We present PLIS, a publicly available, open-source software for the determination of protein-ligand dissociation constants that can be used to characterize biological processes or to shed light on biophysical aspects of interactions. PLIS can analyze data from titration experiments monitored by for instance fluorescence spectroscopy or from nuclear magnetic resonance relaxation dispersion experiments. In addition to analysis of experimental data, PLIS includes functionality for generation of synthetic data, useful for understanding how different parameters effect the data in order to better analyze experiments.
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[NMR paper] Quantitative analysis of protein-ligand interactions by NMR.
Quantitative analysis of protein-ligand interactions by NMR.
Quantitative analysis of protein-ligand interactions by NMR.
Prog Nucl Magn Reson Spectrosc. 2016 Aug;96:47-57
Authors: Furukawa A, Konuma T, Yanaka S, Sugase K
Abstract
Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug...
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08-31-2016 02:34 PM
Quantitative analysis of protein–ligand interactions by NMR
Quantitative analysis of protein–ligand interactions by NMR
Publication date: Available online 3 March 2016
Source:Progress in Nuclear Magnetic Resonance Spectroscopy</br>
Author(s): Ayako Furukawa, Tsuyoshi Konuma, Saeko Yanaka, Kenji Sugase</br>
Protein–ligand interactions have been commonly studied through static structures of the protein–ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein–ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development....
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03-03-2016 08:32 PM
[NMR paper] NMR-based analysis of protein-ligand interactions.
NMR-based analysis of protein-ligand interactions.
NMR-based analysis of protein-ligand interactions.
Anal Bioanal Chem. 2013 Apr 18;
Authors: Cala O, Guillière F, Krimm I
Abstract
Physiological processes are mainly controlled by intermolecular recognition mechanisms involving protein-protein and protein-ligand (low molecular weight molecules) interactions. One of the most important tools for probing these interactions is high-field solution nuclear magnetic resonance (NMR) through protein-observed and ligand-observed experiments, where...
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04-18-2013 10:12 PM
Accuracy and precision of proteinâ??ligand interaction kinetics determined from chemical shift titrations
Accuracy and precision of proteinâ??ligand interaction kinetics determined from chemical shift titrations
Abstract NMR-monitored chemical shift titrations for the study of weak proteinâ??ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K D ) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods...
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10-24-2012 10:28 PM
Increased precision for analysis of proteinâ??ligand dissociation constants determined from chemical shift titrations
Increased precision for analysis of proteinâ??ligand dissociation constants determined from chemical shift titrations
Abstract NMR is ideally suited for the analysis of proteinâ??protein and protein ligand interactions with dissociation constants ranging from ~2 μM to ~1 mM, and with kinetics in the fast exchange regime on the NMR timescale. For the determination of dissociation constants (K D ) of 1:1 proteinâ??protein or proteinâ??ligand interactions using NMR, the protein and ligand concentrations must necessarily be similar in magnitude to the K D , and nonlinear least squares...
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05-01-2012 07:06 AM
Dissecting electrostatic interactions in Bacillus circulans xylanase through NMR-monitored pH titrations.
Dissecting electrostatic interactions in Bacillus circulans xylanase through NMR-monitored pH titrations.
Dissecting electrostatic interactions in Bacillus circulans xylanase through NMR-monitored pH titrations.
J Biomol NMR. 2011 Sep;51(1-2):5-19
Authors: McIntosh LP, Naito D, Baturin SJ, Okon M, Joshi MD, Nielsen JE
Abstract
NMR-monitored pH titration curves of proteins provide a rich source of structural and electrostatic information. Although relatively straightforward to measure, interpreting pH-dependent chemical shift changes to...
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09-30-2011 06:00 AM
Dissecting electrostatic interactions in Bacillus circulans xylanase through NMR-monitored pH titrations.
Dissecting electrostatic interactions in Bacillus circulans xylanase through NMR-monitored pH titrations.
Dissecting electrostatic interactions in Bacillus circulans xylanase through NMR-monitored pH titrations.
J Biomol NMR. 2011 Sep;51(1-2):5-19
Authors: McIntosh LP, Naito D, Baturin SJ, Okon M, Joshi MD, Nielsen JE
Abstract
NMR-monitored pH titration curves of proteins provide a rich source of structural and electrostatic information. Although relatively straightforward to measure, interpreting pH-dependent chemical shift changes...
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09-30-2011 05:59 AM
[NMR paper] Analysis of protein/ligand interactions with NMR diffusion measurements: the importan
Analysis of protein/ligand interactions with NMR diffusion measurements: the importance of eliminating the protein background.
Related Articles Analysis of protein/ligand interactions with NMR diffusion measurements: the importance of eliminating the protein background.
J Magn Reson. 2002 Apr;155(2):217-25
Authors: Derrick TS, McCord EF, Larive CK
Pulsed-field gradient nuclear magnetic resonance (PFG-NMR) is a well-established method for the determination of translational diffusion coefficients. Recently, this method has found applicability in...
Analysis of protein-ligand interactions from titrations and NMR relaxation dispersions
Linear Mode
