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Carbajo D, Ruiz-Sánchez AJ, Nájera F, Pérez-Inestrosa E, Alfonso I. Spontaneous macrocyclization through multiple dynamic cyclic aminal formation. Chem Commun (Camb) 2021; 57:1190-1193. [PMID: 33448267 DOI: 10.1039/d0cc07184f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The use of aminals in dynamic covalent chemistry is slightly underexplored, probably due to their inherent instability. Here we report the spontaneous [2+2] macrocyclization of tetrakis(aminals). Their unexpected stability and structural modularity, the dynamic nature of the connections and their water tolerance make them appealing systems for future applications as stimulus-responsive materials.
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Affiliation(s)
- Daniel Carbajo
- Department of Biological Chemistry, Institute of Advanced Chemistry of Catalonia, IQAC-CSIC c/Jordi Girona 18-26, Barcelona, 08034, Spain.
| | - Antonio Jesús Ruiz-Sánchez
- Universidad de Málaga-IBIMA, Departamento de Química Orgánica, Campus de Teatinos s/n, Málaga-29071, Spain. and Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, Parque Tecnológico de Andalucía, c/Severo Ochoa, 35, Málaga-29590, Spain
| | - Francisco Nájera
- Universidad de Málaga-IBIMA, Departamento de Química Orgánica, Campus de Teatinos s/n, Málaga-29071, Spain. and Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, Parque Tecnológico de Andalucía, c/Severo Ochoa, 35, Málaga-29590, Spain
| | - Ezequiel Pérez-Inestrosa
- Universidad de Málaga-IBIMA, Departamento de Química Orgánica, Campus de Teatinos s/n, Málaga-29071, Spain. and Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, Parque Tecnológico de Andalucía, c/Severo Ochoa, 35, Málaga-29590, Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry, Institute of Advanced Chemistry of Catalonia, IQAC-CSIC c/Jordi Girona 18-26, Barcelona, 08034, Spain.
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2
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Szady‐Chełmieniecka A, Rzuchowska A, Markowska‐Szczupak A, Schilf W, Rozwadowski Z. New “one‐pot” Pd(II) and Zn(II) complexes of Schiff bases, derivatives of 1‐amino‐1‐deoxy‐
d
‐sorbitol: Spectroscopic studies and biological and catalytic activities. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.5485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- A. Szady‐Chełmieniecka
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical Technology and Engineering,West Pomeranian University of Technology Szczecin, al. Piastów 42 71‐065 Szczecin Poland
| | - A. Rzuchowska
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical Technology and Engineering,West Pomeranian University of Technology Szczecin, al. Piastów 42 71‐065 Szczecin Poland
| | - A. Markowska‐Szczupak
- Department of Chemical and Process Engineering, Faculty of Chemical Technology and EngineeringWest Pomeranian University of Technology, Szczecin Szczecin, al. Piastów 42 71‐065 Szczecin Poland
| | - W. Schilf
- Institute of Organic Chemistry, Polish Academy of Sciences ul. Kasprzaka 44 01‐224 Warsaw Poland
| | - Z. Rozwadowski
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical Technology and Engineering,West Pomeranian University of Technology Szczecin, al. Piastów 42 71‐065 Szczecin Poland
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3
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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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4
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Ramanujam V, Charlier C, Bax A. Observation and Kinetic Characterization of Transient Schiff Base Intermediates by CEST NMR Spectroscopy. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Venkatraman Ramanujam
- Laboratory of Chemical Physics National Institute of Diabetes and Digestive and Kidney Diseases Bethesda MD 20892 USA
| | - Cyril Charlier
- Laboratory of Chemical Physics National Institute of Diabetes and Digestive and Kidney Diseases Bethesda MD 20892 USA
| | - Ad Bax
- Laboratory of Chemical Physics National Institute of Diabetes and Digestive and Kidney Diseases Bethesda MD 20892 USA
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5
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Ramanujam V, Charlier C, Bax A. Observation and Kinetic Characterization of Transient Schiff Base Intermediates by CEST NMR Spectroscopy. Angew Chem Int Ed Engl 2019; 58:15309-15312. [PMID: 31449352 DOI: 10.1002/anie.201908416] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Indexed: 01/15/2023]
Abstract
In aqueous solution, many biochemical reaction pathways involve reaction of an aldehyde with an amine, which progresses through generally unstable, hydrated and dehydrated, Schiff base intermediates that often are unobservable by conventional NMR. There are 4 states in the relevant equilibrium: 1) gem-diol, 2) aldehyde, 3) hemiaminal, and 4) Schiff base. For the reaction between protein amino groups and DOPAL, a highly toxic metabolite of dopamine, the 1 H resonances of both the hemiaminal and the dehydrated Schiff base can be observed by CEST NMR, even when their populations fall below 0.1 %. CEST NMR reveals the quantitative exchange kinetics between reactants and Schiff base intermediates, explaining why the Schiff base NMR signals are rarely observed. The reactivity of DOPAL with Nα -amino groups is greater than with lysine Nϵ -amines and, in the presence of O2 , both types of Schiff base DOPAL-peptide intermediates rapidly react with free DOPAL to irreversibly form dicatechol pyrrole adducts.
