51
|
Designing minimalist membrane proteins. Biochem Soc Trans 2020; 47:1233-1245. [PMID: 31671181 PMCID: PMC6824673 DOI: 10.1042/bst20190170] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 12/13/2022]
Abstract
The construction of artificial membrane proteins from first principles is of fundamental interest and holds considerable promise for new biotechnologies. This review considers the potential advantages of adopting a strictly minimalist approach to the process of membrane protein design. As well as the practical benefits of miniaturisation and simplicity for understanding sequence-structure-function relationships, minimalism should also support the abstract conceptualisation of membrane proteins as modular components for synthetic biology. These ideas are illustrated with selected examples that focus upon α-helical membrane proteins, and which demonstrate how such minimalist membrane proteins might be integrated into living biosystems.
Collapse
|
52
|
Chen J, Sitsel A, Benoy V, Sepúlveda MR, Vangheluwe P. Primary Active Ca 2+ Transport Systems in Health and Disease. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a035113. [PMID: 31501194 DOI: 10.1101/cshperspect.a035113] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Calcium ions (Ca2+) are prominent cell signaling effectors that regulate a wide variety of cellular processes. Among the different players in Ca2+ homeostasis, primary active Ca2+ transporters are responsible for keeping low basal Ca2+ levels in the cytosol while establishing steep Ca2+ gradients across intracellular membranes or the plasma membrane. This review summarizes our current knowledge on the three types of primary active Ca2+-ATPases: the sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) pumps, the secretory pathway Ca2+- ATPase (SPCA) isoforms, and the plasma membrane Ca2+-ATPase (PMCA) Ca2+-transporters. We first discuss the Ca2+ transport mechanism of SERCA1a, which serves as a reference to describe the Ca2+ transport of other Ca2+ pumps. We further highlight the common and unique features of each isoform and review their structure-function relationship, expression pattern, regulatory mechanisms, and specific physiological roles. Finally, we discuss the increasing genetic and in vivo evidence that links the dysfunction of specific Ca2+-ATPase isoforms to a broad range of human pathologies, and highlight emerging therapeutic strategies that target Ca2+ pumps.
Collapse
Affiliation(s)
- Jialin Chen
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Aljona Sitsel
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Veronick Benoy
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - M Rosario Sepúlveda
- Department of Cell Biology, Faculty of Sciences, University of Granada, 18071 Granada, Spain
| | - Peter Vangheluwe
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| |
Collapse
|
53
|
Mitra S, Das R, Singh A, Mukhopadhyay MK, Roy G, Ghosh SK. Surface Activities of a Lipid Analogue Room-Temperature Ionic Liquid and Its Effects on Phospholipid Membrane. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:328-339. [PMID: 31826620 DOI: 10.1021/acs.langmuir.9b02716] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
There are great efforts of synthesizing imidazolium-based ionic liquids (ILs) for developing new antibiotics as these molecules have shown strong antibacterial activities. Compared to a single-hydrocarbon-chained IL, the lipid analogues (LAs) with two chains are more effective. In the present study, the LA molecule MeIm(COOH)Me(Oleylamine)Iodide has been synthesized and its surface activities along with the effectiveness in restructuring of a model cellular membrane have been quantified. The molecule is found to be highly surface active as estimated from the area-pressure isotherm of a monolayer of the molecules formed at the air-water interface. The X-ray reflectivity (XRR) studies of a monolayer dip-coated on a hydrophilic substrate have shown the structural properties of the layer which resembles to those of unsaturated phospholipids. The LA molecules are observed to fluidize a phospholipid bilayer formed by the saturated lipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC). At a lower surface pressure, the lipid monolayer of DPPC has exhibited a thickening effect at a low concentration of added LA and a thinning effect at higher concentration. However, at a high surface pressure of the monolayer, the thickness is found to decrease monotonically. The in-plane pressure-dependent interaction of LA molecules with model cellular membrane and the corresponding perturbation in the structure and physical properties of the membrane may be linked to the strong lysing effect of these types of molecules.
Collapse
Affiliation(s)
| | | | - A Singh
- Surface Physics and Material Science Division , Saha Institute of Nuclear Physics , AF Block, Bidhannagar , Kolkata 700064 , India
| | - M K Mukhopadhyay
- Surface Physics and Material Science Division , Saha Institute of Nuclear Physics , AF Block, Bidhannagar , Kolkata 700064 , India
| | | | | |
Collapse
|
54
|
Saleh N, Wang Y, Nissen P, Lindorff-Larsen K. Allosteric modulation of the sarcoplasmic reticulum Ca 2+ ATPase by thapsigargin via decoupling of functional motions. Phys Chem Chem Phys 2019; 21:21991-21995. [PMID: 31552962 DOI: 10.1039/c9cp04736k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The sarcoplasmic reticulum Ca2+-ATPase (SERCA) is a widely studied member of the large family of phosphorylation(P)-type ATPase membrane transporters. Ligands and nucleotide binding naturally modulate the conformational space of P-type ATPases through allosteric inter-domain communications. Whereas many inhibitory ATPase ligands act by directly blocking substrate uptake or release, SERCA is a target for thapsigargin (TG), a plant-derived natural product that allosterically inhibits the transport cycle. While thapsigargin's inhibitory effects on SERCA have been widely studied experimentally, the molecular mechanisms underlying these remain incompletely understood. Here, we apply modelling and molecular simulations to probe the effects of TG binding to the major functional states along SERCA's reaction cycle. Our results provide insight into the atomic-level details of the conformational changes induced by TG binding to SERCA, and suggest mechanisms for its effect. Since other P-type ATPases share closely related reaction cycles, our data suggests that similar modulators might exist for these.
Collapse
Affiliation(s)
- Noureldin Saleh
- Linderstrøm-Lang Centre for Protein Science, Dept. of Biology, University of Copenhagen, Copenhagen, Denmark.
| | | | | | | |
Collapse
|
55
|
Pedersen MC, Wang Y, Tidemand FG, Martel A, Lindorff-Larsen K, Arleth L. PSX, Protein–Solvent Exchange: software for calculation of deuterium-exchange effects in small-angle neutron scattering measurements from protein coordinates. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576719012469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Recent developments in neutron scattering instrumentation and sample handling have enabled studies of more complex biological samples and measurements at shorter exposure times. The experiments are typically conducted in D2O-based buffers to emphasize or diminish scattering from a particular component or to minimize background noise in the experiment. To extract most information from such experiments it is thus desirable to determine accurate estimates of how and when closely bound hydrogen atoms from the biomolecule exchange with the deuterium in the solvent. This article introduces and documents software, PSX, for exploring the effect of hydrogen–deuterium exchange for proteins solubilized in D2O as well as the underlying bioinformatical models. The software aims to be generally applicable for any atomistic structure of a protein and its surrounding environment, and thus captures effects of both heterogenous exchange rates throughout the protein structure and varying the experimental conditions such as pH and temperature. The paper concludes with examples of applications and estimates of the effect in typical scenarios emerging in small-angle neutron scattering on biological macromolecules in solution. The analysis presented here suggests that the common assumption of 90% exchange is in many cases an overestimate with the rapid sample handling systems currently available, which leads to fitting and calibration issues when analysing the data. Source code for the presented software is available from an online repository in which it is published under version 3 of the GNU publishing licence.
Collapse
|
56
|
Interaction of detergents with biological membranes: Comparison of fluorescence assays with filtration protocols and implications for the rates of detergent association, dissociation and flip-flop. PLoS One 2019; 14:e0222932. [PMID: 31618200 PMCID: PMC6795424 DOI: 10.1371/journal.pone.0222932] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/10/2019] [Indexed: 01/05/2023] Open
Abstract
The present study mainly consists of a re-evaluation of the rate at which C12E8, a typical non-ionic detergent used for membrane studies, is able to dissociate from biological membranes, with sarcoplasmic reticulum membrane vesicles being used as an example. Utilizing a brominated derivative of C12E8 and now stopped-flow fluorescence instead of rapid filtration, we found that the rate of dissociation of this detergent from these membranes, merely perturbed with non-solubilizing concentrations of detergent, was significantly faster (t1/2 < 10 ms) than what had previously been determined (t1/2 ~300–400 ms) from experiments based on a rapid filtration protocol using 14C-labeled C12E8 and glass fiber filters (Binding of a non-ionic detergent to membranes: flip-flop rate and location on the bilayer, by Marc le Maire, Jesper Møller and Philippe Champeil, Biochemistry (1987) Vol 26, pages 4803–4810). We here pinpoint a methodological problem of the earlier rapid filtration experiments, and we suggest that the true overall dissociation rate of C12E8 is indeed much faster than previously thought. We also exemplify the case of brominated dodecyl-maltoside, whose kinetics for overall binding to and dissociation from membranes comprise both a rapid and a sower phase, the latter being presumably due to flip-flop between the two leaflets of the membrane. Consequently, equilibrium is reached only after a few seconds for DDM. This work thereby emphasizes the interest of using the fluorescence quenching associated with brominated detergents for studying the kinetics of detergent/membrane interactions, namely association, dissociation and flip-flop rates.
Collapse
|
57
|
Hénault CM, Govaerts C, Spurny R, Brams M, Estrada-Mondragon A, Lynch J, Bertrand D, Pardon E, Evans GL, Woods K, Elberson BW, Cuello LG, Brannigan G, Nury H, Steyaert J, Baenziger JE, Ulens C. A lipid site shapes the agonist response of a pentameric ligand-gated ion channel. Nat Chem Biol 2019; 15:1156-1164. [PMID: 31591563 DOI: 10.1038/s41589-019-0369-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 08/21/2019] [Indexed: 12/11/2022]
Abstract
Phospholipids are key components of cellular membranes and are emerging as important functional regulators of different membrane proteins, including pentameric ligand-gated ion channels (pLGICs). Here, we take advantage of the prokaryote channel ELIC (Erwinia ligand-gated ion channel) as a model to understand the determinants of phospholipid interactions in this family of receptors. A high-resolution structure of ELIC in a lipid-bound state reveals a phospholipid site at the lower half of pore-forming transmembrane helices M1 and M4 and at a nearby site for neurosteroids, cholesterol or general anesthetics. This site is shaped by an M4-helix kink and a Trp-Arg-Pro triad that is highly conserved in eukaryote GABAA/C and glycine receptors. A combined approach reveals that M4 is intrinsically flexible and that M4 deletions or disruptions of the lipid-binding site accelerate desensitization in ELIC, suggesting that lipid interactions shape the agonist response. Our data offer a structural context for understanding lipid modulation in pLGICs.
