1
|
Masand VH, Al-Hussain S, Alzahrani AY, Al-Mutairi AA, Sultan Alqahtani A, Samad A, Alafeefy AM, Jawarkar RD, Zaki MEA. Unveiling dynamics of nitrogen content and selected nitrogen heterocycles in thrombin inhibitors: a ceteris paribus approach. Expert Opin Drug Discov 2024; 19:991-1009. [PMID: 38898679 DOI: 10.1080/17460441.2024.2368743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/12/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Despite the progress in comprehending molecular design principles and biochemical processes associated with thrombin inhibition, there is a crucial need to optimize efforts and curtail the recurrence of synthesis-testing cycles. Nitrogen and N-heterocycles are key features of many anti-thrombin drugs. Hence, a pragmatic analysis of nitrogen and N-heterocycles in thrombin inhibitors is important throughout the drug discovery pipeline. In the present work, the authors present an analysis with a specific focus on understanding the occurrence and distribution of nitrogen and selected N-heterocycles in the realm of thrombin inhibitors. RESEARCH DESIGN AND METHODS A dataset comprising 4359 thrombin inhibitors is used to scrutinize various categories of nitrogen atoms such as ring, non-ring, aromatic, and non-aromatic. In addition, selected aromatic and aliphatic N-heterocycles have been analyzed. RESULTS The analysis indicates that ~62% of thrombin inhibitors possess five or fewer nitrogen atoms. Substituted N-heterocycles have a high occurrence, like pyrrolidine (23.24%), pyridine (20.56%), piperidine (16.10%), thiazole (9.61%), imidazole (7.36%), etc. in thrombin inhibitors. CONCLUSIONS The majority of active thrombin inhibitors contain nitrogen atoms close to 5 and a combination of N-heterocycles like pyrrolidine, pyridine, piperidine, etc. This analysis provides crucial insights to optimize the transformation of lead compounds into potential anti-thrombin inhibitors.
Collapse
Affiliation(s)
- Vijay H Masand
- Department of Chemistry, Vidya Bharati Mahavidyalaya, Amravati, India
| | - Sami Al-Hussain
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Abdullah Y Alzahrani
- Department of Chemistry, Faculty of Science and Arts, King Khalid University, Mohail Asser, Saudi Arabia
| | - Aamal A Al-Mutairi
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Arwa Sultan Alqahtani
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Abdul Samad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tishk International University, Erbil, Iraq
| | - Ahmed M Alafeefy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Universiti Teknologi MARA [UiTM], Bandar Puncak Alam, Selangor, Malaysia
| | - Rahul D Jawarkar
- Department of Medicinal Chemistry and Drug Discovery, Dr Rajendra Gode Institute of Pharmacy, Amravati, India
| | - Magdi E A Zaki
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| |
Collapse
|
2
|
Rastogi S, Chandra A. Free Energy Landscapes of the Tautomeric Interconversion of Pyridoxal 5'-Phosphate Aldimines at the Active Site of Ornithine Decarboxylase in Aqueous Media. J Phys Chem B 2023; 127:8139-8149. [PMID: 37721415 DOI: 10.1021/acs.jpcb.3c04142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
The pyridoxal 5'-phosphate (PLP) acts as a coenzyme for a large number of biochemical reactions. It exists in mainly two bound forms at the active site of the concerned enzyme: the internal aldimine, in which the PLP is bound with the ϵ-amino group of lysine at the active site, and the external aldimine, where the PLP is bound to the substrate amino acid. Both the internal and external aldimines have Schiff base linkage (N-H-O) and can exist in two tautomeric structures of ketoenamine and enolimine forms. In this work, we have investigated the free energy landscape for the tautomeric proton transfer in the internal and external aldimines at the active site of the ornithine decarboxylase enzyme in an aqueous medium. We performed hybrid quantum-classical metadynamics and force field-based molecular dynamics simulations, which revealed that the ketoenamine tautomer is more stable than the enolimine form. The QM/MM metadynamics calculations show that the free energy difference between the ketoenamine and enolimine forms for the internal aldimine is 3.9 kcal/mol, and it is found to be 5.8 kcal/mol for the external aldimine, with the ketoenamine form being more stable in both cases. The results are further supported by calculations of the binding free energies from classical simulations and static quantum chemical calculations in different environments. We have also analyzed the configurational structure of the microenvironment at the active site in order to have better insights into the interactions of the active site residues with the PLP in its two tautomeric forms.
Collapse
Affiliation(s)
- Shreya Rastogi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Karimi P, Sanchooli M. Tuning the resonance-assisted hydrogen bond (RAHB) of malonaldehyde using π-conjugated substituents and presentation of its energy decomposition. J Mol Graph Model 2022; 112:108142. [DOI: 10.1016/j.jmgm.2022.108142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 10/19/2022]
|
5
|
Mueser TC, Drago V, Kovalevsky A, Dajnowicz S. Pyridoxal 5'-phosphate dependent reactions: Analyzing the mechanism of aspartate aminotransferase. Methods Enzymol 2020; 634:333-359. [PMID: 32093839 DOI: 10.1016/bs.mie.2020.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzyme catalysis is the primary activity in energy and information metabolism and enzyme cofactors are key to the catalytic ability of most enzymes. Pyridoxal 5'-phosphate (PLP) cofactor, derived from Vitamin B6, is widely distributed in nature and has significant latitude in catalytic diversity. X-ray crystallography has revealed the structures of diverse PLP dependent enzymes from multiple families. But these structures are incomplete, lacking the positions of protons essential for understanding enzymatic mechanisms. Here, we review the diversity of PLP and discuss the use of neutron crystallography and joint X-ray/neutron refinement of Fold Type I aspartate aminotransferase to visualize the positions of protons in both the internal and external aldimine forms. Strategies used to prepare extremely large crystals required for neutron diffraction and the approach to data refinement including the PLP cofactor are discussed. The observed positions of protons, including one located in a previously unknown low-barrier hydrogen bond, have been used to create more accurate models for computational analysis. The results revealed a new mechanism for the transaminase reaction where hyperconjugation is key to reducing the energy barrier which finally provides a clear explanation of the Dunathan alignment.
