1
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Gou Y, Li T, Wang Y. Active-Site Oxygen Accessibility and Catalytic Loop Dynamics of Plant Aromatic Amino Acid Decarboxylases from Molecular Simulations. Biochemistry 2024; 63:1980-1990. [PMID: 39008055 PMCID: PMC11308512 DOI: 10.1021/acs.biochem.4c00144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 07/05/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024]
Abstract
Aromatic amino acid decarboxylases (AAADs) are pyridoxal-5'-phosphate (PLP)-dependent enzymes that catalyze the decarboxylation of aromatic amino acid l-amino acids. In plants, apart from canonical AAADs that catalyze the straightforward decarboxylation reaction, other members of the AAAD family function as aromatic acetaldehyde synthases (AASs) and catalyze more complex decarboxylation-dependent oxidative deamination. The interconversion between a canonical AAAD and an AAS can be achieved by a single tyrosine-phenylalanine mutation in the large catalytic loop of the enzymes. In this work, we report implicit ligand sampling (ILS) calculations of the canonical l-tyrosine decarboxylase from Papaver somniferum (PsTyDC) that catalyzes l-tyrosine decarboxylation and its Y350F mutant that instead catalyzes the decarboxylation-dependent oxidative deamination of the same substrate. Through comparative analysis of the resulting three-dimensional (3D) O2 free energy profiles, we evaluate the impact of the key tyrosine/phenylalanine mutation on oxygen accessibility to both the wild type and Y350F mutant of PsTyDC. Additionally, using molecular dynamics (MD) simulations of the l-tryptophan decarboxylase from Catharanthus roseus (CrTDC), we further investigate the dynamics of a large catalytic loop known to be indispensable to all AAADs. Results of our ILS and MD calculations shed new light on how key structural elements and loop conformational dynamics underlie the enzymatic functions of different members of the plant AAAD family.
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Affiliation(s)
- Yitao Gou
- Department of Physics, The
Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Tianjie Li
- Department of Physics, The
Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Yi Wang
- Department of Physics, The
Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
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2
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Hecht M, Dullinger P, Silva W, Horinek D, Gschwind RM. Highly acidic N-triflylphosphoramides as chiral Brønsted acid catalysts: the effect of weak hydrogen bonds and multiple acceptors on complex structures and aggregation. Chem Sci 2024; 15:9104-9111. [PMID: 38903236 PMCID: PMC11186309 DOI: 10.1039/d4sc01939c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 04/22/2024] [Indexed: 06/22/2024] Open
Abstract
N-Triflylphosphoramides (NTPAs) represent an important catalyst class in asymmetric catalysis due to their multiple hydrogen bond acceptor sites and acidity, which is increased by several orders of magnitude compared to conventional chiral phosphoric acids (CPAs). Thus, NTPAs allow for several challenging transformations, which are not accessible with CPAs. However, detailed evidence on their hydrogen bonding situation, complex structures and aggregation is still lacking. Therefore, this study covers the hydrogen bonding behavior and structural features of binary NTPA/imine complexes compared to their CPA counterparts. Deviating from the single-well potential hydrogen bonds commonly observed in CPA/imine complexes, the NTPA/imine complexes exhibit a tautomeric equilibrium between two proton positions. Low-temperature NMR at 180 K supported by computer simulations indicates a OHN hydrogen bond between the phosphoramide oxygen and the imine, instead of the mostly proposed NHN H-bond. Furthermore, this study finds no evidence for the existence of dimeric NTPA/NTPA/imine complexes as previously suggested for CPA systems, both synthetically and through NMR studies.
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Affiliation(s)
- Markus Hecht
- Institut für Organische Chemie, Universität Regensburg D-93053 Regensburg Germany
| | - Philipp Dullinger
- Institute of Physical and Theoretical Chemistry, University of Regensburg D-93053 Germany
| | - Wagner Silva
- Institut für Organische Chemie, Universität Regensburg D-93053 Regensburg Germany
| | - Dominik Horinek
- Institute of Physical and Theoretical Chemistry, University of Regensburg D-93053 Germany
| | - Ruth M Gschwind
- Institut für Organische Chemie, Universität Regensburg D-93053 Regensburg Germany
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3
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Tupikina EY, Sigalov MV, Alkhuder O, Tolstoy PM. Charge Relay Without Proton Transfer: Coupling of Two Short Hydrogen Bonds via Imidazole in Models of Catalytic Triad of Serine Protease Active Site. Chemphyschem 2024; 25:e202300970. [PMID: 38563616 DOI: 10.1002/cphc.202300970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/01/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
A homologous series of 20 substituted alcohol-imidazole-acetate model complexes imitating the charge relay system in Ser-His-Asp catalytic triad of serine proteases is considered quantum-chemically. We show qualitatively that the geometries of alcohol-imidazole and imidazole-acetate short hydrogen bonds are strongly coupled via the central imidazole and such complexes are capable of effectively relaying the charge from acetate to alcohol moiety upon relatively small concerted proton displacements. We hypothesize an alternative catalytic mechanism of serine proteases that does not require two complete proton transfers or hydrogen bond breakage between Ser and His residues.
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Affiliation(s)
- Elena Yu Tupikina
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - Mark V Sigalov
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Omar Alkhuder
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - Peter M Tolstoy
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
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4
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Tautomeric Equilibrium in 1-Benzamidoisoquinoline Derivatives. Molecules 2023; 28:molecules28031101. [PMID: 36770775 PMCID: PMC9920963 DOI: 10.3390/molecules28031101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
In this study, the tautomeric equilibrium of a sequence of 1-benzamidoisoquinoline derivatives was investigated with the tools of NMR spectroscopy and computational chemistry. The equilibrium between different tautomers in these systems could be controlled via the substitution effect, and the relative content of the amide form varied from 74% for the strong electron-donating NMe2 substituent to 38% for the strong electron-accepting NO2 group in the phenyl ring. In contrast to the previously investigated 2-phenacylquinoline derivatives, the most stable and thus most abundant tautomer in the 1-benzamidoisoquinoline series except the two most electron-accepting substituents was an amide. The intramolecular hydrogen bond present in the enol tautomer competed with the intermolecular hydrogen bonds created with the solvent molecules and thus was not a sufficient factor to favor this tautomer in the mixture. Although routinely computational studies of tautomeric equilibrium are performed within the continuum solvent models, it is proven here that the inclusion of the explicit solvent is mandatory in order to reproduce the experimental tendencies observed for this type of system, facilitating strong intermolecular hydrogen bonds.
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5
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Brody SI, Buonomo JA, Orimoloye MO, Jia Z, Sharma S, Brown CD, Baughn AD, Aldrich CC. A Nucleophilic Activity-Based Probe Enables Profiling of PLP-Dependent Enzymes. Chembiochem 2023; 24:e202200669. [PMID: 36652345 DOI: 10.1002/cbic.202200669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 01/19/2023]
Abstract
PLP-dependent enzymes represent an important class of highly "druggable" enzymes that perform a wide array of critical reactions to support all organisms. Inhibition of individual members of this family of enzymes has been validated as a therapeutic target for pathologies ranging from infection with Mycobacterium tuberculosis to epilepsy. Given the broad nature of the activities within this family of enzymes, we envisioned a universally acting probe to characterize existing and putative members of the family that also includes the necessary chemical moieties to enable activity-based protein profiling experiments. Hence, we developed a probe that contains an N-hydroxyalanine warhead that acts as a covalent inhibitor of PLP-dependent enzymes, a linear diazirine for UV crosslinking, and an alkyne moiety to enable enrichment of crosslinked proteins. Our molecule was used to study PLP-dependent enzymes in vitro as well as look at whole-cell lysates of M. tuberculosis and assess inhibitory activity. The probe was able to enrich and identify LysA, a PLP-dependent enzyme crucial for lysine biosynthesis, through mass spectrometry. Overall, our study shows the utility of this trifunctional first-generation probe. We anticipate further optimization of probes for PLP-dependent enzymes will enable the characterization of rationally designed covalent inhibitors of PLP-dependent enzymes, which will expedite the preclinical characterization of these important therapeutic targets.
