Solid-state NMR structures of integral membrane proteins

Exploring the World of Membrane Proteins: Techniques and Methods for Understanding Structure, Function, and Dynamics

In eukaryotic cells, membrane proteins play a crucial role. They fall into three categories: intrinsic proteins, extrinsic proteins, and proteins that are essential to the human genome (30% of which is devoted to encoding them). Hydrophobic interactions inside the membrane serve to stabilize integral proteins, which span the lipid bilayer. This review investigates a number of computational and experimental methods used to study membrane proteins. It encompasses a variety of technologies, including electrophoresis, X-ray crystallography, cryogenic electron microscopy (cryo-EM), nuclear magnetic resonance spectroscopy (NMR), biophysical methods, computational methods, and artificial intelligence. The link between structure and function of membrane proteins has been better understood thanks to these approaches, which also hold great promise for future study in the field. The significance of fusing artificial intelligence with experimental data to improve our comprehension of membrane protein biology is also covered in this paper. This effort aims to shed light on the complexity of membrane protein biology by investigating a variety of experimental and computational methods. Overall, the goal of this review is to emphasize how crucial it is to understand the functions of membrane proteins in eukaryotic cells. It gives a general review of the numerous methods used to look into these crucial elements and highlights the demand for multidisciplinary approaches to advance our understanding.

Lipid Membrane Mimetics in Functional and Structural Studies of Integral Membrane Proteins

Integral membrane proteins (IMPs) fulfill important physiological functions by providing cell-environment, cell-cell and virus-host communication; nutrients intake; export of toxic compounds out of cells; and more. However, some IMPs have obliterated functions due to polypeptide mutations, modifications in membrane properties and/or other environmental factors-resulting in damaged binding to ligands and the adoption of non-physiological conformations that prevent the protein from returning to its physiological state. Thus, elucidating IMPs' mechanisms of function and malfunction at the molecular level is important for enhancing our understanding of cell and organism physiology. This understanding also helps pharmaceutical developments for restoring or inhibiting protein activity. To this end, in vitro studies provide invaluable information about IMPs' structure and the relation between structural dynamics and function. Typically, these studies are conducted on transferred from native membranes to membrane-mimicking nano-platforms (membrane mimetics) purified IMPs. Here, we review the most widely used membrane mimetics in structural and functional studies of IMPs. These membrane mimetics are detergents, liposomes, bicelles, nanodiscs/Lipodisqs, amphipols, and lipidic cubic phases. We also discuss the protocols for IMPs reconstitution in membrane mimetics as well as the applicability of these membrane mimetic-IMP complexes in studies via a variety of biochemical, biophysical, and structural biology techniques.

In-Cell Solid-State NMR Analysis of Membrane Proteins

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Membrane Topology of an Ion Channel Detected by Solid-State Nuclear Magnetic Resonance and Paramagnetic Effects

Ion channels are often targeted by toxins or other ligands to modify their channel activities and alter ion conductance. Interactions between toxins and ion channels could result in changes in membrane insertion depth for residues close to the binding site. Paramagnetic solid-state nuclear magnetic resonance (SSNMR) has shown great potential in providing structural information on membrane samples. We used KcsA as a model ion channel to investigate how the paramagnetic effects of Mn²⁺ and Dy³⁺ ions with headgroup-modified chelator lipids would influence the SSNMR signals of membrane proteins in proteoliposomes. Spectral comparisons have shown significant changes of peak intensities for the residues in the loop or terminal regions due to paramagnetic effects corresponding to the close proximity to the membrane surface. Hence, these results demonstrate that paramagnetic SSNMR can be used to detect surface residues based on the topology and membrane insertion properties for integral membrane proteins.

Paramagnetic solid-state NMR of proteins

The paramagnetic properties of metal ions and stable radicals can affect NMR spectra, which can lead to changes in peak intensities, relaxation times and chemical shifts. The changes from paramagnetic effects provide intriguing opportunities for solid-state NMR studies of proteins. In this review, we summarized the trends and progress of paramagnetic solid-state NMR of proteins in the past decade, and showed that paramagnetic effects have great potential applications for sensitivity enhancement, structure determination and topological analysis for microcrystalline proteins, protein complexes, protein aggregates and membrane proteins.

