Literature DB >> 17562185

Vibrational averaging of chemical shift anisotropies in model peptides.

Sishi Tang1, David A Case.   

Abstract

The effects of chemical shift anisotropy (CSA) are evident in line-shapes or side-band analysis in solid-state NMR, in the observed line positions in partially oriented samples, and in relaxation effects in liquid-state studies. In all of these cases, the effective shielding tensor is influenced by fast vibrational averaging in addition to larger-amplitude internal motions and to overall libration or rotation. Here we compute the contributions of vibrational averaging (including zero-point motions) to the CSA relaxation strengths for the nitrogen and carbonyl carbon in two simple peptide models, and for snapshots taken from a path-integral simulation of a small protein. Because the (15)N shielding tensor is determined by all the atoms of the peptide group, it is less influenced by vibrational motion than (for example) the N-H dipolar interaction, which is more sensitive to the motion of the light hydrogen atom. Computed order parameters for CSA averaging are hence much closer to unity than are N-H dipolar order parameters. This leads to a reduction by about 9% in the magnitude of the amide nitrogen CSA that is needed to fit liquid-state relaxation data. Similar considerations apply to the carbonyl carbon shielding tensor, but in this case the differences between dipolar and CSA averaging are smaller. These considerations will be important for making comparisons between CSA tensors extracted from various NMR experiments, and for comparisons to quantum chemical calculations carried out on static conformers.

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Year:  2007        PMID: 17562185     DOI: 10.1007/s10858-007-9164-8

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


  17 in total

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Authors:  V Tsui; L Zhu; T H Huang; P E Wright; D A Case
Journal:  J Biomol NMR       Date:  2000-01       Impact factor: 2.835

2.  Site-specific variations of carbonyl chemical shift anisotropies in proteins.

Authors:  Phineus R L Markwick; Michael Sattler
Journal:  J Am Chem Soc       Date:  2004-09-22       Impact factor: 15.419

3.  Chemical shift anisotropy tensors of carbonyl, nitrogen, and amide proton nuclei in proteins through cross-correlated relaxation in NMR spectroscopy.

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Journal:  J Am Chem Soc       Date:  2005-04-27       Impact factor: 15.419

4.  Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme.

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5.  An accurate and simple quantum model for liquid water.

Authors:  Francesco Paesani; Wei Zhang; David A Case; Thomas E Cheatham; Gregory A Voth
Journal:  J Chem Phys       Date:  2006-11-14       Impact factor: 3.488

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7.  Parameterization of peptide 13C carbonyl chemical shielding anisotropy in molecular dynamics simulations.

Authors:  Daniel M Jordan; K Maria Mills; Ioan Andricioaei; Akash Bhattacharya; Kim Palmo; Erik R P Zuiderweg
Journal:  Chemphyschem       Date:  2007-06-25       Impact factor: 3.102

8.  A comparison of quantum chemical models for calculating NMR shielding parameters in peptides: mixed basis set and ONIOM methods combined with a complete basis set extrapolation.

Authors:  Seongho Moon; David A Case
Journal:  J Comput Chem       Date:  2006-05       Impact factor: 3.376

9.  Characterizing semilocal motions in proteins by NMR relaxation studies.

Authors:  M W Fischer; L Zeng; A Majumdar; E R Zuiderweg
Journal:  Proc Natl Acad Sci U S A       Date:  1998-07-07       Impact factor: 11.205

10.  Limited variations in 15N CSA magnitudes and orientations in ubiquitin are revealed by joint analysis of longitudinal and transverse NMR relaxation.

Authors:  Peter Damberg; Jüri Jarvet; Astrid Gräslund
Journal:  J Am Chem Soc       Date:  2005-02-16       Impact factor: 15.419

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  11 in total

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Authors:  Benjamin J Wylie; Lindsay J Sperling; Andrew J Nieuwkoop; W Trent Franks; Eric Oldfield; Chad M Rienstra
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-03       Impact factor: 11.205

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Journal:  Biophys J       Date:  2008-09-26       Impact factor: 4.033

3.  Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes.

Authors:  Andrea Victora; Heiko M Möller; Thomas E Exner
Journal:  Nucleic Acids Res       Date:  2014-11-17       Impact factor: 16.971

4.  Calculation of chemical shift anisotropy in proteins.

Authors:  Sishi Tang; David A Case
Journal:  J Biomol NMR       Date:  2011-08-26       Impact factor: 2.835

5.  Correlated motions of C'-N and Cα-Cβ pairs in protonated and per-deuterated GB3.

Authors:  Liliya Vugmeyster; Aaron Griffin; Dmitry Ostrovsky; Shibani Bhattacharya; Parker J Nichols; C James McKnight; Beat Vögeli
Journal:  J Biomol NMR       Date:  2018-08-18       Impact factor: 2.835

6.  Effect of local sugar and base geometry on 13C and 15N magnetic shielding anisotropy in DNA nucleosides.

Authors:  Eva Brumovská; Vladimír Sychrovský; Zuzana Vokácová; Jirí Sponer; Bohdan Schneider; Lukás Trantírek
Journal:  J Biomol NMR       Date:  2008-10-14       Impact factor: 2.835

7.  Influence of the O-phosphorylation of serine, threonine and tyrosine in proteins on the amidic ¹⁵N chemical shielding anisotropy tensors.

Authors:  Jiří Emmer; Andrea Vavrinská; Vladimír Sychrovský; Ladislav Benda; Zdeněk Kříž; Jaroslav Koča; Rolf Boelens; Vladimír Sklenář; Lukáš Trantírek
Journal:  J Biomol NMR       Date:  2012-12-01       Impact factor: 2.835

8.  (15)N CSA tensors and (15)N-(1)H dipolar couplings of protein hydrophobic core residues investigated by static solid-state NMR.

Authors:  Liliya Vugmeyster; Dmitry Ostrovsky; Riqiang Fu
Journal:  J Magn Reson       Date:  2015-09-03       Impact factor: 2.229

9.  Phosphorylation-induced changes in backbone dynamics of the dematin headpiece C-terminal domain.

Authors:  Liliya Vugmeyster; C James McKnight
Journal:  J Biomol NMR       Date:  2008-11-22       Impact factor: 2.835

10.  Quantum chemical calculations of amide-15N chemical shift anisotropy tensors for a membrane-bound cytochrome-b5.

Authors:  Manoj Kumar Pandey; Ayyalusamy Ramamoorthy
Journal:  J Phys Chem B       Date:  2013-01-10       Impact factor: 2.991

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