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Affiliation(s)
- Scott I Brody
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Joseph A Buonomo
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Moyosore O Orimoloye
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Ziyi Jia
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Sachin Sharma
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Christopher D Brown
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, 308 Harvard Street SE, Minneapolis, MN 55455, USA
| | - Anthony D Baughn
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, 308 Harvard Street SE, Minneapolis, MN 55455, USA
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6
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Koeppe B, Tolstoy PM, Guo J, Denisov GS, Limbach HH. Combined NMR and UV-Vis Spectroscopic Studies of Models for the Hydrogen Bond System in the Active Site of Photoactive Yellow Protein: H-Bond Cooperativity and Medium Effects. J Phys Chem B 2021; 125:5874-5884. [PMID: 34060830 DOI: 10.1021/acs.jpcb.0c09923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intramolecular hydrogen bonds in aprotic media were studied by combined (simultaneous) NMR and UV-vis spectroscopy. The species under investigation were anionic and featured single or coupled H-bonds between, for example, carboxylic groups and phenolic oxygen atoms (COO···H···OC)-, among phenolic oxygen atoms (CO···H···OC)-, and hydrogen bond chains between a carboxylic group and two phenolic oxygen atoms (COO···H···(OC)···H···OC)-. The last anion may be regarded as a small molecule model for the hydrogen bond system in the active site of wild-type photoactive yellow protein (PYP) while the others mimic the corresponding H-bonds in site-selective mutants. Proton positions in isolated hydrogen bonds and hydrogen bond chains were assessed by calculations for vacuum conditions and spectroscopically for the two media, CD2Cl2 and the liquefied gas mixture CDClF2/CDF3 at low temperatures. NMR parameters allow for the estimation of time-averaged H-bond geometries, and optical spectra give additional information about geometry distributions. Comparison of the results from the various systems revealed the effects of the formation of hydrogen bond chains and changes of medium conditions on the geometry of individual H-bonds. In particular, the proton in a hydrogen bond to a carboxylic group shifts from the phenolic oxygen atom in the system COO-···H-OC to the carboxylic group in COO-H···(OC)-···H-OC as a result of hydrogen bond formation to the additional phenolic donor. Increase in medium polarity may, however, induce the conversion of a structure of a type COO-H···(OC)-···H-OC to the type COO-···H-(OC)···H-OC. Application of these results obtained from the model systems to PYP suggests that both cooperative effects within the hydrogen bond chain and a low-polarity protein environment are prerequisites for the stabilization of negative charge on the cofactor and hence for the spectral tuning of the photoreceptor.
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Affiliation(s)
- Benjamin Koeppe
- J. Heyrovský Institute of Physical Chemistry, Dolejškova 2155/3, 182 23 Prague 8, Czech Republic
| | - Peter M Tolstoy
- Institute of Chemistry, St. Petersburg State University, Universitetskij pr. 26, 198504 St. Petersburg, Russia
| | - Jing Guo
- Department of Radiology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Gleb S Denisov
- Department of Physics, St. Petersburg State University, 198504 St. Petersburg, Russian Federation
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7
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Reviglio AL, Martínez FA, Montero MDA, Garro-Linck Y, Aucar GA, Sperandeo NR, Monti GA. Accurate location of hydrogen atoms in hydrogen bonds of tizoxanide from the combination of experimental and theoretical models. RSC Adv 2021; 11:7644-7652. [PMID: 35423249 PMCID: PMC8695048 DOI: 10.1039/d0ra10609g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/05/2021] [Indexed: 11/25/2022] Open
Abstract
To obtain detailed information about the position of hydrogen atoms in hydrogen bonds, HBs, of crystalline organic molecular compounds is not an easy task. In this work we propose a combination of ssNMR experimental data with theoretical procedures to get such information. Furthermore, the combination of experimental and theoretical models provides us with well-defined grounds to analyse the strength of π-stacking interactions between layers of hydrogen bonded molecules. Two different theoretical models were considered, both approaches being quite different. The first one is a solid-state model, so that the periodicity of a crystalline system underlies calculations of the electronic energy, the electronic density and NMR parameters. The other one is a molecular model in which molecules are taken as isolated monomers, dimers and tetramers. These two models were applied to the tizoxanide, TIZ, molecular crystal though it can widely be applied to any other molecular crystal. By the application of the quantum molecular model it was possible to learn about the way the intermolecular HBs affect the position of hydrogen atoms that belong to HBs in TIZ. This molecule has two intermolecular HBs that stabilize the structure of a basic dimer, but it also has an intramolecular HB in each monomer whose position should be optimized together with the other ones. We found that by doing this it is possible to obtain reliable results of calculations of NMR spectroscopic parameters. Working with the solid-state model we found that any local variation of the TIZ crystalline structure is correlated with the variation of the values of the NMR parameters of each nucleus. The excellent agreement between experimental and calculated chemical shifts leads to the conclusion that the N10-H10 bond distance should be (1.00 ± 0.02) Å.
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Affiliation(s)
- Ana L Reviglio
- FAMAF, UNC Córdoba Argentina
- Instituto de Física Enrique Gaviola (IFEG), CONICET-UNC Córdoba Argentina
| | - Fernando A Martínez
- Institute of Modelling and Innovation on Technology (IMIT), CONICET-UNNE Corrientes Argentina
- Physics Department, Natural and Exact Science Faculty, Northeastern University of Argentina Corrientes Argentina
| | - Marcos D A Montero
- Institute of Modelling and Innovation on Technology (IMIT), CONICET-UNNE Corrientes Argentina
- Physics Department, Natural and Exact Science Faculty, Northeastern University of Argentina Corrientes Argentina
| | - Yamila Garro-Linck
- FAMAF, UNC Córdoba Argentina
- Instituto de Física Enrique Gaviola (IFEG), CONICET-UNC Córdoba Argentina
| | - Gustavo A Aucar
- Institute of Modelling and Innovation on Technology (IMIT), CONICET-UNNE Corrientes Argentina
- Physics Department, Natural and Exact Science Faculty, Northeastern University of Argentina Corrientes Argentina
| | - Norma R Sperandeo
- Departamento de Ciencias Farmacéuticas, FCQ, UNC Córdoba Argentina
- UNITEFA-CONICET Córdoba Argentina
| | - Gustavo A Monti
- FAMAF, UNC Córdoba Argentina
- Instituto de Física Enrique Gaviola (IFEG), CONICET-UNC Córdoba Argentina
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8
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Berg N, Bergwinkl S, Nuernberger P, Horinek D, Gschwind RM. Extended Hydrogen Bond Networks for Effective Proton-Coupled Electron Transfer (PCET) Reactions: The Unexpected Role of Thiophenol and Its Acidic Channel in Photocatalytic Hydroamidations. J Am Chem Soc 2021; 143:724-735. [DOI: 10.1021/jacs.0c08673] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Nele Berg
- Institute of Organic Chemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Sebastian Bergwinkl
- Institute of Physical and Theoretical Chemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Patrick Nuernberger
- Institute of Physical and Theoretical Chemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Dominik Horinek
- Institute of Physical and Theoretical Chemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Ruth M. Gschwind
- Institute of Organic Chemistry, University of Regensburg, D-93053 Regensburg, Germany
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9
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Khorosheva EI, Sharapova SA, Kuramshina GM. Quantum-Chemical Modeling of Interaction between the Most Stable Methylamine-Pyridoxal-5'-Phosphate Tautomers and Water: Structure and Properties of Monohydrates and Dihydrates. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2020. [DOI: 10.1134/s003602442011014x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Hansen PE. Isotope effects on chemical shifts in the study of hydrogen bonded biological systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 120-121:109-117. [PMID: 33198966 DOI: 10.1016/j.pnmrs.2020.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 06/11/2023]
Abstract
This review deals with biological systems and with deuterium isotope effects on chemical shifts caused by the replacement of OH, NH or SH protons by deuterons. Hydrogen bonding is clearly of central importance. Isotope effects on chemical shifts seems very suitable for use in studies of structures and reactions in the interior of proteins, as exchange of the label can be expected to be slow. One-bond deuterium isotope effects on 15N chemical shifts, and two-bond effects on 1H chemical shifts for N(D)Hx systems can be used to gauge hydrogen bond strength in proteins as well as in salt bridges. Solvent isotope effects on 19F chemical shifts show promise in monitoring solvent access. Equilibrium isotope effects need in some cases to be taken into account. Schemes for calculation of deuterium isotope effects on chemical shifts are discussed and it is demonstrated how calculations may be used in the study of complex biological systems.
