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Hansen PE. A Spectroscopic Overview of Intramolecular Hydrogen Bonds of NH…O,S,N Type. Molecules 2021; 26:2409. [PMID: 33919132 PMCID: PMC8122615 DOI: 10.3390/molecules26092409] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/12/2021] [Accepted: 04/18/2021] [Indexed: 02/06/2023] Open
Abstract
Intramolecular NH…O,S,N interactions in non-tautomeric systems are reviewed in a broad range of compounds covering a variety of NH donors and hydrogen bond acceptors. 1H chemical shifts of NH donors are good tools to study intramolecular hydrogen bonding. However in some cases they have to be corrected for ring current effects. Deuterium isotope effects on 13C and 15N chemical shifts and primary isotope effects are usually used to judge the strength of hydrogen bonds. Primary isotope effects are investigated in a new range of magnitudes. Isotope ratios of NH stretching frequencies, νNH/ND, are revisited. Hydrogen bond energies are reviewed and two-bond deuterium isotope effects on 13C chemical shifts are investigated as a possible means of estimating hydrogen bond energies.
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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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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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Jin Y, Richards NG, Waltho JP, Blackburn GM. Metal Fluorides as Analogues for Studies on Phosphoryl Transfer Enzymes. Angew Chem Int Ed Engl 2017; 56:4110-4128. [PMID: 27862756 DOI: 10.1002/anie.201606474] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Indexed: 12/27/2022]
Abstract
The 1994 structure of a transition-state analogue with AlF4- and GDP complexed to G1α, a small G protein, heralded a new field of research into the structure and mechanism of enzymes that manipulate the transfer of phosphoryl (PO3- ) groups. The number of enzyme structures in the PDB containing metal fluorides (MFx ) as ligands that imitate either a phosphoryl or a phosphate group was 357 at the end of 2016. They fall into three distinct geometrical classes: 1) Tetrahedral complexes based on BeF3- that mimic ground-state phosphates; 2) octahedral complexes, primarily based on AlF4- , which mimic "in-line" anionic transition states for phosphoryl transfer; and 3) trigonal bipyramidal complexes, represented by MgF3- and putative AlF30 moieties, which mimic the geometry of the transition state. The interpretation of these structures provides a deeper mechanistic understanding into the behavior and manipulation of phosphate monoesters in molecular biology. This Review provides a comprehensive overview of these structures, their uses, and their computational development.
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Affiliation(s)
- Yi Jin
- Department of Chemistry, University of York, York, YO10 5DD, UK
| | | | | | - G Michael Blackburn
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
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Jin Y, Richards NG, Waltho JP, Blackburn GM. Metallfluoride als Analoga für Studien an Phosphoryltransferenzymen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201606474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yi Jin
- Department of Chemistry; University of York; York YO10 5DD Großbritannien
| | - Nigel G. Richards
- School of Chemistry; Cardiff University; Cardiff CF10 3AT Großbritannien
| | | | - G. Michael Blackburn
- Department of Molecular Biology and Biotechnology; University of Sheffield; Sheffield S10 2TN Großbritannien
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Metal Fluorides: Tools for Structural and Computational Analysis of Phosphoryl Transfer Enzymes. Top Curr Chem (Cham) 2017; 375:36. [PMID: 28299727 PMCID: PMC5480424 DOI: 10.1007/s41061-017-0130-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/01/2017] [Indexed: 10/31/2022]
Abstract
The phosphoryl group, PO3-, is the dynamic structural unit in the biological chemistry of phosphorus. Its transfer from a donor to an acceptor atom, with oxygen much more prevalent than nitrogen, carbon, or sulfur, is at the core of a great majority of enzyme-catalyzed reactions involving phosphate esters, anhydrides, amidates, and phosphorothioates. The serendipitous discovery that the phosphoryl group could be labeled by "nuclear mutation," by substitution of PO3- by MgF3- or AlF4-, has underpinned the application of metal fluoride (MF x ) complexes to mimic transition states for enzymatic phosphoryl transfer reactions, with sufficient stability for experimental analysis. Protein crystallography in the solid state and 19F NMR in solution have enabled direct observation of ternary and quaternary protein complexes embracing MF x transition state models with precision. These studies have underpinned a radically new mechanistic approach to enzyme catalysis for a huge range of phosphoryl transfer processes, as varied as kinases, phosphatases, phosphomutases, and phosphohydrolases. The results, without exception, have endorsed trigonal bipyramidal geometry (tbp) for concerted, "in-line" stereochemistry of phosphoryl transfer. QM computations have established the validity of tbp MF x complexes as reliable models for true transition states, delivering similar bond lengths, coordination to essential metal ions, and virtually identical hydrogen bond networks. The emergence of protein control of reactant orbital overlap between bond-forming species within enzyme transition states is a new challenging theme for wider exploration.
