An Investigation of Weak CH···O Hydrogen Bonds in Maltose Anomers by a Combination of Calculation and Experimental Solid-State NMR Spectroscopy

Yates, Jonathan R.; Pham, Tran N.; Pickard, Chris J.; Mauri, Francesco; Amado, Ana M.; Gil, Ana M.; Brown, Steven P.

doi:10.1021/ja051019a

Cited by 191 publications

(243 citation statements)

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“…1) (23, 66 -69); thus, we sought to verify our experimental chemical shift change using quantum chemistry calculations. Although this combination of techniques has been used to identify CH⅐⅐⅐O hydrogen bonds in small organic molecules (37,70,71) and in computational biology (68), it has, to our knowledge, not yet been applied experimentally in biological macromolecules. Using this combination of techniques, we reasoned that it should be possible to solve for the hydrogen positions and, thus hydrogen bonding patterns, of the AdoMet methyl group within the SET7/9 active site.…”

Section: Resultsmentioning

confidence: 99%

“…Current methods for identifying are difficult to employ for many proteins, including SET7/9. However, NMR spectroscopy holds promise in identifying CH⅐⅐⅐O hydrogen bonds in proteins and other macromolecules via 1 H chemical shift (23,36,37). Recent structural and functional studies have suggested that CH⅐⅐⅐O hydrogen bonds play pivotal roles in substrate binding and catalysis in SET domain KMTs (6,38,39).…”

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Direct Evidence for Methyl Group Coordination by Carbon-Oxygen Hydrogen Bonds in the Lysine Methyltransferase SET7/9

Horowitz¹,

Yesselman²,

Al‐Hashimi

et al. 2011

Journal of Biological Chemistry

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SET domain lysine methyltransferases (KMTs) are S-adenosylmethionine (AdoMet)-dependent enzymes that catalyze the site-specific methylation of lysyl residues in histone and nonhistone proteins. Based on crystallographic and cofactor binding studies, carbon-oxygen (CH⅐⅐⅐O) 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 CH⅐⅐⅐O hydrogen bonding. These findings represent direct, quantitative evidence of CH⅐⅐⅐O 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.Post-translational modifications in proteins are now well recognized as important players in many biological processes. Among these modifications, site-specific lysine methylation by SET domain KMTs 3 is known to be critical to a diverse set of processes within the nucleus, including gene expression, cell cycle progression, and DNA damage response (1, 2). In particular, the human KMT SET7/9 has been shown to methylate lysine residues on many histone and non-histone proteins and is now considered to be important in many cellular pathways (3). Furthermore, SET7/9 has emerged as an archetype for the specificity and catalytic mechanism of the SET domain family due to multiple high resolution crystal structures, NMR analyses, and computational studies on its structure and function (4 -13). Despite these studies, many aspects regarding its methyl transfer reaction mechanism remain unclear, including the possibility that unconventional CH⅐⅐⅐O hydrogen bonds participate in catalysis (6).CH⅐⅐⅐O hydrogen bonding has been recognized as an important interaction in proteins and other biological macromolecules dating back 40 years (14 -17). For example, it has been estimated that 17% of the energy percentage at protein-protein surfaces is due to CH⅐⅐⅐O hydrogen bonding, and at some protein surfaces, that percentage is as high as 40 -50% (18). These hydrogen bonds also have been implicated in enzyme catalysis (19 -23), stabilizing nucleic acid structure (24 -27), as well as interactions with methyl groups in small molecules (28 -32). Despite their importance, experimental characterization of CH⅐⅐⅐O hydrogen bonds in proteins remains challenging. Current methods for identifying are difficult to employ for many proteins, including SET7/9. However, NMR spectroscopy holds promise in identifying CH⅐⅐⅐O hydrogen b...

