Authors: Waudby CA, Ramos A, Cabrita LD, Christodoulou J
Abstract
NMR titration experiments are a rich source of structural, mechanistic, thermodynamic and kinetic information on biomolecular interactions, which can be extracted through the quantitative analysis of resonance lineshapes. However, applications of such analyses are frequently limited by peak overlap inherent to complex biomolecular systems. Moreover, systematic errors may arise due to the analysis of two-dimensional data using theoretical frameworks developed for one-dimensional experiments. Here we introduce a more accurate and convenient method for the analysis of such data, based on the direct quantum mechanical simulation and fitting of entire two-dimensional experiments, which we implement in a new software tool, TITAN (TITration ANalysis). We expect the approach, which we demonstrate for a variety of protein-protein and protein-ligand interactions, to be particularly useful in providing information on multi-step or multi-component interactions.
[NMR paper] Protein Dynamics in the Solid-State from 2H NMR Lineshape Analysis. II: MOMD Applied to C-D, and C-CD3 Probes.
Protein Dynamics in the Solid-State from 2H NMR Lineshape Analysis. II: MOMD Applied to C-D, and C-CD3 Probes.
Related Articles Protein Dynamics in the Solid-State from 2H NMR Lineshape Analysis. II: MOMD Applied to C-D, and C-CD3 Probes.
J Phys Chem B. 2015 Sep 24;
Authors: Meirovitch E, Liang Z, Freed JH
Abstract
Deuterium lineshape analysis from mobile C?-D and C-?CD3 groups has emerged as a particularly useful tool for studying dynamics in the solid-state. The theoretical models devised so far consist typically of sets...
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09-26-2015 05:13 AM
[NMR paper] Proteins Dynamics in the Solid-state from (2)H NMR Lineshape Analysis: a Consistent Perspective.
Proteins Dynamics in the Solid-state from (2)H NMR Lineshape Analysis: a Consistent Perspective.
Related Articles Proteins Dynamics in the Solid-state from (2)H NMR Lineshape Analysis: a Consistent Perspective.
J Phys Chem B. 2015 Jan 16;
Authors: Meirovitch E, Liang Z, Freed JH
Abstract
Deuterium lineshape analysis of CD3 groups emerged as a particularly useful tool for studying ?s - ms protein motions in the solid-state. The models devised so far consist of several independently conceived simple jump-type motions. They are...
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01-17-2015 04:14 PM
Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis
Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis
Abstract The phosphorylation-specific peptidyl-prolyl isomerase Pin1 catalyzes the isomerization of the peptide bond preceding a proline residue between cis and trans isomers. To best understand the mechanisms of Pin1 regulation, rigorous enzymatic assays of isomerization are required. However, most measures of isomerase activity require significant constraints on substrate sequence and only yield rate constants for the cis isomer,
kcatcis and apparent Michaelis constants,
...
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09-30-2011 08:01 PM
Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis.
Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis.
Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis.
J Biomol NMR. 2011 Sep;51(1-2):21-34
Authors: Greenwood AI, Rogals MJ, De S, Lu KP, Kovrigin EL, Nicholson LK
Abstract
The phosphorylation-specific peptidyl-prolyl isomerase Pin1 catalyzes the isomerization of the peptide bond preceding a proline residue between cis and trans isomers. To best understand the mechanisms of Pin1 regulation,...
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09-30-2011 06:00 AM
Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis.
Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis.
Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis.
J Biomol NMR. 2011 Sep;51(1-2):21-34
Authors: Greenwood AI, Rogals MJ, De S, Lu KP, Kovrigin EL, Nicholson LK
Abstract
The phosphorylation-specific peptidyl-prolyl isomerase Pin1 catalyzes the isomerization of the peptide bond preceding a proline residue between cis and trans isomers. To best understand the mechanisms of Pin1 regulation,...
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09-30-2011 05:59 AM
[NMR paper] Addressing the overlap problem in the quantitative analysis of two dimensional NMR sp
Addressing the overlap problem in the quantitative analysis of two dimensional NMR spectra: application to (15)N relaxation measurements.
Related Articles Addressing the overlap problem in the quantitative analysis of two dimensional NMR spectra: application to (15)N relaxation measurements.
J Biomol NMR. 2004 Nov;30(3):347-52
Authors: Tugarinov V, Choy WY, Kupce E, Kay LE
A quantitative analysis of 2D (1)H-(15)N spectra is often complicated by resonance overlap. Here a simple method is presented for resolving overlapped correlations by...
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11-24-2010 10:03 PM
[NMR paper] Inverse methods in two-dimensional NMR spectral analysis.
Inverse methods in two-dimensional NMR spectral analysis.
Related Articles Inverse methods in two-dimensional NMR spectral analysis.
J Magn Reson. 2003 May;162(1):141-57
Authors: van Beek JD, Meier BH, Schäfer H
Solid-state NMR is a valuable technique for the study of disordered materials. Analysis of such spectra usually involves solution of so-called ill-posed inverse problems. Here we present a strategy for the analysis of two-parameter two-dimensional NMR problems and test it on 2D DECODER and DOQSY experiments. Using Monte Carlo tests,...
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11-24-2010 09:01 PM
[NMR paper] Analysis of the backbone dynamics of interleukin-1 beta using two-dimensional inverse
Analysis of the backbone dynamics of interleukin-1 beta using two-dimensional inverse detected heteronuclear 15N-1H NMR spectroscopy.
Related Articles Analysis of the backbone dynamics of interleukin-1 beta using two-dimensional inverse detected heteronuclear 15N-1H NMR spectroscopy.
Biochemistry. 1990 Aug 14;29(32):7387-401
Authors: Clore GM, Driscoll PC, Wingfield PT, Gronenborn AM
The backbone dynamics of uniformly 15N-labeled interleukin-1 beta are investigated by using two-dimensional inverse detected heteronuclear 15N-1H NMR...
Two-Dimensional NMR Lineshape Analysis.
Linear Mode
