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Fick RJ, Horowitz S, McDole BG, Clay MC, Mehl RA, Al-Hashimi HM, Scheiner S, Trievel RC. Structural and Functional Characterization of Sulfonium Carbon-Oxygen Hydrogen Bonding in the Deoxyamino Sugar Methyltransferase TylM1. Biochemistry 2019; 58:2152-2159. [PMID: 30810306 DOI: 10.1021/acs.biochem.8b01141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The N-methyltransferase TylM1 from Streptomyces fradiae catalyzes the final step in the biosynthesis of the deoxyamino sugar mycaminose, a substituent of the antibiotic tylosin. The high-resolution crystal structure of TylM1 bound to the methyl donor S-adenosylmethionine (AdoMet) illustrates a network of carbon-oxygen (CH···O) hydrogen bonds between the substrate's sulfonium cation and residues within the active site. These interactions include hydrogen bonds between the methyl and methylene groups of the AdoMet sulfonium cation and the hydroxyl groups of Tyr14 and Ser120 in the enzyme. To examine the functions of these interactions, we generated Tyr14 to phenylalanine (Y14F) and Ser120 to alanine (S120A) mutations to selectively ablate the CH···O hydrogen bonding to AdoMet. The TylM1 S120A mutant exhibited a modest decrease in its catalytic efficiency relative to that of the wild type (WT) enzyme, whereas the Y14F mutation resulted in an approximately 30-fold decrease in catalytic efficiency. In contrast, site-specific substitution of Tyr14 by the noncanonical amino acid p-aminophenylalanine partially restored activity comparable to that of the WT enzyme. Correlatively, quantum mechanical calculations of the activation barrier energies of WT TylM1 and the Tyr14 mutants suggest that substitutions that abrogate hydrogen bonding with the AdoMet methyl group impair methyl transfer. Together, these results offer insights into roles of CH···O hydrogen bonding in modulating the catalytic efficiency of TylM1.
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Affiliation(s)
- Robert J Fick
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Scott Horowitz
- Department of Chemistry and Biochemistry, Knoebel Institute for Healthy Aging , University of Denver , Denver , Colorado 80208 , United States
| | - Brandon G McDole
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Mary C Clay
- Department of Biochemistry , Duke University , Durham , North Carolina 27710 , United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Hashim M Al-Hashimi
- Department of Biochemistry , Duke University , Durham , North Carolina 27710 , United States
| | - Steve Scheiner
- Department of Chemistry and Biochemistry , Utah State University , Logan , Utah 84322 , United States
| | - Raymond C Trievel
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
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CO, CO2 and H2 adsorption on ZnO, CeO2, and ZnO/CeO2 surfaces: DFT simulations. J Mol Model 2014; 20:2270. [DOI: 10.1007/s00894-014-2270-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 04/23/2014] [Indexed: 11/26/2022]
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Horowitz S, Yesselman JD, Al-Hashimi HM, Trievel RC. Direct evidence for methyl group coordination by carbon-oxygen hydrogen bonds in the lysine methyltransferase SET7/9. J Biol Chem 2011; 286:18658-63. [PMID: 21454678 PMCID: PMC3099682 DOI: 10.1074/jbc.m111.232876] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 03/17/2011] [Indexed: 12/27/2022] Open
Abstract
SET domain lysine methyltransferases (KMTs) are S-adenosylmethionine (AdoMet)-dependent enzymes that catalyze the site-specific methylation of lysyl residues in histone and non-histone proteins. Based on crystallographic and cofactor binding studies, carbon-oxygen (CH · · · O) hydrogen bonds have been proposed to coordinate the methyl groups of AdoMet and methyllysine within the SET domain active site. However, the presence of these hydrogen bonds has only been inferred due to the uncertainty of hydrogen atom positions in x-ray crystal structures. To experimentally resolve the positions of the methyl hydrogen atoms, we used NMR (1)H chemical shift coupled with quantum mechanics calculations to examine the interactions of the AdoMet methyl group in the active site of the human KMT SET7/9. Our results indicated that at least two of the three hydrogens in the AdoMet methyl group engage in CH · · · O hydrogen bonding. These findings represent direct, quantitative evidence of CH · · · O hydrogen bond formation in the SET domain active site and suggest a role for these interactions in catalysis. Furthermore, thermodynamic analysis of AdoMet binding indicated that these interactions are important for cofactor binding across SET domain enzymes.