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Affiliation(s)
- Poul Erik Hansen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark.
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11
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Jansen D, Gramüller J, Niemeyer F, Schaller T, Letzel MC, Grimme S, Zhu H, Gschwind RM, Niemeyer J. What is the role of acid-acid interactions in asymmetric phosphoric acid organocatalysis? A detailed mechanistic study using interlocked and non-interlocked catalysts. Chem Sci 2020; 11:4381-4390. [PMID: 34122895 PMCID: PMC8159434 DOI: 10.1039/d0sc01026j] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/01/2020] [Indexed: 11/21/2022] Open
Abstract
Organocatalysis has revolutionized asymmetric synthesis. However, the supramolecular interactions of organocatalysts in solution are often neglected, although the formation of catalyst aggregates can have a strong impact on the catalytic reaction. For phosphoric acid based organocatalysts, we have now established that catalyst-catalyst interactions can be suppressed by using macrocyclic catalysts, which react predominantly in a monomeric fashion, while they can be favored by integration into a bifunctional catenane, which reacts mainly as phosphoric acid dimers. For acyclic phosphoric acids, we found a strongly concentration dependent behavior, involving both monomeric and dimeric catalytic pathways. Based on a detailed experimental analysis, DFT-calculations and direct NMR-based observation of the catalyst aggregates, we could demonstrate that intermolecular acid-acid interactions have a drastic influence on the reaction rate and stereoselectivity of asymmetric transfer-hydrogenation catalyzed by chiral phosphoric acids.
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Affiliation(s)
- Dennis Jansen
- Faculty of Chemistry (Organic Chemistry) and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7 45141 Essen Germany
| | | | - Felix Niemeyer
- Faculty of Chemistry (Organic Chemistry) and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7 45141 Essen Germany
| | - Torsten Schaller
- Faculty of Chemistry (Organic Chemistry) and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7 45141 Essen Germany
| | - Matthias C Letzel
- Institute of Organic Chemistry, University of Münster Corrensstrasse 40 48149 Münster Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms Universität Bonn Beringstrasse 4 53115 Bonn Germany
| | - Hui Zhu
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms Universität Bonn Beringstrasse 4 53115 Bonn Germany
| | - Ruth M Gschwind
- Organic Chemistry, University of Regensburg 93040 Regensburg Germany
| | - Jochen Niemeyer
- Faculty of Chemistry (Organic Chemistry) and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7 45141 Essen Germany
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12
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Orlandi M. Basic principles of substrate activation through non-covalent bond interactions. PHYSICAL SCIENCES REVIEWS 2020. [DOI: 10.1515/psr-2018-0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
In the last twenty years, chiral Brønsted acid and chiral counteranion catalysis have emerged as a fundamental area of organocatalysis. The development of chiral acidic catalysts has allowed extending many known Brønsted catalyzed reactions to the stereoselective domain. Moreover, the controlled conditions under which these catalysts can be used, allowed accessing reactivity of increasing complexity with extraordinary selectivity levels. However, compared to the explosion of this branch of organocatalysis in an applicative direction, only little has been done to understand and rationalize the observed reaction outcomes. This is due, in part, to the complex nature of the weak interactions (H-bonds, electrostatic, and dispersion interactions) governing this class of reactions. Here we review relevant mechanistic analyses from both chiral Brønsted acid and chiral counteranion directed catalysis. Both experimental and computational work is included that aimed at unveiling the nature of the interactions governing the a number of reactions. These include the: enantioselective reduction of ketoimines with Hantzsch esters; ring opening reactions of epoxides, oxetanes, aziridinium, and sulfonium ions; stereoselective fluorination of allylic alcohols; oxidative aminations of benzylic thioethers (enantioselective Pummerer reaction). These case studies are analyzed and discussed in order to highlight key features and similarities across the different catalytic systems.
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Affiliation(s)
- Manuel Orlandi
- Dipartimento di Scienze Chimiche , Università degli Studi di Padova , via Marzolo 1 , Padova 35131 , Italy
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13
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Rothermel K, Žabka M, Hioe J, Gschwind RM. Disulfonimides versus Phosphoric Acids in Brønsted Acid Catalysis: The Effect of Weak Hydrogen Bonds and Multiple Acceptors on Complex Structures and Reactivity. J Org Chem 2019; 84:13221-13231. [PMID: 31550152 PMCID: PMC6863592 DOI: 10.1021/acs.joc.9b01811] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Indexed: 12/20/2022]
Abstract
In Brønsted acid catalysis, hydrogen bonds play a crucial role for reactivity and selectivity. However, the contribution of weak hydrogen bonds or multiple acceptors has been unclear so far since it is extremely difficult to collect experimental evidence for weak hydrogen bonds. Here, our hydrogen bond and structural access to Brønsted acid/imine complexes was used to analyze BINOL-derived chiral disulfonimide (DSI)/imine complexes. 1H and 15N chemical shifts as well as 1JNH coupling constants revealed for DSI/imine complexes ion pairs with very weak hydrogen bonds. The high acidity of the DSIs leads to a significant weakening of the hydrogen bond as structural anchor. In addition, the five hydrogen bond acceptors of DSI allow an enormous mobility of the imine in the binary DSI complexes. Theoretical calculations predict the hydrogen bonds to oxygen to be energetically less favored; however, their considerable population is corroborated experimentally by NOE and exchange data. Furthermore, an N-alkylimine, which shows excellent reactivity and selectivity in reactions with DSI, reveals an enlarged structural space in complexes with the chiral phosphoric acid TRIP as potential explanation of its reduced reactivity and selectivity. Thus, considering factors such as flexibility and possible hydrogen bond sites is essential for catalyst development in Brønsted acid catalysis.
