scholarly journals Interact: Automated analysis of protein-ligand interactions by 1D and 2D NMR

2018 ◽  
Author(s):  
Pierre Millard ◽  
Guy Lippens
Keyword(s):  
Dissociation Constants ◽  
Chemical Shifts ◽  
Automated Analysis ◽  
2D Nmr ◽  
Nmr Titration ◽  
Protein Ligand Interactions ◽  
Fitting Procedures ◽  
Ligand Interactions ◽  
Titration Data ◽  
Automated Tools

AbstractNMR titration experiments contain rich information on the thermodynamic, kinetic and structural aspects of protein-ligand interactions. Automated tools are required to process the large number of signals typically acquired in these experiments and facilitate quantitative interpretations. We present Interact, a Python script accessible within the Bruker BioSpin TopSpin™ software, which allows automated analysis of both 1D and 2D NMR titration experiments. Interact performs peak picking and annotation of the successive spectra and supports quantitative interpretation of changes in chemical shifts and linewidths induced by the ligand (e.g. to estimate dissociation constants) through different fitting procedures. Interact can be applied to all types of 1D and 2D NMR experiments and all nuclei, hence facilitating routine analysis of existing and forthcoming NMR titration data. Interact was implemented in Python and can be used on Windows, Unix and MacOS platforms. The source code is distributed under OpenSource license at http://github.com/MetaSys-LISBP/Interact.

scholarly journals Protolysis and Complex Formation of Organophosphorus Compounds—Characterization by NMR-Controlled Titrations

Molecules ◽  
2019 ◽  
Vol 24 (18) ◽  
pp. 3238 ◽  
Author(s):  
Hägele
Keyword(s):  
Dissociation Constants ◽  
Organophosphorus Compounds ◽  
Chemical Shifts ◽  
2D Nmr ◽  
Coupling Constants ◽  
Phosphonic Acids ◽  
Specific Chemical ◽  
Hyphenated Technique ◽  
Aminophosphonic Acids ◽  
2D Nmr Spectra

Phosphonic acids, aminophosphonic acids, and phosphonocarboxylic acids are characterized by an advanced hyphenated technique, combining potentiometric titration with NMR spectroscopy. Automated measurements involving 13C, 19F and 31P nuclei lead to “pseudo 2D NMR” spectra, where chemical shifts or coupling constants are correlated with analytical parameters. Dissociation constants, stability constants, dynamic and specific chemical shifts are determined. Macroscopic and microscopic dissociation equilibria are discussed.

scholarly journals Inverse PI by NMR: Analysis of Ligand 1H-Chemical Shifts in the Protein-Bound State

2021 ◽  
Author(s):  
Gerald Platzer ◽  
Moriz Mayer ◽  
Jark Boettcher ◽  
Leonhard Geist ◽  
Julian E. Fuchs ◽  
...  
Keyword(s):  
Chemical Shift ◽  
Chemical Shifts ◽  
Bound State ◽  
Structure Information ◽  
Π Interactions ◽  
Protein Ligand Interactions ◽  
Protein Deuteration ◽  
Ligand Interactions ◽  
A Site ◽  
Ligand Conformation

The study of protein-ligand interactions via protein-based NMR generally relies on the detection of chemical-shift changes induced by ligand binding. However, the chemical shift of the ligand when bound to the protein is rarely discussed, since it is not readily detectable. In this work we use protein deuteration in combination with [1H-1H]-NOESY NMR to extract 1H chemical shift values of the ligand in the bound state. The chemical shift perturbations (CSPs) experienced by the proton ligand resonances (free vs bound) are an extremely rich source of information on protein-ligand complexes. Besides allowing for the detection of intermolecular CH-π interactions and elucidation of the protein-bound ligand conformation, the CSP information can be used to analyse (de)solvation effects in a site-specific manner. In conjunction with crystal structure information, it is possible to distinguish protons whose desolvation penalty is compensated for upon protein-binding, from those that are not. Combined with the previously reported PI by NMR technique for the protein-based detection of intermolecular CH-π interactions, this method represents another important step towards the ultimate goal of Interaction-Based Drug Discovery.

scholarly journals Prediction of Dissociation Constant in Protein-Ligand Interaction

2021 ◽  
Author(s):  
Masatoshi Kawashima
Keyword(s):  
Dissociation Constant ◽  
Dissociation Constants ◽  
Coefficient Of Determination ◽  
Ligand Interaction ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Predicted Values ◽  
Equilibrium Dissociation ◽  
Antigen Antibody ◽  
Antibody Interactions

In protein-ligand interactions, such as antigen-antibody interactions and hormone-receptor interactions, a correlation between the equilibrium dissociation constant <i>K</i><sub>D</sub> and the reduced mass of the protein and ligand was found. The correlation of dissociation constants as p<i>K</i><sub>D</sub> (-log<i>K</i><sub>D</sub>) between literature values and predicted values was confirmed in high coefficient of determination R<sup>2</sup> over 0.98.

scholarly journals Preliminary investigation of deoxyoligonucleotide binding to ribonuclease A using mass spectrometry: An attempt to develop a lab experience for undergraduates

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 340
Author(s):  
Daniel D. Clark
Keyword(s):  
Mass Spectrometry ◽  
Ion Trap ◽  
Dissociation Constants ◽  
Preliminary Investigation ◽  
Accurate Determination ◽  
Ribonuclease A ◽  
Rnase A ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Pancreatic Ribonuclease A

