Related ArticlesConnecting Longitudinal and Transverse Relaxation Rates in Live-Cell NMR.
J Phys Chem B. 2020 Nov 12;:
Authors: Leeb S, Yang F, Oliveberg M, Danielsson J
Abstract
In the cytosolic environment, protein crowding and Brownian motions result in numerous transient encounters. Each such encounter event increases the apparent size of the interacting molecules, leading to slower rotational tumbling. The extent of transient protein complexes formed in live cells can conveniently be quantified by an apparent viscosity, based on NMR-detected spin-relaxation measurements, that is, the longitudinal (T1) and transverse (T2) relaxation. From combined analysis of three different proteins and surface mutations thereof, we find that T2 implies significantly higher apparent viscosity than T1. At first sight, the effect on T1 and T2 seems thus nonunifiable, consistent with previous reports on other proteins. We show here that the T1 and T2 deviation is actually not a inconsistency but an expected feature of a system with fast exchange between free monomers and transient complexes. In this case, the deviation is basically reconciled by a model with fast exchange between the free-tumbling reporter protein and a transient complex with a uniform 143 kDa partner. The analysis is then taken one step further by accounting for the fact that the cytosolic content is by no means uniform but comprises a wide range of molecular sizes. Integrating over the complete size distribution of the cytosolic interaction ensemble enables us to predict both T1 and T2 from a single binding model. The result yields a bound population for each protein variant and provides a quantification of the transient interactions. We finally extend the approach to obtain a correction term for the shape of a database-derived mass distribution of the interactome in the mammalian cytosol, in good accord with the existing data of the cellular composition.
PMID: 33179918 [PubMed - as supplied by publisher]
[NMR paper] Heteronuclear Transverse and Longitudinal Relaxation in AX4 Spin Systems: Application to 15N Relaxations in 15NH4+
Heteronuclear Transverse and Longitudinal Relaxation in AX4 Spin Systems: Application to 15N Relaxations in 15NH4+
Publication date: Available online 28 June 2014
Source:Journal of Magnetic Resonance</br>
Author(s): Nicolas D. Werbeck , D. Flemming Hansen</br>
The equations that describe the time-evolution of transverse and longitudinal 15N magnetisations in tetrahedral ammonium ions, 15NH4 +, are derived from the Bloch-Wangsness-Redfield density operator relaxation theory. It is assumed that the relaxation of the spin-states is dominated by (1) the intra-molecular...
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06-29-2014 02:00 AM
[NMR paper] Live Cell NMR.
Live Cell NMR.
Related Articles Live Cell NMR.
Annu Rev Biophys. 2014 May 6;43:171-192
Authors: Freedberg DI, Selenko P
Abstract
Ever since scientists realized that cells are the basic building blocks of all life, they have been developing tools to look inside them to reveal the architectures and mechanisms that define their biological functions. Whereas "looking into cells" is typically said in reference to optical microscopy, high-resolution in-cell and on-cell nuclear magnetic resonance (NMR) spectroscopy is a powerful method...
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06-05-2014 05:51 PM
[NMR paper] Quantitative comparison of protein dynamics in live cells and in vitro by in-cell (19)F-NMR.
Quantitative comparison of protein dynamics in live cells and in vitro by in-cell (19)F-NMR.
Quantitative comparison of protein dynamics in live cells and in vitro by in-cell (19)F-NMR.
Chem Commun (Camb). 2013 Feb 26;
Authors: Takaoka Y, Kioi Y, Morito A, Otani J, Arita K, Ashihara E, Ariyoshi M, Tochio H, Shirakawa M, Hamachi I
Abstract
Here we describe how a (19)F-probe incorporated into an endogenous protein by a chemical biology method revealed protein dynamics. By explicit determination of ligand-bound and unbound structures with...
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02-27-2013 06:47 PM
Full relaxation matrix analysis of apparent cross-correlated relaxation rates in four-spin systems
Full relaxation matrix analysis of apparent cross-correlated relaxation rates in four-spin systems
January 2013
Publication year: 2013
Source:Journal of Magnetic Resonance, Volume 226</br>
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Cross-correlated relaxation (CCR) rates are an established tool for the extraction of relative bond orientations in biomolecules in solution. CCR between dipolar interactions in four-spin systems is a particularly well-suited mechanism. In this paper, a simple approach to analyze systematic experimental errors is formulated in a subspace of the complete four-spin Hilbert space....
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12-15-2012 09:51 AM
Full relaxation matrix analysis of apparent cross-correlated relaxation rates in four-spin systems
Full relaxation matrix analysis of apparent cross-correlated relaxation rates in four-spin systems
Available online 12 November 2012
Publication year: 2012
Source:Journal of Magnetic Resonance</br>
</br>
Cross-correlated relaxation (CCR) rates are an established tool for the extraction of relative bond orientations in biomolecules in solution. CCR between dipolar interactions in four-spin systems is a particularly well-suited mechanism. In this paper, a simple approach to analyze systematic experimental errors is formulated in a subspace of the complete four-spin...
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12-01-2012 06:10 PM
13C relaxation experiments for aromatic side chains employing longitudinal- and transverse-relaxation optimized NMR spectroscopy
13C relaxation experiments for aromatic side chains employing longitudinal- and transverse-relaxation optimized NMR spectroscopy
Abstract Aromatic side chains are prevalent in protein binding sites, perform functional roles in enzymatic catalysis, and form an integral part of the hydrophobic core of proteins. Thus, it is of great interest to probe the conformational dynamics of aromatic side chains and its response to biologically relevant events. Indeed, measurements of 13C relaxation rates in aromatic moieties have a long history in biomolecular NMR, primarily in the context of...
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07-05-2012 04:13 AM
Quantitative comparison of errors in 15N transverse relaxation rates measured using various CPMG phasing schemes
Quantitative comparison of errors in 15N transverse relaxation rates measured using various CPMG phasing schemes
Abstract Nitrogen-15 Carr-Purcell-Meiboom-Gill (CPMG) transverse relaxation experiment are widely used to characterize protein backbone dynamics and chemical exchange parameters. Although an accurate value of the transverse relaxation rate, R2, is needed for accurate characterization of dynamics, the uncertainty in the R2 value depends on the experimental settings and the details of the data analysis itself. Here, we present an analysis of the impact of CPMG pulse phase...
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04-03-2012 07:56 AM
[NMR paper] NMR spectroscopic detection of protein protons and longitudinal relaxation rates betw
NMR spectroscopic detection of protein protons and longitudinal relaxation rates between 0.01 and 50 MHz.
Related Articles NMR spectroscopic detection of protein protons and longitudinal relaxation rates between 0.01 and 50 MHz.
Angew Chem Int Ed Engl. 2005 Apr 8;44(15):2223-5
Authors: Bertini I, Gupta YK, Luchinat C, Parigi G, Schlörb C, Schwalbe H
Connecting Longitudinal and Transverse Relaxation Rates in Live-Cell NMR.
Linear Mode