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Affiliation(s)
- Venkatraman Ramanujam
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892, USA
| | - Cyril Charlier
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892, USA
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892, USA
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6
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Pilicer SL, Bakhshi PR, Bentley KW, Wolf C. Biomimetic Chirality Sensing with Pyridoxal-5'-phosphate. J Am Chem Soc 2017; 139:1758-1761. [PMID: 28128945 DOI: 10.1021/jacs.6b12056] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Pyridoxal-5'-phosphate (PLP) is introduced to a biomimetic indicator displacement assay for simultaneous determination of the absolute configuration, enantiomeric composition and concentration of unprotected amino acids, amino alcohols and amines. The chiroptical assay is based on fast imine metathesis with a PLP aryl imine probe to capture the target compound for circular dichroism and fluorescence sensing analysis. The substrate binding yields characteristic Cotton effects that provide information about the target compound ee and the synchronous release of the indicator results in a nonenantioselective off-on fluorescence response that is independent of the enantiomeric sample composition and readily correlated to the total analyte concentration.
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Affiliation(s)
- Samantha L Pilicer
- Department of Chemistry, Georgetown University , Washington, D.C. 20057, United States
| | - Pegah R Bakhshi
- Department of Chemistry, Georgetown University , Washington, D.C. 20057, United States
| | - Keith W Bentley
- Department of Chemistry, Georgetown University , Washington, D.C. 20057, United States
| | - Christian Wolf
- Department of Chemistry, Georgetown University , Washington, D.C. 20057, United States
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7
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Sobczyk L, Chudoba D, Tolstoy PM, Filarowski A. Some Brief Notes on Theoretical and Experimental Investigations of Intramolecular Hydrogen Bonding. Molecules 2016; 21:E1657. [PMID: 27918442 PMCID: PMC6273268 DOI: 10.3390/molecules21121657] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 11/18/2016] [Accepted: 11/28/2016] [Indexed: 11/16/2022] Open
Abstract
A review of selected literature data related to intramolecular hydrogen bonding in ortho-hydroxyaryl Schiff bases, ortho-hydroxyaryl ketones, ortho-hydroxyaryl amides, proton sponges and ortho-hydroxyaryl Mannich bases is presented. The paper reports on the application of experimental spectroscopic measurements (IR and NMR) and quantum-mechanical calculations for investigations of the proton transfer processes, the potential energy curves, tautomeric equilibrium, aromaticity etc. Finally, the equilibrium between the intra- and inter-molecular hydrogen bonds in amides is discussed.
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Affiliation(s)
- Lucjan Sobczyk
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie Str., 50-383 Wrocław, Poland.
| | - Dorota Chudoba
- Faculty of Physics, A. Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland.
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia.
| | - Peter M Tolstoy
- Center for Magnetic Resonance, St. Petersburg State University, St. Petersburg 198504, Russia.
| | - Aleksander Filarowski
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie Str., 50-383 Wrocław, Poland.
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia.
