Overview of Probing Protein‐Ligand Interactions Using NMR

Aguirre, Clémentine; Cala, Olivier; Krimm, Isabelle

doi:10.1002/0471140864.ps1718s81

Cited by 28 publications

(19 citation statements)

References 110 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Upon binding the protein, the ligand acquires a large molecular correlation time leading to substantial enhancement of NOE cross relaxation between protons. Thus, protein-bound compounds exhibit strong negative NOEs and significantly shorter mixing times, compared to the small positive NOEs and longer mixing times exhibited by free ligand (27).…”

Section: Characterization Of Compound Binding By Transferred Noesy Nmmentioning

confidence: 99%

Discovery of stimulator binding to a conserved pocket in the heme domain of soluble guanylyl cyclase

Wales

Chen

Breci

et al. 2018

Journal of Biological Chemistry

View full text Add to dashboard Cite

Soluble guanylyl cyclase (sGC) is the receptor for nitric oxide and a highly soughtafter therapeutic target for the management of cardiovascular diseases. New compounds that stimulate sGC show clinical promise, but where these stimulator compounds bind and how they function remains unknown. Here, using a photolyzable diazirine derivative of a novel stimulator compound, IWP-051, and MS analysis, we localized drug binding to the β1 heme domain of sGC proteins from the hawkmoth Manduca sexta and from human. Covalent attachments to the stimulator were also identified in bacterial homologs of the sGC heme domain, referred to as H-NOX domains, including those from Nostoc sp. 7120, Shewanella oneidensis, Shewanella woodyi, and Clostridium botulinum, indicating the binding site is highly conserved. The identification of photoaffinity-labeled peptides was aided by a signature MS fragmentation pattern of general applicability for unequivocal identification of covalently attached compounds. Using NMR, we also examined stimulator binding to sGC from M. sexta and bacterial H-NOX homologs. These data indicated that stimulators bind to a conserved cleft between two subdomains in the sGC heme domain. L23W/T48W substitutions within the binding pocket resulted in a 9-fold decrease in drug response, suggesting the bulkier tryptophan residues directly block stimulator binding.

show abstract

Section: Characterization Of Compound Binding By Transferred Noesy Nmmentioning

confidence: 99%

Discovery of stimulator binding to a conserved pocket in the heme domain of soluble guanylyl cyclase

Wales

Chen

Breci

et al. 2018

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…To gain insight in the molecular basis of complex formation with SELEX-DNA we utilized NMR spectroscopy [41][42][43][44]. The complex was initially examined through chemical shift perturbation (CSP) experiments.…”

Section: Chemical Shift Mapping Reveals a Unique Binding Mode To Selementioning

confidence: 99%

The Molecular Basis of Specific DNA Binding by the BRG1 AT-hook and Bromodomain

Sanchez

Zhang

Evoli

et al. 2019

Preprint

View full text Add to dashboard Cite

AbstractThe ATP-dependent BAF chromatin remodeling complex plays a critical role in gene regulation by modulating chromatin architecture, and is frequently mutated in cancer. Indeed, subunits of the BAF complex are found to be mutated in >20% of human tumors. The mechanism by which BAF properly navigates chromatin is not fully understood, but is thought to involve a multivalent network of histone and DNA contacts. We previously identified a composite domain in the BRG1 ATPase subunit that is capable of associating with both histones and DNA in a multivalent manner. Mapping the DNA binding pocket revealed that it contains several cancer mutations. Here, we utilize SELEX-seq to identify the DNA specificity of this composite domain and NMR spectroscopy and molecular modelling to determine the structural basis of DNA binding. Finally, we demonstrate that cancer mutations in this domain alter the mode of DNA association.

show abstract

“…Several excellent reviews discuss these ligand observing techniques in much more detail. 12,48,49 Protein observed methods for measuring binding events. In contrast to the ligand observed methods, labelling the protein with stable isotopes, typically 15 N, 13 C, or both, can provide residuespecific, structural information about the binding interface, and give a reasonable estimate of binding constants in both fast and slow exchange regimes (see below) [ Fig.…”

Section: Using Nmr To Describe Protein-ligand Interactionsmentioning

confidence: 99%

(S)Pinning down protein interactions by NMR

et al. 2017

View full text Add to dashboard Cite

Protein molecules are highly diverse communication platforms and their interaction repertoire stretches from atoms over small molecules such as sugars and lipids to macromolecules. An important route to understanding molecular communication is to quantitatively describe their interactions. These types of analyses determine the amounts and proportions of individual constituents that participate in a reaction as well as their rates of reactions and their thermodynamics. Although many different methods are available, there is currently no single method able to quantitatively capture and describe all types of protein reactions, which can span orders of magnitudes in affinities, reaction rates, and lifetimes of states. As the more versatile technique, solution NMR spectroscopy offers a remarkable catalogue of methods that can be successfully applied to the quantitative as well as qualitative descriptions of protein interactions. In this review we provide an easy‐access approach to NMR for the non‐NMR specialist and describe how and when solution state NMR spectroscopy is the method of choice for addressing protein ligand interaction. We describe very briefly the theoretical background and illustrate simple protein–ligand interactions as well as typical strategies for measuring binding constants using NMR spectroscopy. Finally, this review provides examples of caveats of the method as well as the options to improve the outcome of an NMR analysis of a protein interaction reaction.

show abstract

Overview of Probing Protein‐Ligand Interactions Using NMR

Cited by 28 publications

References 110 publications

Discovery of stimulator binding to a conserved pocket in the heme domain of soluble guanylyl cyclase

Discovery of stimulator binding to a conserved pocket in the heme domain of soluble guanylyl cyclase

The Molecular Basis of Specific DNA Binding by the BRG1 AT-hook and Bromodomain

(S)Pinning down protein interactions by NMR

Contact Info

Product

Resources

About