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Affiliation(s)
| | | | - Johnny Hioe
- Institute of Organic Chemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Ruth M. Gschwind
- Institute of Organic Chemistry, University of Regensburg, D-93053 Regensburg, Germany
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14
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Lokesh N, Hioe J, Gramüller J, Gschwind RM. Relaxation Dispersion NMR to Reveal Fast Dynamics in Brønsted Acid Catalysis: Influence of Sterics and H-Bond Strength on Conformations and Substrate Hopping. J Am Chem Soc 2019; 141:16398-16407. [PMID: 31545037 PMCID: PMC6863621 DOI: 10.1021/jacs.9b07841] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Indexed: 12/25/2022]
Abstract
NMR provides both structural and dynamic information, which is key to connecting intermediates and to understanding reaction pathways. However, fast exchanging catalytic intermediates are often inaccessible by conventional NMR due its limited time resolution. Here, we show the combined application of the 1H off-resonance R1ρ NMR method and low temperature (185-175 K) to resolve intermediates exchanging on a μs time scale (ns at room temperature). The potential of the approach is demonstrated on chiral phosphoric acid (CPA) catalysts in their complexes with imines. The otherwise inaccessible exchange kinetics of the E-I ⇌ E-II imine conformations and thermodynamic E-I:E-II imine ratios inside the catalyst pocket are experimentally determined and corroborated by calculations. The E-I ⇌ E-II exchange rate constants (kex185 K) for different catalyst-substrate binary complexes varied between 2500 and 19 000 s-1 (τex = 500-50 μs). Theoretical analysis of these exchange rate constants revealed the involvement of an intermediary tilted conformation E-III, which structurally resembles the hydride transfer transition state. The main E-I and E-II exchange pathway is a hydrogen bond strength dependent tilting-switching-tilting mechanism via a bifurcated hydrogen bond as a transition state. The reduction in the sterics of the catalyst showed an accelerated switching process by at least an order of magnitude and enabled an additional rotational pathway. Hence, the exchange process is mainly a function of the intrinsic properties of the 3,3'-substituents of the catalyst. Overall, we believe that the present study opens a new dimension in catalysis via experimental access to structures, populations, and kinetics of catalyst-substrate complexes on the μs time scale by the 1H off-resonance R1ρ method.
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Affiliation(s)
- N. Lokesh
- Institute of Organic Chemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Johnny Hioe
- Institute of Organic Chemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Johannes Gramüller
- Institute of Organic Chemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Ruth M. Gschwind
- Institute of Organic Chemistry, University of Regensburg, D-93053 Regensburg, Germany
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15
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Rothermel K, Melikian M, Hioe J, Greindl J, Gramüller J, Žabka M, Sorgenfrei N, Hausler T, Morana F, Gschwind RM. Internal acidity scale and reactivity evaluation of chiral phosphoric acids with different 3,3'-substituents in Brønsted acid catalysis. Chem Sci 2019; 10:10025-10034. [PMID: 32015815 PMCID: PMC6977555 DOI: 10.1039/c9sc02342a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/02/2019] [Indexed: 12/16/2022] Open
Abstract
NMR H-bond analysis reveals an offset of internal and external acidities of catalysts and allows for a detailed reactivity analysis.
The concept of hydrogen bonding for enhancing substrate binding and controlling selectivity and reactivity is central in catalysis. However, the properties of these key hydrogen bonds and their catalyst-dependent variations are extremely difficult to determine directly by experiments. Here, for the first time the hydrogen bond properties of a whole series of BINOL-derived chiral phosphoric acid (CPA) catalysts in their substrate complexes with various imines were investigated to derive the influence of different 3,3′-substituents on the acidity and reactivity. NMR 1H and 15N chemical shifts and 1JNH coupling constants of these hydrogen bonds were used to establish an internal acidity scale corroborated by calculations. Deviations from calculated external acidities reveal the importance of intermolecular interactions for this key feature of CPAs. For CPAs with similarly sized binding pockets, a correlation of reactivity and hydrogen bond strengths of the catalyst was found. A catalyst with a very small binding pocket showed significantly reduced reactivities. Therefore, NMR isomerization kinetics, population and chemical shift analyses of binary and ternary complexes as well as reaction kinetics were performed to address the steps of the transfer hydrogenation influencing the overall reaction rate. The results of CPAs with different 3,3′-substituents show a delicate balance between the isomerization and the ternary complex formation to be rate-determining. For CPAs with an identical acidic motif and similar sterics, reactivity and internal acidity correlated inversely. In cases where higher sterical demand within the binary complex hinders the binding of the second substrate, the correlation between acidity and reactivity breaks down.
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Affiliation(s)
- Kerstin Rothermel
- Institut für Organische Chemie , Universität Regensburg , Universitätsstraße 31 , D-93053 Regensburg , Germany .
| | - Maxime Melikian
- Institut für Organische Chemie , Universität Regensburg , Universitätsstraße 31 , D-93053 Regensburg , Germany .
| | - Johnny Hioe
- Institut für Organische Chemie , Universität Regensburg , Universitätsstraße 31 , D-93053 Regensburg , Germany .
| | - Julian Greindl
- Institut für Organische Chemie , Universität Regensburg , Universitätsstraße 31 , D-93053 Regensburg , Germany .
| | - Johannes Gramüller
- Institut für Organische Chemie , Universität Regensburg , Universitätsstraße 31 , D-93053 Regensburg , Germany .
| | - Matej Žabka
- Institut für Organische Chemie , Universität Regensburg , Universitätsstraße 31 , D-93053 Regensburg , Germany .
| | - Nils Sorgenfrei
- Institut für Organische Chemie , Universität Regensburg , Universitätsstraße 31 , D-93053 Regensburg , Germany .
| | - Thomas Hausler
- Institut für Organische Chemie , Universität Regensburg , Universitätsstraße 31 , D-93053 Regensburg , Germany .
| | - Fabio Morana
- Institut für Organische Chemie , Universität Regensburg , Universitätsstraße 31 , D-93053 Regensburg , Germany .
| | - Ruth M Gschwind
- Institut für Organische Chemie , Universität Regensburg , Universitätsstraße 31 , D-93053 Regensburg , Germany .
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16
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Koeppe B, Pylaeva SA, Allolio C, Sebastiani D, Nibbering ETJ, Denisov GS, Limbach HH, Tolstoy PM. Polar solvent fluctuations drive proton transfer in hydrogen bonded complexes of carboxylic acid with pyridines: NMR, IR and ab initio MD study. Phys Chem Chem Phys 2018; 19:1010-1028. [PMID: 27942642 DOI: 10.1039/c6cp06677a] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We study a series of intermolecular hydrogen-bonded 1 : 1 complexes formed by chloroacetic acid with 19 substituted pyridines and one aliphatic amine dissolved in CD2Cl2 at low temperature by 1H and 13C NMR and FTIR spectroscopy. The hydrogen bond geometries in these complexes vary from molecular (O-HN) to zwitterionic (O-H-N+) ones, while NMR spectra show the formation of short strong hydrogen bonds in intermediate cases. Analysis of C[double bond, length as m-dash]O stretching and asymmetric CO2- stretching bands in FTIR spectra reveal the presence of proton tautomerism. On the basis of these data, we construct the overall proton transfer pathway. In addition to that, we also study by use of ab initio molecular dynamics the complex formed by chloroacetic acid with 2-methylpyridine, surrounded by 71 CD2Cl2 molecules, revealing a dual-maximum distribution of hydrogen bond geometries in solution. The analysis of the calculated trajectory shows that the proton jumps between molecular and zwitterionic forms are indeed driven by dipole-dipole solvent-solute interactions, but the primary cause of the jumps is the formation/breaking of weak CHO bonds from solvent molecules to oxygen atoms of the carboxylate group.