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8
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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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9
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Gamov G, Zavalishin M, Khokhlova A, Sharnin V. Influence of aqueous dimethyl sulfoxide on pyridoxine protonation and tautomerization. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.06.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Mehr SHM, Patrick BO, MacLachlan MJ. Stabilization of a Strained Heteroradialene by Peripheral Electron Delocalization. Org Lett 2016; 18:1840-3. [DOI: 10.1021/acs.orglett.6b00577] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- S. Hessam M. Mehr
- Department of Chemistry, University of British Columbia, 2036
Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Brian O. Patrick
- Department of Chemistry, University of British Columbia, 2036
Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Mark J. MacLachlan
- Department of Chemistry, University of British Columbia, 2036
Main Mall, Vancouver, BC V6T 1Z1, Canada
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11
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Young RP, Caulkins BG, Borchardt D, Bulloch DN, Larive CK, Dunn MF, Mueller LJ. Solution-State (17)O Quadrupole Central-Transition NMR Spectroscopy in the Active Site of Tryptophan Synthase. Angew Chem Int Ed Engl 2015; 55:1350-4. [PMID: 26661504 DOI: 10.1002/anie.201508898] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Indexed: 11/09/2022]
Abstract
Oxygen is an essential participant in the acid-base chemistry that takes place within many enzyme active sites, yet has remained virtually silent as a probe in NMR spectroscopy. Here, we demonstrate the first use of solution-state (17)O quadrupole central-transition NMR spectroscopy to characterize enzymatic intermediates under conditions of active catalysis. In the 143 kDa pyridoxal-5'-phosphate-dependent enzyme tryptophan synthase, reactions of the α-aminoacrylate intermediate with the nucleophiles indoline and 2-aminophenol correlate with an upfield shift of the substrate carboxylate oxygen resonances. First principles calculations suggest that the increased shieldings for these quinonoid intermediates result from the net increase in the charge density of the substrate-cofactor π-bonding network, particularly at the adjacent α-carbon site.
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Affiliation(s)
- Robert P Young
- Department of Chemistry, University of California, Riverside, Riverside, CA, 92521, USA
| | - Bethany G Caulkins
- Department of Chemistry, University of California, Riverside, Riverside, CA, 92521, USA
| | - Dan Borchardt
- Department of Chemistry, University of California, Riverside, Riverside, CA, 92521, USA
| | - Daryl N Bulloch
- Department of Chemistry, University of California, Riverside, Riverside, CA, 92521, USA
| | - Cynthia K Larive
- Department of Chemistry, University of California, Riverside, Riverside, CA, 92521, USA
| | - Michael F Dunn
- Department of Biochemistry, University of California, Riverside, Riverside, CA, 92521, USA
| | - Leonard J Mueller
- Department of Chemistry, University of California, Riverside, Riverside, CA, 92521, USA.
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12
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Young RP, Caulkins BG, Borchardt D, Bulloch DN, Larive CK, Dunn MF, Mueller LJ. Solution‐State
17
O Quadrupole Central‐Transition NMR Spectroscopy in the Active Site of Tryptophan Synthase. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508898] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Robert P. Young
- Department of Chemistry University of California, Riverside Riverside CA 92521 USA
| | - Bethany G. Caulkins
- Department of Chemistry University of California, Riverside Riverside CA 92521 USA
| | - Dan Borchardt
- Department of Chemistry University of California, Riverside Riverside CA 92521 USA
| | - Daryl N. Bulloch
- Department of Chemistry University of California, Riverside Riverside CA 92521 USA
| | - Cynthia K. Larive
- Department of Chemistry University of California, Riverside Riverside CA 92521 USA
| | - Michael F. Dunn
- Department of Biochemistry University of California, Riverside Riverside CA 92521 USA
| | - Leonard J. Mueller
- Department of Chemistry University of California, Riverside Riverside CA 92521 USA
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13
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Kozlecki T, Tolstoy PM, Kwocz A, Vovk MA, Kochel A, Polowczyk I, Tretyakov PY, Filarowski A. Conformational state of β-hydroxynaphthylamides: Barriers for the rotation of the amide group around CN bond and dynamics of the morpholine ring. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 149:254-262. [PMID: 25965172 DOI: 10.1016/j.saa.2015.04.052] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 04/14/2015] [Accepted: 04/16/2015] [Indexed: 06/04/2023]
Abstract
Three β-hydroxynaphthylamides (morpholine, pyrrolidine and dimethylamine derivatives) have been synthesized and their conformational state was analyzed by NMR, X-ray and DFT calculations. In aprotic solution the molecules contain intramolecular OHO hydrogen bonds, which change into intermolecular ones in solid state. The energy barriers for the amide group rotation around the CN bond were estimated from the line shape analysis of (1)H and (13)C NMR signals. A tentative correlation between the barrier height and the strength of OHO bond was proposed. Calculations of the potential energy profiles for the rotations around CC and CN bonds were done. In case of morpholine derivative experimental indications of additional dynamics: chair-chair 'ring flip' in combination with the twisting around CC bond were obtained and confirmed by quantum chemistry calculations.