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Noroozi Pesyan N, Rashidnejad H. Isotopic splitting patterns in the (13) C NMR spectra of some partially deuterated 1-aryl-2-(phenyldiazenyl)butane-1,3-dione and 4-hydroxy-3-(phenyldiazenyl)-2H-chromen-2-one: evidence for elucidation of tautomeric forms. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2016; 54:358-364. [PMID: 26776053 DOI: 10.1002/mrc.4390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 10/20/2015] [Accepted: 10/29/2015] [Indexed: 06/05/2023]
Abstract
Nuclear magnetic resonance spectra of synthesized azo dyes derived from aniline derivatives in reaction with benzoylacetone and 4-hydroxycoumarin were studied in both CDCl3 and (CD3 )2 SO (two drops of D2 O were added into solutions of dyes). All dyes showed intramolecular hydrogen bonding. Dyes derived from o-nitro aniline in the reaction with benzoylacetone, and 4-hydroxycoumarin showed bifurcated intramolecular hydrogen bonds. The solvent-substrate proton exchange of dyes derived from benzoylacetone and 4-hydroxycoumarin was examined in the presence of two drops of D2 O. Among ten dye samples, two dyes derived from benzoylacetone did not show deuteration, three dyes showed partial deuteration and five dyes showed full deuteration under similar conditions. For the partially deuterated dyes the β-isotope effect in (13) C splitting was investigated and was used for the determination of the predominant tautomeric form.
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Affiliation(s)
- Nader Noroozi Pesyan
- Faculty of Chemistry, Department of Organic Chemistry, Urmia University, 57159, Urmia, Iran
| | - Hamid Rashidnejad
- Faculty of Chemistry, Department of Organic Chemistry, Urmia University, 57159, Urmia, Iran
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Pietrzak M, Grech E, Nowicka-Scheibe J, Hansen PE. Deuterium isotope effects on 13C chemical shifts of negatively charged NH…N systems. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:683-688. [PMID: 24038402 DOI: 10.1002/mrc.4000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Revised: 06/21/2013] [Accepted: 07/22/2013] [Indexed: 06/02/2023]
Abstract
Deuterium isotope effects on (13)C chemical shifts are investigated in anions of 1,8-bis(4-toluenesulphonamido)naphthalenes together with N,N-(naphthalene-1,8-diyl)bis(2,2,2-trifluoracetamide) all with bis(1,8-dimethylamino)napthaleneH(+) as counter ion. These compounds represent both "static" and equilibrium cases. NMR assignments of the former have been revised. The NH proton is deuteriated. The isotope effects on (13)C chemical shifts are rather unusual in these strongly hydrogen bonded systems between a NH and a negatively charged nitrogen atom. The formal four-bond effects are found to be negative indicating transmission via the hydrogen bond. In addition, unusual long range effects are seen. Structures, (1)H and (13)C NMR chemical shifts and changes in nuclear shieldings upon deuteriation are calculated using density functional theory methods.
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Affiliation(s)
- Mariusz Pietrzak
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224, Warsaw, Poland
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Baxter NJ, Bowler MW, Alizadeh T, Cliff MJ, Hounslow AM, Wu B, Berkowitz DB, Williams NH, Blackburn GM, Waltho JP. Atomic details of near-transition state conformers for enzyme phosphoryl transfer revealed by MgF-3 rather than by phosphoranes. Proc Natl Acad Sci U S A 2010; 107:4555-60. [PMID: 20164409 PMCID: PMC2842025 DOI: 10.1073/pnas.0910333106] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Prior evidence supporting the direct observation of phosphorane intermediates in enzymatic phosphoryl transfer reactions was based on the interpretation of electron density corresponding to trigonal species bridging the donor and acceptor atoms. Close examination of the crystalline state of beta-phosphoglucomutase, the archetypal phosphorane intermediate-containing enzyme, reveals that the trigonal species is not PO-3 , but is MgF-3 (trifluoromagnesate). Although MgF-3 complexes are transition state analogues rather than phosphoryl group transfer reaction intermediates, the presence of fluorine nuclei in near-transition state conformations offers new opportunities to explore the nature of the interactions, in particular the independent measures of local electrostatic and hydrogen-bonding distributions using 19F NMR. Measurements on three beta-PGM-MgF-3 -sugar phosphate complexes show a remarkable relationship between NMR chemical shifts, primary isotope shifts, NOEs, cross hydrogen bond F...H-N scalar couplings, and the atomic positions determined from the high-resolution crystal structure of the beta-PGM-MgF--3 -G6P complex. The measurements provide independent validation of the structural and isoelectronic MgF--3 model of near-transition state conformations.