The Perpendicular Orientation of Amphotericin B Methyl Ester in Hydrated Lipid Bilayers Supports the Barrel-Stave Model

The clinically important antibiotic amphotericin B (AmB) is a membrane-active natural product that targets membrane sterol. The antimicrobial activity of AmB is generally attributed to its membrane permeabilization, which occurs when a pore is formed across a lipid bilayer. In this study, the molecular orientation of AmB was investigated using solid-state nuclear magnetic resonance (NMR) to better understand the mechanism of antifungal activity. The methyl ester of AmB (AME) labeled with NMR isotopes, d₃-AME, and its fluorinated and/or ¹³C-labeled derivatives were prepared. All of the AmB derivatives showed similar membrane-disrupting activities and ultraviolet spectra in phospholipid liposomes, suggesting that their molecular assemblies in membranes closely mimic those of AmB. Solid-state ²H NMR measurements of d₃-AME in a hydrated membrane showed that the mobility of AME molecules depends on concentration and temperature. At a 1:5:45 AME:Erg:dimyristoylphosphatidylcholine ratio, AME became sufficiently mobilized to observe the motional averaging of quadrupole coupling. On the basis of the rotational averaging effect of ¹⁹F chemical shift anisotropy, ²H quadrupolar splitting, and ¹³C-¹⁹F dipolar coupling of 14β-F-AMEs, we deduced that the molecular axis of AME is predominantly parallel to the normal of a lipid bilayer. This result supports the barrel-stave model as a molecular assembly of AmB in membranes.

Effects of chelator lipids, paramagnetic metal ions and trehalose on liposomes by solid-state NMR

The effects of various lipid bound paramagnetic metal ions on liposomes prepared in the presence of trehalose and chelator lipids are evaluated to observe site-specific signal changes on liposome samples with optimal resolution in solid-state NMR spectroscopy. We found that Mn²⁺, Gd³⁺ and Dy³⁺ have different influences on the lipid ¹³C sites depending on their penetration depths into the bilayer, which can be extracted as distance information. The trehalose-liposome mixture is efficiently packed into solid-state NMR rotors and provides optimal resolution at reasonable instrument temperatures (10-50 °C). The effectiveness and convenience of the trehalose preparation for studying a membrane protein in liposomes are demonstrated by a membrane sample with a model membrane peptide to show that trehalose is useful to prepare consistent and stable membrane protein liposome samples for solid-state NMR.

Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies

Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents.

Efflux proteins at the blood-brain barrier: review and bioinformatics analysis

1. Efflux proteins at the blood-brain barrier provide a mechanism for export of waste products of normal metabolism from the brain and help to maintain brain homeostasis. They also prevent entry into the brain of a wide range of potentially harmful compounds such as drugs and xenobiotics. 2. Conversely, efflux proteins also hinder delivery of therapeutic drugs to the brain and central nervous system used to treat brain tumours and neurological disorders. For bypassing efflux proteins, a comprehensive understanding of their structures, functions and molecular mechanisms is necessary, along with new strategies and technologies for delivery of drugs across the blood-brain barrier. 3. We review efflux proteins at the blood-brain barrier, classified as either ATP-binding cassette (ABC) transporters (P-gp, BCRP, MRPs) or solute carrier (SLC) transporters (OATP1A2, OATP1A4, OATP1C1, OATP2B1, OAT3, EAATs, PMAT/hENT4 and MATE1). 4. This includes information about substrate and inhibitor specificity, structural organisation and mechanism, membrane localisation, regulation of expression and activity, effects of diseases and conditions and the principal technique used for in vivo analysis of efflux protein activity: positron emission tomography (PET). 5. We also performed analyses of evolutionary relationships, membrane topologies and amino acid compositions of the proteins, and linked these to structure and function.

Backbone assignment of perdeuterated proteins by solid-state NMR using proton detection and ultrafast magic-angle spinning

Solid-state NMR (ssNMR) is a technique that allows the study of protein structure and dynamics at atomic detail. In contrast to X-ray crystallography and cryo-electron microscopy, proteins can be studied under physiological conditions-for example, in a lipid bilayer and at room temperature (0-35 °C). However, ssNMR requires considerable amounts (milligram quantities) of isotopically labeled samples. In recent years, ¹H-detection of perdeuterated protein samples has been proposed as a method of alleviating the sensitivity issue. Such methods are, however, substantially more demanding to the spectroscopist, as compared with traditional ¹³C-detected approaches. As a guide, this protocol describes a procedure for the chemical shift assignment of the backbone atoms of proteins in the solid state by ¹H-detected ssNMR. It requires a perdeuterated, uniformly ¹³C- and ¹⁵N-labeled protein sample with subsequent proton back-exchange to the labile sites. The sample needs to be spun at a minimum of 40 kHz in the NMR spectrometer. With a minimal set of five 3D NMR spectra, the protein backbone and some of the side-chain atoms can be completely assigned. These spectra correlate resonances within one amino acid residue and between neighboring residues; taken together, these correlations allow for complete chemical shift assignment via a 'backbone walk'. This results in a backbone chemical shift table, which is the basis for further analysis of the protein structure and/or dynamics by ssNMR. Depending on the spectral quality and complexity of the protein, data acquisition and analysis are possible within 2 months.