Structure and Dynamic Properties of Membrane Proteins using NMR

Abstract

Integral membrane proteins are one of the most challenging groups of macromolecules despite their apparent conformational simplicity. They manage and drive transport, circulate information, and participate in cellular movements via interactions with other proteins and through intricate conformational changes. Their structural and functional decoding is challenging and has imposed demanding experimental development. Solution nuclear magnetic resonance (NMR) spectroscopy is one of the techniques providing the capacity to make a significant difference in the deciphering of the membrane protein structure‐function paradigm. The method has evolved dramatically during the last decade resulting in a plethora of new experiments leading to a significant increase in the scientific repertoire for studying membrane proteins. Besides solving the three‐dimensional structures using state‐of‐the‐art approaches, a large variety of developments of well‐established techniques are available providing insight into membrane protein flexibility, dynamics, and interactions. Inspired by the speed of development in the application of new strategies, by invention of methods to measure solvent accessibility and describe low‐populated states, this review seeks to introduce the vast possibilities solution NMR can offer to the study of membrane protein structure‐function analyses with special focus on applicability. © 2012 American Physiological Society. Compr Physiol 2:1491‐1539, 2012.

Understanding single‐pass transmembrane receptor signaling from a structural viewpoint—what are we missing?

“…Within the currently feasible size range is, e.g., organic solvents, detergents, and bicelles, where the latter two represent the most widely used systems to solubilize membrane proteins for NMR studies. Several excellent reviews are available describing the broader palette of membrane‐mimicking solvents for solution‐state NMR spectroscopy as well as detailing the process of structure determination of membrane proteins by this technique . Importantly, it is well established that membrane mimetics may influence the quality of the collected data as well as the structural properties of membrane proteins significantly , and it is likely that certain types of helix–helix interactions are exaggerated or reduced in membrane mimetics of varying types .…”

“…As evident from Table and outlined above, only a modest number of NOE restraints have been collected on the currently solved SPTMR‐TMD structures as a group. The reason for the poor output of NOEs from single‐pass TMDs is probably multifold, with increased linewidth due to the large‐sized micelle–protein complexes, few protein–protein contacts, and transient interactions as the suspected main causes . With the inadequacy of the usual primary NMR‐work horse, the NOE, additional restraints, as well as new or optimized NMR methods are evidently needed to increase the qualities of the structures of these proteins.…”

Can proteins be intrinsically disordered inside a membrane?

“…42 Furthermore, the addition of lipids dramatically increase the tumbling time of the protein with associated problems for solutions NMR which is a difficult problem even for well-behaved membrane proteins. 43 However, if the conformational exchange falls in appropriate time scales, NMR can be very powerful as described in the preceding section.…”

Exploiting Hydrophobicity for Efficient Production of Transmembrane Helices for Structure Determination by NMR Spectroscopy

“…5 This significant underrepresentation constitutes a critical bottleneck in the molecular understanding of many important biological systems and predominantly originates from the methodological challenges associated with structural studies of membrane proteins. 6 Significant progress in structure determination of membrane proteins by NMR spectroscopy has occurred within the past decade, 5 but the growth in available structures remains hampered by three major obstacles. First, the establishment of a recombinant production protocol allowing for isotope labeling as well as a high yield is considered a major bottleneck.…”

“…Currently, integral membrane proteins constitute only 2.2% of the RCSB Protein Data Bank (PDB) repository, and of these, ∼70% are of prokaryotic origin . This significant under-representation constitutes a critical bottleneck in the molecular understanding of many important biological systems and predominantly originates from the methodological challenges associated with structural studies of membrane proteins …”