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Affiliation(s)
- Nicola J. Baxter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Matthew W. Bowler
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, F-38043 Grenoble, France
| | - Tooba Alizadeh
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Matthew J. Cliff
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Andrea M. Hounslow
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Bin Wu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588
| | - David B. Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588
| | - Nicholas H. Williams
- Centre for Chemical Biology, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom; and
| | - G. Michael Blackburn
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Jonathan P. Waltho
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
- Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, M1 7DN, United Kingdom
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Toledo EJ, Custodio R, Ramalho TC, Porto MEG, Magriotis ZM. Electrical field effects on dipole moment, structure and energetic of (H2O)n (2⩽n⩽15) cluster. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.08.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Sośnicki JG. Michael addition of nitroalkanes to nonactivated α,β-unsaturated δ-thiolactams: reactivity, diastereoselectivity, and comparison to α,β-unsaturated δ-lactams. Tetrahedron 2009. [DOI: 10.1016/j.tet.2008.12.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Liu A, Wang J, Lu Z, Yao L, Li Y, Yan H. Hydrogen-bond detection, configuration assignment and rotamer correction of side-chain amides in large proteins by NMR spectroscopy through protium/deuterium isotope effects. Chembiochem 2009; 9:2860-71. [PMID: 18973166 DOI: 10.1002/cbic.200800467] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The configuration and hydrogen-bonding network of side-chain amides in a 35 kDa protein were determined by measuring differential and trans-hydrogen-bond H/D isotope effects by using the isotopomer-selective (IS)-TROSY technique, which leads to a reliable recognition and correction of erroneous rotamers that are frequently found in protein structures. First, the differential two-bond isotope effects on carbonyl (13)C' shifts, which are defined as Delta(2)Delta(13)C'(ND) = (2)Delta(13)C'(ND(E))-(2)Delta(13)C'(ND(Z)), provide a reliable means for the configuration assignment for side-chain amides, because environmental effects (hydrogen bonds and charges, etc.) are greatly attenuated over the two bonds that separate the carbon and hydrogen atoms, and the isotope effects fall into a narrow range of positive values. Second and more importantly, the significant variations in the differential one-bond isotope effects on (15)N chemical shifts, which are defined as Delta(1)Delta(15)N(D) = (1)Delta(15)N(D(E))-(1)Delta(15)N(D(Z)) can be correlated with hydrogen-bonding interactions, particularly those involving charged acceptors. The differential one-bond isotope effects are additive, with major contributions from intrinsic differential conjugative interactions between the E and Z configurations, H-bonding interactions, and charge effects. Furthermore, the pattern of trans-H-bond H/D isotope effects can be mapped onto more complicated hydrogen-bonding networks that involve bifurcated hydrogen-bonds. Third, the correlations between Delta(1)Delta(15)N(D) and hydrogen-bonding interactions afford an effective means for the correction of erroneous rotamer assignments of side-chain amides. Rotamer correction by differential isotope effects is not only robust, but also simple and can be applied to large proteins.
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Affiliation(s)
- Aizhuo Liu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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Borowiak T, Dutkiewicz G, Sośnicki JG, Jagodziński TS, Hansen PE. Secondary thioamide group deformations in different surroundings: The case of intramolecular NH···N hydrogen bond – An X-ray study combined with theoretical calculations. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2008.06.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Hansen PE. Isotope effect on chemical shifts in hydrogen-bonded systems. J Labelled Comp Radiopharm 2007. [DOI: 10.1002/jlcr.1440] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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