Abstract Biological function of proteins relies on conformational transitions and binding of specific ligands. Proteinā??ligand interactions are thermodynamically and kinetically coupled to conformational changes in protein structures as conceptualized by the models of pre-existing equilibria and induced fit. NMR spectroscopy is particularly sensitive to complex ligand-binding modesā??NMR line-shape analysis can provide for thermodynamic and kinetic constants of ligand-binding equilibria with the site-specific resolution. However, broad use of line shape analysis is hampered by complexity of NMR line shapes in multi-state systems. To facilitate interpretation of such spectral patterns, I computationally explored systems where isomerization or dimerization of a protein (receptor) molecule is coupled to binding of a ligand. Through an extensive analysis of multiple exchange regimes for a family of three-state models, I identified signature features to guide an NMR experimentalist in recognizing specific interaction mechanisms. Results show that distinct multi-state models may produce very similar spectral patterns. I also discussed aggregation of a receptor as a possible source of spurious three-state line shapes and provided specific suggestions for complementary experiments that can ensure reliable mechanistic insight.
Content Type Journal Article
Category Article
Pages 1-14
DOI 10.1007/s10858-012-9636-3
Authors
Evgenii L. Kovrigin, Department of Chemistry, Marquette University, PO Box 1881, Milwaukee, WI 53201, USA
The feasibility of parameterizing four-state equilibria using relaxation dispersion measurements
The feasibility of parameterizing four-state equilibria using relaxation dispersion measurements
Abstract Coupled equilibria play important roles in controlling information flow in biochemical systems, including allosteric molecules and multidomain proteins. In the simplest case, two equilibria are coupled to produce four interconverting states. In this study, we assessed the feasibility of determining the degree of coupling between two equilibria in a four-state system via relaxation dispersion measurements. A major bottleneck in this effort is the lack of efficient approaches to...
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[NMR paper] Perturbation of the conformational equilibria in Ras by selective mutations as studie
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FEBS Lett. 2004 Dec 17;578(3):305-10
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Ras regulates a variety of different signal transduction pathways acting as molecular switch. It was shown by liquid and solid-state (31)P NMR spectroscopy that Ras exists in the...
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[NMR paper] Flavonoid binding to a multi-drug-resistance transporter protein: an STD-NMR study.
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Authors: Nissler L, Gebhardt R, Berger S
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Several NMR screening techniques have been developed in recent years to aid in the identification of lead drug compounds. These NMR methods have traditionally been used for protein targets, and here we examine their applicability for an RNA target. We used the SHAPES compound library to test three different NMR...
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We have determined by (15)N, (1)H, and (13)C NMR, the chemical behavior of the six histidines in subtilisin BPN' and their PMSF and peptide boronic acid complexes in aqueous solution as a...
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BACKGROUND: Recently, it has been shown that nuclear magnetic resonance (NMR) may be used to identify ligands that bind to low molecular weight protein drug targets. Recognizing the utility of NMR as a very sensitive method for detecting binding, we have...
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Low-affinity platelet factor 4 (LA-PF4), unlike another related, sequentially homologous (about 50%) platelet-specific protein, platelet factor 4 (PF4), is an active mitogenic and chemotactic...
NMR line shapes and multi-state binding equilibria
Linear Mode
