz Mart University , 17020, Çanakkale , Turkey
| | - Muharrem Dinçer
- a Department of Physics , Faculty of Arts and Sciences, Ondokuz Mayıs University , 55139, Samsun , Turkey
| | - Nilgün Ö. Kalaycıoğlu
- b Department of Chemistry , Faculty of Science, Erciyes University , 38039, Kayseri , Turkey
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21
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Martyniak A, Panek J, Jezierska-Mazzarello A, Filarowski A. Triple hydrogen bonding in a circular arrangement: ab initio, DFT and first-principles MD studies of tris-hydroxyaryl enamines. J Comput Aided Mol Des 2012; 26:1045-53. [PMID: 22955961 PMCID: PMC3474916 DOI: 10.1007/s10822-012-9597-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Accepted: 08/29/2012] [Indexed: 11/17/2022]
Abstract
First-principles Car-Parrinello molecular dynamics, ab initio (MP2) and density functional schemes have been used to explore the tautomeric equilibrium in three tris(amino(R)methylidene)cyclohexane-1,3,5-triones (R = hydrogen, methyl or phenyl group). The dynamic nature of the cyclic hydrogen bonding has been studied by the first-principles MD method. The comparison of the results obtained by aforesaid methods has been accomplished on the basis of calculations of structural and spectroscopic characteristics of the compounds. The conformational analysis of the studied compounds has been carried out at the MP2/6-31+G(d,p) and B3LYP/6-31+G(d,p) levels of theory. The influence of steric and electronic effects on the cyclic hydrogen bonding has been analysed. The extent of the proton delocalization has been modified by the substituents according to the sequence: hydrogen < phenyl < methyl. This fact is verified by the spectroscopic and structural data as well as the energy potential curve. A prevalence of the keto-enamine tautomeric form has been observed in the static ab initio and DFT models, and confirmed by the first-principles MD.
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Affiliation(s)
- Agata Martyniak
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie str., 50-383 Wrocław, Poland
| | - Jarosław Panek
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie str., 50-383 Wrocław, Poland
| | | | - Aleksander Filarowski
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie str., 50-383 Wrocław, Poland
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22
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Casasnovas R, Adrover M, Ortega-Castro J, Frau J, Donoso J, Muñoz F. C–H Activation in Pyridoxal-5′-phosphate Schiff Bases: The Role of the Imine Nitrogen. A Combined Experimental and Computational Study. J Phys Chem B 2012; 116:10665-75. [DOI: 10.1021/jp303678n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rodrigo Casasnovas
- Institut
d’Investigació en Ciènces de la Salut (IUNICS),
Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Miquel Adrover
- Institut
d’Investigació en Ciènces de la Salut (IUNICS),
Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Joaquin Ortega-Castro
- Institut
d’Investigació en Ciènces de la Salut (IUNICS),
Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Juan Frau
- Institut
d’Investigació en Ciènces de la Salut (IUNICS),
Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Josefa Donoso
- Institut
d’Investigació en Ciènces de la Salut (IUNICS),
Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Francisco Muñoz
- Institut
d’Investigació en Ciènces de la Salut (IUNICS),
Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
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23
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Koşar B, Albayrak C, Ersanlı CC, Odabaşoğlu M, Büyükgüngör O. Molecular structure, spectroscopic investigations, second-order nonlinear optical properties and intramolecular proton transfer of (E)-5-(diethylamino)-2-[(4-propylphenylimino)methyl]phenol: a combined experimental and theoretical study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 93:1-9. [PMID: 22465762 DOI: 10.1016/j.saa.2012.03.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 02/23/2012] [Accepted: 03/03/2012] [Indexed: 05/31/2023]
Abstract
This work presents a combined experimental and theoretical study on an ortho-hydroxy Schiff base compound, (E)-5-(diethylamino)-2-[(4-propylphenylimino)methyl]phenol. The crystal structure and spectroscopic properties of the compound have been determined by using X-ray diffraction, IR and UV-vis spectroscopy techniques. The electronic structure, vibrational frequencies and electronic absorption spectra have been investigated from the calculative point of view. A relaxed potential energy surface scan has been performed based on the optimized geometry of OH tautomeric form to describe the potential energy barrier belonging to intramolecular proton transfer and to observe the effects of transfer on the molecular geometry. The second-order nonlinear optical properties have been investigated based on the first static hyperpolarizability (β) by using the density functional theory.