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Affiliation(s)
- Tomasz Kozlecki
- Wroclaw University of Technology, Faculty of Chemistry, Division of Chemical Engineering, 50-373 Wrocław, Poland
| | - Peter M Tolstoy
- St. Petersburg State University, Center for Magnetic Resonance, 198504 St. Petersburg, Russia.
| | - Agnieszka Kwocz
- Faculty of Chemistry, University of Wrocław, 50-383 Wrocław, Poland
| | - Mikhail A Vovk
- St. Petersburg State University, Center for Magnetic Resonance, 198504 St. Petersburg, Russia
| | - Andrzej Kochel
- Faculty of Chemistry, University of Wrocław, 50-383 Wrocław, Poland
| | - Izabela Polowczyk
- Wroclaw University of Technology, Faculty of Chemistry, Division of Chemical Engineering, 50-373 Wrocław, Poland
| | | | - Aleksander Filarowski
- Faculty of Chemistry, University of Wrocław, 50-383 Wrocław, Poland; The Joint Institute for Nuclear Research, Frank Laboratory of Neutron Physics, 141980 Dubna, Russia.
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14
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Catalytic roles of βLys87 in tryptophan synthase: (15)N solid state NMR studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1194-9. [PMID: 25688830 DOI: 10.1016/j.bbapap.2015.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 10/24/2022]
Abstract
The proposed mechanism for tryptophan synthase shows βLys87 playing multiple catalytic roles: it bonds to the PLP cofactor, activates C4' for nucleophilic attack via a protonated Schiff base nitrogen, and abstracts and returns protons to PLP-bound substrates (i.e. acid-base catalysis). ε-¹⁵N-lysine TS was prepared to access the protonation state of βLys87 using ¹⁵N solid-state nuclear magnetic resonance (SSNMR) spectroscopy for three quasi-stable intermediates along the reaction pathway. These experiments establish that the protonation state of the ε-amino group switches between protonated and neutral states as the β-site undergoes conversion from one intermediate to the next during catalysis, corresponding to mechanistic steps where this lysine residue has been anticipated to play alternating acid and base catalytic roles that help steer reaction specificity in tryptophan synthase catalysis. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications. Guest Editors: Andrea Mozzarelli and Loredano Pollegioni.
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15
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Stojanovski BM, Breydo L, Hunter GA, Uversky VN, Ferreira GC. Catalytically active alkaline molten globular enzyme: Effect of pH and temperature on the structural integrity of 5-aminolevulinate synthase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2145-54. [PMID: 25240868 DOI: 10.1016/j.bbapap.2014.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 08/27/2014] [Accepted: 09/10/2014] [Indexed: 11/30/2022]
Abstract
5-Aminolevulinate synthase (ALAS), a pyridoxal-5'phosphate (PLP)-dependent enzyme, catalyzes the first step of heme biosynthesis in mammals. Circular dichroism (CD) and fluorescence spectroscopies were used to examine the effects of pH (1.0-3.0 and 7.5-10.5) and temperature (20 and 37°C) on the structural integrity of ALAS. The secondary structure, as deduced from far-UV CD, is mostly resilient to pH and temperature changes. Partial unfolding was observed at pH2.0, but further decreasing pH resulted in acid-induced refolding of the secondary structure to nearly native levels. The tertiary structure rigidity, monitored by near-UV CD, is lost under acidic and specific alkaline conditions (pH10.5 and pH9.5/37°C), where ALAS populates a molten globule state. As the enzyme becomes less structured with increased alkalinity, the chiral environment of the internal aldimine is also modified, with a shift from a 420nm to 330nm dichroic band. Under acidic conditions, the PLP cofactor dissociates from ALAS. Reaction with 8-anilino-1-naphthalenesulfonic acid corroborates increased exposure of hydrophobic clusters in the alkaline and acidic molten globules, although the reaction is more pronounced with the latter. Furthermore, quenching the intrinsic fluorescence of ALAS with acrylamide at pH1.0 and 9.5 yielded subtly different dynamic quenching constants. The alkaline molten globule state of ALAS is catalytically active (pH9.5/37°C), although the kcat value is significantly decreased. Finally, the binding of 5-aminolevulinate restricts conformational fluctuations in the alkaline molten globule. Overall, our findings prove how the structural plasticity of ALAS contributes to reaching a functional enzyme.