Collapse
Affiliation(s)
- Timothy C Mueser
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH, United States.
| | - Victoria Drago
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH, United States
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Steven Dajnowicz
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH, United States; Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| |
Collapse
|
6
|
Intramolecular Hydrogen Bonds in Normal and Sterically Compressed o-Hydroxy Aromatic Aldehydes. Isotope Effects on Chemical Shifts and Hydrogen Bond Strength. Molecules 2019; 24:molecules24244533. [PMID: 31835750 PMCID: PMC6943505 DOI: 10.3390/molecules24244533] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/24/2019] [Accepted: 12/03/2019] [Indexed: 11/17/2022] Open
Abstract
A number of o-hydroxy aromatic aldehydes have been synthesized to illustrate the effect of steric compression and O···O distances on the intramolecular hydrogen bond and the hydrogen bond energies. Hydrogen bond energies have been calculated using the 'hb and out' method using either the MP2 method or the B3LYP functional with the basis set 6-311++G(d,p). However, several compounds cannot be treated this way. Hydrogen bond energies are also determined using electron densities at bond critical points and these results are in good agreement with the results of the 'hb and out' model. Two-bond deuterium isotope effects on 13C chemical shifts are suggested as an experimental way to obtain information on hydrogen bond energies as they easily can be measured. Isotope effects on aldehyde proton chemical shifts have also been measured. The former show very good correlation with the hydrogen bond energies and the latter are related to short O···O distances. Short O···O distances can be obtained as the result of short C=C bond lengths, conjugative effects, and steric compression of the aldehyde group. Short O···O distances are in general related to high hydrogen bond energies in these intramolecularly hydrogen-bonded systems of resonance assisted hydrogen bond (RAHB) type.
Collapse
|
7
|
Synthesis of [ 13C₃]-B6 Vitamers Labelled at Three Consecutive Positions Starting from [ 13C₃]-Propionic Acid. MOLECULES (BASEL, SWITZERLAND) 2018; 23:molecules23092117. [PMID: 30142892 PMCID: PMC6225105 DOI: 10.3390/molecules23092117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 08/16/2018] [Accepted: 08/18/2018] [Indexed: 12/31/2022]
Abstract
[13C3]-labelled vitamers (PN, PL and PM) of the B6 group were prepared starting from [13C3]-propionic acid. [13C3]-PN was synthesized in ten linear steps with an overall yield of 17%. Hereby, higher alkyl homologues of involved esters showed a positive impact on the reaction outcome of the intermediates in the chosen synthetic route. Oxidation of [13C3]-PN to [13C3]-PL was undertaken using potassium permanganate and methylamine followed by acid hydrolysis of the imine derivative. [13C3]-PM could be prepared from the oxime derivative of [13C3]-PN by hydrogenation with palladium.
Collapse
|
8
|
Direct visualization of critical hydrogen atoms in a pyridoxal 5'-phosphate enzyme. Nat Commun 2017; 8:955. [PMID: 29038582 PMCID: PMC5643538 DOI: 10.1038/s41467-017-01060-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/15/2017] [Indexed: 11/13/2022] Open
Abstract
Enzymes dependent on pyridoxal 5′-phosphate (PLP, the active form of vitamin B6) perform a myriad of diverse chemical transformations. They promote various reactions by modulating the electronic states of PLP through weak interactions in the active site. Neutron crystallography has the unique ability of visualizing the nuclear positions of hydrogen atoms in macromolecules. Here we present a room-temperature neutron structure of a homodimeric PLP-dependent enzyme, aspartate aminotransferase, which was reacted in situ with α-methylaspartate. In one monomer, the PLP remained as an internal aldimine with a deprotonated Schiff base. In the second monomer, the external aldimine formed with the substrate analog. We observe a deuterium equidistant between the Schiff base and the C-terminal carboxylate of the substrate, a position indicative of a low-barrier hydrogen bond. Quantum chemical calculations and a low-pH room-temperature X-ray structure provide insight into the physical phenomena that control the electronic modulation in aspartate aminotransferase. Pyridoxal 5’-phosphate (PLP) is a ubiquitous co factor for diverse enzymes, among them aspartate aminotransferase. Here the authors use neutron crystallography, which allows the visualization of the positions of hydrogen atoms, and computation to characterize the catalytic mechanism of the enzyme.
Collapse
|
9
|
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.