Collapse
Affiliation(s)
- Camille M Hénault
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Cedric Govaerts
- Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université libre de Bruxelles, Brussels, Belgium
| | - Radovan Spurny
- Laboratory of Structural Neurobiology, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Marijke Brams
- Laboratory of Structural Neurobiology, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | | | - Joseph Lynch
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | | | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Genevieve L Evans
- Laboratory of Structural Neurobiology, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Kristen Woods
- Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ, USA.,Department of Physics, Rutgers University-Camden, Camden, NJ, USA
| | - Benjamin W Elberson
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, TTUHSC, Lubbock, TX, USA
| | - Luis G Cuello
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, TTUHSC, Lubbock, TX, USA
| | - Grace Brannigan
- Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ, USA.,Department of Physics, Rutgers University-Camden, Camden, NJ, USA
| | - Hugues Nury
- University Grenoble Alpes, CNRS, IBS, Grenoble, France
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - John E Baenziger
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada.
| | - Chris Ulens
- Laboratory of Structural Neurobiology, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
| |
Collapse
|
58
|
Conrard L, Tyteca D. Regulation of Membrane Calcium Transport Proteins by the Surrounding Lipid Environment. Biomolecules 2019; 9:E513. [PMID: 31547139 PMCID: PMC6843150 DOI: 10.3390/biom9100513] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 12/11/2022] Open
Abstract
Calcium ions (Ca2+) are major messengers in cell signaling, impacting nearly every aspect of cellular life. Those signals are generated within a wide spatial and temporal range through a large variety of Ca2+ channels, pumps, and exchangers. More and more evidences suggest that Ca2+ exchanges are regulated by their surrounding lipid environment. In this review, we point out the technical challenges that are currently being overcome and those that still need to be defeated to analyze the Ca2+ transport protein-lipid interactions. We then provide evidences for the modulation of Ca2+ transport proteins by lipids, including cholesterol, acidic phospholipids, sphingolipids, and their metabolites. We also integrate documented mechanisms involved in the regulation of Ca2+ transport proteins by the lipid environment. Those include: (i) Direct interaction inside the protein with non-annular lipids; (ii) close interaction with the first shell of annular lipids; (iii) regulation of membrane biophysical properties (e.g., membrane lipid packing, thickness, and curvature) directly around the protein through annular lipids; and (iv) gathering and downstream signaling of several proteins inside lipid domains. We finally discuss recent reports supporting the related alteration of Ca2+ and lipids in different pathophysiological events and the possibility to target lipids in Ca2+-related diseases.
Collapse
Affiliation(s)
- Louise Conrard
- CELL Unit, de Duve Institute and Université catholique de Louvain, UCL B1.75.05, avenue Hippocrate, 75, B-1200 Brussels, Belgium
| | - Donatienne Tyteca
- CELL Unit, de Duve Institute and Université catholique de Louvain, UCL B1.75.05, avenue Hippocrate, 75, B-1200 Brussels, Belgium.
| |
Collapse
|
59
|
Corey RA, Vickery ON, Sansom MSP, Stansfeld PJ. Insights into Membrane Protein-Lipid Interactions from Free Energy Calculations. J Chem Theory Comput 2019; 15:5727-5736. [PMID: 31476127 PMCID: PMC6785801 DOI: 10.1021/acs.jctc.9b00548] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Integral membrane proteins are regulated
by specific interactions
with lipids from the surrounding bilayer. The structures of protein–lipid
complexes can be determined through a combination of experimental
and computational approaches, but the energetic basis of these interactions
is difficult to resolve. Molecular dynamics simulations provide the
primary computational technique to estimate the free energies of these
interactions. We demonstrate that the energetics of protein–lipid
interactions may be reliably and reproducibly calculated using three
simulation-based approaches: potential of mean force calculations,
alchemical free energy perturbation, and well-tempered metadynamics.
We employ these techniques within the framework of a coarse-grained
force field and apply them to both bacterial and mammalian membrane
protein–lipid systems. We demonstrate good agreement between
the different techniques, providing a robust framework for their automated
implementation within a pipeline for annotation of newly determined
membrane protein structures.
Collapse
Affiliation(s)
- Robin A Corey
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Owen N Vickery
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Mark S P Sansom
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Phillip J Stansfeld
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| |
Collapse
|
60
|
Autoinhibition and activation mechanisms of the eukaryotic lipid flippase Drs2p-Cdc50p. Nat Commun 2019; 10:4142. [PMID: 31515475 PMCID: PMC6742660 DOI: 10.1038/s41467-019-12191-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/23/2019] [Indexed: 12/14/2022] Open
Abstract
The heterodimeric eukaryotic Drs2p-Cdc50p complex is a lipid flippase that maintains cell membrane asymmetry. The enzyme complex exists in an autoinhibited form in the absence of an activator and is specifically activated by phosphatidylinositol-4-phosphate (PI4P), although the underlying mechanisms have been unclear. Here we report the cryo-EM structures of intact Drs2p-Cdc50p isolated from S. cerevisiae in apo form and in the PI4P-activated form at 2.8 Å and 3.3 Å resolution, respectively. The structures reveal that the Drs2p C-terminus lines a long groove in the cytosolic regulatory region to inhibit the flippase activity. PIP4 binding in a cytosol-proximal membrane region triggers a 90° rotation of a cytosolic helix switch that is located just upstream of the inhibitory C-terminal peptide. The rotation of the helix switch dislodges the C-terminus from the regulatory region, activating the flippase.
Collapse
|
61
|
Barrera EE, Machado MR, Pantano S. Fat SIRAH: Coarse-Grained Phospholipids To Explore Membrane-Protein Dynamics. J Chem Theory Comput 2019; 15:5674-5688. [PMID: 31433946 DOI: 10.1021/acs.jctc.9b00435] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The capability to handle highly heterogeneous molecular assemblies in a consistent manner is among the greatest challenges faced when deriving simulation parameters. This is particularly the case for coarse-grained (CG) simulations in which chemical functional groups are lumped into effective interaction centers for which transferability between different chemical environments is not guaranteed. Here, we introduce the parametrization of a set of CG phospholipids compatible with the latest version of the SIRAH force field for proteins. The newly introduced lipid species include different acylic chain lengths and partial unsaturation, as well as polar and acidic head groups that show a very good reproduction of structural membrane determinants, such as areas per lipid, thickness, order parameter, etc., and their dependence with temperature. Simulation of membrane proteins showed unprecedented accuracy in the unbiased description of the thickness-dependent membrane-protein orientation in systems where this information is experimentally available (namely, the SarcoEndoplasmic Reticulum Calcium-SERCA-pump and its regulator Phospholamban). The interactions that lead to this faithful reproduction can be traced down to the single amino acid-lipid interaction level and show full agreement with biochemical data present in the literature. Finally, the present parametrization is implemented in the GROMACS and AMBER simulation packages facilitating its use by a wide portion of the biocomputing community.
Collapse
Affiliation(s)
- Exequiel E Barrera
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
| | - Matías R Machado
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
| | - Sergio Pantano
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay.,Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , Shanghai 201210 , China
| |
Collapse
|
62
|
Abstract
Infections arising from multidrug-resistant pathogenic bacteria are spreading rapidly throughout the world and threaten to become untreatable. The origins of resistance are numerous and complex, but one underlying factor is the capacity of bacteria to rapidly export drugs through the intrinsic activity of efflux pumps. In this Review, we describe recent advances that have increased our understanding of the structures and molecular mechanisms of multidrug efflux pumps in bacteria. Clinical and laboratory data indicate that efflux pumps function not only in the drug extrusion process but also in virulence and the adaptive responses that contribute to antimicrobial resistance during infection. The emerging picture of the structure, function and regulation of efflux pumps suggests opportunities for countering their activities.
Collapse
|
63
|
Hiraizumi M, Yamashita K, Nishizawa T, Nureki O. Cryo-EM structures capture the transport cycle of the P4-ATPase flippase. Science 2019; 365:1149-1155. [PMID: 31416931 DOI: 10.1126/science.aay3353] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/06/2019] [Indexed: 12/13/2022]
Abstract
In eukaryotic membranes, type IV P-type adenosine triphosphatases (P4-ATPases) mediate the translocation of phospholipids from the outer to the inner leaflet and maintain lipid asymmetry, which is critical for membrane trafficking and signaling pathways. Here, we report the cryo-electron microscopy structures of six distinct intermediates of the human ATP8A1-CDC50a heterocomplex at resolutions of 2.6 to 3.3 angstroms, elucidating the lipid translocation cycle of this P4-ATPase. ATP-dependent phosphorylation induces a large rotational movement of the actuator domain around the phosphorylation site in the phosphorylation domain, accompanied by lateral shifts of the first and second transmembrane helices, thereby allowing phosphatidylserine binding. The phospholipid head group passes through the hydrophilic cleft, while the acyl chain is exposed toward the lipid environment. These findings advance our understanding of the flippase mechanism and the disease-associated mutants of P4-ATPases.