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Affiliation(s)
- Bosko M Stojanovski
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Leonid Breydo
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Gregory A Hunter
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; USF Health Byrd Alzheimer's Research Institute, University of South Florida, Tampa, FL 33612, USA; Biology Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Gloria C Ferreira
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Department of Chemistry, University of South Florida, Tampa, FL 33612, USA.
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16
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Caulkins B, Bastin B, Yang C, Neubauer TJ, Young RP, Hilario E, Huang YMM, Chang CEA, Fan L, Dunn MF, Marsella MJ, Mueller LJ. Protonation states of the tryptophan synthase internal aldimine active site from solid-state NMR spectroscopy: direct observation of the protonated Schiff base linkage to pyridoxal-5'-phosphate. J Am Chem Soc 2014; 136:12824-7. [PMID: 25148001 PMCID: PMC4183654 DOI: 10.1021/ja506267d] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Indexed: 11/29/2022]
Abstract
The acid-base chemistry that drives catalysis in pyridoxal-5'-phosphate (PLP)-dependent enzymes has been the subject of intense interest and investigation since the initial identification of PLP's role as a coenzyme in this extensive class of enzymes. It was first proposed over 50 years ago that the initial step in the catalytic cycle is facilitated by a protonated Schiff base form of the holoenzyme in which the linking lysine ε-imine nitrogen, which covalently binds the coenzyme, is protonated. Here we provide the first (15)N NMR chemical shift measurements of such a Schiff base linkage in the resting holoenzyme form, the internal aldimine state of tryptophan synthase. Double-resonance experiments confirm the assignment of the Schiff base nitrogen, and additional (13)C, (15)N, and (31)P chemical shift measurements of sites on the PLP coenzyme allow a detailed model of coenzyme protonation states to be established.
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Affiliation(s)
- Bethany
G. Caulkins
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Baback Bastin
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Chen Yang
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Thomas J. Neubauer
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Robert P. Young
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Eduardo Hilario
- Department
of Biochemistry, University of California, Riverside, California 92521, United States
| | - Yu-ming M. Huang
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Chia-en A. Chang
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Li Fan
- Department
of Biochemistry, University of California, Riverside, California 92521, United States
| | - Michael F. Dunn
- Department
of Biochemistry, University of California, Riverside, California 92521, United States
| | - Michael J. Marsella
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Leonard J. Mueller
- Department
of Chemistry, University of California, Riverside, California 92521, United States
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17
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Impact of metal cation complexation and protonation on tautomeric and resonance forms of the oxaalkyl Schiff bases derived from 5-substituted salicylaldehyde and 2-hydroxy-1-naphthlaldehyde. Struct Chem 2014. [DOI: 10.1007/s11224-014-0447-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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18
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Chan-Huot M, Dos A, Zander R, Sharif S, Tolstoy PM, Compton S, Fogle E, Toney MD, Shenderovich I, Denisov GS, Limbach HH. NMR Studies of Protonation and Hydrogen Bond States of Internal Aldimines of Pyridoxal 5′-Phosphate Acid–Base in Alanine Racemase, Aspartate Aminotransferase, and Poly-l-lysine. J Am Chem Soc 2013; 135:18160-75. [DOI: 10.1021/ja408988z] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Monique Chan-Huot
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
- Ecole Normale Supérieure, Laboratoire des BioMolécules, 24 rue Lhomond, 75231 Cedex 05, Paris, France
| | - Alexandra Dos
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Reinhard Zander
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Shasad Sharif
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Peter M. Tolstoy
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
- Department
of Chemistry, St. Petersburg State University, Universitetskij pr. 26, 198504 St. Petersburg, Russian Federation
| | - Shara Compton
- Department
of Chemistry, University of California—Davis, One Shields Avenue, Davis, California 95616, United States
- Department
of Chemistry, Widener University, One University Place, Chester, Pennsylvania 19013, United States
| | - Emily Fogle
- Department
of Chemistry, University of California—Davis, One Shields Avenue, Davis, California 95616, United States
- Department of Chemistry & Biochemistry, CalPoly, San Luis Obispo, California 93407, United States
| | - Michael D. Toney
- Department
of Chemistry, University of California—Davis, One Shields Avenue, Davis, California 95616, United States
| | - Ilya Shenderovich
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
- University of Regensburg, Universitätsstr.