Collapse
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,
| |
Collapse
|
10
|
Gökcan H, Monard G, Sungur Konuklar FA. Molecular dynamics simulations of apo, holo, and inactivator bound GABA-at reveal the role of active site residues in PLP dependent enzymes. Proteins 2016; 84:875-91. [PMID: 26800298 DOI: 10.1002/prot.24991] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 12/24/2015] [Accepted: 12/29/2015] [Indexed: 11/08/2022]
Abstract
The pyridoxal 5-phosphate (PLP) cofactor is a significant organic molecule in medicinal chemistry. It is often found covalently bound to lysine residues in proteins to form PLP dependent enzymes. An example of this family of PLP dependent enzymes is γ-aminobutyric acid aminotransferase (GABA-AT) which is responsible for the degradation of the neurotransmitter GABA. Its inhibition or inactivation can be used to prevent the reduction of GABA concentration in brain which is the source of several neurological disorders. As a test case for PLP dependent enzymes, we have performed molecular dynamics simulations of GABA-AT to reveal the roles of the protein residues and its cofactor. Three different states have been considered: the apoenzyme, the holoenzyme, and the inactive state obtained after the suicide inhibition by vigabatrin. Different protonation states have also been considered for PLP and two key active site residues: Asp298 and His190. Together, 24 independent molecular dynamics trajectories have been simulated for a cumulative total of 2.88 µs. Our results indicate that, unlike in aqueous solution, the PLP pyridine moiety is protonated in GABA-AT. This is a consequence of a pKa shift triggered by a strong charge-charge interaction with an ionic "diad" formed by Asp298 and His190 that would help the activation of the first half-reaction of the catalytic mechanism in GABA-AT: the conversion of PLP to free pyridoxamine phosphate (PMP). In addition, our MD simulations exhibit additional strong hydrogen bond networks between the protein and PLP: the phosphate group is held in place by the donation of at least three hydrogen bonds while the carbonyl oxygen of the pyridine ring interacts with Gln301; Phe181 forms a π-π stacking interaction with the pyridine ring and works as a gate keeper with the assistance of Val300. All these interactions are hypothesized to help maintain free PMP in place inside the protein active site to facilitate the second half-reaction in GABA-AT: the regeneration of PLP-bound GABA-AT (i.e., the holoenzyme). Proteins 2016; 84:875-891. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Hatice Gökcan
- Universite De Lorraine, UMR 7565 SRSMC, Boulevard Des Aiguillettes B.P. 70239, Vandoeuvre-les-Nancy, 54506, France.,CNRS, UMR 7565 SRSMC, Boulevard Des Aiguillettes B.P. 70239, Vandoeuvre-les-Nancy, 54506, France.,Computational Science and Engineering Division, Informatics Institute, Ayazağa Campus, Maslak, Istanbul, 34496, Turkey
| | - Gerald Monard
- Universite De Lorraine, UMR 7565 SRSMC, Boulevard Des Aiguillettes B.P. 70239, Vandoeuvre-les-Nancy, 54506, France.,CNRS, UMR 7565 SRSMC, Boulevard Des Aiguillettes B.P. 70239, Vandoeuvre-les-Nancy, 54506, France
| | - F Aylin Sungur Konuklar
- Computational Science and Engineering Division, Informatics Institute, Ayazağa Campus, Maslak, Istanbul, 34496, Turkey
| |
Collapse
|
11
|
Pylaeva S, Allolio C, Koeppe B, Denisov GS, Limbach HH, Sebastiani D, Tolstoy PM. Proton transfer in a short hydrogen bond caused by solvation shell fluctuations: an ab initio MD and NMR/UV study of an (OHO)(-) bonded system. Phys Chem Chem Phys 2015; 17:4634-44. [PMID: 25586486 DOI: 10.1039/c4cp04727c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We present a joint experimental and quantum chemical study on the influence of solvent dynamics on the protonation equilibrium in a strongly hydrogen bonded phenol-acetate complex in CD2Cl2. Particular attention is given to the correlation of the proton position distribution with the internal conformation of the complex itself and with fluctuations of the aprotic solvent. Specifically, we have focused on a complex formed by 4-nitrophenol and tetraalkylammonium-acetate in CD2Cl2. Experimentally we have used combined low-temperature (1)H and (13)C NMR and UV-vis spectroscopy and showed that a very strong OHO hydrogen bond is formed with proton tautomerism (PhOH···(-)OAc and PhO(-)···HOAc forms, both strongly hydrogen bonded). Computationally, we have employed ab initio molecular dynamics (70 and 71 solvent molecules, with and without the presence of a counter-cation, respectively). We demonstrate that the relative motion of the counter-cation and the "free" carbonyl group of the acid plays the major role in the OHO bond geometry and causes proton "jumps", i.e. interconversion of PhOH···(-)OAc and PhO(-)···HOAc tautomers. Weak H-bonds between CH(CD) groups of the solvent and the oxygen atom of carbonyl stabilize the PhOH···(-)OAc type of structures. Breaking of CH···O bonds shifts the equilibrium towards PhO(-)···HOAc form.
Collapse
Affiliation(s)
- Svetlana Pylaeva
- Department of Physics, St. Petersburg State University, Ulianovskaya st. 3, 198504 St. Petersburg, Russia.
| | | | | | | | | | | | | |
Collapse
|
12
|
|
13
|
Nitoker N, Major DT. Understanding the Reaction Mechanism and Intermediate Stabilization in Mammalian Serine Racemase Using Multiscale Quantum-Classical Simulations. Biochemistry 2014; 54:516-27. [DOI: 10.1021/bi500984m] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Neta Nitoker
- Department
of Chemistry and
the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department
of Chemistry and
the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
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
| |
Collapse
|
16
|
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]
|
17
|
Shoji M, Hanaoka K, Ujiie Y, Tanaka W, Kondo D, Umeda H, Kamoshida Y, Kayanuma M, Kamiya K, Shiraishi K, Machida Y, Murakawa T, Hayashi H. A QM/MM Study of the l-Threonine Formation Reaction of Threonine Synthase: Implications into the Mechanism of the Reaction Specificity. J Am Chem Soc 2014; 136:4525-33. [DOI: 10.1021/ja408780c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mitsuo Shoji
- Center
for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba 305-8577, Japan
- Graduate
School of Pure and Applied Sciences, University of Tsukuba, Tennodai
1-1-1, Tsukuba 305-8571, Japan
| | - Kyohei Hanaoka
- Graduate
School of Pure and Applied Sciences, University of Tsukuba, Tennodai
1-1-1, Tsukuba 305-8571, Japan
| | - Yuzuru Ujiie
- Graduate
School of Pure and Applied Sciences, University of Tsukuba, Tennodai
1-1-1, Tsukuba 305-8571, Japan
| | - Wataru Tanaka
- Graduate
School of Pure and Applied Sciences, University of Tsukuba, Tennodai
1-1-1, Tsukuba 305-8571, Japan
| | - Daiki Kondo
- Graduate
School of Pure and Applied Sciences, University of Tsukuba, Tennodai
1-1-1, Tsukuba 305-8571, Japan
| | - Hiroaki Umeda
- Center
for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba 305-8577, Japan
| | - Yoshikazu Kamoshida
- Information
Technology Center, The University of Tokyo, Yayoi 2-11-16,
Bunkyo-ku, Tokyo 113-8658, Japan
| | - Megumi Kayanuma
- Graduate
School of Systems and Information Engineering, University of Tsukuba, Tennodai 1-1-1, Tsukuba 305-8573, Japan
| | - Katsumasa Kamiya
- Center
for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba 305-8577, Japan
| | - Kenji Shiraishi
- Center
for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba 305-8577, Japan
| | - Yasuhiro Machida
- Department
of Chemistry, Osaka Medical College, Takatsuki 569-8686, Japan
| | - Takeshi Murakawa
- Department
of Biochemistry, Osaka Medical College, Takatsuki 569-8686, Japan
| | - Hideyuki Hayashi
- Department
of Chemistry, Osaka Medical College, Takatsuki 569-8686, Japan
| |
Collapse
|
18
|
Zhao L, Li W, Plog A, Xu Y, Buntkowsky G, Gutmann T, Zhang K. Multi-responsive cellulose nanocrystal–rhodamine conjugates: an advanced structure study by solid-state dynamic nuclear polarization (DNP) NMR. Phys Chem Chem Phys 2014; 16:26322-9. [DOI: 10.1039/c4cp04096a] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Monitoring stimuli-responsive cellulose nanocrystals with surface-attached rhodamine spiroamide of low amount using DNP-enhanced ssNMR spectroscopy.