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Affiliation(s)
- B Koeppe
- Department of Chemistry, Humboldt-Universität zu Berlin, Germany
| | - S A Pylaeva
- Institute of Chemistry, Martin-Luther Universität Halle-Wittenberg, Germany.
| | - C Allolio
- Institute of Chemistry, Martin-Luther Universität Halle-Wittenberg, Germany.
| | - D Sebastiani
- Institute of Chemistry, Martin-Luther Universität Halle-Wittenberg, Germany.
| | - E T J Nibbering
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin, Germany.
| | - G S Denisov
- Department of Physics, St.Petersburg State University, Russia
| | - H-H Limbach
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Germany
| | - P M Tolstoy
- Center for Magnetic Resonance, St. Petersburg State University, Russia.
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17
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Renzi P, Hioe J, Gschwind RM. Enamine/Dienamine and Brønsted Acid Catalysis: Elusive Intermediates, Reaction Mechanisms, and Stereoinduction Modes Based on in Situ NMR Spectroscopy and Computational Studies. Acc Chem Res 2017; 50:2936-2948. [PMID: 29172479 PMCID: PMC6300316 DOI: 10.1021/acs.accounts.7b00320] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
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Over the years, the field of enantioselective organocatalysis has
seen unparalleled growth in the development of novel synthetic applications
with respect to mechanistic investigations. Reaction optimization
appeared to be rather empirical than rational. This offset between
synthetic development and mechanistic understanding was and is generally
due to the difficulties in detecting reactive intermediates and the
inability to experimentally evaluate transition states. Thus, the
first key point for mechanistic studies is detecting elusive intermediates
and characterizing them in terms of their structure, stability, formation
pathways, and kinetic properties. The second key point is evaluating
the importance of these intermediates and their properties in the
transition state. In the past 7 years, our group has addressed
the problems with
detecting elusive intermediates in organocatalysis by means of NMR
spectroscopy and eventually theoretical calculations. Two main activation
modes were extensively investigated: secondary amine catalysis and,
very recently, Brønsted acid catalysis. Using these examples,
we discuss potential methods to stabilize intermediates via intermolecular
interactions; to elucidate their structures, formation pathways and
kinetics; to change the kinetics of the reactions; and to address
their relevance in transition states. The elusive enamine in proline-catalyzed
aldol reactions is used as an example of the stabilization of intermediates
via inter- and intramolecular interactions; the determination of kinetics
on its formation pathway is discussed. Classical structural characterization
of intermediates is described using prolinol and prolinol ether enamines
and dienamines. The Z/E dilemma
for the second double bond of the dienamines shows how the kinetics
of a reaction can be changed to allow for the detection of reaction
intermediates. We recently started to investigate substrate–catalyst
complexes in the field of Brønsted acid catalysis. These studies
on imine/chiral phosphoric acid complexes show that an appropriate
combination of highly developed NMR and theoretical methods can provide
detailed insights into the complicated structures, exchange kinetics,
and H-bonding properties of chiral ion pairs. Furthermore, the merging
of these structural investigations and photoisomerization even allowed
the active transition state combinations to be determined for the
first time on the basis of experimental data only, which is the gold
standard in mechanistic investigations and was previously thought
to be exclusively the domain of theoretical calculations. Thus,
this Account summarizes our recent mechanistic work in the
field of organocatalysis and explains the potential methods for addressing
the central questions in mechanistic studies: stabilization of intermediates,
elucidation of structures and formation pathways, and addressing transition
state combinations experimentally.
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Affiliation(s)
- Polyssena Renzi
- Institut für Organische Chemie, Universität Regensburg, D-95053 Regensburg, Germany
| | - Johnny Hioe
- Institut für Organische Chemie, Universität Regensburg, D-95053 Regensburg, Germany
| | - Ruth M. Gschwind
- Institut für Organische Chemie, Universität Regensburg, D-95053 Regensburg, Germany
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18
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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: 34] [Impact Index Per Article: 4.9] [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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19
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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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20
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Shigeta A, Ito S, Inoue K, Okitsu T, Wada A, Kandori H, Kawamura I. Solid-State Nuclear Magnetic Resonance Structural Study of the Retinal-Binding Pocket in Sodium Ion Pump Rhodopsin. Biochemistry 2017; 56:543-550. [PMID: 28040890 DOI: 10.1021/acs.biochem.6b00999] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The recently identified Krokinobacter rhodopsin 2 (KR2) functions as a light-driven sodium ion pump. The structure of the retinal-binding pocket of KR2 offers important insights into the mechanisms of KR2, which has motif of Asn112, Asp116, and Gln123 (NDQ) that is common among sodium ion pump rhodopsins but is unique among other microbial rhodopsins. Here we present solid-state nuclear magnetic resonance (NMR) characterization of retinal and functionally important residues in the vicinity of retinal in the ground state. We assigned chemical shifts of retinal C14 and C20 atoms, and Tyr218Cζ, Lys255Cε, and the protonated Schiff base of KR2 in lipid environments at acidic and neutral pH. 15N NMR signals of the protonated Schiff base showed a twist around the N-Cε bond under neutral conditions, compared with other microbial rhodopsins. These data indicated that the location of the counterion Asp116 is one helical pitch toward the cytoplasmic side. In acidic environments, the 15N Schiff base signal was shifted to a lower field, indicating that protonation of Asp116 induces reorientation during interactions between the Schiff base and Asp116. In addition, the Tyr218 residue in the vicinity of retinal formed a weak hydrogen bond with Asp251, a temporary Na+-binding site during the photocycle. These features may indicate unique mechanisms of sodium ion pumps.
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Affiliation(s)
- Arisu Shigeta
- Graduate School of Engineering, Yokohama National University , Hodogaya-ku, Yokohama 240-8501, Japan
| | - Shota Ito
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,PRESTO, Japan Science and Technology Agency (JST) , 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Takashi Okitsu
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University , Higashinada-ku, Kobe 658-8558, Japan
| | - Akimori Wada
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University , Higashinada-ku, Kobe 658-8558, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Izuru Kawamura
- Graduate School of Engineering, Yokohama National University , Hodogaya-ku, Yokohama 240-8501, Japan
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21
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Sorgenfrei N, Hioe J, Greindl J, Rothermel K, Morana F, Lokesh N, Gschwind RM. NMR Spectroscopic Characterization of Charge Assisted Strong Hydrogen Bonds in Brønsted Acid Catalysis. J Am Chem Soc 2016; 138:16345-16354. [PMID: 27936674 PMCID: PMC5266430 DOI: 10.1021/jacs.6b09243] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Indexed: 01/10/2023]
Abstract
Hydrogen bonding plays a crucial role in Brønsted acid catalysis. However, the hydrogen bond properties responsible for the activation of the substrate are still under debate. Here, we report an in depth study of the properties and geometries of the hydrogen bonds in (R)-TRIP imine complexes (TRIP: 3,3'-Bis(2,4,6-triisopropylphenyl)-1,1'-binaphthyl-2,2'-diylhydrogen phosphate). From NMR spectroscopic investigations 1H and 15N chemical shifts, a Steiner-Limbach correlation, a deuterium isotope effect as well as quantitative values of 1JNH,2hJPH and 3hJPN were used to determine atomic distances (rOH, rNH, rNO) and geometry information. Calculations at SCS-MP2/CBS//TPSS-D3/def2-SVP-level of theory provided potential surfaces, atomic distances and angles. In addition, scalar coupling constants were computed at TPSS-D3/IGLO-III. The combined experimental and theoretical data reveal mainly ion pair complexes providing strong hydrogen bonds with an asymmetric single well potential. The geometries of the hydrogen bonds are not affected by varying the steric or electronic properties of the aromatic imines. Hence, the strong hydrogen bond reduces the degree of freedom of the substrate and acts as a structural anchor in the (R)-TRIP imine complex.
