Literature DB >> 19455282

Deuterium isotope effects on 15N backbone chemical shifts in proteins.

Jens Abildgaard1, Poul Erik Hansen, Marlon N Manalo, Andy LiWang.   

Abstract

Quantum mechanical calculations are presented that predict that one-bond deuterium isotope effects on the (15)N chemical shift of backbone amides of proteins, (1)Delta(15)N(D), are sensitive to backbone conformation and hydrogen bonding. A quantitative empirical model for (1)Delta(15)N(D) including the backbone dihedral angles, Phi and Psi, and the hydrogen bonding geometry is presented for glycine and amino acid residues with aliphatic side chains. The effect of hydrogen bonding is rationalized in part as an electric-field effect on the first derivative of the nuclear shielding with respect to N-H bond length. Another contributing factor is the effect of increased anharmonicity of the N-H stretching vibrational state upon hydrogen bonding, which results in an altered N-H/N-D equilibrium bond length ratio. The N-H stretching anharmonicity contribution falls off with the cosine of the N-H...O bond angle. For residues with uncharged side chains a very good prediction of isotope effects can be made. Thus, for proteins with known secondary structures, (1)Delta(15)N(D) can provide insights into hydrogen bonding geometries.

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Year:  2009        PMID: 19455282      PMCID: PMC2697368          DOI: 10.1007/s10858-009-9316-0

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  11 in total

Review 1.  Use of chemical shifts in macromolecular structure determination.

Authors:  D S Wishart; D A Case
Journal:  Methods Enzymol       Date:  2001       Impact factor: 1.600

2.  Quantification of H/D isotope effects on protein hydrogen-bonds by h3JNC' and 1JNC' couplings and peptide group 15N and 13C' chemical shifts.

Authors:  Victor A Jaravine; Florence Cordier; Stephan Grzesiek
Journal:  J Biomol NMR       Date:  2004-07       Impact factor: 2.835

3.  A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams. 1991.

Authors:  Daniel S Garrett; Robert Powers; Angela M Gronenborn; G Marius Clore
Journal:  J Magn Reson       Date:  2011-12       Impact factor: 2.229

4.  The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy.

Authors:  D S Wishart; B D Sykes; F M Richards
Journal:  Biochemistry       Date:  1992-02-18       Impact factor: 3.162

5.  Structure of ubiquitin refined at 1.8 A resolution.

Authors:  S Vijay-Kumar; C E Bugg; W J Cook
Journal:  J Mol Biol       Date:  1987-04-05       Impact factor: 5.469

6.  Computational and empirical trans-hydrogen bond deuterium isotope shifts suggest that N1-N3 A:U hydrogen bonds of RNA are shorter than those of A:T hydrogen bonds of DNA.

Authors:  Yong-Ick Kim; Marlon N Manalo; Lisa M Peréz; Andy LiWang
Journal:  J Biomol NMR       Date:  2006-04       Impact factor: 2.835

7.  NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

Authors:  F Delaglio; S Grzesiek; G W Vuister; G Zhu; J Pfeifer; A Bax
Journal:  J Biomol NMR       Date:  1995-11       Impact factor: 2.835

8.  Differential deuterium isotope shifts and one-bond 1H-13C scalar couplings in the conformational analysis of protein glycine residues.

Authors:  D M LeMaster; J C LaIuppa; D M Kushlan
Journal:  J Biomol NMR       Date:  1994-11       Impact factor: 2.835

9.  Hydrogen-bond detection, configuration assignment and rotamer correction of side-chain amides in large proteins by NMR spectroscopy through protium/deuterium isotope effects.

Authors:  Aizhuo Liu; Jifeng Wang; Zhenwei Lu; Lishan Yao; Yue Li; Honggao Yan
Journal:  Chembiochem       Date:  2008-11-24       Impact factor: 3.164

10.  Relationship between nuclear magnetic resonance chemical shift and protein secondary structure.

Authors:  D S Wishart; B D Sykes; F M Richards
Journal:  J Mol Biol       Date:  1991-11-20       Impact factor: 5.469

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  5 in total

1.  Partially-deuterated samples of HET-s(218-289) fibrils: assignment and deuterium isotope effect.

Authors:  Albert A Smith; Francesco Ravotti; Emilie Testori; Riccardo Cadalbert; Matthias Ernst; Anja Böckmann; Beat H Meier
Journal:  J Biomol NMR       Date:  2017-01-10       Impact factor: 2.835

2.  15N detection harnesses the slow relaxation property of nitrogen: Delivering enhanced resolution for intrinsically disordered proteins.

Authors:  Sandeep Chhabra; Patrick Fischer; Koh Takeuchi; Abhinav Dubey; Joshua J Ziarek; Andras Boeszoermenyi; Daniel Mathieu; Wolfgang Bermel; Norman E Davey; Gerhard Wagner; Haribabu Arthanari
Journal:  Proc Natl Acad Sci U S A       Date:  2018-02-05       Impact factor: 11.205

3.  Accurate measurements of the effects of deuteration at backbone amide positions on the chemical shifts of ¹⁵N, ¹³Cα, ¹³Cβ, ¹³CO and ¹Hα nuclei in proteins.

Authors:  Daoning Zhang; Vitali Tugarinov
Journal:  J Biomol NMR       Date:  2013-04-24       Impact factor: 2.835

4.  Deuterium isotope shifts for backbone ¹H, ¹⁵N and ¹³C nuclei in intrinsically disordered protein α-synuclein.

Authors:  Alexander S Maltsev; Jinfa Ying; Ad Bax
Journal:  J Biomol NMR       Date:  2012-09-08       Impact factor: 2.835

5.  The Strong β-CF3 Shielding Effect in Hexafluoroisopropanol and 100 Other Organic Solvents Revisited with 17O NMR Spectroscopy.

Authors:  Annika Bernhardt; Harald Kelm; Frederic W Patureau
Journal:  ChemCatChem       Date:  2018-02-23       Impact factor: 5.686

  5 in total

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