Collapse
Affiliation(s)
- Li Zhao
- Eduard-Zintl-Institute for Inorganic Chemistry and Physical Chemistry
- Technical University Darmstadt
- D-64287 Darmstadt, Germany
| | - Wei Li
- Ernst-Berl-Institute for Chemical Engineering and Macromolecular Science
- Technical University Darmstadt
- 64287 Darmstadt, Germany
| | - Andreas Plog
- Center of Smart Interfaces
- Technical University Darmstadt
- 64287 Darmstadt, Germany
| | - Yeping Xu
- Eduard-Zintl-Institute for Inorganic Chemistry and Physical Chemistry
- Technical University Darmstadt
- D-64287 Darmstadt, Germany
| | - Gerd Buntkowsky
- Eduard-Zintl-Institute for Inorganic Chemistry and Physical Chemistry
- Technical University Darmstadt
- D-64287 Darmstadt, Germany
| | - Torsten Gutmann
- Eduard-Zintl-Institute for Inorganic Chemistry and Physical Chemistry
- Technical University Darmstadt
- D-64287 Darmstadt, Germany
| | - Kai Zhang
- Ernst-Berl-Institute for Chemical Engineering and Macromolecular Science
- Technical University Darmstadt
- 64287 Darmstadt, Germany
| |
Collapse
|
19
|
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.
Collapse
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.
| |
Collapse
|
20
|
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
| |
Collapse
|
21
|
Toney MD. Aspartate aminotransferase: an old dog teaches new tricks. Arch Biochem Biophys 2013; 544:119-27. [PMID: 24121043 DOI: 10.1016/j.abb.2013.10.002] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 09/28/2013] [Accepted: 10/01/2013] [Indexed: 11/29/2022]
Abstract
Aspartate aminotransferase (AAT) is a prototypical pyridoxal 5'-phosphate (PLP) dependent enzyme that catalyzes the reversible interconversion of l-aspartate and α-ketoglutarate with oxalacetate and l-glutamate via a ping-pong catalytic cycle in which the pyridoxamine 5'-phosphate enzyme form is an intermediate. There is a bountiful literature on AAT that spans approximately 60years, and much fundamental mechanistic information on PLP dependent reactions has been gained from its study. Here, we review our recent work on AAT, where we again used it as a test bed for fundamental concepts in PLP chemistry. First, we discuss the role that coenzyme protonation state plays in controlling reaction specificity, then ground state destabilization via hyperconjugation in the external aldimine intermediate is examined. The third topic is light enhancement of catalysis of Cα-H deprotonation by PLP in solution and in AAT, which occurs through a triplet state of the external aldimine intermediate. Lastly, we consider recent advances in our analyses of enzyme multiple sequence alignments for the purpose of predicting mutations that are required to interconvert structurally similar but catalytically distinct enzymes, and the application of our program JANUS to the conversion of AAT into tyrosine aminotransferase.
Collapse
Affiliation(s)
- Michael D Toney
- Department of Chemistry, University of California, Davis, Davis, CA 95616, USA.
| |
Collapse
|
22
|
Mueller LJ, Dunn MF. NMR crystallography of enzyme active sites: probing chemically detailed, three-dimensional structure in tryptophan synthase. Acc Chem Res 2013; 46:2008-17. [PMID: 23537227 DOI: 10.1021/ar3003333] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
NMR crystallography--the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry--offers unprecedented insight into three-dimensional, chemically detailed structure. Initially, researchers used NMR crystallography to refine diffraction data from organic and inorganic solids. Now we are applying this technique to explore active sites in biomolecules, where it reveals chemically rich detail concerning the interactions between enzyme site residues and the reacting substrate. Researchers cannot achieve this level of detail from X-ray, NMR,or computational methodologies in isolation. For example, typical X-ray crystal structures (1.5-2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate but do not directly identify the protonation states. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but they rely on researcher-specified chemical details. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which scientists can develop models of the active site using computational chemistry; they can then distinguish these models by comparing calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at the highest possible resolution. In this Account, we detail our first steps in the development of NMR crystallography applied to enzyme catalysis. We begin with a brief introduction to NMR crystallography and then define the process that we have employed to probe the active site in the β-subunit of tryptophan synthase with unprecedented atomic-level resolution. This approach has resulted in a novel structural hypothesis for the protonation state of the quinonoid intermediate in tryptophan synthase and its surprising role in directing the next step in the catalysis of L-Trp formation.
Collapse
Affiliation(s)
- Leonard J. Mueller
- 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
| |
Collapse
|
23
|
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.