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Affiliation(s)
- Nils Sorgenfrei
- Institut für Organische
Chemie, Universität Regensburg, D-93053 Regensburg, Germany
| | - Johnny Hioe
- Institut für Organische
Chemie, Universität Regensburg, D-93053 Regensburg, Germany
| | - Julian Greindl
- Institut für Organische
Chemie, Universität Regensburg, D-93053 Regensburg, Germany
| | - Kerstin Rothermel
- Institut für Organische
Chemie, Universität Regensburg, D-93053 Regensburg, Germany
| | - Fabio Morana
- Institut für Organische
Chemie, Universität Regensburg, D-93053 Regensburg, Germany
| | - N. Lokesh
- Institut für Organische
Chemie, Universität Regensburg, D-93053 Regensburg, Germany
| | - Ruth M. Gschwind
- Institut für Organische
Chemie, Universität Regensburg, D-93053 Regensburg, Germany
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22
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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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23
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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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24
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Kucherov S, Bureiko S, Denisov G. Anticooperativity of FHF hydrogen bonds in clusters of the type F− × (HF)n, RF × (HF)n and XF × (HF)n, R = alkyl and X = H, Br, Cl, F. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.10.066] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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25
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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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26
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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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27
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Isotope effects on chemical shifts in the study of intramolecular hydrogen bonds. Molecules 2015; 20:2405-24. [PMID: 25647577 PMCID: PMC6272349 DOI: 10.3390/molecules20022405] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 12/17/2014] [Accepted: 01/05/2015] [Indexed: 11/16/2022] Open
Abstract
The paper deals with the use of isotope effects on chemical shifts in characterizing intramolecular hydrogen bonds. Both so-called resonance-assisted (RAHB) and non-RAHB systems are treated. The importance of RAHB will be discussed. Another very important issue is the borderline between “static” and tautomeric systems. Isotope effects on chemical shifts are particularly useful in such studies. All kinds of intramolecular hydrogen bonded systems will be treated, typical hydrogen bond donors: OH, NH, SH and NH+, typical acceptors C=O, C=N, C=S C=N−. The paper will be deal with both secondary and primary isotope effects on chemical shifts. These two types of isotope effects monitor the same hydrogen bond, but from different angles.
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28
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Kwiatek A, Mielke Z. Conformational isomerism of pyridoxal. Infrared matrix isolation and theoretical studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 135:1099-1106. [PMID: 25173527 DOI: 10.1016/j.saa.2014.07.067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 07/08/2014] [Accepted: 07/18/2014] [Indexed: 06/03/2023]
Abstract
A combined matrix isolation FTIR and theoretical DFT/B3LYP/6-311++G(2p,2d) study of pyridoxal was performed. The calculations resulted in five stable PLHB conformers stabilized by intramolecular O-H⋯O bonding between phenolic OH and carbonyl C=O groups and another thirteen conformers in which OH or/and aldehyde groups are rotated by 180° around CO or/and CC bonds leading, respectively, to formation of PLO, PLA and PLOA conformers. The analysis of the spectra of the as-deposited matrix indicated that two most stable PLHB1 and PLHB2 conformers with intramolecular hydrogen bond are present in the matrix. The exposure of the PL/Ar matrix to mercury lamp radiation (λ>345 nm) induced conformational change of PLHB isomers to PLOA ones.
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Affiliation(s)
- Anna Kwiatek
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Zofia Mielke
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland.
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29
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Shenderovich IG, Lesnichin SB, Tu C, Silverman DN, Tolstoy PM, Denisov GS, Limbach HH. NMR studies of active-site properties of human carbonic anhydrase II by using (15) N-labeled 4-methylimidazole as a local probe and histidine hydrogen-bond correlations. Chemistry 2014; 21:2915-29. [PMID: 25521423 DOI: 10.1002/chem.201404083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 11/12/2014] [Indexed: 12/24/2022]
Abstract
By using a combination of liquid and solid-state NMR spectroscopy, (15) N-labeled 4-methylimidazole (4-MI) as a local probe of the environment has been studied: 1) in the polar, wet Freon CDF3 /CDF2 Cl down to 130 K, 2) in water at pH 12, and 3) in solid samples of the mutant H64A of human carbonic anhydrase II (HCA II). In the latter, the active-site His64 residue is replaced by alanine; the catalytic activity is, however, rescued by the presence of 4-MI. For the Freon solution, it is demonstrated that addition of water molecules not only catalyzes proton tautomerism but also lifts its quasidegeneracy. The possible hydrogen-bond clusters formed and the mechanism of the tautomerism are discussed. Information about the imidazole hydrogen-bond geometries is obtained by establishing a correlation between published (1) H and (15) N chemical shifts of the imidazole rings of histidines in proteins. This correlation is useful to distinguish histidines embedded in the interior of proteins and those at the surface, embedded in water. Moreover, evidence is obtained that the hydrogen-bond geometries of His64 in the active site of HCA II and of 4-MI in H64A HCA II are similar. Finally, the degeneracy of the rapid tautomerism of the neutral imidazole ring His64 reported by Shimahara et al. (J. Biol. Chem.- 2007, 282, 9646) can be explained with a wet, polar, nonaqueous active-site conformation in the inward conformation, similar to the properties of 4-MI in the Freon solution. The biological implications for the enzyme mechanism are discussed.
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Affiliation(s)
- Ilya G Shenderovich
- University of Regensburg, Universitätsstrasse 31, 93053 Regensburg (Germany).
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30
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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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31
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Dutta Banik S, Chandra A. A Hybrid QM/MM Simulation Study of Intramolecular Proton Transfer in the Pyridoxal 5′-Phosphate in the Active Site of Transaminase: Influence of Active Site Interaction on Proton Transfer. J Phys Chem B 2014; 118:11077-89. [DOI: 10.1021/jp506196m] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology, Kanpur, India 208016
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32
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Pang J, Scrutton NS, Sutcliffe MJ. Quantum Mechanics/Molecular Mechanics Studies on the Mechanism of Action of Cofactor Pyridoxal 5′-Phosphate in Ornithine 4,5-Aminomutase. Chemistry 2014; 20:11390-401. [DOI: 10.1002/chem.201402759] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Indexed: 02/02/2023]
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33
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Ortegón-Reyna D, Garcías-Morales C, Padilla-Martínez I, García-Báez E, Aríza-Castolo A, Peraza-Campos A, Martínez-Martínez F. NMR structural study of the prototropic equilibrium in solution of Schiff bases as model compounds. Molecules 2013; 19:459-81. [PMID: 24384925 PMCID: PMC6271073 DOI: 10.3390/molecules19010459] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/12/2013] [Accepted: 12/13/2013] [Indexed: 11/16/2022] Open
Abstract
An NMR titration method has been used to simultaneously measure the acid dissociation constant (pKa) and the intramolecular NHO prototropic constant ΔKNHO on a set of Schiff bases. The model compounds were synthesized from benzylamine and substituted ortho-hydroxyaldehydes, appropriately substituted with electron-donating and electron-withdrawing groups to modulate the acidity of the intramolecular NHO hydrogen bond. The structure in solution was established by 1H-, 13C- and 15N-NMR spectroscopy. The physicochemical parameters of the intramolecular NHO hydrogen bond (pKa, ΔKNHO and ΔΔG°) were obtained from 1H-NMR titration data and pH measurements. The Henderson-Hasselbalch data analysis indicated that the systems are weakly acidic, and the predominant NHO equilibrium was established using Polster-Lachmann δ-diagram analysis and Perrin model data linearization.
