Opportunities and Challenges of Backbone, Sidechain, and RDC Experiments to Study Membrane Protein Dynamics in a Detergent-Free Lipid Environment Using Solution State NMR.

Stefan Bibow

doi:10.3389/fmolb.2019.00103

Abstract

Whereas solution state NMR provided a wealth of information on the dynamics landscape of soluble proteins, only few studies have investigated membrane protein dynamics in a detergent-free lipid environment. Recent developments of smaller nanodiscs and other lipid-scaffolding polymers, such as styrene maleic acid (SMA), however, open new and promising avenues to explore the function-dynamics relationship of membrane proteins as well as between membrane proteins and their surrounding lipid environment. Favorably sized lipid-bilayer nanodiscs, established membrane protein reconstitution protocols and sophisticated solution NMR relaxation methods probing dynamics over a wide range of timescales will eventually reveal unprecedented lipid-membrane protein interdependencies that allow us to explain things we have not been able to explain so far. In particular, methyl group dynamics resulting from CEST, CPMG, ZZ exchange, and RDC experiments are expected to provide new and surprising insights due to their proximity to lipids, their applicability in large 100+ kDa assemblies and their simple labeling due to the availability of commercial precursors. This review summarizes the recent developments of membrane protein dynamics with a special focus on membrane protein dynamics in lipid-bilayer nanodiscs. Opportunities and challenges of backbone, side chain and RDC dynamics applied to membrane proteins are discussed. Solution-state NMR and lipid nanodiscs bear great potential to change our molecular understanding of lipid-membrane protein interactions.

Highlights

In 1985, the first membrane protein (MP) structure was determined (Deisenhofer et al, 1985)
Those low-q bicelle preparations are necessary for solution NMR to obtain sharp and interpretable NMR spectra since they retain a fast tumbling of the membrane protein
It is surprising that there are still only a few solution state NMR publications that investigate MP backbone dynamics in a lipid environment. This is certainly a result of at least three aspects: (i) the difficulty to work with membrane proteins; (ii) the difficulties arising from the usage of bicelles; (iii) the recency of smaller nanodiscs that can provide high-quality spectra in a very reproducible manner

Summary

Stefan Bibow*

Specialty section: This article was submitted to Structural Biology, a section of the journal Frontiers in Molecular Biosciences. Whereas solution state NMR provided a wealth of information on the dynamics landscape of soluble proteins, only few studies have investigated membrane protein dynamics in a detergent-free lipid environment. Recent developments of smaller nanodiscs and other lipid-scaffolding polymers, such as styrene maleic acid (SMA), open new and promising avenues to explore the function-dynamics relationship of membrane proteins as well as between membrane proteins and their surrounding lipid environment. Sized lipid-bilayer nanodiscs, established membrane protein reconstitution protocols and sophisticated solution NMR relaxation methods probing dynamics over a wide range of timescales will eventually reveal unprecedented lipid-membrane protein interdependencies that allow us to explain things we have not been able to explain so far. This review summarizes the recent developments of membrane protein dynamics with a special focus on membrane protein dynamics in lipid-bilayer nanodiscs. Solution-state NMR and lipid nanodiscs bear great potential to change our molecular understanding of lipid-membrane protein interactions

INTRODUCTION

BACKBONE RESONANCES AS PROBES FOR MEMBRANE PROTEIN DYNAMICS

METHYL GROUPS AS PROBES FOR MEMBRANE PROTEIN DYNAMICS

Findings

CONCLUSION