scholarly journals NMR structures of membrane proteins in phospholipid bilayers

2014 ◽  
Vol 47 (3) ◽  
pp. 249-283 ◽  
Author(s):  
Jasmina Radoicic ◽  
George J. Lu ◽  
Stanley J. Opella
Keyword(s):  
Membrane Proteins ◽  
Phospholipid Bilayers ◽  
Phospholipid Bilayer ◽  
Side Chain ◽  
Physiological Conditions ◽  
X Ray Crystallography ◽  
Nmr Structures ◽  
Lipid Environment ◽  
And Function

AbstractMembrane proteins have always presented technical challenges for structural studies because of their requirement for a lipid environment. Multiple approaches exist including X-ray crystallography and electron microscopy that can give significant insights into their structure and function. However, nuclear magnetic resonance (NMR) is unique in that it offers the possibility of determining the structures of unmodified membrane proteins in their native environment of phospholipid bilayers under physiological conditions. Furthermore, NMR enables the characterization of the structure and dynamics of backbone and side chain sites of the proteins alone and in complexes with both small molecules and other biopolymers. The learning curve has been steep for the field as most initial studies were performed under non-native environments using modified proteins until ultimately progress in both techniques and instrumentation led to the possibility of examining unmodified membrane proteins in phospholipid bilayers under physiological conditions. This review aims to provide an overview of the development and application of NMR to membrane proteins. It highlights some of the most significant structural milestones that have been reached by NMR spectroscopy of membrane proteins, especially those accomplished with the proteins in phospholipid bilayer environments where they function.

Biophysical methods toolbox to study ABC exporter structure and function

2017 ◽  
Vol 398 (2) ◽  
pp. 229-235
Author(s):  
Thomas Marcellino ◽  
Vasundara Srinivasan
Keyword(s):  
Membrane Proteins ◽  
Abc Transporter ◽  
Integrated Approach ◽  
Structure And Function ◽  
Dynamic Membrane ◽  
Biophysical Characterization ◽  
Intermediate States ◽  
And Function

Abstract ABC exporters are highly dynamic membrane proteins that span a huge spectrum of different conformations. A detailed integrated approach of cellular, biochemical and biophysical characterization of these ‘open’, ‘closed’ and other intermediate states is central to understanding their function. Almost 40 years after the discovery of the first ABC transporter, thanks to the enormous development in methodologies, a picture is slowly emerging to visualize how these fascinating molecules transport their substrates. This mini review summarizes some of the biophysical tools that have made a major impact in understanding the function of the ABC exporters.

Cryo-Electron Microscopy: Moving Beyond X-Ray Crystal Structures for Drug Receptors and Drug Development

2020 ◽  
Vol 60 (1) ◽  
pp. 51-71 ◽  
Author(s):  
Javier García-Nafría ◽  
Christopher G. Tate
Keyword(s):  
Membrane Proteins ◽  
G Protein ◽  
Rational Design ◽  
Protein Complexes ◽  
Host Cells ◽  
X Ray ◽  
X Ray Crystallography ◽  
Receptor Modulation ◽  
Lipid Environment ◽  
Drug Receptors

Electron cryo-microscopy (cryo-EM) has revolutionized structure determination of membrane proteins and holds great potential for structure-based drug discovery. Here we discuss the potential of cryo-EM in the rational design of therapeutics for membrane proteins compared to X-ray crystallography. We also detail recent progress in the field of drug receptors, focusing on cryo-EM of two protein families with established therapeutic value, the γ-aminobutyric acid A receptors (GABAARs) and G protein–coupled receptors (GPCRs). GABAARs are pentameric ion channels, and cryo-EM structures of physiological heteromeric receptors in a lipid environment have uncovered the molecular basis of receptor modulation by drugs such as diazepam. The structures of ten GPCR–G protein complexes from three different classes of GPCRs have now been determined by cryo-EM. These structures give detailed insights into molecular interactions with drugs, GPCR–G protein selectivity, how accessory membrane proteins alter receptor–ligand pharmacology, and the mechanism by which HIV uses GPCRs to enter host cells.

scholarly journals Cholesterol in sarcoplasmic reticulum and the physiological significance of membrane fluidity

1981 ◽  
Vol 196 (2) ◽  
pp. 505-511 ◽  
Author(s):  
A Johannsson ◽  
C A Keightley ◽  
G A Smith ◽  
J C Metcalfe
Keyword(s):  
Sarcoplasmic Reticulum ◽  
Membrane Proteins ◽  
Atpase Activity ◽  
Membrane Fluidity ◽  
Operating Conditions ◽  
Phospholipid Bilayer ◽  
General Question ◽  
Rabbit Muscle ◽  
Large Decrease ◽  
Physiological Conditions