31, 93040 Regensburg, Germany
| | - Gleb S. Denisov
- Institute
of Physics, St. Petersburg State University, 198504 St. Petersburg, Russian Federation
| | - Hans-Heinrich Limbach
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
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19
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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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20
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Filarowski A, Hansen PE. Secondary Isotope Effects on 13C and 15N Chemical Shifts of Schiff Bases Revisited. ACTA ACUST UNITED AC 2013. [DOI: 10.1524/zpch.2013.0378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
An analysis is presented of secondary deuterium isotope effects on 15N and 13C chemical shifts of the methylamine Schiff base of 4,6-dimethoxysalicylaldehyde. It is shown that for this compound existing as an equilibrium between an OH and a NH-form, the secondary isotope effects depend on the OH/NH ratio giving a function with a maximum and a minimum.
Secondary deuterium isotope effects on 13C and 15N chemical shifts are compared in a broader range of compounds and the above trend is confirmed. Changes in the dielectric constants of the medium with temperature are found to be rather unimportant for the change in equilibrium. Equilibrium isotope effects on chemical shifts are shown to be important. The magnitudes of the isotope effects are correlated both to intrinsic and equilibrium isotope effects. The latter correlate to the shape of the two-potential well, the energy difference and the difference in chemical shifts of the two tautomers.
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21
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Spectroscopic studies of amino acid ionic liquid-supported Schiff bases. Molecules 2013; 18:4986-5004. [PMID: 23629755 PMCID: PMC6269710 DOI: 10.3390/molecules18054986] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/08/2013] [Accepted: 04/17/2013] [Indexed: 11/16/2022] Open
Abstract
Amino acid ionic liquid-supported Schiff bases, derivatives of salicylaldehyde and various amino acids (l-threonine, l-valine, l-leucine, l-isoleucine and l-histidine) have been investigated by means of various spectroscopic techniques (NMR, UV-Vis, IR, MS) and deuterium isotope effects on 13C-NMR chemical shifts. The results have shown that in all studied amino acid ionic liquid-supported Schiff bases (except the l-histidine derivative) a proton transfer equilibrium exists and the presence of the COO− group stabilizes the proton transferred NH-form.
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22
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Grebner C, Kästner J, Thiel W, Engels B. A New Tabu-Search-Based Algorithm for Solvation of Proteins. J Chem Theory Comput 2012; 9:814-21. [DOI: 10.1021/ct300898d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Christoph Grebner
- Julius-Maximilians-Universität
Würzburg, Institut für Physikalische und
Theoretische Chemie, Emil-Fischer-Straße 42, D-97074 Würzburg,
Germany
| | - Johannes Kästner
- Universität
Stuttgart,
Institut für Theoretische Chemie, Pfaffenwaldring 55, D-70569
Stuttgart, Germany
| | - Walter Thiel
- Max-Planck-Institut
für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an
der Ruhr, Germany
| | - Bernd Engels
- Julius-Maximilians-Universität
Würzburg, Institut für Physikalische und
Theoretische Chemie, Emil-Fischer-Straße 42, D-97074 Würzburg,
Germany
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23
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24
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Xiao X, Liu M, Rong C, Xue F, Li S, Xie Y, Shi Y. An Efficient Asymmetric Biomimetic Transamination of α-Keto Esters to Chiral α-Amino Esters. Org Lett 2012; 14:5270-3. [DOI: 10.1021/ol302427d] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiao Xiao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Mao Liu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Chao Rong
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Fazhen Xue
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Songlei Li
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Ying Xie
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Yian Shi
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
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25
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Xue F, Xiao X, Wang H, Shi Y. The effect of benzyl amine on the efficiency of the base-catalyzed transamination of α-keto esters. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.06.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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26