Collapse
|
24
|
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
| |
Collapse
|
25
|
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
| |
Collapse
|
26
|
Vilanova B, Gallardo JM, Caldés C, Adrover M, Ortega-Castro J, Muñoz F, Donoso J. Formation of Schiff Bases of O-Phosphorylethanolamine and O-Phospho-d,l-serine with Pyridoxal 5′-Phosphate. Experimental and Theoretical Studies. J Phys Chem A 2012; 116:1897-905. [DOI: 10.1021/jp2116033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bartolomé Vilanova
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
| | - Jessica M. Gallardo
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
| | - Catalina Caldés
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
| | - Miquel Adrover
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
| | - Joaquín Ortega-Castro
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
| | - Francisco Muñoz
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
| | - Josefa Donoso
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
| |
Collapse
|
27
|
Mukherjee T, Pessoa JC, Kumar A, Sarkar AR. Synthesis, spectroscopic characterization, insulin-enhancment, and competitive DNA binding activity of a new Zn(ii) complex with a vitamin B6 derivative—a new fluorescence probe for Zn(ii). Dalton Trans 2012; 41:5260-71. [DOI: 10.1039/c2dt12298g] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
28
|
Sparr C, Salamanova E, Schweizer WB, Senn HM, Gilmour R. Theoretical and X-ray crystallographic evidence of a fluorine-imine gauche effect: an addendum to Dunathan's stereoelectronic hypothesis. Chemistry 2011; 17:8850-7. [PMID: 21732444 DOI: 10.1002/chem.201100644] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Indexed: 11/07/2022]
Abstract
The preference of β-fluoroimines to adopt a gauche conformation has been studied by single-crystal X-ray diffraction analysis and DFT methods. Empirical and theoretical evidence for a preferential gauche arrangement around the NCCF torsion angle (φ) is presented ((E)-2-fluoro-N-(4-nitrobenzylidene)ethanamine: φ(NCCF) =70.0°). In the context of this study, the analysis of a pyridoxal-derived β-fluoroaldimine was performed, a species that is implicated in the inhibition of pyridoxal phosphate (PLP)-dependent enzymes by β-fluoroamine derivatives. The gauche preference of the internal aldimine (=NCH(2)CH(2)F) that can be rationalized by stereoelectronic arguments does not hold for the corresponding external system (N=CHCH(2)F) (E(min) when φ(NCCF) =120°). Moreover, the C-F bond is lengthened by more than 0.02 Å at φ(NCCF) =±90°, when it is exactly antiperiplanar to the conjugated imine. This activation of the C-F σ bond by an adjacent π system constitutes an addendum to Dunathan's stereoelectronic hypothesis.
Collapse
Affiliation(s)
- Christof Sparr
- Swiss Federal Institute of Technology (ETH) Zürich, Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, Zürich, Switzerland
| | | | | | | | | |
Collapse
|
29
|
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.
Collapse
Affiliation(s)
- Hans-Heinrich Limbach
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraβe 3, D-14195, Germany.
| | | | | | | | | | | | | |
Collapse
|
30
|
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.
Collapse
Affiliation(s)
- Yen-Lin Lin
- Department of Chemistry, Digital Technology Center and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | | | |
Collapse
|
31
|
Abstract
A mixed centroid path integral and free energy perturbation method (PI-FEP/UM) has been used to investigate the primary carbon and secondary hydrogen kinetic isotope effects (KIEs) in the amino acid decarboxylation of L-Dopa catalyzed by the enzyme L-Dopa decarboxylase (DDC) along with the corresponding uncatalyzed reaction in water. DDC is a pyridoxal 5'-phosphate (PLP) dependent enzyme. The cofactor undergoes an internal proton transfer between the zwitterionic protonated Schiff base configuration and the neutral hydroxyimine tautomer. It was found that the cofactor PLP makes significant contributions to lowering the decarboxylation barrier, while the enzyme active site provides further stabilization of the transition state. Interestingly, the O-protonated configuration is preferred both in the Michaelis complex and at the decarboxylation transition state. The computed kinetic isotope effects (KIE) on the carboxylate C-13 are consistent with that observed on decarboxylation reactions of other PLP-dependent enzymes, whereas the KIEs on the α carbon and secondary proton, which can easily be validated experimentally, may be used as a possible identification for the active form of the PLP tautomer in the active site of DDC.
