The investigation of structural propensities of proteins is essential for understanding how they function at the molecular level. NMR, offering atomic-scale information, is often the method of choice. One of the available techniques relies on the cross-correlated relaxation (CCR) effect, whose magnitude is related to local spatial conformation. Application of these methods is difficult if the protein under investigation exhibits high mobility, because NMR observables like CCR rates and chemical shifts present themselves as mere averages of an underlying ensemble distribution. Furthermore, relaxation observables are a convolution of structural and dynamical components. Despite these challenges, it is possible to infer the underlying structural ensemble by combining information from several CCR rates with a different geometrical dependence. In this paper, we present a set of eight CCR experiments tailored for proteins of a highly dynamic nature. Analyzed together, they yield a distribution of backbone dihedral angles for each residue of the protein. The experiments were validated on the folded protein ubiquitin using PDB-deposited NMR structures for comparison. Extraordinary peak separation, achieved by evolving four different chemical shifts, allows for the application of this method to intrinsically disordered proteins in future studies.
TRACT revisited: an algebraic solution for determining overall rotational correlation times from cross-correlated relaxation rates
TRACT revisited: an algebraic solution for determining overall rotational correlation times from cross-correlated relaxation rates
Abstract
Accurate rotational correlation times ( \({\tau }_{\text{c}}\) ) are critical for quantitative analysis of fast timescale NMR dynamics. As molecular weights increase, the classic derivation of \({\tau }_{c}\) using transverse and longitudinal relaxation rates...
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09-04-2021 10:34 AM
Cross-correlated relaxation rates between protein backbone Hā??X dipolar interactions
Cross-correlated relaxation rates between protein backbone Hā??X dipolar interactions
Abstract
The relaxation interference between dipoleā??dipole interactions of two separate spin pairs carries structural and dynamics information. In particular, when compared to individual dynamic behavior of those spin pairs, such cross-correlated relaxation (CCR) rates report on the correlation between the spin pairs. We have recently mapped out correlated motion along the backbone of the protein GB3, using CCR rates among and between consecutive HNā??N and...
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03-13-2017 02:54 AM
[NMR images] Table 1. Definition of dihedral angles, the expected dihedral angle ...
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Table 1. Definition of dihedral angles, the expected dihedral angle ...
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NMR pictures
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06-18-2013 07:21 AM
[NMR paper] Anisotropy of Rotational Diffusion, Dipole-Dipole Cross-Correlated NMR Relaxation and Angles between Bond Vectors in Proteins.
Anisotropy of Rotational Diffusion, Dipole-Dipole Cross-Correlated NMR Relaxation and Angles between Bond Vectors in Proteins.
Related Articles Anisotropy of Rotational Diffusion, Dipole-Dipole Cross-Correlated NMR Relaxation and Angles between Bond Vectors in Proteins.
Chemphyschem. 2001 Sep 17;2(8-9):539-43
Authors: Deschamps M, Bodenhausen G
Abstract
Cross correlations between the fluctuations of dipolar (13) C(?) -(1) H(?) interactions yield information about the relative orientation of successive (13) C(?) -(1) H(?) bond vectors...
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05-22-2013 04:43 PM
[NMR paper] Probing Local Backbone Geometries in Intrinsically Disordered Proteins by Cross-Correlated NMR Relaxation.
Probing Local Backbone Geometries in Intrinsically Disordered Proteins by Cross-Correlated NMR Relaxation.
Probing Local Backbone Geometries in Intrinsically Disordered Proteins by Cross-Correlated NMR Relaxation.
Angew Chem Int Ed Engl. 2013 Mar 20;
Authors: Stanek J, Saxena S, Geist L, Konrat R, Ko?mi?ski W
Abstract
Ab ultra-high-resolution NMR experiment for the measurement of intraresidue (1) H(i)-(15) N(i)-(13) C'(i) dipolar-chemical shift anisotropy relaxation interference is employed to extract information about local backbone...
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03-23-2013 06:36 PM
[NMR paper] Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone ?, ? and side-chain ?(1) and ?(2) dihedral angles.
Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone ?, ? and side-chain ?(1) and ?(2) dihedral angles.
Related Articles Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone ?, ? and side-chain ?(1) and ?(2) dihedral angles.
J Chem Theory Comput. 2012 Sep 11;8(9):3257-3273
Authors: Best RB, Zhu X, Shim J, Lopes PE, Mittal J, Feig M, Mackerell AD
Abstract
While the quality of the current CHARMM22/CMAP additive force field for...
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02-03-2013 10:19 AM
Side chain: backbone projections in aromatic and ASX residues from NMR cross-correlated relaxation
Side chain: backbone projections in aromatic and ASX residues from NMR cross-correlated relaxation
Abstract The measurements of cross-correlated relaxation rates between HNā??N and CĪ²ā??CĪ³ intraresidual and sequential dipolar interactions is demonstrated in ASN, ASP and aromatic residues. The experiment can be used for deuterated samples and no additional knowledge such as Karplus parametrizations is required for the analysis. The data constitutes a new type of information since no other method relates the CĪ²ā??CĪ³ bond to HNā??N. Using this method the dominant populations of rotamer...
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01-09-2011 12:46 PM
[NMR paper] Automated NMR determination of protein backbone dihedral angles from cross-correlated
Automated NMR determination of protein backbone dihedral angles from cross-correlated spin relaxation.
Related Articles Automated NMR determination of protein backbone dihedral angles from cross-correlated spin relaxation.
J Biomol NMR. 2002 Apr;22(4):349-63
Authors: Kloiber K, Schüler W, Konrat R
The simultaneous interpretation of a suite of dipole-dipole and dipole-CSA cross-correlation rates involving the backbone nuclei 13Calpha, 1Halpha, 13CO, 15N and 1HN can be used to resolve the ambiguities associated with each individual...
A complete set of cross-correlated relaxation experiments for determining the protein backbone dihedral angles
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