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Kovaříček P, Lehn JM. Merging Constitutional and Motional Covalent Dynamics in Reversible Imine Formation and Exchange Processes. J Am Chem Soc 2012; 134:9446-55. [DOI: 10.1021/ja302793c] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Petr Kovaříček
- Laboratoire de Chimie
Supramoléculaire, Institut de Science et d’Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, 8 allée Gaspard Monge, Strasbourg 67000, France
| | - Jean-Marie Lehn
- Laboratoire de Chimie
Supramoléculaire, Institut de Science et d’Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, 8 allée Gaspard Monge, Strasbourg 67000, France
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27
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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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28
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Balakrishnan A, Paramasivam S, Chakraborty S, Polenova T, Jordan F. Solid-state nuclear magnetic resonance studies delineate the role of the protein in activation of both aromatic rings of thiamin. J Am Chem Soc 2012; 134:665-72. [PMID: 22092024 PMCID: PMC3257386 DOI: 10.1021/ja209856x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Knowledge of the state of ionization and tautomerization of heteroaromatic cofactors when enzyme-bound is essential for formulating a detailed stepwise mechanism via proton transfers, the most commonly observed contribution to enzyme catalysis. In the bifunctional coenzyme, thiamin diphosphate (ThDP), both aromatic rings participate in catalysis, the thiazolium ring as an electrophilic covalent catalyst and the 4'-aminopyrimidine as acid-base catalyst involving its 1',4'-iminopyrimidine tautomeric form. Two of four ionization and tautomeric states of ThDP are well characterized via circular dichroism spectral signatures on several ThDP superfamily members. Yet, the method is incapable of providing information about specific proton locations, which in principle may be accessible via NMR studies. To determine the precise ionization/tautomerization states of ThDP during various stages of the catalytic cycle, we report the first application of solid-state NMR spectroscopy to ThDP enzymes, whose large mass (160,000-250,000 Da) precludes solution NMR approaches. Three de novo synthesized analogues, [C2,C6'-(13)C(2)]ThDP, [C2-(13)C]ThDP, and [N4'-(15)N]ThDP used with three enzymes revealed that (a) binding to the enzymes activates both the 4'-aminopyrimidine (via pK(a) elevation) and the thiazolium rings (pK(a) suppression); (b) detection of a pre-decarboxylation intermediate analogue using [C2,C6'-(13)C(2)]ThDP, enables both confirmation of covalent bond formation and response in 4'-aminopyrimidine ring's tautomeric state to intermediate formation, supporting the mechanism we postulate; and (c) the chemical shift of bound [N4'-(15)N]ThDP provides plausible models for the participation of the 1',4'-iminopyrimidine tautomer in the mechanism. Unprecedented detail is achieved about proton positions on this bifunctional coenzyme on large enzymes in their active states.
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Affiliation(s)
| | | | | | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE
| | - Frank Jordan
- Department of Chemistry, Rutgers University, Newark, NJ 07102
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29
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Sparr C, Salamanova E, Schweizer WB, Senn HM, Gilmour R. Theoretical and X-ray crystallographic evidence of a fluorine-imine gauche effect: an addendum to Dunathan's stereoelectronic hypothesis. Chemistry 2011; 17:8850-7. [PMID: 21732444 DOI: 10.1002/chem.201100644] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Indexed: 11/07/2022]
Abstract
The preference of β-fluoroimines to adopt a gauche conformation has been studied by single-crystal X-ray diffraction analysis and DFT methods. Empirical and theoretical evidence for a preferential gauche arrangement around the NCCF torsion angle (φ) is presented ((E)-2-fluoro-N-(4-nitrobenzylidene)ethanamine: φ(NCCF) =70.0°). In the context of this study, the analysis of a pyridoxal-derived β-fluoroaldimine was performed, a species that is implicated in the inhibition of pyridoxal phosphate (PLP)-dependent enzymes by β-fluoroamine derivatives. The gauche preference of the internal aldimine (=NCH(2)CH(2)F) that can be rationalized by stereoelectronic arguments does not hold for the corresponding external system (N=CHCH(2)F) (E(min) when φ(NCCF) =120°). Moreover, the C-F bond is lengthened by more than 0.02 Å at φ(NCCF) =±90°, when it is exactly antiperiplanar to the conjugated imine. This activation of the C-F σ bond by an adjacent π system constitutes an addendum to Dunathan's stereoelectronic hypothesis.