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Affiliation(s)
- Başak Koşar
- Department of Science Education, Sinop University, Sinop 57000, Turkey.
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24
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Gökcan H, Konuklar FAS. Theoretical study on HF elimination and aromatization mechanisms: a case of pyridoxal 5' phosphate-dependent enzyme. J Org Chem 2012; 77:5533-43. [PMID: 22646918 DOI: 10.1021/jo3005815] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyridoxal 5-phosphate (PLP), the phosphorylated and the oxidized form of vitamin B6 is an organic cofactor. PLP forms a Schiff base with the ϵ-amino group of a lysine residue of PLP-dependent enzymes. γ-Aminobutyric acid (GABA) aminotransferase is a PLP-dependent enzyme that degrades GABA to succinic semialdehyde, while reduction of GABA concentration in the brain causes convolution besides several neurological diseases. The fluorine-containing substrate analogues for the inactivation of the GABA-AT are synthesized extensively in cases where the inactivation mechanisms involve HF elimination. Although two proposed mechanisms are present for the HF elimination, the details of the base-induced HF elimination are not well identified. In this density functional theory (DFT) study, fluorine-containing substrate analogue, 5-amino-2-fluorocyclohex-3-enecarboxylic acid, is particularly chosen in order to explain the details of the HF elimination reactions. On the other hand, the experimental studies revealed that aromatization competes with Michael addition mechanism in the presence of 5-amino-2-fluorocyclohex-3-enecarboxylic acid. The results allowed us to draw a conclusion for the nature of HF elimination, besides the elucidation of the mechanism preference for the inactivation mechanism. Furthermore, the solvent phase calculations carried out in this study ensure that the proton transfer steps should be assisted either by a water molecule or a base for lower activation energy barriers.
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Affiliation(s)
- Hatice Gökcan
- Informatics Institute, Computational Science and Engineering Programme, Istanbul Technical University, Ayazağa Campus 34469, Maslak, Istanbul, Turkey
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25
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Makins C, Miros FN, Scrutton NS, Wolthers KR. Role of histidine 225 in adenosylcobalamin-dependent ornithine 4,5-aminomutase. Bioorg Chem 2012; 40:39-47. [DOI: 10.1016/j.bioorg.2011.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 08/05/2011] [Accepted: 08/08/2011] [Indexed: 12/01/2022]
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26
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Adrover M, Caldés C, Vilanova B, Frau J, Donoso J, Muñoz F. Towards a detailed description of pyridoxamine tautomeric species. NEW J CHEM 2012. [DOI: 10.1039/c2nj40230k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Studies on molecular structure and tautomerism of a vitamin B6 analog with density functional theory. J Mol Model 2011; 18:1993-2001. [PMID: 21877155 DOI: 10.1007/s00894-011-1214-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 08/07/2011] [Indexed: 10/17/2022]
Abstract
This work presents a computational study on the molecular structure and tautomeric equilibria of a novel Schiff base L derived from pyridoxal (PL) and o-phenylenediamine by using the density functional method B3LYP with basis sets 6-31 G(d,p), 6-31++G(d,p), 6-311 G(d,p) and 6-311++G(d,p). The optimized geometrical parameters obtained by B3LYP/6-31 G(d,p) method showed the best agreement with the experimental values. Tautomeric stability study of L inferred that the enolimine form is more stable than its ketoenamine form in both gas phase and solution. However, protonation of the pyridoxal nitrogen atom (LH) have accelerated the formation of ketoenamine form, and therefore, both ketoenamine and enolimine forms could be present in acidic media.