Vesicles of sarcoplasmic reticulum from rabbit muscle can be loaded with cholesterol to at least 20 mol% with respect to endogenous sarcoplasmic-reticulum phospholipid without effect on the ATPase activity at 32 degrees C. This applies both to sarcoplasmic-reticulum vesicles in which the ATPase activity is stably coupled to Ca2+ accumulation, and to sarcoplasmic-reticulum vesicles in which the sarcoplasmic-reticulum ATPase is activated severalfold by fully uncoupling the enzyme from net Ca2+ accumulation. Since the incorporation of cholesterol causes a large decrease in fluidity of sarcoplasmic-reticulum phospholipid bilayer, these results for sarcoplasmic reticulum raise the more general question of whether bilayer fluidity is important in modulating the function of membrane proteins under physiological conditions as is widely assumed, or whether the function of membrane proteins may be effectively buffered under normal operating conditions against changes in bilayer fluidity due to extraneous agents.

scholarly journals Towards a native environment: structure and function of membrane proteins in lipid bilayers by NMR

2021 ◽  
Author(s):  
Kai Xue ◽  
Kumar Tekwani Movellan ◽  
Xizhou Cecily Zhang ◽  
Eszter E. Najbauer ◽  
Marcel C. Forster ◽  
...  
Keyword(s):  
Solid State ◽  
Membrane Proteins ◽  
Small Molecules ◽  
Lipid Bilayers ◽  
Biological Samples ◽  
Solid State Nmr ◽  
Structure And Function ◽  
Versatile Technique ◽  
And Function

Solid-state NMR (ssNMR) is a versatile technique that can be used for the characterization of various materials, ranging from small molecules to biological samples, including membrane proteins, as reviewed here.

scholarly journals Structural Characterization of an Alternative Mode of Tigecycline Binding to the Bacterial Ribosome

2015 ◽  
Vol 59 (5) ◽  
pp. 2849-2854 ◽  
Author(s):  
Andreas Schedlbauer ◽  
Tatsuya Kaminishi ◽  
Borja Ochoa-Lizarralde ◽  
Neha Dhimole ◽  
Shu Zhou ◽  
...  
Keyword(s):  
Ribosomal Subunit ◽  
Resistance Mechanisms ◽  
Side Chain ◽  
Alternative Mode ◽  
X Ray Crystallography ◽  
Bacterial Ribosome ◽  
A Site

ABSTRACTAlthough both tetracycline and tigecycline inhibit protein synthesis by sterically hindering the binding of tRNA to the ribosomal A site, tigecycline shows increased efficacy in bothin vitroandin vivoactivity assays and escapes the most common resistance mechanisms associated with the tetracycline class of antibiotics. These differences in activities are attributed to thetert-butyl-glycylamido side chain found in tigecycline. Our structural analysis by X-ray crystallography shows that tigecycline binds the bacterial 30S ribosomal subunit with its tail in an extended conformation and makes extensive interactions with the 16S rRNA nucleotide C1054. These interactions restrict the mobility of C1054 and contribute to the antimicrobial activity of tigecycline, including its resistance to the ribosomal protection proteins.

scholarly journals Mass spectrometry of membrane protein complexes

2019 ◽  
Vol 400 (7) ◽  
pp. 813-829 ◽  
Author(s):  
Julian Bender ◽  
Carla Schmidt
Keyword(s):  
Mass Spectrometry ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Membrane Protein Complexes ◽  
Hydrophobic Nature ◽  
Alternative Approaches ◽  
Lipid Environment ◽  
And Function

Abstract Membrane proteins are key players in the cell. Due to their hydrophobic nature they require solubilising agents such as detergents or membrane mimetics during purification and, consequently, are challenging targets in structural biology. In addition, their natural lipid environment is crucial for their structure and function further hampering their analysis. Alternative approaches are therefore required when the analysis by conventional techniques proves difficult. In this review, we highlight the broad application of mass spectrometry (MS) for the characterisation of membrane proteins and their interactions with lipids. We show that MS unambiguously identifies the protein and lipid components of membrane protein complexes, unravels their three-dimensional arrangements and further provides clues of protein-lipid interactions.

scholarly journals The power, pitfalls and potential of the nanodisc system for NMR-based studies

2016 ◽  
Vol 397 (12) ◽  
pp. 1335-1354 ◽  
Author(s):  
Aldino Viegas ◽  
Thibault Viennet ◽  
Manuel Etzkorn
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Membrane Proteins ◽  
Lipid Bilayer ◽  
Structure And Function ◽  
Fundamental Importance ◽  
Future Studies ◽  
And Function ◽  
Unique Potential

Abstract The choice of a suitable membrane mimicking environment is of fundamental importance for the characterization of structure and function of membrane proteins. In this respect, usage of the lipid bilayer nanodisc technology provides a unique potential for nuclear magnetic resonance (NMR)-based studies. This review summarizes the recent advances in this field, focusing on (i) the strengths of the system, (ii) the bottlenecks that may be faced, and (iii) promising capabilities that may be explored in future studies.