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Affiliation(s)
- David Ortegón-Reyna
- Laboratorio de Posgrado, Facultad de Ciencias Químicas, Universidad de Colima, Km 9 Carretera Colima-Coquimatlán, Colima 28400, Mexico.
| | - Cesar Garcías-Morales
- Laboratorio de Posgrado, Facultad de Ciencias Químicas, Universidad de Colima, Km 9 Carretera Colima-Coquimatlán, Colima 28400, Mexico.
| | - Itzia Padilla-Martínez
- Laboratorio de Posgrado, Facultad de Ciencias Químicas, Universidad de Colima, Km 9 Carretera Colima-Coquimatlán, Colima 28400, Mexico.
| | - Efren García-Báez
- Laboratorio de Posgrado, Facultad de Ciencias Químicas, Universidad de Colima, Km 9 Carretera Colima-Coquimatlán, Colima 28400, Mexico.
| | - Armando Aríza-Castolo
- Laboratorio de Posgrado, Facultad de Ciencias Químicas, Universidad de Colima, Km 9 Carretera Colima-Coquimatlán, Colima 28400, Mexico.
| | - Ana Peraza-Campos
- Laboratorio de Posgrado, Facultad de Ciencias Químicas, Universidad de Colima, Km 9 Carretera Colima-Coquimatlán, Colima 28400, Mexico.
| | - Francisco Martínez-Martínez
- Laboratorio de Posgrado, Facultad de Ciencias Químicas, Universidad de Colima, Km 9 Carretera Colima-Coquimatlán, Colima 28400, Mexico.
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34
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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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35
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Resonance assisted hydrogen bonds in open-chain and cyclic structures of malonaldehyde enol: A theoretical study. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.04.069] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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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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37
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Koeppe B, Guo J, Tolstoy PM, Denisov GS, Limbach HH. Solvent and H/D isotope effects on the proton transfer pathways in heteroconjugated hydrogen-bonded phenol-carboxylic acid anions observed by combined UV-vis and NMR spectroscopy. J Am Chem Soc 2013; 135:7553-66. [PMID: 23607931 DOI: 10.1021/ja400611x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heteroconjugated hydrogen-bonded anions A···H···X(-) of phenols (AH) and carboxylic/inorganic acids (HX) dissolved in CD2Cl2 and CDF3/CDF2Cl have been studied by combined low-temperature UV-vis and (1)H/(13)C NMR spectroscopy (UVNMR). The systems constitute small molecular models of hydrogen-bonded cofactors in proteins such as the photoactive yellow protein (PYP). Thus, the phenols studied include the PYP cofactor 4-hydroxycinnamic acid methyl thioester, and the more acidic 4-nitrophenol and 2-chloro-4-nitrophenol which mimic electronically excited cofactor states. It is shown that the (13)C chemical shifts of the phenolic residues of A···H···X(-), referenced to the corresponding values of A···H···A(-), constitute excellent probes for the average proton positions. These shifts correlate with those of the H-bonded protons, as well as with the H/D isotope effects on the (13)C chemical shifts. A combined analysis of UV-vis and NMR data was employed to elucidate the proton transfer pathways in a qualitative way. Dual absorption bands of the phenolic moiety indicate a double-well situation for the shortest OHO hydrogen bonds studied. Surprisingly, when the solvent polarity is low the carboxylates are protonated whereas the proton shifts toward the phenolic oxygens when the polarity is increased. This finding indicates that because of stronger ion-dipole interactions small anions are stabilized at high solvent polarity and large anions exhibiting delocalized charges at low solvent polarities. It also explains the large acidity difference of phenols and carboxylic acids in water, and the observation that this difference is strongly reduced in the interior of proteins when both partners form mutual hydrogen bonds.
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Affiliation(s)
- Benjamin Koeppe
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany
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38
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Galić N, Brođanac I, Kontrec D, Miljanić S. Structural investigations of aroylhydrazones derived from nicotinic acid hydrazide in solid state and in solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 107:263-270. [PMID: 23434553 DOI: 10.1016/j.saa.2013.01.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 12/21/2012] [Accepted: 01/10/2013] [Indexed: 06/01/2023]
Abstract
Structural forms of aroylhydrazones derived from nicotinic acid hydrazide have been studied in the solid state by FT-IR spectroscopy and in solution by NMR, UV-Vis and ATR spectroscopy. The studied compounds were N'-benzylidene-3-pyridinecarbohydrazide (1), N'-(2,4-dihydroxyphenylmethylidene)-3-pyridinecarbohydrazide (2), N'-(5-chloro-2-hydroxyphenylmethylidene)-3-pyridinecarbohydrazide (3), and N'-(3,5-dichloro-2-hydroxymethoxyphenylmethylidene)-3-pyridinecarbohydrazide (4). The compound 1 adopted the most stable ketoamine form (form I, -CO-NH-N=C-) in the solid state as well as in various organic solvents. In mixtures of organic solvents with water the UV-Vis and ATR spectra implied intermolecular hydrogen bonding of 1 with water molecules. The presence of both tautomeric forms I and II (form II, -COH=N-N=C-) was proposed for the solid substance and highly concentrated solutions of 2, whereas form I was detected as the predominant one in diluted solutions. For compounds 3 and 4 a coexistence of forms I and III (form III, -CO-NH-NH-C=C-CO-) was noticed in the solid state and in polar protic organic solvents. The conversion to form III was induced by increasing the water content in the solvent mixtures. This process was the most pronounced for compound 4. When exposed to daylight, an appearance of a new band was observed during time in the UV-Vis spectrum of 4 in organic solvent/water 1/1 mixtures, which implied that tautomeric interconversion was most likely followed by E/Z isomerisation.
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Affiliation(s)
- Nives Galić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia.
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39
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40
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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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41
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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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42
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Ip BCK, Shenderovich IG, Tolstoy PM, Frydel J, Denisov GS, Buntkowsky G, Limbach HH. NMR Studies of Solid Pentachlorophenol-4-Methylpyridine Complexes Exhibiting Strong OHN Hydrogen Bonds: Geometric H/D Isotope Effects and Hydrogen Bond Coupling Cause Isotopic Polymorphism. J Phys Chem A 2012; 116:11370-87. [DOI: 10.1021/jp305863n] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Brenda C. K. Ip
- Institut für Chemie und
Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin,
Germany
| | - Ilya G. Shenderovich
- Institut für Chemie und
Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin,
Germany
- St. Petersburg State University, 198504 St. Petersburg, Russian Federation
| | - Peter M. Tolstoy
- Institut für Chemie und
Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin,
Germany
- St. Petersburg State University, 198504 St. Petersburg, Russian Federation
| | - Jaroslaw Frydel
- Institut für Chemie und
Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin,
Germany
| | - Gleb S. Denisov
- St. Petersburg State University, 198504 St. Petersburg, Russian Federation
| | - Gerd Buntkowsky
- Eduard-Zintl-Institut für
Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Petersenstr. 20, D-64287 Darmstadt, Germany
| | - Hans-Heinrich Limbach
- Institut für Chemie und
Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin,
Germany
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43
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Guo J, Tolstoy PM, Koeppe B, Golubev NS, Denisov GS, Smirnov SN, Limbach HH. Hydrogen Bond Geometries and Proton Tautomerism of Homoconjugated Anions of Carboxylic Acids Studied via H/D Isotope Effects on 13C NMR Chemical Shifts. J Phys Chem A 2012; 116:11180-8. [DOI: 10.1021/jp304943h] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jing Guo
- Institut für Chemie und
Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany
| | - Peter M. Tolstoy
- Department of Chemistry, St. Petersburg State University, Universitetsky Pr.