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28
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Griswold WR, Toney MD. Role of the pyridine nitrogen in pyridoxal 5'-phosphate catalysis: activity of three classes of PLP enzymes reconstituted with deazapyridoxal 5'-phosphate. J Am Chem Soc 2011; 133:14823-30. [PMID: 21827189 DOI: 10.1021/ja2061006] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pyridoxal 5'-phosphate (PLP; vitamin B(6))-catalyzed reactions have been well studied, both on enzymes and in solution, due to the variety of important reactions this cofactor catalyzes in nitrogen metabolism. Three functional groups are central to PLP catalysis: the C4' aldehyde, the O3' phenol, and the N1 pyridine nitrogen. In the literature, the pyridine nitrogen has traditionally been assumed to be protonated in enzyme active sites, with the protonated pyridine ring providing resonance stabilization of carbanionic intermediates. This assumption is certainly correct for some PLP enzymes, but the structures of other active sites are incompatible with protonation of N1, and, consequently, these enzymes are expected to use PLP in the N1-unprotonated form. For example, aspartate aminotransferase protonates the pyridine nitrogen for catalysis of transamination, while both alanine racemase and O-acetylserine sulfhydrylase are expected to maintain N1 in the unprotonated, formally neutral state for catalysis of racemization and β-elimination. Herein, kinetic results for these three enzymes reconstituted with 1-deazapyridoxal 5'-phosphate, an isosteric analogue of PLP lacking the pyridine nitrogen, are compared to those for the PLP enzyme forms. They demonstrate that the pyridine nitrogen is vital to the 1,3-prototropic shift central to transamination, but not to reactions catalyzed by alanine racemase or O-acetylserine sulfhydrylase. Not all PLP enzymes require the electrophilicity of a protonated pyridine ring to enable formation of carbanionic intermediates. It is proposed that modulation of cofactor electrophilicity plays a central role in controlling reaction specificity in PLP enzymes.
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Affiliation(s)
- Wait R Griswold
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, USA
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29
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Griswold WR, Fisher AJ, Toney MD. Crystal structures of aspartate aminotransferase reconstituted with 1-deazapyridoxal 5'-phosphate: internal aldimine and stable L-aspartate external aldimine. Biochemistry 2011; 50:5918-24. [PMID: 21627105 DOI: 10.1021/bi200436y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The 1.8 Å resolution crystal structures of Escherichia coli aspartate aminotransferase reconstituted with 1-deazapyridoxal 5'-phosphate (deazaPLP; 2-formyl-3-hydroxy-4-methylbenzyl phosphate) in the internal aldimine and L-aspartate external aldimine forms are reported. The L-aspartate·deazaPLP external aldimine is extraordinarily stable (half-life of >20 days), allowing crystals of this intermediate to be grown by cocrystallization with L-aspartate. This structure is compared to that of the α-methyl-L-aspartate·PLP external aldimine. Overlays with the corresponding pyridoxal 5'-phosphate (PLP) aldimines show very similar orientations of deazaPLP with respect to PLP. The lack of a hydrogen bond between Asp222 and deazaPLP, which serves to "anchor" PLP in the active site, releases strain in the deazaPLP internal aldimine that is enforced in the PLP internal aldimine [Hayashi, H., Mizuguchi, H., Miyahara, I., Islam, M. M., Ikushiro, H., Nakajima, Y., Hirotsu, K., and Kagamiyama, H. (2003) Biochim. Biophys. Acta1647, 103] as evidenced by the planarity of the pyridine ring and the Schiff base linkage with Lys258. Additionally, loss of this anchor causes a 10° greater tilt of deazaPLP toward the substrate in the external aldimine. An important mechanistic difference between the L-aspartate·deazaPLP and α-methyl-L-aspartate·PLP external aldimines is a hydrogen bond between Gly38 and Lys258 in the former, positioning the catalytic base above and approximately equidistant between Cα and C4'. In contrast, in the α-methyl-L-aspartate·PLP external aldimine, the ε-amino group of Lys258 is rotated ~70° to form a hydrogen bond to Tyr70 because of the steric bulk of the methyl group.