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Direct Evidence for Methyl Group Coordination by Carbon-Oxygen Hydrogen Bonds in the Lysine Methyltransferase SET7/9

Horowitz¹,

Yesselman²,

Al‐Hashimi

et al. 2011

Journal of Biological Chemistry

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“…However, it is only with the development of 1 H homonuclear decoupling schemes suitable for application under moderate to fast MAS frequencies, e.g., Frequency-Switched Lee-Goldburg (FSLG), 5 Phase-Modulated Lee-Goldburg (PMLG), 6 and DUMBO, 7 coupled with advances in RF consoles, that such experiments have started to be more widely employed. 8,9 For example, 13 C, 1 H heteronuclear correlation (HETCOR) experiments at moderate to fast MAS frequencies 10,11 have been widely applied to a variety of significant material types, such as proteins, 12,13 pharmaceuticals, 14,15 silica-supported catalytic complexes, 16,17 organic-templated microporous materials, 18 inorganic-organic hybrid materials, 19 as well as chemical problems, such as the characterisation of weak hydrogen bonding in sugars 20 and the solution of structures from powder diffraction data. 21 Heteronuclear 13 C{ 1 H} spin-echo experiments employing 1 H homonuclear decoupling during the a) Author to whom correspondence should be addressed.…”

Section: Introductionmentioning

confidence: 99%

Unexpected effects of third-order cross-terms in heteronuclear spin systems under simultaneous radio-frequency irradiation and magic-angle spinning NMR

Tatton

Frantsuzov

Brown

et al. 2012

The Journal of Chemical Physics

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(2012) 'Unexpected e ects of third-order cross-terms in heteronuclear spin systems under simultaneous radio-frequency irradiation and magic-angle spinning NMR. ', Journal of chemical physics., 136 (8). 084503.Further information on publisher's website: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-pro t purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details.

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“…The principal components of the resulting shielding tensor were obtained by diagonalizing its symmetric part. Chemical shifts are measured relative to a reference frequency with their direction opposite to the shielding, so the isotropic chemical shift was calculated from the isotropic average of the shielding tensor according to [31][32][33]. To compare with experimental data two-dimensional anisotropic-isotropic correlation spectra were simulated using SIMPSON from the calculated principal components of all 16 1 H sites using the measured B1 distribution and the experimental ν2 linewidths obtained from the 1 H ultrafast MAS spectrum.…”

Section: Computationalmentioning

confidence: 99%

1 H CSA parameters by ultrafast MAS NMR: Measurement and applications to structure refinement

Miah

Cresswell

Iuga

et al. 2017

Solid State Nuclear Magnetic Resonance

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A 1 H anisotropic-isotropic chemical shift correlation experiment which employs symmetry-based recoupling sequences to reintroduce the chemical shift anisotropy in ν1 and ultrafast MAS to resolve 1 H sites in ν2 is described. This experiment is used to measure 1 H shift parameters for L-ascorbic acid, a compound with a relatively complex hydrogen-bonding network in the solid. The 1 H CSAs of hydrogen-bonded sites with resolved isotropic shifts can be extracted directly from the recoupled lineshapes. In combination with DFT calculations, hydrogen positions in crystal structures obtained from X-ray and neutron diffraction are refined by comparison with simulations of the full two-dimensional NMR spectrum. The improved resolution afforded by the second dimension allows even unresolved hydrogen-bonded sites 1 H to be assigned and their shift parameters to be obtained.

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An Investigation of Weak CH···O Hydrogen Bonds in Maltose Anomers by a Combination of Calculation and Experimental Solid-State NMR Spectroscopy

Cited by 191 publications

References 47 publications

Direct Evidence for Methyl Group Coordination by Carbon-Oxygen Hydrogen Bonds in the Lysine Methyltransferase SET7/9

Direct Evidence for Methyl Group Coordination by Carbon-Oxygen Hydrogen Bonds in the Lysine Methyltransferase SET7/9

Unexpected effects of third-order cross-terms in heteronuclear spin systems under simultaneous radio-frequency irradiation and magic-angle spinning NMR

1 H CSA parameters by ultrafast MAS NMR: Measurement and applications to structure refinement

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