Collapse
Affiliation(s)
- Masahiro Hiraizumi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Discovery Technology Laboratories, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida, Aoba-ku, Yokohama, 227-0033, Japan
| | - Keitaro Yamashita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| |
Collapse
|
64
|
McGruer V, Pasparakis C, Grosell M, Stieglitz JD, Benetti DD, Greer JB, Schlenk D. Deepwater Horizon crude oil exposure alters cholesterol biosynthesis with implications for developmental cardiotoxicity in larval mahi-mahi (Coryphaena hippurus). Comp Biochem Physiol C Toxicol Pharmacol 2019; 220:31-35. [PMID: 30851416 DOI: 10.1016/j.cbpc.2019.03.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 03/05/2019] [Indexed: 12/18/2022]
Abstract
During the spring and summer of 2010, the Deepwater Horizon (DWH) oil well released over three million barrels of crude oil into the Gulf of Mexico. As the oil dispersed it contaminated ecosystems that support numerous Gulf species including mahi-mahi (Coryphaena hippurus). The timing of the spill, and location of the surface slick, coincided with the spawning of many species in the region, raising concerns over embryonic and larval exposure. Numerous abnormalities due to crude oil exposure have been documented in fish early life stages, including cardiotoxicity; however, knowledge of the molecular mechanisms that cause these phenotypes is still limited. Several transcriptomic studies have presented cholesterol biosynthesis as one of the top enriched pathways following PAH exposure. In this study we exposed mahi-mahi embryos to DWH oil collected from the surface slick. At exposures ranging from ∑PAH 1.69 μg/L to ∑PAH 5.99 μg/L, the resulting larvae demonstrated significant increases in farnesyl-diphosphate farnesyltransferase 1 (fdft1) and an upward trend in 3-Hydroxy-3-Methylglutaryl-CoA Reductase (hmgcr) expression, genes that encode key enzymes in the cholesterol biosynthetic pathway. In addition to the increased expression of genes in cholesterol biosynthetic pathway, a significant decrease in total cholesterol was observed in larval homogenates, at ∑PAH 8.3 μg/L. These data confirm earlier transcriptomic studies and show that oil may diminish cholesterol and adversely impact numerous cellular functions due to altered membrane stability.
Collapse
Affiliation(s)
- Victoria McGruer
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA; Department of Environmental Sciences, University of California, Riverside, CA 92521, USA.
| | - Christina Pasparakis
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA.
| | - Martin Grosell
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA.
| | - John D Stieglitz
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA.
| | - Daniel D Benetti
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA.
| | - Justin B Greer
- Department of Environmental Sciences, University of California, Riverside, CA 92521, USA.
| | - Daniel Schlenk
- Department of Environmental Sciences, University of California, Riverside, CA 92521, USA.
| |
Collapse
|
65
|
Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP. Emerging Diversity in Lipid-Protein Interactions. Chem Rev 2019; 119:5775-5848. [PMID: 30758191 PMCID: PMC6509647 DOI: 10.1021/acs.chemrev.8b00451] [Citation(s) in RCA: 264] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Indexed: 02/07/2023]
Abstract
Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable membrane environment for proteins to being embedded in to detailed roles in complicated and well-regulated protein functions. Experimental and computational advances are converging in a rapidly expanding research area of lipid-protein interactions. Experimentally, the database of high-resolution membrane protein structures is growing, as are capabilities to identify the complex lipid composition of different membranes, to probe the challenging time and length scales of lipid-protein interactions, and to link lipid-protein interactions to protein function in a variety of proteins. Computationally, more accurate membrane models and more powerful computers now enable a detailed look at lipid-protein interactions and increasing overlap with experimental observations for validation and joint interpretation of simulation and experiment. Here we review papers that use computational approaches to study detailed lipid-protein interactions, together with brief experimental and physiological contexts, aiming at comprehensive coverage of simulation papers in the last five years. Overall, a complex picture of lipid-protein interactions emerges, through a range of mechanisms including modulation of the physical properties of the lipid environment, detailed chemical interactions between lipids and proteins, and key functional roles of very specific lipids binding to well-defined binding sites on proteins. Computationally, despite important limitations, molecular dynamics simulations with current computer power and theoretical models are now in an excellent position to answer detailed questions about lipid-protein interactions.
Collapse
Affiliation(s)
- Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Besian I. Sejdiu
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haydee Mesa-Galloso
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haleh Abdizadeh
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Sergei Yu. Noskov
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| |
Collapse
|
66
|
Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
Collapse
Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
| |
Collapse
|
67
|
Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
Collapse
Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
68
|
Zhang XC, Zhang H. P-type ATPases use a domain-association mechanism to couple ATP hydrolysis to conformational change. BIOPHYSICS REPORTS 2019. [DOI: 10.1007/s41048-019-0087-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
|
69
|
Dutta D, Ullah A, Bibi S, Fliegel L. Functional Analysis of Conserved Transmembrane Charged Residues and a Yeast Specific Extracellular Loop of the Plasma Membrane Na +/H + Antiporter of Schizosaccharomyces pombe. Sci Rep 2019; 9:6191. [PMID: 30996236 PMCID: PMC6470128 DOI: 10.1038/s41598-019-42658-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/01/2019] [Indexed: 01/20/2023] Open
Abstract
The Na+/H+ exchanger of the plasma membrane of S. pombe (SpNHE1) removes excess intracellular sodium in exchange for an extracellular proton. We examined the functional role of acidic amino acids of a yeast specific periplasmic extracellular loop 6 (EL6) and of Glu74 and Arg77 of transmembrane segment 3. Glu74 and Arg77 are conserved in yeast species while Glu74 is conserved throughout various phyla. The mutation E74A caused a minor effect, while mutation R77A had a larger effect on the ability of SpNHE1 to confer salt tolerance. Mutation of both residues to Ala or Glu also eliminated the ability to confer salt tolerance. Arg341 and Arg342 were also necessary for SpNHE1 transport in S. pombe. Deletion of 3 out of 4 acidic residues (Asp389, Glu390, Glu392, Glu397) of EL6 did not greatly affect SpNHE1 function while deletion of all did. Replacement of EL6 with a segment from the plant Na+/H+ exchanger SOS1 also did not affect function. We suggest that EL6 forms part of a cation coordination sphere, attracting cations for transport but that the region is not highly specific for the location of acidic charges. Overall, we identified a number of polar amino acids important in SpNHE1 function.
Collapse
Affiliation(s)
- Debajyoti Dutta
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Asad Ullah
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Sana Bibi
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Larry Fliegel
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada.
| |
Collapse
|
70
|
Abstract
Of all the macromolecular assemblies of life, the least understood is the biomembrane. This is especially true in regard to its atomic structure. Ideas on biomembranes, developed in the last 200 years, culminated in the fluid mosaic model of the membrane. In this essay, I provide a historical outline of how we arrived at our current understanding of biomembranes and the models we use to describe them. A selection of direct experimental findings on the nano-scale structure of biomembranes is taken up to discuss their physical nature, and special emphasis is put on the surprising insights that arise from atomic scale descriptions.
Collapse
|
71
|
Espinoza-Fonseca LM. Probing the effects of nonannular lipid binding on the stability of the calcium pump SERCA. Sci Rep 2019; 9:3349. [PMID: 30833659 PMCID: PMC6399444 DOI: 10.1038/s41598-019-40004-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/07/2019] [Indexed: 01/14/2023] Open
Abstract
The calcium pump SERCA is a transmembrane protein that is critical for calcium transport in cells. SERCA resides in an environment made up largely by the lipid bilayer, so lipids play a central role on its stability and function. Studies have provided insights into the effects of annular and bulk lipids on SERCA activation, but the role of a nonannular lipid site in the E2 intermediate state remains elusive. Here, we have performed microsecond molecular dynamics simulations to probe the effects of nonannular lipid binding on the stability and structural dynamics of the E2 state of SERCA. We found that the structural integrity and stability of the E2 state is independent of nonannular lipid binding, and that occupancy of a lipid molecule at this site does not modulate destabilization of the E2 state, a step required to initiate the transition toward the competent E1 state. We also found that binding of the nonannular lipid does not induce direct allosteric control of the intrinsic functional dynamics the E2 state. We conclude that nonannular lipid binding is not necessary for the stability of the E2 state, but we speculate that it becomes functionally significant during the E2-to-E1 transition of the pump.
Collapse
Affiliation(s)
- L Michel Espinoza-Fonseca
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.
| |
Collapse
|
72
|
Nguyen GH, Tran TN, Podgorski MN, Bell SG, Supuran CT, Donald WA. Nanoscale Ion Emitters in Native Mass Spectrometry for Measuring Ligand-Protein Binding Affinities. ACS CENTRAL SCIENCE 2019; 5:308-318. [PMID: 30834319 PMCID: PMC6396573 DOI: 10.1021/acscentsci.8b00787] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Indexed: 05/20/2023]
Abstract
Electrospray ionization (ESI) mass spectrometry (MS) is a crucial method for rapidly determining the interactions between small molecules and proteins with ultrahigh sensitivity. However, nonvolatile molecules and salts that are often necessary to stabilize the native structures of protein-ligand complexes can readily adduct to protein ions, broaden spectral peaks, and lower signal-to-noise ratios in native MS. ESI emitters with narrow tip diameters (∼250 nm) were used to significantly reduce the extent of adduction of salt and nonvolatile molecules to protein complexes to more accurately measure ligand-protein binding constants than by use of conventional larger-bore emitters under these conditions. As a result of decreased salt adduction, peaks corresponding to protein-ligand complexes that differ in relative molecular weight by as low as 0.06% can be readily resolved. For low-molecular-weight anion ligands formed from sodium salts, anion-bound and unbound protein ions that differ in relative mass by 0.2% were completely baseline resolved using nanoscale emitters, which was not possible under these conditions using conventional emitters. Owing to the improved spectral resolution obtained using narrow-bore emitters and an analytically derived equation, K d values were simultaneously obtained for at least six ligands to a single druggable protein target from one spectrum for the first time. This research suggests that ligand-protein binding constants can be directly and accurately measured from solutions with high concentrations of nonvolatile buffers and salts by native MS.