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Affiliation(s)
- Scott Horowitz
- Chemistry, and Biophysics, University of Michigan, Ann Arbor, Michigan 48109
| | - Joseph D. Yesselman
- Chemistry, and Biophysics, University of Michigan, Ann Arbor, Michigan 48109
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Afonin AV, Ushakov IA, Pavlov DV, Ivanov AV, Mikhaleva AI. Study of conformations and hydrogen bonds in the configurational isomers of pyrrole-2-carbaldehyde oxime by 1H, 13C and 15N NMR spectroscopy combined with MP2 and DFT calculations and NBO analysis. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48:685-692. [PMID: 20623827 DOI: 10.1002/mrc.2650] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The (1)H, (13)C and (15)N NMR studies have shown that the E and Z isomers of pyrrole-2-carbaldehyde oxime adopt preferable conformation with the syn orientation of the oxime group with respect to the pyrrole ring. The syn conformation of E and Z isomers of pyrrole-2-carbaldehyde oxime is stabilized by the N-H...N and N-H...O intramolecular hydrogen bonds, respectively. The N-H...N hydrogen bond in the E isomer causes the high-frequency shift of the bridge proton signal by about 1 ppm and increase the (1)J(N, H) coupling by approximately 3 Hz. The bridge proton shows further deshielding and higher increase of the (1)J(N, H) coupling constant due to the strengthening of the N-H...O hydrogen bond in the Z isomer. The MP2 calculations indicate that the syn conformation of E and Z isomers is by approximately 3.5 kcal/mol energetically less favorable than the anti conformation. The calculations of (1)H shielding and (1)J(N, H) coupling in the syn and anti conformations allow the contribution to these constants from the N-H...N and N-H...O hydrogen bondings to be estimated. The NBO analysis suggests that the N-H...N hydrogen bond in the E isomer is a pure electrostatic interaction while the charge transfer from the oxygen lone pair to the antibonding orbital of the N-H bond through the N-H...O hydrogen bond occurs in the Z isomer.
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Affiliation(s)
- Andrei V Afonin
- Institute of Chemistry, Siberian Branch of the Russian Academy of Science, Favorski St 1, 664033 Irkutsk, Russia
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Cooperativity of multiple H-bonds in influencing structural and spectroscopic features of the peptide unit of proteins. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2009.10.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Scheiner S. Identification of spectroscopic patterns of CH...O H-bonds in proteins. J Phys Chem B 2009; 113:10421-7. [PMID: 19575539 DOI: 10.1021/jp9035138] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Ab initio calculations are used to identify characteristics of vibrational and NMR spectra that signal the involvement of a protein backbone in a CH...O H-bond and that distinguish this sort of interaction from other H-bonds in which a protein might participate. Glycine and alanine dipeptides, in both their C7 and C5 minimum-energy structures, are paired with formamide in a number of different H-bonding arrangements. The CH...O H-bond is characterized by a small contraction of the C-H bond length, along with a blue shift in its stretching frequency, accompanied by an intensification of this vibrational band. In the context of NMR spectra, the bridging CH proton's chemical shift is moved downfield by 1-2 ppm. The aforementioned features are not produced by other H-bonds in which the protein backbone might participate, such as NH proton donation or accepting a proton via the peptide C=O.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322-0300, USA.