Deoxyoligonucleotide binding to bovine pancreatic ribonuclease A (RNase A) was investigated using electrospray ionization ion-trap mass spectrometry (ESI-IT-MS). Deoxyoligonucleotides included CCCCC (dC5) and CCACC (dC2AC2).  This work was an attempt to develop a biochemistry lab experience that would introduce undergraduates to the use of mass spectrometry for the analysis of protein-ligand interactions.  Titration experiments were performed using a fixed RNase A concentration and variable deoxyoligonucleotide concentrations.  Samples at equilibrium were infused directly into the mass spectrometer under native conditions.  For each deoxyoligonucleotide, mass spectra showed one-to-one binding stoichiometry, with marked increases in the total ion abundance of ligand-bound RNase A complexes as a function of concentration, but the accurate determination of dC5 and dC2AC2 dissociation constants was problematic.

scholarly journals Layer-wise relevance propagation of InteractionNet explains protein–ligand interactions at the atom level

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Hyeoncheol Cho ◽  
Eok Kyun Lee ◽  
Insung S. Choi
Keyword(s):  
Dissociation Constants ◽  
Structural Information ◽  
Three Dimensional ◽  
Graph Representation ◽  
Ligand Complex ◽  
Covalent Bonds ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Atom Level ◽  
Graph Neural Networks

AbstractDevelopment of deep-learning models for intermolecular noncovalent (NC) interactions between proteins and ligands has great potential in the chemical and pharmaceutical tasks, including structure–activity relationship and drug design. It still remains an open question how to convert the three-dimensional, structural information of a protein–ligand complex into a graph representation in the graph neural networks (GNNs). It is also difficult to know whether a trained GNN model learns the NC interactions properly. Herein, we propose a GNN architecture that learns two distinct graphs—one for the intramolecular covalent bonds in a protein and a ligand, and the other for the intermolecular NC interactions between the protein and the ligand—separately by the corresponding covalent and NC convolutional layers. The graph separation has some advantages, such as independent evaluation on the contribution of each convolutional step to the prediction of dissociation constants, and facile analysis of graph-building strategies for the NC interactions. In addition to its prediction performance that is comparable to that of a state-of-the art model, the analysis with an explainability strategy of layer-wise relevance propagation shows that our model successfully predicts the important characteristics of the NC interactions, especially in the aspect of hydrogen bonding, in the chemical interpretation of protein–ligand binding.

scholarly journals Non‐Stationary Complementary Non‐Uniform Sampling (NOSCO NUS) for Fast Acquisition of Serial 2D NMR Titration Data

2020 ◽  
Vol 59 (52) ◽  
pp. 23496-23499
Author(s):  
Javier A. Romero ◽  
Ewa K. Nawrocka ◽  
Alexandra Shchukina ◽  
Francisco J. Blanco ◽  
Tammo Diercks ◽  
...  
Keyword(s):  
2D Nmr ◽  
Nmr Titration ◽  
Uniform Sampling ◽  
Fast Acquisition ◽  
Titration Data ◽  
Non Uniform Sampling

Interaction of troponin I and troponin C: 19F NMR studies of the binding of the inhibitory troponin I peptide to turkey skeletal troponin C

1991 ◽  
Vol 69 (9) ◽  
pp. 674-681 ◽  
Author(s):  
A. Patricia Campbell ◽  
Paul J. Cachia ◽  
Brian D. Sykes
Keyword(s):  
Calcium Binding ◽  
Troponin I ◽  
Dissociation Constants ◽  
Chemical Shifts ◽  
Troponin C ◽  
Resonance Spectroscopy ◽  
Nmr Studies ◽  
Binding Model ◽  
Peptide Binding Site ◽  
Titration Data

We have used 19F nuclear magnetic resonance spectroscopy to study the interaction of the inhibitory region of troponin (TnI) with apo- and calcium(II)-saturated turkey skeletal troponin C (TnC), using the synthetic TnI analogue Nα-acetyl[19FPhe106]TnI(104–115)amide. Dissociation constants of Kd = (3.7 ± 3.1) × 10−5 M for the apo interaction and Kd = (4.8 ± 1.8) × 10−5 M for the calcium(II)-saturated interaction were obtained using a 1:1 binding model of peptide to protein. The 19F NMR chemical shifts for the F-phenylalanine of the bound peptide are different from the apo- and calcium-saturated protein, indicating a different environment for the bound peptide. The possibility of 2:1 binding of the peptide to Ca(II)-saturated TnC was tested by calculating the fit of the experimental titration data to a series of theoretical binding curves in which the dissociation constants for the two hypothetical binding sites were varied. We obtained the best fit for 0.056 mM ≤ Kd1 ≤ 0.071 mM and 0.5 mM ≤ Kd2 ≤ 2.0 mM. These results allow the possibility of a second peptide binding site on calcium(II)-saturated TnC with an affinity 10- to 20-fold weaker than that of the first site.Key words: tropinin C, tropinin I, calcium binding, NMR studies, muscle proteins.

Studies of protein–ligand interactions by NMR

2003 ◽  
Vol 31 (5) ◽  
pp. 1006-1009 ◽  
Author(s):  
J. Clarkson ◽  
I.D. Campbell
Keyword(s):  
Chemical Shift ◽  
Structure Determination ◽  
Dissociation Constants ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Ligand Complex ◽  
Protein Ligand Interactions ◽  
Small Proteins ◽  
Ligand Interactions

Solution-state NMR has become an accepted method for studying the structure of small proteins in solution. This has resulted in over 3000 NMR-based co-ordinate sets being deposited in the Protein Databank. It is becoming increasingly apparent, however, that NMR is also a very powerful tool for accessing interactions between macromolecules and various ligands. These interactions can be assessed at a wide variety of levels, e.g. qualitative screening of libraries of pharmaceuticals and ‘chemical shift mapping’. Dissociation constants can sometimes be obtained in such cases. Another example would be the complete three-dimensional structure determination of a protein–ligand complex. Here we briefly describe a few of the principles involved and illustrate the method with recent examples.

Sign in / Sign up

Export Citation Format

Share Document