A guide to quantifying membrane protein dynamics in lipids and other native‐like environments by solution‐state <scp>NMR</scp> spectroscopy

Bibow, Stefan; Hiller, Sebastian

doi:10.1111/febs.14639

Cited by 20 publications

(18 citation statements)

References 109 publications

(156 reference statements)

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“…Choice of lipid environment can be pivotal for interrogation of membrane protein structure, dynamics, & function. [22][23][24][25][26] We have incorporated pSRII and OmpW into both detergent micelles as well as lipid bilayers in order to assess the potential role of membrane environment in membrane protein fast-timescale side chain dynamics. Due to their small size, micelles result in higher-quality, more comprehensive NMR data.…”

Section: Membrane Mimetic Has Little Impact On Fast Internal Motions mentioning

confidence: 99%

“…Bilayers represent a more native-like environment for membrane proteins, yet form very large assemblies, limiting signal-to-noise. Comparisons of membrane protein dynamics between lipid conditions have been restricted to limited raw backbone relaxation data; 22,23,26 we aimed here to quantitatively assess lipid environment effects by comparing dynamics directly through calculation of methyl order parameters. The NMR chemical shifts of pSRII & OmpW incorporated into micelles and bilayers are very comparable, though there are notable shifts in the OmpW 13 C-methyl spectrum likely due to change in detergent/lipid head group (Fig.…”

Section: Membrane Mimetic Has Little Impact On Fast Internal Motions mentioning

confidence: 99%

“…These comparisons suggest that fast-timescale motions are less sensitive to membrane mimetic than previously anticipated. 22,26 Due to the apparent lack of dependence of fast-timescale dynamics on lipid environment for both membrane protein systems, we pursued more detailed investigations of micelleincorporated proteins due to the improved data quality. Approximately 90/146 methyl probes in pSRII and 55/65 in OmpW had O 2 axis values sufficiently determined with acceptable precision (error < 0.10) with an average error of ± 0.038 for pSRII (see Fig.…”

Section: Membrane Mimetic Has Little Impact On Fast Internal Motions mentioning

confidence: 99%

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Membrane Proteins Have Distinct Fast Internal Motion and Residual Conformational Entropy

O’Brien

Fuglestad

Lessen

et al. 2020

Preprint

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AbstractFor a variety of reasons, the internal motions of integral membrane proteins have largely eluded comprehensive experiential characterization. Here, the fast side chain dynamics of the 7-transmembrane helix protein sensory rhodopsin II and the beta-barrel bacterial outer membrane channel protein W have been characterized in lipid bilayers and detergent micelles by solution NMR relaxation techniques. Though of quite different topologies, both proteins are found to have a similar and striking distribution of methyl-bearing amino acid side chain motion that is independent of membrane mimetic. The methyl-bearing side chains of both proteins, on average, are more dynamic in the ps-ns time regime than any soluble protein characterized to date. Approximately one third of methyl-bearing side chains exhibit extreme rotameric averaging on this timescale. Accordingly, both proteins retain an extraordinary residual conformational entropy in the folded state, which provides a counterbalance to the absence of the hydrophobic effect that normally stabilizes the folded state of water-soluble proteins. Furthermore, the large reservoir of conformational entropy that is observed provides the potential to greatly influence the thermodynamics underlying a plethora of membrane protein functions including ligand binding, allostery and signaling.

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Section: Membrane Mimetic Has Little Impact On Fast Internal Motions mentioning

confidence: 99%

Section: Membrane Mimetic Has Little Impact On Fast Internal Motions mentioning

confidence: 99%

Section: Membrane Mimetic Has Little Impact On Fast Internal Motions mentioning

confidence: 99%

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Membrane Proteins Have Distinct Fast Internal Motion and Residual Conformational Entropy

O’Brien

Fuglestad

Lessen

et al. 2020

Preprint

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“…However, only a few studies reported the lipidomics of bacteria under cold stress, which are possibly due to the complexity and distinct types of lipids that can be found in different bacteria. Also, the most commonly used methods for the analysis of lipids in bacteria are thin-layer chromatography (TLC, reviewed by Fuchs [10]), gas chromatography (GC) [11,12], and nuclear magnetic resonance (NMR) [13,14], which offer limited information. Now, some methods based on mass spectrometry (MS) have been used for the detailed analysis of bacterial cell membranes lipidomics, including directly analyzing lipid extracts by matrix-assisted laser desorption ionization (MALDI) [15,16], liquid chromatography (LC) [17], and electrospray ionization (ESI) [16,18,19] coupled to MS.…”

Section: Introductionmentioning

confidence: 99%

Quantitative Analysis of Cold Stress Inducing Lipidomic Changes in Shewanella putrefaciens Using UHPLC-ESI-MS/MS

et al. 2019

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Shewanella putrefaciens is a well-known specific spoilage organism (SSO) and cold-tolerant microorganism in refrigerated fresh marine fish. Cold-adapted mechanism includes increased fluidity of lipid membranes by the ability to finely adjust lipids composition. In the present study, the lipid profile of S. putrefaciens cultivated at 30, 20, 10, 4, and 0 °C was explored using ultra-high-pressure liquid chromatography/electrospray ionization tandem mass spectrometry (UHPLC-ESI-MS/MS) to discuss the effect of lipid composition on cold-adapted tolerance. Lipidomic analysis detected a total of 27 lipid classes and 606 lipid molecular species in S. putrefaciens cultivated at 30, 20, 10, 4, and 0 °C. S. putrefaciens cultivated at 30 °C (SP-30) had significantly higher content of glycerolipids, sphingolipids, saccharolipids, and fatty acids compared with that at 0 °C (SP-0); however, the lower content of phospholipids (13.97%) was also found in SP-30. PE (30:0), PE (15:0/15:0), PE (31:0), PA (33:1), PE (32:1), PE (33:1), PE (25:0), PC (22:0), PE (29:0), PE (34:1), dMePE (15:0/16:1), PE (31:1), dMePE (15:1/15:0), PG (34:2), and PC (11:0/11:0) were identified as the most abundant lipid molecular species in S. putrefaciens cultivated at 30, 20, 10, 4, and 0 °C. The increase of PG content contributes to the construction of membrane lipid bilayer and successfully maintains membrane integrity under cold stress. S. putrefaciens cultivated at low temperature significantly increased the total unsaturated liquid contents but decreased the content of saturated liquid contents.

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“…(C) The multidrug transporter EmrE alternates between the outward- and inward-open state about 5 times per second (PDB: 3B5D). Figure modified with permission from Bibow and Hiller (2018).…”

Section: Introductionmentioning

confidence: 99%

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

Bibow

2019

Front. Mol. Biosci.

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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.

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A guide to quantifying membrane protein dynamics in lipids and other native‐like environments by solution‐state NMR spectroscopy

Cited by 20 publications

References 109 publications

Membrane Proteins Have Distinct Fast Internal Motion and Residual Conformational Entropy

Membrane Proteins Have Distinct Fast Internal Motion and Residual Conformational Entropy

Quantitative Analysis of Cold Stress Inducing Lipidomic Changes in Shewanella putrefaciens Using UHPLC-ESI-MS/MS

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

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