26, 198504, St. Petersburg, Russia
| | - Benjamin Koeppe
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
| | - Nikolai S. Golubev
- Department of Physics, St. Petersburg State University, Uljanovskaja 1, 198504,
St. Petersburg, Russia
| | - Gleb S. Denisov
- Department of Physics, St. Petersburg State University, Uljanovskaja 1, 198504,
St. Petersburg, Russia
| | - Sergei N. Smirnov
- Department of Chemistry, St. Petersburg State University, Universitetsky Pr.
26, 198504, St. Petersburg, Russia
| | - Hans-Heinrich Limbach
- Institut für Chemie und
Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany
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Bharath SR, Bisht S, Harijan RK, Savithri HS, Murthy MRN. Structural and mutational studies on substrate specificity and catalysis of Salmonella typhimurium D-cysteine desulfhydrase. PLoS One 2012; 7:e36267. [PMID: 22574144 PMCID: PMC3344862 DOI: 10.1371/journal.pone.0036267] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Accepted: 04/04/2012] [Indexed: 11/19/2022] Open
Abstract
Salmonella typhimurium DCyD (StDCyD) is a fold type II pyridoxal 5′ phosphate (PLP)-dependent enzyme that catalyzes the degradation of D-Cys to H2S and pyruvate. It also efficiently degrades β-chloro-D-alanine (βCDA). D-Ser is a poor substrate while the enzyme is inactive with respect to L-Ser and 1-amino-1-carboxy cyclopropane (ACC). Here, we report the X-ray crystal structures of StDCyD and of crystals obtained in the presence of D-Cys, βCDA, ACC, D-Ser, L-Ser, D-cycloserine (DCS) and L-cycloserine (LCS) at resolutions ranging from 1.7 to 2.6 Å. The polypeptide fold of StDCyD consisting of a small domain (residues 48–161) and a large domain (residues 1–47 and 162–328) resembles other fold type II PLP dependent enzymes. The structures obtained in the presence of D-Cys and βCDA show the product, pyruvate, bound at a site 4.0–6.0 Å away from the active site. ACC forms an external aldimine complex while D- and L-Ser bind non-covalently suggesting that the reaction with these ligands is arrested at Cα proton abstraction and transimination steps, respectively. In the active site of StDCyD cocrystallized with DCS or LCS, electron density for a pyridoxamine phosphate (PMP) was observed. Crystals soaked in cocktail containing these ligands show density for PLP-cycloserine. Spectroscopic observations also suggest formation of PMP by the hydrolysis of cycloserines. Mutational studies suggest that Ser78 and Gln77 are key determinants of enzyme specificity and the phenolate of Tyr287 is responsible for Cα proton abstraction from D-Cys. Based on these studies, a probable mechanism for the degradation of D-Cys by StDCyD is proposed.
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Affiliation(s)
| | - Shveta Bisht
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Rajesh K. Harijan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | - Mathur R. N. Murthy
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- * E-mail:
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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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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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47
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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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48
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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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49
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Lin YL, Gao J, Rubinstein A, Major DT. Molecular dynamics simulations of the intramolecular proton transfer and carbanion stabilization in the pyridoxal 5'-phosphate dependent enzymes L-dopa decarboxylase and alanine racemase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1438-46. [PMID: 21600315 DOI: 10.1016/j.bbapap.2011.05.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 04/28/2011] [Accepted: 05/03/2011] [Indexed: 10/18/2022]
Abstract
Molecular dynamics simulations using a combined quantum mechanical and molecular mechanical (QM/MM) potential have been carried out to investigate the internal proton transfer equilibrium of the external aldimine species in l-dopa decarboxylase, and carbanion stabilization by the enzyme cofactor in the active site of alanine racemase. Solvent effects lower the free energy of the O-protonated PLP tautomer both in aqueous solution and in the active site, resulting a free energy difference of about -1 kcal/mol relative to the N-protonated Schiff base in the enzyme. The external aldimine provides the dominant contribution to lowering the free energy barrier for the spontaneous decarboxylation of l-dopa in water, by a remarkable 16 kcal/mol, while the enzyme l-dopa decarboxylase further lowers the barrier by 8 kcal/mol. Kinetic isotope effects were also determined using a path integral free energy perturbation theory on the primary (13)C and the secondary (2)H substitutions. In the case of alanine racemase, if the pyridine ring is unprotonated as that in the active site, there is destabilizing contribution to the formation of the α-carbanion in the gas phase, although when the pyridine ring is protonated the contribution is stabilizing. In aqueous solution and in alanine racemase, the α-carbanion is stabilized both when the pyridine ring is protonated and unprotonated. The computational studies illustrated in this article show that combined QM/MM simulations can help provide a deeper understanding of the mechanisms of PLP-dependent enzymes. This article is part of a Special Issue entitled: Pyridoxal Phosphate Enzymology.
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Affiliation(s)
- Yen-Lin Lin
- Department of Chemistry, Digital Technology Center and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
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50
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Koeppe B, Tolstoy PM, Limbach HH. Reaction pathways of proton transfer in hydrogen-bonded phenol-carboxylate complexes explored by combined UV-vis and NMR spectroscopy. J Am Chem Soc 2011; 133:7897-908. [PMID: 21534587 DOI: 10.1021/ja201113a] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Combined low-temperature NMR/UV-vis spectroscopy (UVNMR), where optical and NMR spectra are measured in the NMR spectrometer under the same conditions, has been set up and applied to the study of H-bonded anions A··H··X(-) (AH = 1-(13)C-2-chloro-4-nitrophenol, X(-) = 15 carboxylic acid anions, 5 phenolates, Cl(-), Br(-), I(-), and BF(4)(-)). In this series, H is shifted from A to X, modeling the proton-transfer pathway. The (1)H and (13)C chemical shifts and the H/D isotope effects on the latter provide information about averaged H-bond geometries. At the same time, red shifts of the π-π* UV-vis absorption bands are observed which correlate with the averaged H-bond geometries. However, on the UV-vis time scale, different tautomeric states and solvent configurations are in slow exchange. The combined data sets indicate that the proton transfer starts with a H-bond compression and a displacement of the proton toward the H-bond center, involving single-well configurations A-H···X(-). In the strong H-bond regime, coexisting tautomers A··H···X(-) and A(-)···H··X are observed by UV. Their geometries and statistical weights change continuously when the basicity of X(-) is increased. Finally, again a series of single-well structures of the type A(-)···H-X is observed. Interestingly, the UV-vis absorption bands are broadened inhomogeneously because of a distribution of H-bond geometries arising from different solvent configurations.
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Affiliation(s)
- Benjamin Koeppe
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany
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