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The Journal of Biological Chemistry 2021Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out... (Review)
Review
Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact.
Topics: Databases, Protein; History, 20th Century; History, 21st Century; Membrane Proteins; Protein Conformation; Structure-Activity Relationship
PubMed: 33744283
DOI: 10.1016/j.jbc.2021.100557 -
The Journal of Membrane Biology Feb 2021Membrane proteins govern critical cellular processes and are central to human health and associated disease. Understanding of membrane protein function is obscured by... (Review)
Review
Membrane proteins govern critical cellular processes and are central to human health and associated disease. Understanding of membrane protein function is obscured by the vast ranges of structural dynamics-both in the spatial and time regime-displayed in the protein and surrounding membrane. The membrane lipids have emerged as allosteric modulators of membrane protein function, which further adds to the complexity. In this review, we discuss several examples of membrane dependency. A particular focus is on how molecular dynamics (MD) simulation have aided to map membrane protein dynamics and how enhanced sampling methods can enable observing the otherwise inaccessible biological time scale. Also, time-resolved X-ray scattering in solution is highlighted as a powerful tool to track membrane protein dynamics, in particular when combined with MD simulation to identify transient intermediate states. Finally, we discuss future directions of how to further develop this promising approach to determine structural dynamics of both the protein and the surrounding lipids.
Topics: Humans; Membrane Proteins
PubMed: 33409541
DOI: 10.1007/s00232-020-00165-8 -
FEBS Letters Jul 2015Cell-free protein production has become a core technology in the rapidly spreading field of synthetic biology. In particular the synthesis of membrane proteins, highly... (Review)
Review
Cell-free protein production has become a core technology in the rapidly spreading field of synthetic biology. In particular the synthesis of membrane proteins, highly problematic proteins in conventional cellular production systems, is an ideal application for cell-free expression. A large variety of artificial as well as natural environments for the optimal co-translational folding and stabilization of membrane proteins can rationally be designed. The high success rate of cell-free membrane protein production allows to focus on individually selected targets and to modulate their functional and structural properties with appropriate supplements. The efficiency and robustness of lysates from Escherichia coli strains allow a wide diversity of applications and we summarize current strategies for the successful production of high quality membrane protein samples.
Topics: Cell-Free System; Escherichia coli; Membrane Proteins; Protein Biosynthesis; Protein Folding; Recombinant Proteins
PubMed: 25937121
DOI: 10.1016/j.febslet.2015.04.045 -
Annual Review of Cell and Developmental... Oct 2017Proper localization of membrane proteins is essential for the function of biological membranes and for the establishment of organelle identity within a cell. Molecular... (Review)
Review
Proper localization of membrane proteins is essential for the function of biological membranes and for the establishment of organelle identity within a cell. Molecular machineries that mediate membrane protein biogenesis need to not only achieve a high degree of efficiency and accuracy, but also prevent off-pathway aggregation events that can be detrimental to cells. The posttranslational targeting of tail-anchored proteins (TAs) provides tractable model systems to probe these fundamental issues. Recent advances in understanding TA-targeting pathways reveal sophisticated molecular machineries that drive and regulate these processes. These findings also suggest how an interconnected network of targeting factors, cochaperones, and quality control machineries together ensures robust membrane protein biogenesis.
Topics: Animals; Humans; Membrane Proteins; Models, Biological; Protein Sorting Signals; Protein Transport
PubMed: 28992441
DOI: 10.1146/annurev-cellbio-100616-060839 -
Biochemistry and Cell Biology =... Dec 2016Membrane proteins are still heavily under-represented in the protein data bank (PDB), owing to multiple bottlenecks. The typical low abundance of membrane proteins in... (Review)
Review
Membrane proteins are still heavily under-represented in the protein data bank (PDB), owing to multiple bottlenecks. The typical low abundance of membrane proteins in their natural hosts makes it necessary to overexpress these proteins either in heterologous systems or through in vitro translation/cell-free expression. Heterologous expression of proteins, in turn, leads to multiple obstacles, owing to the unpredictability of compatibility of the target protein for expression in a given host. The highly hydrophobic and (or) amphipathic nature of membrane proteins also leads to challenges in producing a homogeneous, stable, and pure sample for structural studies. Circumventing these hurdles has become possible through the introduction of novel protein production protocols; efficient protein isolation and sample preparation methods; and, improvement in hardware and software for structural characterization. Combined, these advances have made the past 10-15 years very exciting and eventful for the field of membrane protein structural biology, with an exponential growth in the number of solved membrane protein structures. In this review, we focus on both the advances and diversity of protein production and purification methods that have allowed this growth in structural knowledge of membrane proteins through X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM).
Topics: Animals; Crystallography, X-Ray; Humans; Membrane Proteins
PubMed: 27010607
DOI: 10.1139/bcb-2015-0143 -
The FEBS Journal Oct 2021Membrane proteins play critical physiological roles in all organisms, from ion transport and signal transduction to multidrug resistance. Elucidating their 3D structures... (Review)
Review
Membrane proteins play critical physiological roles in all organisms, from ion transport and signal transduction to multidrug resistance. Elucidating their 3D structures is essential for understanding their functions, and this information can also be exploited for structure-aided drug discovery efforts. In this regard, X-ray crystallography has been the most widely used technique for determining the high-resolution 3D structures of membrane proteins. However, the success of this technique is dependent on efficient protein extraction, solubilization, stabilization, and generating diffracting crystals. Each of these steps can impose great challenges for membrane protein crystallographers. In this review, the process of generating membrane protein crystals from protein extraction and solubilization to structure determination is discussed. In addition, the current methods for precrystallization screening and a few strategies to increase the chance of crystallizing challenging membrane proteins are introduced.