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Scheiner S, Kar T. Spectroscopic and Structural Signature of the CH−O Hydrogen Bond. J Phys Chem A 2008; 112:11854-60. [DOI: 10.1021/jp806984g] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322-0300
| | - Tapas Kar
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322-0300
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Kongsted J, Aidas K, Mikkelsen KV, Sauer SPA. On the Accuracy of Density Functional Theory to Predict Shifts in Nuclear Magnetic Resonance Shielding Constants due to Hydrogen Bonding. J Chem Theory Comput 2008; 4:267-77. [DOI: 10.1021/ct700285j] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jacob Kongsted
- Department of Theoretical Chemistry, Chemical Center, University of Lund, P.O. Box 124, S-221 00 Lund, Sweden
| | - Kestutis Aidas
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Kurt V. Mikkelsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Stephan P. A. Sauer
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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Afonin AV, Ushakov IA, Sobenina LN, Stepanova ZV, Petrova OV, Trofimov BA. Different types of hydrogen bonds in 2-substituted pyrroles and 1-vinyl pyrroles as monitored by (1)H, (13)C and (15)N NMR spectroscopy and ab initio calculations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2006; 44:59-65. [PMID: 16259054 DOI: 10.1002/mrc.1727] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
According to the (1)H, (13)C and (15)N NMR spectroscopic data and ab initio calculations, the strong N--H...O intramolecular hydrogen bond in the Z-isomers of 2-(2-acylethenyl)pyrroles causes the decrease in the absolute size of the (1)J(N,H) coupling constant by 2 Hz in CDCl(3) and by 4.5 Hz in DMSO-d(6), the deshielding of the proton and nitrogen by 5-6 and 15 ppm, respectively, and the lengthening of the N--H link by 0.025 A. The N--H...N intramolecular hydrogen bond in the 2(2'-pyridyl)pyrrole leads to the increase of the (1)J(N,H) coupling constant by 3 Hz, the deshielding of the proton by 1.5 ppm and the lengthening of the N--H link by 0.004 A. The C--H...N intramolecular hydrogen bond in the 1-vinyl-2-(2'-pyridyl)-pyrrole results in the increase of the (1)J(C,H) coupling constant by 5 Hz, the deshielding of the proton by 1 ppm and the shortening of the C--H link by 0.003 A. Different behavior of the coupling constants and length of the covalent links under the hydrogen bond influence originate from the different nature of the hydrogen bonding (predominantly covalent or electrostatic), which depends in turn on the geometry of the hydrogen bridge. The Fermi-contact mechanism only is responsible for the increase of the coupling constant in the case of the predominantly electrostatic hydrogen bonding, whereas both Fermi-contact and paramagnetic spin-orbital mechanisms bring about the decrease of coupling constant in the case of the predominantly covalent hydrogen bonding.
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Affiliation(s)
- Andrei V Afonin
- Institute of Chemistry, Favorsky St. 1, 664033 Irkutsk, Russia.
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Affiliation(s)
- Tapas Kar
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300
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Electronic Mechanisms of Intra and Intermolecular J Couplings in Systems with C-H···O Interactions. Int J Mol Sci 2003. [DOI: 10.3390/i4040203] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Vorobyov I, Yappert MC, DuPré DB. Hydrogen Bonding in Monomers and Dimers of 2-Aminoethanol. J Phys Chem A 2002. [DOI: 10.1021/jp013211e] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Igor Vorobyov
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - M. Cecilia Yappert
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - Donald B. DuPré
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
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Abstract
Although the peptide C(alpha)H group has historically not been thought to form hydrogen bonds within proteins, ab initio quantum calculations show it to be a potent proton donor. Its binding energy to a water molecule lies in the range between 1.9 and 2.5 kcal/mol for nonpolar and polar amino acids; the hydrogen bond (H-bond) involving the charged lysine residue is even stronger than a conventional OH..O interaction. The preferred H-bond lengths are quite uniform, about 3.32 A. Formation of each interaction results in a downfield shift of the bridging hydrogen's chemical shift and a blue shift in the C(alpha)H stretching frequency, potential diagnostics of the presence of such an H-bond within a protein.
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Affiliation(s)
- S Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan 84322-0300, USA.
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