Collapse
Affiliation(s)
- Giang
T. H. Nguyen
- School
of Chemistry, University of New South Wales, Dalton Building, Sydney, New South Wales 2052, Australia
| | - Thinh N. Tran
- School
of Electrical Engineering and Telecommunications, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Matthew N. Podgorski
- Department
of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Stephen G. Bell
- Department
of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Claudiu T. Supuran
- Department
of Neuroscience, Psychology, Drug Research and Child’s Health,
Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - William A. Donald
- School
of Chemistry, University of New South Wales, Dalton Building, Sydney, New South Wales 2052, Australia
- Phone: +61 (2) 9385 8827. E-mail:
| |
Collapse
|
73
|
Sweadner KJ, Arystarkhova E, Penniston JT, Swoboda KJ, Brashear A, Ozelius LJ. Genotype-structure-phenotype relationships diverge in paralogs ATP1A1, ATP1A2, and ATP1A3. NEUROLOGY-GENETICS 2019; 5:e303. [PMID: 30842972 PMCID: PMC6384024 DOI: 10.1212/nxg.0000000000000303] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/08/2018] [Indexed: 11/15/2022]
Abstract
Objective We tested the assumption that closely related genes should have similar pathogenic variants by analyzing >200 pathogenic variants in a gene family with high neurologic impact and high sequence identity, the Na,K-ATPases ATP1A1, ATP1A2, and ATP1A3. Methods Data sets of disease-associated variants were compared. Their equivalent positions in protein crystal structures were used for insights into pathogenicity and correlated with the phenotype and conservation of homology. Results Relatively few mutations affected the corresponding amino acids in 2 genes. In the membrane domain of ATP1A3 (primarily expressed in neurons), variants producing milder neurologic phenotypes had different structural positions than variants producing severe phenotypes. In ATP1A2 (primarily expressed in astrocytes), membrane domain variants characteristic of severe phenotypes in ATP1A3 were absent from patient data. The known variants in ATP1A1 fell into 2 distinct groups. Sequence conservation was an imperfect indicator: it varied among structural domains, and some variants with demonstrated pathogenicity were in low conservation sites. Conclusions Pathogenic variants varied between genes despite high sequence identity, and there is a genotype-structure-phenotype relationship in ATP1A3 that correlates with neurologic outcomes. The absence of "severe" pathogenic variants in ATP1A2 patients predicts that they will manifest either in a different tissue or by death in utero and that new ATP1A1 variants will produce additional phenotypes. It is important that some variants in poorly conserved amino acids are nonetheless pathogenic and could be incorrectly predicted to be benign.
Collapse
Affiliation(s)
- Kathleen J Sweadner
- Department of Neurosurgery (K.J. Sweadner, E.A., J.T.P.), Center for Human Genetics Research (K.J. Swoboda), and Department of Neurology, (K.J. Swoboda, L.J.O.) Massachusetts General Hospital, Boston; and the Department of Neurology (A.B.), Wake Forest School of Medicine, Winston-Salem, NC
| | - Elena Arystarkhova
- Department of Neurosurgery (K.J. Sweadner, E.A., J.T.P.), Center for Human Genetics Research (K.J. Swoboda), and Department of Neurology, (K.J. Swoboda, L.J.O.) Massachusetts General Hospital, Boston; and the Department of Neurology (A.B.), Wake Forest School of Medicine, Winston-Salem, NC
| | - John T Penniston
- Department of Neurosurgery (K.J. Sweadner, E.A., J.T.P.), Center for Human Genetics Research (K.J. Swoboda), and Department of Neurology, (K.J. Swoboda, L.J.O.) Massachusetts General Hospital, Boston; and the Department of Neurology (A.B.), Wake Forest School of Medicine, Winston-Salem, NC
| | - Kathryn J Swoboda
- Department of Neurosurgery (K.J. Sweadner, E.A., J.T.P.), Center for Human Genetics Research (K.J. Swoboda), and Department of Neurology, (K.J. Swoboda, L.J.O.) Massachusetts General Hospital, Boston; and the Department of Neurology (A.B.), Wake Forest School of Medicine, Winston-Salem, NC
| | - Allison Brashear
- Department of Neurosurgery (K.J. Sweadner, E.A., J.T.P.), Center for Human Genetics Research (K.J. Swoboda), and Department of Neurology, (K.J. Swoboda, L.J.O.) Massachusetts General Hospital, Boston; and the Department of Neurology (A.B.), Wake Forest School of Medicine, Winston-Salem, NC
| | - Laurie J Ozelius
- Department of Neurosurgery (K.J. Sweadner, E.A., J.T.P.), Center for Human Genetics Research (K.J. Swoboda), and Department of Neurology, (K.J. Swoboda, L.J.O.) Massachusetts General Hospital, Boston; and the Department of Neurology (A.B.), Wake Forest School of Medicine, Winston-Salem, NC
| |
Collapse
|
74
|
Dai Q, Zhao H, Cao H, Yang J, Zhao W, Wang T, Liu L, Fan Z, Wang G. Photo-triggered conversion of hydrophilic fluorescent biomimetic nanostructures for cell imaging. Chem Commun (Camb) 2019; 55:596-599. [PMID: 30480678 DOI: 10.1039/c8cc07197g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Fluorescent nanoarchitectures, such as hydrophobic micelles and hydrophilic vesicles decorated with fluorescent carbon nanoparticles, were fabricated from one fatty acid by means of photo-triggering. The biomimetic nanostructures, like cell membrane structures, have applications in fluorescence imaging in both the cell cytoplasm and nucleus. Besides, hydrophobic micelles can be used as very stable fluorescent inks.
Collapse
Affiliation(s)
- Qin Dai
- Beijing Engineering Research Center of Process Pollution Control, Division of Environment Technology and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
| | | | | | | | | | | | | | | | | |
Collapse
|
75
|
Effect of Cholesterol on the Dipole Potential of Lipid Membranes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1115:135-154. [DOI: 10.1007/978-3-030-04278-3_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
76
|
Flayhan A, Mertens HDT, Ural-Blimke Y, Martinez Molledo M, Svergun DI, Löw C. Saposin Lipid Nanoparticles: A Highly Versatile and Modular Tool for Membrane Protein Research. Structure 2018; 26:345-355.e5. [PMID: 29413323 PMCID: PMC5807053 DOI: 10.1016/j.str.2018.01.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/27/2017] [Accepted: 01/10/2018] [Indexed: 11/30/2022]
Abstract
Saposin-derived lipid nanoparticles (SapNPs) are a new alternative tool for membrane protein reconstitution. Here we demonstrate the potential and advantages of SapNPs. We show that SapA has the lowest lipid specificity for SapNP formation. These nanoparticles are modular and offer a tunable range of size and composition depending on the stoichiometric ratio of lipid and saposin components. They are stable and exhibit features typical of lipid-bilayer systems. Our data suggest that SapNPs are versatile and can adapt to membrane proteins of various sizes and architectures. Using SapA and various types of lipids we could reconstitute membrane proteins of different transmembrane cross-sectional areas (from 14 to 56 transmembrane α helices). SapNP-reconstituted proteins bound their respective ligands and were more heat stable compared with the detergent-solubilized form. Moreover, SapNPs encircle membrane proteins in a compact way, allowing structural investigations of small membrane proteins in a detergent-free environment using small-angle X-ray scattering. SapA shows the lowest lipid specificity for SapNP formation SapNPs are versatile and can adapt to MPs of various sizes and architectures SapNP-reconstituted MPs are more stable than in detergent SapNPs encapsulate MPs in a compact manner
Collapse
Affiliation(s)
- Ali Flayhan
- Centre for Structural Systems Biology (CSSB), DESY, Notkestrasse 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | - Haydyn D T Mertens
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | - Yonca Ural-Blimke
- Centre for Structural Systems Biology (CSSB), DESY, Notkestrasse 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | - Maria Martinez Molledo
- Centre for Structural Systems Biology (CSSB), DESY, Notkestrasse 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), DESY, Notkestrasse 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22607 Hamburg, Germany; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, 17177 Stockholm, Sweden.
| |
Collapse
|
77
|
Sørensen TLM, Hjorth-Jensen SJ, Oksanen E, Andersen JL, Olesen C, Møller JV, Nissen P. Membrane-protein crystals for neutron diffraction. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1208-1218. [PMID: 30605135 DOI: 10.1107/s2059798318012561] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/05/2018] [Indexed: 11/10/2022]
Abstract
Neutron macromolecular crystallography (NMX) has the potential to provide the experimental input to address unresolved aspects of transport mechanisms and protonation in membrane proteins. However, despite this clear scientific motivation, the practical challenges of obtaining crystals that are large enough to make NMX feasible have so far been prohibitive. Here, the potential impact on feasibility of a more powerful neutron source is reviewed and a strategy for obtaining larger crystals is formulated, exemplified by the calcium-transporting ATPase SERCA1. The challenges encountered at the various steps in the process from crystal nucleation and growth to crystal mounting are explored, and it is demonstrated that NMX-compatible membrane-protein crystals can indeed be obtained.