Collapse
Affiliation(s)
- Yen-lin Lin
- Department of Chemistry, Digital Technology Center and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | | |
Collapse
|
32
|
Lai J, Niks D, Wang Y, Domratcheva T, Barends TRM, Schwarz F, Olsen RA, Elliott DW, Fatmi MQ, Chang CEA, Schlichting I, Dunn MF, Mueller LJ. X-ray and NMR Crystallography in an Enzyme Active Site: The Indoline Quinonoid Intermediate in Tryptophan Synthase. J Am Chem Soc 2010; 133:4-7. [DOI: 10.1021/ja106555c] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jinfeng Lai
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Dimitri Niks
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Yachong Wang
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Tatiana Domratcheva
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Thomas R. M. Barends
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Friedrich Schwarz
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Ryan A. Olsen
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Douglas W. Elliott
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - M. Qaiser Fatmi
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Chia-en A. Chang
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Ilme Schlichting
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Michael F. Dunn
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Leonard J. Mueller
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| |
Collapse
|
33
|
Chan-Huot M, Sharif S, Tolstoy PM, Toney MD, Limbach HH. NMR Studies of the Stability, Protonation States, and Tautomerism of 13C- and 15N-Labeled Aldimines of the Coenzyme Pyridoxal 5′-Phosphate in Water. Biochemistry 2010; 49:10818-30. [DOI: 10.1021/bi101061m] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Monique Chan-Huot
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany
| | - Shasad Sharif
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany
| | - Peter M. Tolstoy
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany
| | - Michael D. Toney
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Hans-Heinrich Limbach
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany
| |
Collapse
|
34
|
Alkorta I, Elguero J, Popelier PL. Thermodynamic and kinetic effects of Lewis acid complexation on a Schiff base present in two tautomeric forms. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1813] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
35
|
Tolstoy PM, Guo J, Koeppe B, Golubev NS, Denisov GS, Smirnov SN, Limbach HH. Geometries and Tautomerism of OHN Hydrogen Bonds in Aprotic Solution Probed by H/D Isotope Effects on 13C NMR Chemical Shifts. J Phys Chem A 2010; 114:10775-82. [DOI: 10.1021/jp1027146] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Peter M. Tolstoy
- Institute of Chemistry and Biochemistry, Free University of Berlin, Germany, and V. A. Fock Institute of Physics, St. Petersburg State University, Russia
| | - Jing Guo
- Institute of Chemistry and Biochemistry, Free University of Berlin, Germany, and V. A. Fock Institute of Physics, St. Petersburg State University, Russia
| | - Benjamin Koeppe
- Institute of Chemistry and Biochemistry, Free University of Berlin, Germany, and V. A. Fock Institute of Physics, St. Petersburg State University, Russia
| | - Nikolai S. Golubev
- Institute of Chemistry and Biochemistry, Free University of Berlin, Germany, and V. A. Fock Institute of Physics, St. Petersburg State University, Russia
| | - Gleb S. Denisov
- Institute of Chemistry and Biochemistry, Free University of Berlin, Germany, and V. A. Fock Institute of Physics, St. Petersburg State University, Russia
| | - Sergei N. Smirnov
- Institute of Chemistry and Biochemistry, Free University of Berlin, Germany, and V. A. Fock Institute of Physics, St. Petersburg State University, Russia
| | - Hans-Heinrich Limbach
- Institute of Chemistry and Biochemistry, Free University of Berlin, Germany, and V. A. Fock Institute of Physics, St. Petersburg State University, Russia
| |
Collapse
|
36
|
|
37
|
Rubinstein A, Major DT. Understanding Catalytic Specificity in Alanine Racemase from Quantum Mechanical and Molecular Mechanical Simulations of the Arginine 219 Mutant. Biochemistry 2010; 49:3957-64. [DOI: 10.1021/bi1002629] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Amir Rubinstein
- Department of Chemistry and Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| |
Collapse
|
38
|
Study of the protonation (methylation) position and tautomeric structure of thiopyrimidine derivatives by 2D 1H—15H NMR HSQC/HMBC. Experimental approach and theoretical modeling. Russ Chem Bull 2010. [DOI: 10.1007/s11172-009-0008-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
39
|
Lin YL, Gao J. Internal proton transfer in the external pyridoxal 5'-phosphate Schiff base in dopa decarboxylase. Biochemistry 2010; 49:84-94. [PMID: 19938875 DOI: 10.1021/bi901790e] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Combined quantum mechanical and molecular mechanical (QM/MM) simulations of dopa decarboxylase have been carried out to elucidate the factors that contribute to the tautomeric equilibrium of the intramolecular proton transfer in the external PLP-L-dopa Schiff base. The presence of a carboxylate anion on the alpha-carbon of the Schiff base stabilizes the zwitterions and shifts the equilibrium in favor of the oxoenamine tautomer (protonated Schiff base). Moreover, protonation of the PLP pyridine nitrogen further drives the equilibrium toward the oxoenamine direction. On the other hand, solvent effects favor the hydroxyimine configuration, although the equilibrium favors the oxoenamine isomer with a methyl group as the substituent on the imino nitrogen. In dopa decarboxylase, the hydroxyimine form of the PLP(H+)-L-dopa Schiff base is predicted to be the major isomer with a relative free energy of -1.3 kcal/mol over that of the oxoenamine isomer. Both Asp271 and Lys303 stabilize the hydroxyimine configuration through hydrogen-bonding interactions with the pyridine nitrogen of the PLP and the imino nitrogen of the Schiff base, respectively. Interestingly, Thr246 plays a double role in the intramolecular proton transfer process, in which it initially donates a hydrogen bond to the phenolate oxygen in the oxoenamine configuration and then switches to a hydrogen bond acceptor from the phenolic hydroxyl group in the hydroxyimine tautomer.
Collapse
Affiliation(s)
- Yen-lin Lin
- Department of Chemistry and Digital Technology Center, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | | |
Collapse
|
40
|
Dos A, Schimming V, Chan-Huot M, Limbach HH. Effects of hydration on the acid–base interactions and secondary structures of poly-l-lysine probed by 15N and 13C solid state NMR. Phys Chem Chem Phys 2010; 12:10235-45. [DOI: 10.1039/c002730h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
41
|
Bueno C, Pavez P, Salazar R, Encinas MV. Photophysics and photochemical studies of the vitamin B6 group and related derivatives. Photochem Photobiol 2009; 86:39-46. [PMID: 19930123 DOI: 10.1111/j.1751-1097.2009.00643.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The photophysics and photochemical properties of vitamin B6 constituents and analogs were studied as function of pH and solvent. The pK of the phenolic oxygen and the pyridine ring nitrogen depends on the electron donor-acceptor ability of the 4-substituent, and agrees with the calculated proton affinity. For all studied compounds, the fluorescence properties showed that the phenolic oxygen is 8 units more acidic in the lowest singlet excited state than in the ground state. The pyridine N-atom is slightly more basic in the excited state. At pH of biological significance, pH 6-8, pyridoxamine and 4-pyridoxic acid are the more efficient chromophores with higher fluorescence yield and longer lifetime. Spectroscopic studies showed that the tautomeric equilibrium depends on the nature of the 4-substituent. The quenching of the singlet excited state of pyridoxamine and 4-pyridoxic acid by amino acids, free or in a peptide, and DNA bases at pH 7 was studied by time-resolved fluorescence techniques. The quenching rate constants are well correlated with the redox properties of the pyridoxinic compound and amino acids, and are related to the free energy change in the electron transfer process. Guanosine and pyrimidine bases also are efficient quenchers, involving an electron transfer reaction.