Topics: Animals; Crystallization; Crystallography, X-Ray; Humans; Membrane Proteins; Protein Conformation
PubMed: 33340246
DOI: 10.1111/febs.15676 -
Biomolecules Mar 2014Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic... (Review)
Review
Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins. In comparison, advances in the membrane protein folding field lag far behind. Although membrane proteins constitute about a third of the proteins encoded in known genomes, stability studies on membrane proteins have been impaired due to experimental limitations. Furthermore, no systematic experimental strategies are available for folding these biomolecules in vitro. Common denaturing agents such as chaotropes usually do not work on helical membrane proteins, and ionic detergents have been successful denaturants only in few cases. Refolding a membrane protein seems to be a craftsman work, which is relatively straightforward for transmembrane β-barrel proteins but challenging for α-helical membrane proteins. Additional complexities emerge in multidomain membrane proteins, data interpretation being one of the most critical. In this review, we will describe some recent efforts in understanding the folding mechanism of membrane proteins that have been reversibly refolded allowing both thermodynamic and kinetic analysis. This information will be discussed in the context of current paradigms in the protein folding field.
Topics: Animals; Humans; Kinetics; Membrane Proteins; Protein Conformation; Protein Folding; Thermodynamics
PubMed: 24970219
DOI: 10.3390/biom4010354 -
Chemistry and Physics of Lipids Jan 2019The concept of a memtein as the minimal unit of membrane function is proposed here, and refers to the complex of a membrane protein together with a continuous layer of... (Review)
Review
The concept of a memtein as the minimal unit of membrane function is proposed here, and refers to the complex of a membrane protein together with a continuous layer of biological lipid molecules. The elucidation of the atomic resolution structures and specific interactions within memteins remains technically challenging. Nonetheless, we argue that these entities are critical endpoints for the postgenomic era, being essential units of cellular function that mediate signal transduction and trafficking. Their biological mechanisms and molecular compositions can be resolved using native nanodiscs formed by poly(styrene-co-maleic acid) (SMA) copolymers. These amphipathic polymers rapidly and spontaneously fragment membranes into water-soluble discs holding a section of bilayer. This allows structures of complexes found in vivo to be prepared without resorting to synthetic detergents or artificial lipids. The ex situ structures of memteins can be resolved by methods including cryo-electron microscopy (cEM), X-ray crystallography (XRC), NMR spectroscopy and mass spectrometry (MS). Progress in the field demonstrates that memteins are better representations of how biology actually works in membranes than naked proteins devoid of lipid, spurring on further advances in polymer chemistry to resolve their details.
Topics: Humans; Lipid Bilayers; Lipids; Membrane Proteins; Molecular Structure
PubMed: 30508515
DOI: 10.1016/j.chemphyslip.2018.11.008 -
Science China. Life Sciences Jan 2015Membrane proteins are involved in various critical biological processes, and studying membrane proteins represents a major challenge in protein biochemistry. As shown by... (Review)
Review
Membrane proteins are involved in various critical biological processes, and studying membrane proteins represents a major challenge in protein biochemistry. As shown by both structural and functional studies, the membrane environment plays an essential role for membrane proteins. In vitro studies are reliant on the successful reconstitution of membrane proteins. This review describes the interaction between detergents and lipids that aids the understanding of the reconstitution processes. Then the techniques of detergent removal and a few useful techniques to refine the formed proteoliposomes are reviewed. Finally the applications of reconstitution techniques to study membrane proteins involved in Ca(2+) signaling are summarized.
Topics: Detergents; In Vitro Techniques; Membrane Proteins; Microscopy, Electron; Structure-Activity Relationship
PubMed: 25576454
DOI: 10.1007/s11427-014-4769-0 -
Current Biology : CB Apr 2018One-fourth of eukaryotic genes code for integral membrane proteins, nearly all of which are inserted and assembled at the endoplasmic reticulum (ER). The defining... (Review)
Review
One-fourth of eukaryotic genes code for integral membrane proteins, nearly all of which are inserted and assembled at the endoplasmic reticulum (ER). The defining feature of membrane proteins is one or more transmembrane domains (TMDs). During membrane protein biogenesis, TMDs are selectively recognized, shielded, and chaperoned into the lipid bilayer, where they often assemble with other TMDs. If maturation fails, exposed TMDs serve as a cue for engagement of degradation pathways. Thus, TMD-recognition factors in the cytosol and ER are essential for membrane protein biogenesis and quality control. Here, we discuss the growing assortment of cytosolic and membrane-embedded TMD-recognition factors, the pathways within which they operate, and mechanistic principles of recognition.
Topics: Animals; Cytosol; Endoplasmic Reticulum; Humans; Membrane Proteins; Molecular Chaperones; Protein Biosynthesis; Protein Domains; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 29689233
DOI: 10.1016/j.cub.2018.02.004