Collapse
Affiliation(s)
- Thomas Lykke Møller Sørensen
- Department of Molecular Biology and Genetics - DANDRITE, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark
| | - Samuel John Hjorth-Jensen
- Department of Molecular Biology and Genetics - DANDRITE, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark
| | - Esko Oksanen
- European Spallation Source ERIC, PO Box 176, 22100 Lund, Sweden
| | | | - Claus Olesen
- Department of Biomedicine, Aarhus University, Ole Worn Alle 3, DK-8000 Aarhus C, Denmark
| | - Jesper Vuust Møller
- Department of Biomedicine, Aarhus University, Ole Worn Alle 3, DK-8000 Aarhus C, Denmark
| | - Poul Nissen
- Department of Molecular Biology and Genetics - DANDRITE, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark
| |
Collapse
|
78
|
Mechanism of the E2 to E1 transition in Ca 2+ pump revealed by crystal structures of gating residue mutants. Proc Natl Acad Sci U S A 2018; 115:12722-12727. [PMID: 30482857 DOI: 10.1073/pnas.1815472115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Ca2+-ATPase of sarcoplasmic reticulum (SERCA1a) pumps two Ca2+ per ATP hydrolyzed from the cytoplasm and two or three protons in the opposite direction. In the E2 state, after transferring Ca2+ into the lumen of sarcoplasmic reticulum, all of the acidic residues that coordinate Ca2+ are thought to be protonated, including the gating residue Glu309. Therefore a Glu309Gln substitution is not expected to significantly perturb the structure. Here we report crystal structures of the Glu309Gln and Glu309Ala mutants of SERCA1a under E2 conditions. The Glu309Gln mutant exhibits, unexpectedly, large structural rearrangements in both the cytoplasmic and transmembrane domains, apparently uncoupling them. However, the structure definitely represents E2 and, together with the help of quantum chemical calculations, allows us to postulate a mechanism for the E2 → E1 transition triggered by deprotonation of Glu309.
Collapse
|
79
|
Michalak M, Agellon LB. Stress Coping Strategies in the Heart: An Integrated View. Front Cardiovasc Med 2018; 5:168. [PMID: 30519562 PMCID: PMC6258784 DOI: 10.3389/fcvm.2018.00168] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/02/2018] [Indexed: 12/15/2022] Open
Abstract
The heart is made up of an ordered amalgam of cardiac cell types that work together to coordinate four major processes, namely energy production, electrical conductance, mechanical work, and tissue remodeling. Over the last decade, a large body of information has been amassed regarding how different cardiac cell types respond to cellular stress that affect the functionality of their elaborate intracellular membrane networks, the cellular reticular network. In the context of the heart, the manifestations of stress coping strategies likely differ depending on the coping strategy outcomes of the different cardiac cell types, and thus may underlie the development of distinct cardiac disorders. It is not clear whether all cardiac cell types have similar sensitivity to cellular stress, how specific coping response strategies modify their unique roles, and how their metabolic status is communicated to other cells within the heart. Here we discuss our understanding of the roles of specialized cardiac cells that together make the heart function as an organ with the ability to pump blood continuously and follow a regular rhythm.
Collapse
Affiliation(s)
- Marek Michalak
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Luis B Agellon
- School of Human Nutrition, McGill University, Ste. Anne de Bellevue, QC, Canada
| |
Collapse
|
80
|
Abstract
Robertson recounts the historical experiments that gave rise to our current understanding of cell membranes. In 1918, the year the Journal of General Physiology was founded, there was little understanding of the structure of the cell membrane. It was evident that cells had invisible barriers separating the cytoplasm from the external solution. However, it would take decades before lipid bilayers were identified as the essential constituent of membranes. It would take even longer before it was accepted that there existed hydrophobic proteins that were embedded within the membrane and that these proteins were responsible for selective permeability in cells. With a combination of intuitive experiments and quantitative thinking, the last century of cell membrane research has led us to a molecular understanding of the structure of the membrane, as well as many of the proteins embedded within. Now, research is turning toward a physical understanding of the reactions of membrane proteins and lipids in this unique and incredibly complex solvent environment.
Collapse
Affiliation(s)
- Janice L Robertson
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA
| |
Collapse
|
81
|
Lee J, Pothula KR, Kleinekathöfer U, Im W. Simulation Study of Occk5 Functional Properties in Pseudomonas aeruginosa Outer Membranes. J Phys Chem B 2018; 122:8185-8192. [DOI: 10.1021/acs.jpcb.8b07109] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Joonseong Lee
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Karunakar R. Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| |
Collapse
|
82
|
Wäldchen F, Becher S, Esch P, Kompauer M, Heiles S. Selective phosphatidylcholine double bond fragmentation and localisation using Paternò-Büchi reactions and ultraviolet photodissociation. Analyst 2018; 142:4744-4755. [PMID: 29142996 DOI: 10.1039/c7an01158j] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The effect of double bond functionalisation for selective double bond localisation by ultraviolet photodissociation of phosphatidylcholines is investigated. Paternò-Büchi reactions in nanoESI emitter tips enable attachment of acetophenone to double bonds of unsaturated phosphatidylcholines after 100 s of 254 nm light irradiation with about 50-80% reaction yield. Functionalized phosphatidylcholines dissociate upon 266 nm irradiation yielding double bond selective fragment ions in contrast to results for ultraviolet photodissociation of unmodified lipids. Ultraviolet photodissociation of Paternò-Büchi modified lipids results in a selectivity increase of up to 2.2 towards double bond localisation compared collision-induced dissociation experiments. Double bond localisation is also possible with ultraviolet photodissociation when alkali metal ion attachment to Paternò-Büchi modified phosphatidylcholines occurs in contrast to classic collision-induced dissociation experiments. The developed methodology is used to differentiate lipid double bond isomers and applied to phosphatidylcholines from egg yolk to identify 15 phosphatidylcholines. Results from this study demonstrate that locally depositing energy in close vicinity to cleavable bonds via ultraviolet photodissociation can result in increased dissociation selectivity. This method can help to disentangle contributions from different structural elements in complex tandem mass spectra of lipids and aid to the structural characterization of phospholipids in a "top-down" approach.
Collapse
Affiliation(s)
- Fabian Wäldchen
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany.
| | | | | | | | | |
Collapse
|
83
|
Cohen BE. Membrane Thickness as a Key Factor Contributing to the Activation of Osmosensors and Essential Ras Signaling Pathways. Front Cell Dev Biol 2018; 6:76. [PMID: 30087894 PMCID: PMC6066546 DOI: 10.3389/fcell.2018.00076] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/25/2018] [Indexed: 12/17/2022] Open
Abstract
The cell membrane provides a functional link between the external environment and the replicating DNA genome by using ligand-gated receptors and chemical signals to activate signaling transduction pathways. However, increasing evidence has also indicated that the phospholipid bilayer itself by altering various physical parameters serves as a sensor that regulate membrane proteins in a specific manner. Changes in thickness and/or curvature of the membrane have been shown to be induced by mechanical forces and transmitted through the transmembrane helices of several types of mechanosensitive (MS) ion channels underlying functions such as osmoregulation in bacteria and sensory processing in mammalian cells. This review focus on recent protein functional and structural data indicating that the activation of bacterial and yeast osmosensors is consistent with thickness-induced tilting changes of the transmembrane domains of these proteins. Membrane thinning in combination with curvature changes may also lead to the lateral transfer of the small lipid-anchored GTPases Ras1 and H-Ras out of lipid rafts for clustering and signaling. The modulation of signaling pathways by amphiphilic peptides and the membrane-active antibiotics colistin and Amphotericin B is also discussed.
Collapse
Affiliation(s)
- B Eleazar Cohen
- Division of External Activities, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| |
Collapse
|
84
|
Fernández-de Gortari E, Espinoza-Fonseca LM. Structural basis for relief of phospholamban-mediated inhibition of the sarcoplasmic reticulum Ca 2+-ATPase at saturating Ca 2+ conditions. J Biol Chem 2018; 293:12405-12414. [PMID: 29934304 DOI: 10.1074/jbc.ra118.003752] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/21/2018] [Indexed: 11/06/2022] Open
Abstract
Sarcoplasmic reticulum Ca2+-ATPase (SERCA) is critical for cardiac Ca2+ transport. Reversal of phospholamban (PLB)-mediated SERCA inhibition by saturating Ca2+ conditions operates as a physiological rheostat to reactivate SERCA function in the absence of PLB phosphorylation. Here, we performed extensive atomistic molecular dynamics simulations to probe the structural mechanism of this process. Simulation of the inhibitory complex at superphysiological Ca2+ concentrations ([Ca2+] = 10 mm) revealed that Ca2+ ions interact primarily with SERCA and the lipid headgroups, but not with PLB's cytosolic domain or the cytosolic side of the SERCA-PLB interface. At this [Ca2+], a single Ca2+ ion was translocated from the cytosol to the transmembrane transport sites. We used this Ca2+-bound complex as an initial structure to simulate the effects of saturating Ca2+ at physiological conditions ([Ca2+]total ≈ 400 μm). At these conditions, ∼30% of the Ca2+-bound complexes exhibited structural features consistent with an inhibited state. However, in ∼70% of the Ca2+-bound complexes, Ca2+ moved to transport site I, recruited Glu771 and Asp800, and disrupted key inhibitory contacts involving the conserved PLB residue Asn34 Structural analysis showed that Ca2+ induces only local changes in interresidue inhibitory interactions, but does not induce repositioning or changes in PLB structural dynamics. Upon relief of SERCA inhibition, Ca2+ binding produced a site I configuration sufficient for subsequent SERCA activation. We propose that at saturating [Ca2+] and in the absence of PLB phosphorylation, binding of a single Ca2+ ion in the transport sites rapidly shifts the equilibrium toward a noninhibited SERCA-PLB complex.