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Affiliation(s)
- Christof Sparr
- Swiss Federal Institute of Technology (ETH) Zürich, Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, Zürich, Switzerland
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30
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Limbach HH, Chan-Huot M, Sharif S, Tolstoy PM, Shenderovich IG, Denisov GS, Toney MD. Critical hydrogen bonds and protonation states of pyridoxal 5'-phosphate revealed by NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1426-37. [PMID: 21703367 DOI: 10.1016/j.bbapap.2011.06.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 06/04/2011] [Accepted: 06/07/2011] [Indexed: 12/01/2022]
Abstract
In this contribution we review recent NMR studies of protonation and hydrogen bond states of pyridoxal 5'-phosphate (PLP) and PLP model Schiff bases in different environments, starting from aqueous solution, the organic solid state to polar organic solution and finally to enzyme environments. We have established hydrogen bond correlations that allow one to estimate hydrogen bond geometries from (15)N chemical shifts. It is shown that protonation of the pyridine ring of PLP in aspartate aminotransferase (AspAT) is achieved by (i) an intermolecular OHN hydrogen bond with an aspartate residue, assisted by the imidazole group of a histidine side chain and (ii) a local polarity as found for related model systems in a polar organic solvent exhibiting a dielectric constant of about 30. Model studies indicate that protonation of the pyridine ring of PLP leads to a dominance of the ketoenamine form, where the intramolecular OHN hydrogen bond of PLP exhibits a zwitterionic state. Thus, the PLP moiety in AspAT carries a net positive charge considered as a pre-requisite to initiate the enzyme reaction. However, it is shown that the ketoenamine form dominates in the absence of ring protonation when PLP is solvated by polar groups such as water. Finally, the differences between acid-base interactions in aqueous solution and in the interior of proteins are discussed. This article is part of a special issue entitled: Pyridoxal Phosphate Enzymology.
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Affiliation(s)
- Hans-Heinrich Limbach
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraβe 3, D-14195, Germany.
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31
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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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32
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Fleischmann M, Drettwan D, Sugiono E, Rueping M, Gschwind RM. Brønsted Acid Catalysis: Hydrogen Bonding versus Ion Pairing in Imine Activation. Angew Chem Int Ed Engl 2011; 50:6364-9. [DOI: 10.1002/anie.201101385] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Indexed: 11/08/2022]
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33
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Fleischmann M, Drettwan D, Sugiono E, Rueping M, Gschwind RM. Brønsted Acid Catalysis: Hydrogen Bonding versus Ion Pairing in Imine Activation. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101385] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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34
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Cerqueira NMFSA, Fernandes PA, Ramos MJ. Computational Mechanistic Studies Addressed to the Transimination Reaction Present in All Pyridoxal 5′-Phosphate-Requiring Enzymes. J Chem Theory Comput 2011; 7:1356-68. [DOI: 10.1021/ct1002219] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- N. M. F. S. A. Cerqueira
- REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - P. A. Fernandes
- REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - M. J. Ramos
- REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, s/n, 4169-007 Porto, Portugal
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35
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Lai J, Niks D, Wang Y, Domratcheva T, Barends TRM, Schwarz F, Olsen RA, Elliott DW, Fatmi MQ, Chang CEA, Schlichting I, Dunn MF, Mueller LJ. X-ray and NMR Crystallography in an Enzyme Active Site: The Indoline Quinonoid Intermediate in Tryptophan Synthase. J Am Chem Soc 2010; 133:4-7. [DOI: 10.1021/ja106555c] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jinfeng Lai
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Dimitri Niks
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Yachong Wang
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Tatiana Domratcheva
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Thomas R. M. Barends
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Friedrich Schwarz
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Ryan A. Olsen
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Douglas W. Elliott
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - M. Qaiser Fatmi
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Chia-en A. Chang
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Ilme Schlichting
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Michael F. Dunn
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Leonard J. Mueller
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
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