Full relaxation matrix analysis of apparent cross-correlated relaxation rates in four-spin systems

Vögeli, Beat

doi:10.1016/j.jmr.2012.11.002

Cited by 3 publications

(3 citation statements)

References 38 publications

(73 reference statements)

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“…Corrections to the apparent CCR rates were calculated with a full matrix analysis as outlined in reference .…”

Section: Methodsmentioning

confidence: 99%

“…2) Non-negligible corrections to the CCRs have been calculated from a full relaxation-matrix analysis. 47 3) The orientations of the H N -N and H α -C α bond vectors that have been used, were previously determined to an accuracy of ca. 3 degrees from RDCs measured under multiple alignment conditions.…”

Section: Introductionmentioning

confidence: 99%

“…(1) All CCR rates were measured with at least two methods that are as different as possible in order to obtain insight into systematic errors in addition to random errors inherent to each method. (2) Non-negligible corrections to the CCRs have been calculated from a full relaxation-matrix analysis . (3) The orientations of the H N –N and H α –C α bond vectors that have been used were previously determined to an accuracy of ca.…”

Section: Introductionmentioning

confidence: 99%

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Direct Investigation of Slow Correlated Dynamics in Proteins via Dipolar Interactions

2016

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The synchronization of native state motions as they transition between microstates influences catalysis kinetics, mediates allosteric interactions and reduces the conformational entropy of proteins. However, it has proven difficult to describe native microstates because they are usually minimally frustrated and may interconvert on the μs-ms time scale. Direct observation of concerted equilibrium fluctuations would therefore be an important tool for describing protein native states. Here we propose a strategy that relates NMR cross-correlated relaxation (CCR) rates between dipolar interactions to residual dipolar couplings (RDCs) of individual consecutive HN–N and Hα–Cα bonds, which act as a proxy for the peptide planes and the side chains respectively. Using Xplor-NIH ensemble structure calculations restrained with the RDC and CCR data we observe collective motions on time scales slower than nanoseconds in the backbone for GB3. To directly access the correlations from CCR we develop a structure-free data analysis. The resulting dynamic correlation map is consistent with the ensemble-restrained simulations and reveals a complex network. In general we find that the bond motions are on average slightly correlated, and that the local environment dominates many observations. Despite this, some patterns are typical over entire secondary structure elements. In the β-sheet, nearly all bonds are weakly correlated and there is an approximately binary alternation in correlation intensity corresponding to the solvent exposure/shielding alternation of the side chains. For α-helices there is also a weak correlation in the HN-N bonds and the degree of correlation involving Hα-Cα bonds is directly affected by side-chain fluctuations, while loops show complex and non-uniform behavior.

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“…Corrections to the apparent CCR rates were calculated with a full matrix analysis as outlined in reference .…”

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Direct Investigation of Slow Correlated Dynamics in Proteins via Dipolar Interactions

2016

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Distance‐independent Cross‐correlated Relaxation and Isotropic Chemical Shift Modulation in Protein Dynamics Studies

Vögeli

Vugmeyster

2018

ChemPhysChem

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Cross-correlated relaxation (CCR) in multiple-quantum coherences differs from other relaxation phenomena in its theoretical ability to be mediated across an infinite distance. The two interfering relaxation mechanisms may be dipolar interactions, chemical shift anisotropies, chemical shift modulations or quadrupolar interactions. These properties make multiple-quantum CCR an attractive probe for structure and dynamics of biomacromolecules not accessible from other measurements. Here, we review the use of multiple-quantum CCR measurements in dynamics studies of proteins. We compile a list of all experiments proposed for CCR rate measurements, provide an overview of the theory with a focus on protein dynamics, and present applications to various protein systems.

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Cross-correlated relaxation rates between protein backbone H–X dipolar interactions

Vögeli

2017

J Biomol NMR

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Full relaxation matrix analysis of apparent cross-correlated relaxation rates in four-spin systems

Cited by 3 publications

References 38 publications

Direct Investigation of Slow Correlated Dynamics in Proteins via Dipolar Interactions

Direct Investigation of Slow Correlated Dynamics in Proteins via Dipolar Interactions

Distance‐independent Cross‐correlated Relaxation and Isotropic Chemical Shift Modulation in Protein Dynamics Studies

Cross-correlated relaxation rates between protein backbone H–X dipolar interactions

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