Overview on the Use of NMR to Examine Protein Structure

Breukels, Vincent; Konijnenberg, Albert; Nabuurs, Sanne M.; Doreleijers, Jurgen F.; Kovalevskaya, Nadezda V.; Vuister, Geerten W.

doi:10.1002/0471140864.ps1705s64

Cited by 10 publications

(8 citation statements)

References 189 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…NMR is a spectroscopic technique that employs an inherent property of many nuclei called 'spin' to yield spectra of various nuclei of biological interest, e.g. 1 H, 13 C, 15 N and 31 P. NMR's exquisite (bio-)chemical usefulness originates from its ability to discriminate the different nuclei in a biomolecule. The electronic environment of each nucleus slightly modifies its exact resonance frequency through a process called chemical shielding and consequently the positions of various peaks in the NMR spectrum are specific for each nucleus in the molecule.…”

Section: Chemical Shift and Exchangementioning

confidence: 99%

See 1 more Smart Citation

Simple high‐resolution NMR spectroscopy as a tool in molecular biology

Mureddu

Vuister

2019

The FEBS Journal

Self Cite

View full text Add to dashboard Cite

NMR is one of the major techniques for investigating the structure, dynamics and interactions between biomolecules. However, non‐experts often experience NMR experimentation and data analysis as intimidating. We discuss a simple yet powerful NMR technique, the so‐called chemical shift perturbation (CSP) analysis, as a tool to elucidate macromolecular interactions in small‐ and medium‐sized complexes, including protein‐protein, protein‐drug, and protein‐DNA/RNA interactions. We discuss current software packages for NMR data analysis and present a new interactive graphical tool implemented in CcpNmr AnalysisAssign version‐3, which can drastically reduce the time required for the CSP analysis. Lastly, we illustrate the usefulness of a protein three‐dimensional structure for interpretation of the CSP data.

show abstract

Section: Chemical Shift and Exchangementioning

confidence: 99%

“…It is based on the notion that the interactions are facilitated by the specific molecular shapes and, as has nowadays become evident, also their dynamical changes. Together these are crucial in determining the affinities that drive the assembly of the macromolecular complexes [1].…”

Section: Introductionmentioning

confidence: 99%

Simple high‐resolution NMR spectroscopy as a tool in molecular biology

Mureddu

Vuister

2019

The FEBS Journal

Self Cite

View full text Add to dashboard Cite

show abstract

“…Triple resonance NMR spectra were collected on a Varian INOVA 750-MHz magnet with triple resonance 1 H 13 C 15 N cryoprobe. The standard array of triple resonance and NOESY experiments were collected for determining protein structure [51] with distance restraint calibration and assignments optimized by the combined automated NOE assignment and structure determination module (CANDID) of the CYANA software package [52,53]. This structure determination process was initiated during the screening process and fragment hits were compared to this preliminary ensemble before that structure was technically ready for PDB deposition.…”

Section: Nmr-based Modeling Of Target Proteinmentioning

confidence: 99%

Identifying Ortholog Selective Fragment Molecules for Bacterial Glutaredoxins by NMR and Affinity Enhancement by Modification with an Acrylamide Warhead

et al. 2019

View full text Add to dashboard Cite

Illustrated here is the development of a new class of antibiotic lead molecules targeted at Pseudomonas aeruginosa glutaredoxin (PaGRX). This lead was produced to (a) circumvent efflux-mediated resistance mechanisms via covalent inhibition while (b) taking advantage of species selectivity to target a fundamental metabolic pathway. This work involved four components: a novel workflow for generating protein specific fragment hits via independent nuclear magnetic resonance (NMR) measurements, NMR-based modeling of the target protein structure, NMR guided docking of hits, and synthetic modification of the fragment hit with a vinyl cysteine trap moiety, i.e., acrylamide warhead, to generate the chimeric lead. Reactivity of the top warhead-fragment lead suggests that the ortholog selectivity observed for a fragment hit can translate into a substantial kinetic advantage in the mature warhead lead, which bodes well for future work to identify potent, species specific drug molecules targeted against proteins heretofore deemed undruggable.

show abstract

“…The 3-D structure of protein-ligand complexes can then be determined via heteronuclear experiments recorded on 13 C-, 15 N-, or 2 H-labeled protein samples. The structure resolution requires molecular dynamics calculations with experimental NMR restraints resulting from chemical shifts, scalar couplings, Nuclear Overhauser Effects (NOEs), paramagnetic interactions, or dipolar couplings (Breukels et al, 2011). These methods are limited in their routine use to proteins with low molecular weights (<30 kDa) to avoid large efforts in both labeling strategies and resonance assignment.…”

Section: Introductionmentioning

confidence: 99%

Overview of Probing Protein‐Ligand Interactions Using NMR

2015

View full text Add to dashboard Cite

Nuclear magnetic resonance (NMR) is a powerful technique for the study and characterization of protein-ligand interactions. In this unit we review both experiments where the NMR spectrum of the protein is observed (protein-observed NMR experiments) and those where the NMR spectra of the ligand is observed (ligand-observed NMR experiments) for the identification of binding partners, the measurement of protein-ligand affinity, the design of molecules that are active against biological targets such as proteins, and the assessment of the binding modes of the ligands. Ligand-observed methods discussed in this unit are Nuclear Overhauser Effect (NOE)-based approaches, with well-known experiments such as the Saturation Transfer Difference, Water-Ligand Observed via Gradient Spectroscopy (WaterLOGSY), and transferred-Nuclear Overhauser Effect Spectroscopy (tr-NOESY) experiments, and also the INPHARMA experiment. Regarding protein-observed experiments, this unit focuses on the use of chemical shift perturbations observed in protein-NMR spectra upon ligand binding. Also discussed is how these chemical shift perturbations can be used for the analysis of protein-ligand complexes, including fast structure determination when combined with docking.

show abstract

Overview on the Use of NMR to Examine Protein Structure

Cited by 10 publications

References 189 publications

Simple high‐resolution NMR spectroscopy as a tool in molecular biology

Simple high‐resolution NMR spectroscopy as a tool in molecular biology

Identifying Ortholog Selective Fragment Molecules for Bacterial Glutaredoxins by NMR and Affinity Enhancement by Modification with an Acrylamide Warhead

Overview of Probing Protein‐Ligand Interactions Using NMR

Contact Info

Product

Resources

About