Collapse
Affiliation(s)
- Claudia Bueno
- Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | | | | | | |
Collapse
|
42
|
Crugeiras J, Rios A, Riveiros E, Richard JP. Substituent effects on the thermodynamic stability of imines formed from glycine and aromatic aldehydes: implications for the catalytic activity of pyridoxal-5'-phosphate. J Am Chem Soc 2009; 131:15815-24. [PMID: 19807092 PMCID: PMC2788968 DOI: 10.1021/ja906230n] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Equilibrium constants for addition of glycine to substituted benzaldehydes to form the corresponding imines and pK(a)'s for ionization of the iminium ions were determined by (1)H NMR analysis in D(2)O. The introduction of a phenoxide anion substituent into the aromatic ring of benzaldehyde leads to a substantial increase in the pK(a) of the iminium ion from 6.3 to 10.2 for p-hydroxybenzaldehyde and to 12.1 for salicylaldehyde. An analysis of the differential effect of ortho- versus para-substitution shows that the iminium ion to salicylaldehyde is stabilized by an intramolecular hydrogen bond in aqueous solution, with an estimated energy ca. 3 kcal/mol larger than can be accounted for by a simple electrostatic interaction. A comparison of the o-O(-) substituent effect on the acidity of the iminium ions of glycine to benzaldehyde and 4-pyridine-carboxaldehyde provides evidence for the existence of an internal hydrogen bond of similar strength in pyridoxal 5'-phosphate (PLP) iminium ions in water. The effects of other ring substituents on the stability of PLP iminium ions are discussed.
Collapse
Affiliation(s)
- Juan Crugeiras
- Departamento de Química Física, Facultad de Química, Universidad de Santiago, 15782
| | - Ana Rios
- Departamento de Química Física, Facultad de Química, Universidad de Santiago, 15782
| | - Enrique Riveiros
- Departamento de Química Física, Facultad de Química, Universidad de Santiago, 15782
| | - John P. Richard
- Santiago de Compostela, Spain and Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, USA
| |
Collapse
|
43
|
Reddy TS, Rameshwar N, Bhudevi B, Reddy AR. Structure dependent prototropy in 4-hydroxy-3-formylideneamino-1-methyl/phenylquinolin-2-ones. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2009; 73:916-921. [PMID: 19477678 DOI: 10.1016/j.saa.2009.04.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Revised: 03/31/2009] [Accepted: 04/15/2009] [Indexed: 05/27/2023]
Abstract
The electronic absorption spectra of 4-hydroxy-3-formyl quinolin-2-ones and their Schiff bases were investigated in various solvents of varying polarity. The three aromatic transitions of napthalene in quinolin-2-one are shifted to longer wavelength on their transformation to anils. Electron-donating group in the anils lead to enolimine form, while electron-withdrawing group leads to an equilibrium mixture of enolimine and ketoamine forms and the Schiff base derived from alkyl amine exist in ketoamine form. The prototropic interconversion of enolimine and ketoimine forms in the anils with the electron-withdrawing substituted anils is further supported by proton NMR studies. The spectral shifts are solvent dependent. Dipolar aprotic solvents bring bathochromic shift while polar protic solvents cause blue shift in the longer wavelength absorption maxima. In the case of Schiff bases substituted by electron-donating group the bathochromic shift is directly related to the polarity of the solvents.
Collapse
Affiliation(s)
- T Sheshashena Reddy
- Department of Chemistry, University College of Science, Osmania University Campus, Osmania University, Hyderabad 500007, Andhra Pradesh, India
| | | | | | | |
Collapse
|
44
|
Dos A, Schimming V, Huot MC, Limbach HH. Acid-Induced Amino Side-Chain Interactions and Secondary Structure of Solid Poly-l-lysine Probed by 15N and 13C Solid State NMR and ab Initio Model Calculations. J Am Chem Soc 2009; 131:7641-53. [DOI: 10.1021/ja901082a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexandra Dos
- Institut für Chemie und Biochemie, Takustrasse 3, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Volkmar Schimming
- Institut für Chemie und Biochemie, Takustrasse 3, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Monique Chan Huot
- Institut für Chemie und Biochemie, Takustrasse 3, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Hans-Heinrich Limbach
- Institut für Chemie und Biochemie, Takustrasse 3, Freie Universität Berlin, D-14195 Berlin, Germany
| |
Collapse
|
45
|
Dos A, Schimming V, Tosoni S, Limbach HH. Acid−Base Interactions and Secondary Structures of Poly-l-Lysine Probed by 15N and 13C Solid State NMR and Ab initio Model Calculations. J Phys Chem B 2008; 112:15604-15. [DOI: 10.1021/jp806551u] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexandra Dos
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, and Dipartimento Chimica IFM, University of Torino, Via P. Giuria 7, 10125 Torino, Italy
| | - Volkmar Schimming
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, and Dipartimento Chimica IFM, University of Torino, Via P. Giuria 7, 10125 Torino, Italy
| | - Sergio Tosoni
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, and Dipartimento Chimica IFM, University of Torino, Via P. Giuria 7, 10125 Torino, Italy
| | - Hans-Heinrich Limbach
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, and Dipartimento Chimica IFM, University of Torino, Via P. Giuria 7, 10125 Torino, Italy
| |
Collapse
|
46
|
Perona A, Sanz D, Claramunt RM, Elguero J. NMR studies of novel Schiff bases derived from L-alpha-amino methyl esters and 3-hydroxypyridin-4-carboxaldehyde. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2008; 46:930-938. [PMID: 18618628 DOI: 10.1002/mrc.2278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Schiff bases of 3-hydroxypyridin-4-carboxaldehyde and L-alpha-amino esters as well as those derived from the structurally related amines lacking the ester function have been synthesised. In two cases a tetrahydro-1H-imidazo[4,5-c]pyridine was formed as a by-product. (1)H, (13)C, (15)N-NMR spectral data and density functional theory (DFT) calculations established the structure of all compounds.
