In the case of soluble proteins, chemical shift mapping is used to identify the intermolecular interfaces when the NOE-based calculations of spatial structure of the molecular assembly are impossible or impracticable. However, the reliability of the membrane protein interface mapping based on chemical shifts or other relevant parameters was never assessed. In the present work, we investigate the predictive power of various NMR parameters that can be used for mapping of helixâ??helix interfaces in dimeric TM domains. These parameters are studied on a dataset containing three structures of helical dimers obtained for two different proteins in various membrane mimetics. We conclude that the amide chemical shifts have very little predictive value, while the methyl chemical shifts could be used to predict interfaces, though with great care. We suggest an approach based on conversion of the carbon NMR relaxation parameters of methyl groups into parameters of motion, and one of such values, the characteristic time of methyl rotation, appears to be a reliable sensor of interhelix contacts in transmembrane domains. The carbon NMR relaxation parameters of methyl groups can be measured accurately and with high sensitivity and resolution, making the proposed parameter a useful tool for investigation of protein-protein interfaces even in large membrane proteins. An approach to build the models of transmembrane dimers based on perturbations of methyl parameters and TMDOCK software is suggested.
Dynamics of Methyl Groups in Membrane Proteins Studied by Deterium Solid State NMR Relaxation
Dynamics of Methyl Groups in Membrane Proteins Studied by Deterium Solid State NMR Relaxation
Publication date: 16 February 2016
Source:Biophysical Journal, Volume 110, Issue 3, Supplement 1</br>
Author(s): Xiaolin Xu, Andrey V. Struts, Aswini Kumar Giri, Trivikram R. Molugu, Charitha Guruge, Samira Faylough, Carolina L. Nascimento, Nasri Nesnas, Victor J. Hruby, Michael F. Brown</br>
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02-17-2016 07:50 PM
[NMR paper] Methyl groups as NMR probes for biomolecular interactions.
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Authors: Wiesner S, Sprangers R
Abstract
Intermolecular interactions are indispensible for biological function. Here we discuss how novel NMR techniques can provide unique insights into the assembly, dynamics and regulation of biomolecular complexes. We focus on applications that exploit the methyl TROSY effect and show that methodological advances...
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09-26-2015 07:56 PM
[NMR paper] Recent Progresses in Studying Helix-helix Interactions in Proteins by Incorporating the Wenxiang Diagram into the NMR Spectroscopy.
Recent Progresses in Studying Helix-helix Interactions in Proteins by Incorporating the Wenxiang Diagram into the NMR Spectroscopy.
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Curr Top Med Chem. 2015 Aug 18;
Authors: Zhou GP, Chen D, Liao S, Sun L, Huang RB
Abstract
All residues in an alpha helix can be characterized and dispositioned on a 2D the wenxiang diagram, which possesses the following features: (1) the relative...
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08-20-2015 07:36 PM
[NMR paper] Origin of Abrupt Rise in Deuteron NMR Longitudinal Relaxation Times of Protein Methyl Groups Below 90 K.
Origin of Abrupt Rise in Deuteron NMR Longitudinal Relaxation Times of Protein Methyl Groups Below 90 K.
Origin of Abrupt Rise in Deuteron NMR Longitudinal Relaxation Times of Protein Methyl Groups Below 90 K.
J Phys Chem B. 2013 Apr 29;
Authors: Vugmeyster L, Ostrovsky D, Lipton AS
Abstract
In order to examine the origin of the abrupt change in the temperature dependence of 2H NMR longitudinal relaxation times observed previously for methyl groups of L69 in the hydrophobic core of villin headpiece protein at around 90 K (Vugmeyster et...
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05-01-2013 11:46 AM
Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methylâ??methyl nuclear overhauser enhancement spectroscopy
Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methylâ??methyl nuclear overhauser enhancement spectroscopy
Abstract Methyl-transverse relaxation optimized spectroscopy is rapidly becoming the preferred NMR technique for probing structure and dynamics of very large proteins up to ~1 MDa in molecular size. Data interpretation, however, necessitates assignment of methyl groups which still presents a very challenging and time-consuming process. Here we demonstrate that, in combination with a known 3D structure, paramagnetic...
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09-26-2011 06:42 AM
Selective 1H-13C NMR spectroscopy of methyl groups in residually protonated samples of large proteins
Selective 1H-13C NMR spectroscopy of methyl groups in residually protonated samples of large proteins
Abstract Methyl 13CHD2 isotopomers of all methyl-containing amino-acids can be observed in residually protonated samples of large proteins obtained from -glucose/D2O-based bacterial media, with sensitivity sufficient for a number of NMR applications. Selective detection of some subsets of methyl groups (Alaβ, Thrγ2) is possible using simple â??out-and-backâ?? NMR methodology. Such selective methyl-detected â??out-and-backâ?? NMR experiments allow complete assignments of threonine γ2...
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01-09-2011 12:46 PM
[NMR paper] Methyl groups as probes for proteins and complexes in in-cell NMR experiments.
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Authors: Serber Z, Straub W, Corsini L, Nomura AM, Shimba N, Craik CS, Ortiz de Montellano P, Dötsch V
Studying protein components of large intracellular complexes by in-cell NMR has so far been impossible because the backbone resonances are unobservable due to their slow tumbling rates. We describe a methodology that overcomes...
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11-24-2010 09:51 PM
[NMR paper] Cross-correlated relaxation enhanced 1H[bond]13C NMR spectroscopy of methyl groups in
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J Am Chem Soc. 2003 Aug 27;125(34):10420-8
Authors: Tugarinov V, Hwang PM, Ollerenshaw JE, Kay LE
A comparison of HSQC and HMQC pulse schemes for recording (1)H(13)C correlation maps of protonated methyl groups in highly deuterated proteins is presented....
NMR relaxation parameters of methyl groups as a tool to map the interfaces of helixâ??helix interactions in membrane proteins
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