NMR Methods for Structural Characterization of Protein-Protein Complexes.

Jeffrey A Purslow,Balabhadra Khatiwada,Vincenzo Venditti,Marvin J Bayro

doi:10.3389/fmolb.2020.00009

Jeffrey A Purslow, Balabhadra Khatiwada + Show 2 more

Open Access

https://doi.org/10.3389/fmolb.2020.00009

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Abstract

Protein-protein interactions and the complexes thus formed are critical elements in a wide variety of cellular events that require an atomic-level description to understand them in detail. Such complexes typically constitute challenging systems to characterize and drive the development of innovative biophysical methods. NMR spectroscopy techniques can be applied to extract atomic resolution information on the binding interfaces, intermolecular affinity, and binding-induced conformational changes in protein-protein complexes formed in solution, in the cell membrane, and in large macromolecular assemblies. Here we discuss experimental techniques for the characterization of protein-protein complexes in both solution NMR and solid-state NMR spectroscopy. The approaches include solvent paramagnetic relaxation enhancement and chemical shift perturbations (CSPs) for the identification of binding interfaces, and the application of intermolecular nuclear Overhauser effect spectroscopy and residual dipolar couplings to obtain structural constraints of protein-protein complexes in solution. Complementary methods in solid-state NMR are described, with emphasis on the versatility provided by heteronuclear dipolar recoupling to extract intermolecular constraints in differentially labeled protein complexes. The methods described are of particular relevance to the analysis of membrane proteins, such as those involved in signal transduction pathways, since they can potentially be characterized by both solution and solid-state NMR techniques, and thus outline key developments in this frontier of structural biology.

Highlights

The function and survival of cellular organisms are reliant on the ability of cell societies to transfer essential information through communication networks commonly referred to as signaling pathways
Albeit solvent-PRE experiments provide a wealth of structural information on macromolecular complexes, a major drawback is their inability of extracting thermodynamic parameters on protein-protein interactions
Albeit chemical shift perturbations (CSPs) and solvent PRE analysis are powerful tools for distinguishing binding interfaces, structure-activity relationships, and KD values (Nerli et al, 2018; Nitsche and Otting, 2018), additional structural information on the proteinprotein complex can be derived by combining CSP and/or solvent-PRE data with molecular docking simulations

Summary

INTRODUCTION

The function and survival of cellular organisms are reliant on the ability of cell societies to transfer essential information through communication networks commonly referred to as signaling pathways. The resulting cellular responses of such pathways are mediated by numerous biomolecular interactions that are crucial for regulating various vital biological processes including signal transduction, gene regulation, enzyme catalysis, immune response, signal processing, encoding, and integration (Hunter et al, 2000; Wong and Scott, 2004; Kholodenko, 2006; Anglister et al, 2016). Several important pathologies such as cancer, chronic inflammatory syndrome, and diabetes are commonly dependent upon the malfunction of one or more steps within a signaling pathway (Yarden and Sliwkowski, 2001; Fischer et al, 2003; Gray et al, 2003; Solinas et al, 2007; Wang et al, 2013; Vlahopoulos et al, 2015). The continuous technological advances in solution and solid state NMR are establishing NMR methods as fundamental investigation tools for obtaining insights into the biochemistry of signal transduction pathways

EXPERIMENTS

Dephasing Methods

CONCLUSIONS

DATA AVAILABILITY STATEMENT