Collapse
Affiliation(s)
- Almudena Perona
- Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias, UNED, Senda del Rey 9, E-28040 Madrid, Spain.
| | | | | | | |
Collapse
|
47
|
Rozwadowski Z, Nowak-Wydra B. Chiral recognition of Schiff bases by 15N NMR spectroscopy in the presence of a dirhodium complex. Deuterium isotope effect on 15N chemical shift of the optically active Schiff bases and their dirhodium tetracarboxylate adducts. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2008; 46:974-978. [PMID: 18666208 DOI: 10.1002/mrc.2280] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Optically active Schiff bases, derivatives of ortho-hydroxyaldehydes and their adducts with dirhodium tetracarboxylate complexes have been studied by (15)N NMR spectroscopy. The position of the equilibrium of Schiff bases, as well as their adducts, has been established on the basis of measurements of deuterium isotope effects on (15)N chemical shifts. At the equilibrium state, the formation of the adducts with dirhodium complexes shifted the proton-transfer equilibrium towards the NH-form.
Collapse
Affiliation(s)
- Z Rozwadowski
- Institute of Chemistry and Environmental Protection, Szczecin University of Technology, Al. Piastów 42, 70-065 Szczecin, Poland.
| | | |
Collapse
|
48
|
Schweitzer A, Gutmann T, Wächtler M, Breitzke H, Buchholz A, Plass W, Buntkowsky G. (51)V solid-state NMR investigations and DFT studies of model compounds for vanadium haloperoxidases. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2008; 34:52-67. [PMID: 18342494 DOI: 10.1016/j.ssnmr.2008.02.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Indexed: 05/26/2023]
Abstract
Three cis-dioxovanadium(V) complexes with similar N-salicylidenehydrazide ligands modeling hydrogen bonding interactions of vanadate relevant for vanadium haloperoxidases are studied by (51)V solid-state NMR spectroscopy. Their parameters describing the quadrupolar and chemical shift anisotropy interactions (quadrupolar coupling constant C(Q), asymmetry of the quadrupolar tensor eta(Q), isotropic chemical shift delta(iso), chemical shift anisotropy delta(sigma), asymmetry of the chemical shift tensor eta(sigma) and the Euler angles alpha, beta and gamma) are determined both experimentally and theoretically using DFT methods. A comparative study of different methods to determine the NMR parameters by numerical simulation of the spectra is presented. Detailed theoretical investigations on the DFT level using various basis sets and structural models show that by useful choice of the methodology, the calculated parameters agree to the experimental ones in a very good manner.
Collapse
Affiliation(s)
- Annika Schweitzer
- Institut für Physikalische Chemie, Friedrich-Schiller-Universität Jena, Helmholtzweg 4, D-07743 Jena, Germany
| | | | | | | | | | | | | |
Collapse
|
49
|
A catalytic mechanism that explains a low catalytic activity of serine dehydratase like-1 from human cancer cells: Crystal structure and site-directed mutagenesis studies. Biochim Biophys Acta Gen Subj 2008; 1780:809-18. [DOI: 10.1016/j.bbagen.2008.01.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 01/29/2008] [Accepted: 01/30/2008] [Indexed: 11/23/2022]
|
50
|
Kozlov AV, Semenov VE, Mikhailov AS, Aganov AV, Smith MB, Reznik VS, Latypov SK. Preferential Protonation and Methylation Site of Thiopyrimidine Derivatives in Solution: NMR Data. J Phys Chem B 2008; 112:3259-67. [DOI: 10.1021/jp710952r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Artem V. Kozlov
- Institute of Organic and Physical Chemistry, Arbuzov Str. 8, Kazan, 420088, Russian Federation, Kazan State University, Kazan, 420008, Russian Federation, and University of Connecticut, 55 North Eagleville Road, 4-60, Storrs, Connecticut 06269-3060
| | - Vyacheslav E. Semenov
- Institute of Organic and Physical Chemistry, Arbuzov Str. 8, Kazan, 420088, Russian Federation, Kazan State University, Kazan, 420008, Russian Federation, and University of Connecticut, 55 North Eagleville Road, 4-60, Storrs, Connecticut 06269-3060
| | - Anatoliy S. Mikhailov
- Institute of Organic and Physical Chemistry, Arbuzov Str. 8, Kazan, 420088, Russian Federation, Kazan State University, Kazan, 420008, Russian Federation, and University of Connecticut, 55 North Eagleville Road, 4-60, Storrs, Connecticut 06269-3060
| | - Albert V. Aganov
- Institute of Organic and Physical Chemistry, Arbuzov Str. 8, Kazan, 420088, Russian Federation, Kazan State University, Kazan, 420008, Russian Federation, and University of Connecticut, 55 North Eagleville Road, 4-60, Storrs, Connecticut 06269-3060
| | - Michael B. Smith
- Institute of Organic and Physical Chemistry, Arbuzov Str. 8, Kazan, 420088, Russian Federation, Kazan State University, Kazan, 420008, Russian Federation, and University of Connecticut, 55 North Eagleville Road, 4-60, Storrs, Connecticut 06269-3060
| | - Vladimir S. Reznik
- Institute of Organic and Physical Chemistry, Arbuzov Str. 8, Kazan, 420088, Russian Federation, Kazan State University, Kazan, 420008, Russian Federation, and University of Connecticut, 55 North Eagleville Road, 4-60, Storrs, Connecticut 06269-3060
| | - Shamil K. Latypov
- Institute of Organic and Physical Chemistry, Arbuzov Str. 8, Kazan, 420088, Russian Federation, Kazan State University, Kazan, 420008, Russian Federation, and University of Connecticut, 55 North Eagleville Road, 4-60, Storrs, Connecticut 06269-3060
| |
Collapse
|