Collapse
Affiliation(s)
- Eli Fernández-de Gortari
- From the Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan 48109
| | - L Michel Espinoza-Fonseca
- From the Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan 48109
| |
Collapse
|
85
|
Abstract
Outer-membrane porins are often considered as passive conduits of small molecules across lipid bilayers. Using native mass spectrometry experiments we identify a pH-sensitive lipid-binding mechanism of outer membrane porin F, which enables increased threading of a colicin-derived peptide through open channels. Supported by molecular dynamics simulations and channel recording experiments, we posit that this mechanism attenuates channel opening in response to changes in environmental conditions, specifically pH. These findings have important consequences for mass spectrometry experiments, wherein the role of charge is often overlooked, and they also could help provide understanding of antibiotics that gain access to Gram-negative bacteria through porin-mediated pathways. Strong interactions between lipids and proteins occur primarily through association of charged headgroups and amino acid side chains, rendering the protonation status of both partners important. Here we use native mass spectrometry to explore lipid binding as a function of charge of the outer membrane porin F (OmpF). We find that binding of anionic phosphatidylglycerol (POPG) or zwitterionic phosphatidylcholine (POPC) to OmpF is sensitive to electrospray polarity while the effects of charge are less pronounced for other proteins in outer or mitochondrial membranes: the ferripyoverdine receptor (FpvA) or the voltage-dependent anion channel (VDAC). Only marginal charge-induced differences were observed for inner membrane proteins: the ammonia channel (AmtB) or the mechanosensitive channel. To understand these different sensitivities, we performed an extensive bioinformatics analysis of membrane protein structures and found that OmpF, and to a lesser extent FpvA and VDAC, have atypically high local densities of basic and acidic residues in their lipid headgroup-binding regions. Coarse-grained molecular dynamics simulations, in mixed lipid bilayers, further implicate changes in charge by demonstrating preferential binding of anionic POPG over zwitterionic POPC to protonated OmpF, an effect not observed to the same extent for AmtB. Moreover, electrophysiology and mass-spectrometry–based ligand-binding experiments, at low pH, show that POPG can maintain OmpF channels in open conformations for extended time periods. Since the outer membrane is composed almost entirely of anionic lipopolysaccharide, with similar headgroup properties to POPG, such anionic lipid binding could prevent closure of OmpF channels, thereby increasing access of antibiotics that use porin-mediated pathways.
Collapse
|
86
|
Gupta K, Li J, Liko I, Gault J, Bechara C, Wu D, Hopper JTS, Giles K, Benesch JLP, Robinson CV. Identifying key membrane protein lipid interactions using mass spectrometry. Nat Protoc 2018; 13:1106-1120. [PMID: 29700483 PMCID: PMC6049616 DOI: 10.1038/nprot.2018.014] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
With the recent success in determining membrane protein structures, further detailed understanding of the identity and function of the bound lipidome is essential. Using an approach that combines high-energy native mass spectrometry (HE-nMS) and solution-phase lipid profiling, this protocol can be used to determine the identity of the endogenous lipids that directly interact with a protein. Furthermore, this method can identify systems in which such lipid binding has a major role in regulating the oligomeric assembly of membrane proteins. The protocol begins with recording of the native mass spectrum of the protein of interest, under successive delipidation conditions, to determine whether delipidation leads to disruption of the oligomeric state. Subsequently, we propose using a bipronged strategy: first, an HE-nMS platform is used that allows dissociation of the detergent micelle at the front end of the instrument. This allows for isolation of the protein-lipid complex at the quadrupole and successive fragmentation at the collision cell, which leads to identification of the bound lipid masses. Next, simultaneous coupling of this with in-solution LC-MS/MS-based identification of extracted lipids reveals the complete identity of the interacting lipidome that copurifies with the proteins. Assimilation of the results of these two sets of experiments divulges the complete identity of the set of lipids that directly interact with the membrane protein of interest, and can further delineate its role in maintaining the oligomeric state of the protein. The entire procedure takes 2 d to complete.
Collapse
Affiliation(s)
- Kallol Gupta
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Jingwen Li
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Idlir Liko
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Joseph Gault
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Cherine Bechara
- Department of Chemistry, University of Oxford, Oxford, UK
- Institut de Genomique Fonctionnelle, CNRS UMR-5203, INSERM U1191, University of Montpellier, Montpellier, France
| | - Di Wu
- Department of Chemistry, University of Oxford, Oxford, UK
| | | | | | | | | |
Collapse
|
87
|
Structural Lipids Enable the Formation of Functional Oligomers of the Eukaryotic Purine Symporter UapA. Cell Chem Biol 2018; 25:840-848.e4. [PMID: 29681524 PMCID: PMC6058078 DOI: 10.1016/j.chembiol.2018.03.011] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/27/2018] [Accepted: 03/22/2018] [Indexed: 11/25/2022]
Abstract
The role of membrane lipids in modulating eukaryotic transporter assembly and function remains unclear. We investigated the effect of membrane lipids in the structure and transport activity of the purine transporter UapA from Aspergillus nidulans. We found that UapA exists mainly as a dimer and that two lipid molecules bind per UapA dimer. We identified three phospholipid classes that co-purified with UapA: phosphatidylcholine, phosphatidylethanolamine (PE), and phosphatidylinositol (PI). UapA delipidation caused dissociation of the dimer into monomers. Subsequent addition of PI or PE rescued the UapA dimer and allowed recovery of bound lipids, suggesting a central role of these lipids in stabilizing the dimer. Molecular dynamics simulations predicted a lipid binding site near the UapA dimer interface. Mutational analyses established that lipid binding at this site is essential for formation of functional UapA dimers. We propose that structural lipids have a central role in the formation of functional, dimeric UapA. Mass spectrometry reveals specific lipid binding to the eukaryotic transporter UapA Interfacial lipids stabilize the functional UapA dimer MD simulations reveal the lipid binding sites Mutagenesis of a lipid binding site disrupts UapA dimerization and function in vivo
Collapse
|
88
|
Maki-Yonekura S, Matsuoka R, Yamashita Y, Shimizu H, Tanaka M, Iwabuki F, Yonekura K. Hexameric and pentameric complexes of the ExbBD energizer in the Ton system. eLife 2018; 7:35419. [PMID: 29661272 PMCID: PMC5903867 DOI: 10.7554/elife.35419] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/18/2018] [Indexed: 01/18/2023] Open
Abstract
Gram-negative bacteria import essential nutrients such as iron and vitamin B12 through outer membrane receptors. This process utilizes proton motive force harvested by the Ton system made up of three inner membrane proteins, ExbB, ExbD and TonB. ExbB and ExbD form the proton channel that energizes uptake through TonB. Recently, crystal structures suggest that the ExbB pentamer is the scaffold. Here, we present structures of hexameric complexes of ExbB and ExbD revealed by X-ray crystallography and single particle cryo-EM. Image analysis shows that hexameric and pentameric complexes coexist, with the proportion of hexamer increasing with pH. Channel current measurement and 2D crystallography support the existence and transition of the two oligomeric states in membranes. The hexameric complex consists of six ExbB subunits and three ExbD transmembrane helices enclosed within the central channel. We propose models for activation/inactivation associated with hexamer and pentamer formation and utilization of proton motive force. Many biological processes that are essential for life are powered by the flow of ions across the membranes of cells. Similar to how energy is stored in the water behind a dam, energy is also stored when the concentration of ions on one side of a biological membrane is higher than it is on the other. When these ions then flow down this concentration gradient, the energy can be harnessed to power other processes. In many bacteria, the concentration of hydrogen ions, or protons, is higher on the outside of the cell. When the protons flow down the concentration gradient, a protein complex called the Ton system in the bacteria’s inner membrane harnesses the energy to transport various compounds, including essential nutrients, across the outer membrane, which is about 20 nanometres away. Toxins, and viruses that infect bacteria, can also hijack the Ton system to gain entry into these cells. This means that the Ton system could perhaps be targeted via drugs to treat bacterial infections. Though the Ton system is important, structural information on this protein family is limited. The Ton complex is composed of three proteins – ExbB, ExbD and TonB – located in the bacteria’s inner membrane. ExbB and ExbD together form a channel for the protons and the complex made from these two proteins can be thought of as the system’s engine. Maki-Yonekura et al. wanted to understand how the ExbB / ExbD complex works, which was challenging because the complex was not well suited to any single structural biology technique. To get around this issue, a combination of two techniques called X-ray crystallography and single particle cryo-EM were used. This approached revealed that the two proteins form complexes made up of either five or six ExbB subunits with one or three ExbD subunits, respectively. It also showed that the proteins transition between the two forms in a cell’s membrane. More of the larger six-unit complex (also called a “hexamer”) formed at higher pH. This is consistent with the increased flow of protons through the channel when the local conditions inside the cell become less acidic. Based on these results, Maki-Yonekura et al. propose that some subunits in the core of the complex rotate to harness the energy from the flow of protons, and the number of subunits in the complex changes when it switches to become active or inactive. The discoveries may provide a new vision of dynamic membrane biology. Further studies are now needed to see how general this mechanism is in biology, and the new structural information could also be used to help develop more anti-bacterial drugs.
Collapse
Affiliation(s)
| | - Rei Matsuoka
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Sayo, Japan
| | - Yoshiki Yamashita
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Sayo, Japan
| | - Hirofumi Shimizu
- Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Maiko Tanaka
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Sayo, Japan
| | - Fumie Iwabuki
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Sayo, Japan
| | - Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Sayo, Japan
| |
Collapse
|
89
|
Chakravarty S, Ung AR, Moore B, Shore J, Alshamrani M. A Comprehensive Analysis of Anion-Quadrupole Interactions in Protein Structures. Biochemistry 2018; 57:1852-1867. [PMID: 29482321 PMCID: PMC6051350 DOI: 10.1021/acs.biochem.7b01006] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The edgewise interactions of anions with phenylalanine (Phe) aromatic rings in proteins, known as anion-quadrupole interactions, have been well studied. However, the anion-quadrupole interactions of the tyrosine (Tyr) and tryptophan (Trp) rings have been less well studied, probably because these have been considered weaker than interactions of anions hydrogen bonded to Trp/Tyr side chains. Distinguishing such hydrogen bonding interactions, we comprehensively surveyed the edgewise interactions of certain anions (aspartate, glutamate, and phosphate) with Trp, Tyr, and Phe rings in high-resolution, nonredundant protein single chains and interfaces (protein-protein, DNA/RNA-protein, and membrane-protein). Trp/Tyr anion-quadrupole interactions are common, with Trp showing the highest propensity and average interaction energy for this type of interaction. The energy of an anion-quadrupole interaction (-15.0 to 0.0 kcal/mol, based on quantum mechanical calculations) depends not only on the interaction geometry but also on the ring atom. The phosphate anions at DNA/RNA-protein interfaces interact with aromatic residues with energies comparable to that of aspartate/glutamate anion-quadrupole interactions. At DNA-protein interfaces, the frequency of aromatic ring participation in anion-quadrupole interactions is comparable to that of positive charge participation in salt bridges, suggesting an underappreciated role for anion-quadrupole interactions at DNA-protein (or membrane-protein) interfaces. Although less frequent than salt bridges in single-chain proteins, we observed highly conserved anion-quadrupole interactions in the structures of remote homologues, and evolutionary covariance-based residue contact score predictions suggest that conserved anion-quadrupole interacting pairs, like salt bridges, contribute to polypeptide folding, stability, and recognition.
