Protein-inhibitor interaction studies using NMR

Ishima, Rieko

doi:10.2174/9781608059621115010007

Cited by 13Advanced NMR Techniques and ApplicationsProtein Structure and DynamicsProtein Interaction Studies and Fluorescence Analysis

Protein-inhibitor interaction studies using NMR

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Ishima, Rieko·2015·Applications of NMR Spectroscopy

DOI 10.2174/9781608059621115010007PMC PMC4562695

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Abstract

Solution-state NMR has been widely applied to determine the three-dimensional structure, dynamics, and molecular interactions of proteins. The designs of experiments used in protein NMR differ from those used for small-molecule NMR, primarily because the information available prior to an experiment, such as molecular mass and knowledge of the primary structure, is unique for proteins compared to small molecules. In this review article, protein NMR for structural biology is introduced with comparisons to small-molecule NMR, such as descriptions of labeling strategies and the effects of molecular dynamics on relaxation. Next, applications for protein NMR are reviewed, especially practical aspects for protein-observed ligand-protein interaction studies. Overall, the following topics are described: (1) characteristics of protein NMR, (2) methods to detect protein-ligand interactions by NMR, and (3) practical aspects of carrying out protein-observed inhibitor-protein interaction studies.

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The crystal structure of reverse transcriptase with beta-thujaplicinol showed the inhibitor in the active site chelating two Mn2+ ions and provided insight into the inhibition mechanism.
“The crystal structure of RT with a hydroxytropolone inhibitor, β-thujaplicinol, showed the inhibitor in the active-site with chelation of two Mn2+ (Figure 5a) and prompted postulation on how RNA/DNA substrate interaction with the inhibitors may occur, providing insight into the mechanism of inhibition [77].”
From Retroviral RNase H: structure, mechanism, and inhibition (2021) · cites this paper as [77]
Section 4.3 discusses NMR studies of a different RT inhibitor, BHMP07, and the References list work on hydroxylated tropolones. Searches for β-thujaplicinol and for a crystal structure showing chelation of two Mn2+ ions found no passage in our copy addressing the claimed structure or its proposed inhibition mechanism. (LLM, conf=0.72)
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Authors: Ishima, R.
Affiliations: University of Pittsburgh (US)
Corresponding author: Ishima, Rieko
ORCID: Ishima, Rieko
Venue: Applications of NMR Spectroscopy
Publisher: BENTHAM SCIENCE PUBLISHERS
Published: 2015-02-09
Volume: 1
Pages: 143-181
DOI: 10.2174/9781608059621115010007
PMC: PMC4562695
OpenAlex: W654319949
Cited by: 13
References: 208
Citations by year: 2023: 1 · 2021: 3 · 2020: 3 · 2019: 1 · 2018: 1 · 2017: 1 · 2016: 3
FWCI: 2.81
Type: book chapter
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: BENTHAM SCIENCE PUBLISHERS eBooks (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Funders: National Institute of General Medical Sciences (R01GM105401)
Topics: Physical Sciences › Chemistry › Spectroscopy › Advanced NMR Techniques and Applications
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Interaction Studies and Fluorescence Analysis
Keywords: protein-inhibitor interactions, protein-ligand interactions, solution NMR, protein structure determination, protein dynamics, structural biology

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Protein-inhibitor interaction studies using NMR

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