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Affiliation(s)
- Wait R Griswold
- Department of Chemistry, University of California, Davis, California 95616, United States
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30
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Controlling reaction specificity in pyridoxal phosphate enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1407-18. [PMID: 21664990 DOI: 10.1016/j.bbapap.2011.05.019] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 05/18/2011] [Accepted: 05/25/2011] [Indexed: 11/20/2022]
Abstract
Pyridoxal 5'-phosphate enzymes are ubiquitous in the nitrogen metabolism of all organisms. They catalyze a wide variety of reactions including racemization, transamination, decarboxylation, elimination, retro-aldol cleavage, Claisen condensation, and others on substrates containing an amino group, most commonly α-amino acids. The wide variety of reactions catalyzed by PLP enzymes is enabled by the ability of the covalent aldimine intermediate formed between substrate and PLP to stabilize carbanionic intermediates at Cα of the substrate. This review attempts to summarize the mechanisms by which reaction specificity can be achieved in PLP enzymes by focusing on three aspects of these reactions: stereoelectronic effects, protonation state of the external aldimine intermediate, and interaction of the carbanionic intermediate with the protein side chains present in the active site. This article is part of a Special Issue entitled: Pyridoxal Phosphate Enzymology.
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31
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Bruno A, Amori L, Costantino G. Addressing the Conformational Flexibility of Serine Racemase by Combining Targeted Molecular Dynamics, Conformational Sampling and Docking Studies. Mol Inform 2011; 30:317-28. [DOI: 10.1002/minf.201000162] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 12/22/2010] [Indexed: 11/06/2022]
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32
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Kosar B, Albayrak Ç, Odabaşoğlu M, Büyükgüngör O. Molecular structure of (Z)-6-[(5-chloro-2-hydroxyphenylamino) methylene]-3-(diethylamino)cyclohexa-2,4-dienone: A combined experimental and theoretical study. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2010.12.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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33
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Durak AT, Gökcan H, Konuklar FAS. Theoretical studies on the inactivation mechanism of γ-aminobutyric acid aminotransferase. Org Biomol Chem 2011; 9:5162-71. [DOI: 10.1039/c1ob05146f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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He S, Tan Y, Xiao X, Zhu L, Guo Y, Li M, Tian A, Pu X, Wong NB. Substituent effects on electronic character of the CN group and trans/cis isomerization in the C-substituted imine derivatives: A computational study. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.03.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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35
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Ortega-Castro J, Adrover M, Frau J, Salvà A, Donoso J, Muñoz F. DFT Studies on Schiff Base Formation of Vitamin B6 Analogues. Reaction between a Pyridoxamine-Analogue and Carbonyl Compounds. J Phys Chem A 2010; 114:4634-40. [DOI: 10.1021/jp909156m] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. Ortega-Castro
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, Cra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - M. Adrover
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, Cra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - J. Frau
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, Cra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - A. Salvà
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, Cra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - J. Donoso
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, Cra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - F. Muñoz
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, Cra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
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36
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Guzow K, Milewska M, Czaplewski C, Wiczk W. A DFT/TD DFT study of the structure and spectroscopic properties of 5-methyl-2-(8-quinolinyl)benzoxazole and its complexes with Zn(II) ion. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2010; 75:773-781. [PMID: 20022554 DOI: 10.1016/j.saa.2009.11.053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2009] [Revised: 11/16/2009] [Accepted: 11/27/2009] [Indexed: 05/28/2023]
Abstract
The structure and spectroscopic properties of 5-methyl-2-(8-quinolinyl)benzoxazole and its complexes with Zn(II) ion were studied using a DFT and TD DFT methods with def2-TZVP basis set. It was shown that the type of functional used (B3-LYP or pbe0) implemented in TURBOMOLE package does not have essential influence on the geometry (small differences in bond length, valence and dihedral angles) of studied compounds in both ground and excited states. However, significant differences were obtained for the position of vertical absorption and emission transition but not for the oscillator strength of transition. Application of pbe0 functional seems to reproduce better the experimental spectrum.
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Affiliation(s)
- Katarzyna Guzow
- Faculty of Chemistry, University of Gdansk, 80-952 Gdansk, Sobieskiego 18, Poland
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