Collapse
Affiliation(s)
- Suvobrata Chakravarty
- Chemistry & Biochemistry, South Dakota State University, Brookings, SD, USA, 57007
- BioSNTR, Brookings, SD, USA, 57007
| | - Adron R. Ung
- Chemistry & Biochemistry, South Dakota State University, Brookings, SD, USA, 57007
| | - Brian Moore
- University Networking and Research Computing, South Dakota State University, Brookings, SD, USA, 57007
| | - Jay Shore
- Chemistry & Biochemistry, South Dakota State University, Brookings, SD, USA, 57007
| | - Mona Alshamrani
- Chemistry & Biochemistry, South Dakota State University, Brookings, SD, USA, 57007
| |
Collapse
|
90
|
Fajardo VA, Mikhaeil JS, Leveille CF, Tupling AR, LeBlanc PJ. Elevated whole muscle phosphatidylcholine: phosphatidylethanolamine ratio coincides with reduced SERCA activity in murine overloaded plantaris muscles. Lipids Health Dis 2018. [PMID: 29534725 PMCID: PMC5851149 DOI: 10.1186/s12944-018-0687-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND An increase in phosphatidylcholine:phosphatidylethanolamine (PC:PE) and a decrease in fatty acyl chain length, monounsaturated:polyunsaturated (MUFA:PUFA) fatty acyl ratio reduces SERCA activity in liposomes and in mouse models of obesity and muscular dystrophy. We have previously shown that maximal SERCA activity is significantly reduced in mechanically overloaded (OVL) plantaris, however, whether changes in PC:PE ratio or fatty acyl composition may contribute to the alterations in maximal SERCA activity remain unknown. Here, we tested the hypotheses that in OVL plantaris 1) PC:PE ratio would negatively correlate with maximal SERCA activity and 2) PC fatty acyl chain length (ACL) and/or MUFA:PUFA ratio would positively correlate with maximal SERCA activity. METHODS To overload plantaris in mice, we transected the soleus and gastrocnemius tendons from one leg, while the contralateral leg underwent a sham surgery. After two weeks, plantaris muscles were extracted, homogenized and processed for SERCA activity and lipid analyses. Specifically, we performed HPTLC densitometry to examine changes in PC, PE, and the ratio of PC:PE. We also performed gas chromatography to assess any potential changes to fatty acyl composition. RESULTS SERCA activity was significantly reduced in OVL plantaris compared with sham. Coinciding with this, we found a significant increase in PC but not PE in OVL plantaris. In turn, there was an increase in PC:PE but did not reach significance (p = 0.09). However, we found a significant negative correlation between PC:PE and maximal SERCA activity. Fatty acyl composition of PE remained similar between OLV and sham and PC demonstrated higher percent mole fraction of 17:1, 18:1, and ACL compared to sham. In addition, PC ACL, % MUFA, % PUFA, or MUFA:PUFA did not significantly correlate with maximal SERCA activity. CONCLUSIONS Our results indicate that the phospholipid headgroup PC:PE negatively correlated and could potentially contribute to reductions in SERCA activity seen in functionally overloaded plantaris. In contrast, fatty acyl chain (ACL, % MUFA, % PUFA, MUFA:PUFA) did not correlate with maximal SERCA activity. Future studies will determine whether altering PC:PE with genetic and dietary interventions can influence SERCA activity and ultimately change the physiological outcome in response to muscle overloading.
Collapse
Affiliation(s)
- Val A Fajardo
- Department of Health Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada.,Centre for Bone and Muscle Health, Faculty of Applied Health Sciences, Brock University, St. Catharines, ON, Canada
| | - John S Mikhaeil
- Department of Health Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada.,Centre for Bone and Muscle Health, Faculty of Applied Health Sciences, Brock University, St. Catharines, ON, Canada
| | - Cameron F Leveille
- Department of Health Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada.,Centre for Bone and Muscle Health, Faculty of Applied Health Sciences, Brock University, St. Catharines, ON, Canada
| | - A Russell Tupling
- Department of Kinesiology, University of Waterloo, Waterloo, ON, Canada
| | - Paul J LeBlanc
- Department of Health Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada. .,Centre for Bone and Muscle Health, Faculty of Applied Health Sciences, Brock University, St. Catharines, ON, Canada.
| |
Collapse
|
91
|
Gianfrancesco MA, Paquot N, Piette J, Legrand-Poels S. Lipid bilayer stress in obesity-linked inflammatory and metabolic disorders. Biochem Pharmacol 2018; 153:168-183. [PMID: 29462590 DOI: 10.1016/j.bcp.2018.02.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/15/2018] [Indexed: 12/13/2022]
Abstract
The maintenance of the characteristic lipid compositions and physicochemical properties of biological membranes is essential for their proper function. Mechanisms allowing to sense and restore membrane homeostasis have been identified in prokaryotes for a long time and more recently in eukaryotes. A membrane remodeling can result from aberrant metabolism as seen in obesity. In this review, we describe how such lipid bilayer stress can account for the modulation of membrane proteins involved in the pathogenesis of obesity-linked inflammatory and metabolic disorders. We address the case of the Toll-like receptor 4 that is implicated in the obesity-related low grade inflammation and insulin resistance. The lipid raft-mediated TLR4 activation is promoted by an enrichment of the plasma membrane with saturated lipids or cholesterol increasing the lipid phase order. We discuss of the plasma membrane Na, K-ATPase that illustrates a new concept according to which direct interactions between specific residues and particular lipids determine both stability and activity of the pump in parallel with indirect effects of the lipid bilayer. The closely related sarco(endo)-plasmic Ca-ATPase embedded in the more fluid ER membrane seems to be more sensitive to a lipid bilayer stress as demonstrated by its inactivation in cholesterol-loaded macrophages or its inhibition mediated by an increased PtdCho/PtdEtn ratio in obese mice hepatocytes. Finally, we describe the model recently proposed for the activation of the conserved IRE-1 protein through alterations in the ER membrane lipid packing and thickness. Such IRE-1 activation could occur in response to abnormal lipid synthesis and membrane remodeling as observed in hepatocytes exposed to excess nutrients. Since the IRE-1/XBP1 branch also stimulates the lipid synthesis, this pathway could create a vicious cycle "lipogenesis-ER lipid bilayer stress-lipogenesis" amplifying hepatic ER pathology and the obesity-linked systemic metabolic defects.
Collapse
Affiliation(s)
- Marco A Gianfrancesco
- Laboratory of Immunometabolism and Nutrition, GIGA-I3, University of Liège, Liège, Belgium; Division of Diabetes, Nutrition and Metabolic Disorders, Department of Medicine, University Hospital of Liège, Liège, Belgium
| | - Nicolas Paquot
- Laboratory of Immunometabolism and Nutrition, GIGA-I3, University of Liège, Liège, Belgium; Division of Diabetes, Nutrition and Metabolic Disorders, Department of Medicine, University Hospital of Liège, Liège, Belgium
| | - Jacques Piette
- Laboratory of Virology and Immunology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium
| | - Sylvie Legrand-Poels
- Laboratory of Immunometabolism and Nutrition, GIGA-I3, University of Liège, Liège, Belgium; Laboratory of Virology and Immunology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium.
| |
Collapse
|
92
|
Zheng Y, Cui Q. Multiple Pathways and Time Scales for Conformational Transitions in apo-Adenylate Kinase. J Chem Theory Comput 2018; 14:1716-1726. [PMID: 29378407 DOI: 10.1021/acs.jctc.7b01064] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The open/close transition in adenylate kinase (AK) is regarded as a representative example for large-scale conformational transition in proteins, yet its mechanism remains unclear despite numerous experimental and computational studies. Using extensive (∼50 μs) explicit solvent atomistic simulations and Markov state analysis, we shed new lights on the mechanism of this transition in the apo form of AK. The closed basin of apo AK features an open NMP domain while the LID domain closes and rotates toward it. Therefore, although the computed structural properties of the closed ensemble are consistent with previously reported FRET and PRE measurements, our simulations suggest that NMP closure is likely to follow AMP binding, in contrast to the previous interpretation of FRET and PRE data that the apo state was able to sample the fully closed conformation for "ligand selection". The closed state ensemble is found to be kinetically heterogeneous; multiple pathways and time scales are associated with the open/close transition, providing new clues to the disparate time scales observed in different experiments. Besides interdomain interactions, a novel mutual information analysis identifies specific intradomain interactions that correlate strongly to transition kinetics, supporting observations from previous chimera experiments. While our results underscore the role of internal domain properties in determining the kinetics of open/close transition in apo AK, no evidence is observed for any significant degree of local unfolding during the transition. These observations about AK have general implications to our view of conformational states, transition pathways, and time scales of conformational changes in proteins. The key features and time scales of observed transition pathways are robust and similar from simulations using two popular fixed charge force fields.