Nanodisc characterization by analytical ultracentrifugation

2017 ◽  
Vol 6 (1) ◽  
pp. 3-14 ◽  
Author(s):  
Sayaka Inagaki ◽  
Rodolfo Ghirlando
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Analytical Ultracentrifugation ◽  
Size Composition ◽  
Functional Studies ◽  
Lipid Environment ◽  
The Many ◽  
Sample Homogeneity ◽  
Simple Fashion

AbstractDue to their unique properties, tunable size, and ability to provide a near native lipid environment, nanodiscs have found widespread use for the structural and functional studies of reconstituted membrane proteins. They have also been developed, albeit in a few applications, for therapeutic and biomedical use. For these studies and applications, it is essential to characterize the nanodisc preparations in terms of their monodispersity, size, and composition, as these can influence the properties of the membrane protein of interest. Of the many biophysical methods utilized for the study and characterization of nanodiscs, we show that analytical ultracentrifugation is able to report on sample homogeneity, shape, size, composition, and membrane protein stoichiometry or oligomerization state in a direct and simple fashion. The method is truly versatile and does not require nanodisc modification or disassembly.

scholarly journals N-Amino-imidazol-2-one (Nai) Residues as Tools for Peptide Mimicry: Synthesis, Conformational Analysis and Biomedical Applications

Synthesis ◽  
2022 ◽  
Author(s):  
William D. Lubell ◽  
Yousra Hamdane ◽  
Julien Poupart
Keyword(s):  
Conformational Analysis ◽  
Biomedical Applications ◽  
Biologically Active ◽  
Synthetic Methods ◽  
Side Chain ◽  
Peptide Backbone ◽  
X Ray Crystallography ◽  
Side Chain Conformation ◽  
Peptide Mimicry ◽  
And Function

Abstract N-Amino-imidazol-2-one (Nai) residues are tools for studying peptide-backbone and side-chain conformation and function. Recent methods for substituted Nai residue synthesis, conformational analysis by X-ray crystallography and computation, and biomedical applications are reviewed, demonstrating the utility of this constrained residue to favor biologically active turn conformers with defined χ-dihedral angle orientations.1 Introduction2 Synthetic Methods3 Conformational Analysis4 Biomedical Applications5 Conclusions

scholarly journals New Insights on Structure and Function of Sialyltransferases

2014 ◽  
Vol 70 (a1) ◽  
pp. C482-C482
Author(s):  
Gesa Volkers ◽  
Liam Worrall ◽  
Emilie Lameignere ◽  
Natalie Strynadka
Keyword(s):  
Sialic Acid ◽  
Schwann Cells ◽  
Molecular Mechanisms ◽  
Neuronal Development ◽  
X Ray Crystallography ◽  
Mechanism Of Catalysis ◽  
Function Relationship ◽  
And Function ◽  
Relationship Of

Sialic acids are a unique posttranslational modification at the terminus of glycoproteins and -lipids. Proteins modified with oligomers of sialic acid add a repellent charge to cell surfaces, which is a crucial feature in cell migration and axonal growth during early brain development. Varied expression levels of sialic acid are linked to tumor malignancy in neuroblastoma, schizophrenia, autism and bipolar disorder but the lack thereof is linked to impaired neuronal development. On the other hand, overexpression of sialic acid oligomers in Schwann cells promotes the peripheral regeneration of lesioned nerves and improves the ability of Schwann cells to migrate into damaged tissue and to remyelinate central nervous system axons. In order to understand the molecular mechanisms of sialylation, our project focuses on the structural characterization of enzymes of the mammalian and bacterial glycosyltransferase families 29 and 42. The proteins of interest were expressed in insect cells and structural studies were undertaken by x-ray crystallography. Kinetics, SEC MALS and glycan array data will shed light on mechanism of catalysis and acceptor specificity. Altogether, the results of this study will promote further understanding of the structure-function relationship of sialyltransferases.

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