Collapse
Affiliation(s)
- Yuqing Zheng
- Graduate Program in Biophysics and Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53706 , United States
| | - Qiang Cui
- Graduate Program in Biophysics and Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53706 , United States
| |
Collapse
|
93
|
|
94
|
Wei P, Song G, Shi M, Zhou Y, Liu Y, Lei J, Chen P, Yin L. Substrate analog interaction with MCR-1 offers insight into the rising threat of the plasmid-mediated transferable colistin resistance. FASEB J 2018; 32:1085-1098. [PMID: 29079699 DOI: 10.1096/fj.201700705r] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Colistin is considered a last-resort antibiotic against most gram-negative bacteria. Recent discoveries of a plasmid-mediated, transferable mobilized colistin-resistance gene ( mcr-1) on all continents have heralded the imminent emergence of pan-drug-resistant superbacteria. The inner-membrane protein MCR-1 can catalyze the transfer of phosphoethanolamine (PEA) to lipid A, resulting in colistin resistance. However, little is known about the mechanism, and few drugs exist to address this issue. We present crystal structures revealing the MCR-1 catalytic domain (cMCR-1) as a monozinc metalloprotein with ethanolamine (ETA) and d-glucose, respectively, thus highlighting 2 possible substrate-binding pockets in the MCR-1-catalyzed PEA transfer reaction. Mutation of the residues involved in ETA and d-glucose binding impairs colistin resistance in recombinant Escherichia coli containing full-length MCR-1. Partial analogs of the substrate are used for cocrystallization with cMCR-1, providing valuable information about the family of PEA transferases. One of the analogs, ETA, causes clear inhibition of polymyxin B resistance, highlighting its potential for drug development. These data demonstrate the crucial role of the PEA- and lipid A-binding pockets and provide novel insights into the structure-based mechanisms, important drug-target hot spots, and a drug template for further drug development to combat the urgent, rising threat of MCR-1-mediated antibiotic resistance.-Wei, P., Song, G., Shi, M., Zhou, Y., Liu, Y., Lei, J., Chen, P., Yin, L. Substrate analog interaction with MCR-1 offers insight into the rising threat of the plasmid-mediated transferable colistin resistance.
Collapse
Affiliation(s)
- Pengcheng Wei
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Guangji Song
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mengyang Shi
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yafei Zhou
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yang Liu
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jun Lei
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Peng Chen
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lei Yin
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, China
| |
Collapse
|
95
|
Abstract
Experimental methods for the characterization of protein complexes have been instrumental in achieving our current understanding of the protein universe and continue to progress with each year that passes. In this chapter, we review some of the most important tools and techniques in the field, covering the important points in X-ray crystallography, cryo-electron microscopy, NMR spectroscopy, and mass spectrometry. Novel developments are making it possible to study large protein complexes at near-atomic resolutions, and we also now have the ability to study the dynamics and assembly pathways of protein complexes across a range of sizes.
Collapse
Affiliation(s)
- Jonathan N Wells
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK.
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
96
|
Oka T. Small-Angle X-ray Crystallography on Single-Crystal Regions of Inverse Bicontinuous Cubic Phases: Lipid Bilayer Structures and Gaussian Curvature-Dependent Fluctuations. J Phys Chem B 2017; 121:11399-11409. [PMID: 29172522 DOI: 10.1021/acs.jpcb.7b08589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
I report for the first time an X-ray crystallographic study on single-crystal regions of cubic phases of a lyotropic liquid crystal. The single-crystal regions of three inverse bicontinuous cubic phases of a lipid, monoolein, diffracted X-ray only in small-angle regions, but amplitudes of structure factors were determined from the small-angle X-ray diffraction data with high accuracy. Structure factors from lipid bilayer models with constant thickness were optimized to amplitudes obtained from the X-ray data. By using amplitudes of the structure factors from X-ray data and phases from the models, electron density maps of three cubic phases were reconstructed. Lipid bilayer membranes, consisting of high density head regions and low density tail regions, were clearly distinguished in the electron density maps. Water regions had slightly lower density than that of the lipid head regions and were clearly visible for two of the cubic phases. Centers of bilayer membranes were located on the corresponding triply periodic minimal surfaces in the maps. Electron density data indicated Gaussian curvature-dependent fluctuations of bilayer membranes: the smaller the Gaussian curvature is, the larger the fluctuation becomes. The technique described in this report is expected to bring new knowledge in the structural research of lyotropic liquid crystals.
Collapse
Affiliation(s)
- Toshihiko Oka
- Department of Physics, Faculty of Science, and ‡Nanomaterials Research Division, Research Institute of Electronics, Shizuoka University , Shizuoka 422-8529, Japan
| |
Collapse
|
97
|
Dutta D, Fliegel L. Structure and function of yeast and fungal Na + /H + antiporters. IUBMB Life 2017; 70:23-31. [PMID: 29219228 DOI: 10.1002/iub.1701] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 11/21/2017] [Indexed: 12/22/2022]
Abstract
Sodium proton antiporters (or sodium proton exchangers [NHEs]) are a critical family of membrane proteins that exchange sodium for protons across cell membranes. In yeast and plants, their primary function is to keep the sodium concentration low inside the cytoplasm. One class of NHE constitutively expressed in yeast is the plasma membrane Na+ /H+ antiporter, and another class is expressed on the endosomal/vacuolar membrane. At present, four bacterial plasma membrane antiporter structures are known and nuclear magnetic resonance structures are available for the membrane spanning transmembrane helices of mammalian and yeast NHEs. Additionally, a vast amount of mutational data are available on the role of individual amino acids and critical motifs involved in transport. We combine this information to obtain a more detailed picture of the yeast NHE plasma membrane protein and review mechanisms of transport, conserved motifs, unique residues important in function, and regulation of these proteins. The Na+ /H+ antiporter of Schizosaccharomyces pombe, SpNHE1, is an interesting model protein in an easy to study system and is representative of fungal Na+ /H+ antiporters. © IUBMB Life, 70(1):23-31, 2018.
Collapse
Affiliation(s)
- Debajyoti Dutta
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Larry Fliegel
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
98
|
Ravishankar H, Barth A, Andersson M. Probing the activity of a recombinant Zn 2+ -transporting P-type ATPase. Biopolymers 2017; 109. [PMID: 29168553 DOI: 10.1002/bip.23087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/16/2017] [Accepted: 10/25/2017] [Indexed: 01/25/2023]
Abstract
P-type ATPase proteins maintain cellular homeostasis and uphold critical concentration gradients by ATP-driven ion transport across biological membranes. Characterization of single-cycle dynamics by time-resolved X-ray scattering techniques in solution could resolve structural intermediates not amendable to for example crystallization or cryo-electron microscopy sample preparation. To pave way for such time-resolved experiments, we used biochemical activity measurements, Attenuated Total Reflectance (ATR) and time-dependent Fourier-Transform Infra-Red (FTIR) spectroscopy to identify optimal conditions for activating a Zn2+ -transporting Type-I ATPase from Shigella sonnei (ssZntA) at high protein concentration using caged ATP. The highest total activity was observed at a protein concentration of 25 mg/mL, at 310 K, pH 7, and required the presence of 20% (v/v) glycerol as stabilizing agent. Neither the presence of caged ATP nor increasing lipid-to-protein ratio affected the hydrolysis activity significantly. This work also paves way for characterization of recombinant metal-transporting (Type-I) ATPase mutants with medical relevance.
Collapse
Affiliation(s)
- H Ravishankar
- Science for Life Laboratory, Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Solna, SE-171 21, Sweden
| | - A Barth
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-106 91, Sweden
| | - M Andersson
- Science for Life Laboratory, Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Solna, SE-171 21, Sweden
| |
Collapse
|
99
|
Dutta D, Shin K, Rainey JK, Fliegel L. Transmembrane Segment XI of the Na +/H + Antiporter of S. pombe is a Critical Part of the Ion Translocation Pore. Sci Rep 2017; 7:12793. [PMID: 29038548 PMCID: PMC5643542 DOI: 10.1038/s41598-017-12701-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/18/2017] [Indexed: 01/01/2023] Open
Abstract
The Na+/H+ exchanger of the plasma membrane of S. pombe (SpNHE1) removes intracellular sodium in exchange for an extracellular proton. We examined the structure and functional role of amino acids 360–393 of putative transmembrane (TM) segment XI of SpNHE1. Structural analysis suggested that it had a helical propensity over amino acids 360–368, an extended region from 369–378 and was helical over amino acids 379–386. TM XI was sensitive to side chain alterations. Mutation of eight amino acids to alanine resulted in loss of one or both of LiCl or NaCl tolerance when re-introduced into SpNHE1 deficient S. pombe. Mutation of seven other amino acids had minor effects. Analysis of structure and functional mutations suggested that Glu361 may be involved in cation coordination on the cytoplasmic face of the protein with a negative charge in this position being important. His367, Ile371 and Gly372 were important in function. Ile371 may have important hydrophobic interactions with other residues and Gly372 may be important in maintaining an extended conformation. Several residues from Val377 to Leu384 are important in function possibly involved in hydrophobic interactions with other amino acids. We suggest that TM XI forms part of the ion translocation core of this Na+/H+ exchanger.
Collapse
Affiliation(s)
- Debajyoti Dutta
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Kyungsoo Shin
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Jan K Rainey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.,Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Larry Fliegel
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada.
| |
Collapse
|
100
|
Yamasaki K, Daiho T, Danko S, Yasuda S, Suzuki H. Nanodisc-based kinetic assays reveal distinct effects of phospholipid headgroups on the phosphoenzyme transition of sarcoplasmic reticulum Ca 2+-ATPase. J Biol Chem 2017; 292:20218-20227. [PMID: 29032359 DOI: 10.1074/jbc.m117.816702] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/10/2017] [Indexed: 01/08/2023] Open
Abstract
Sarco(endo)plasmic reticulum Ca2+-ATPase catalyzes ATP-driven Ca2+ transport from the cytoplasm to the lumen and is critical for a range of cell functions, including muscle relaxation. Here, we investigated the effects of the headgroups of the 1-palmitoyl-2-oleoyl glycerophospholipids phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), and phosphatidylglycerol (PG) on sarcoplasmic reticulum (SR) Ca2+-ATPase embedded into a nanodisc, a lipid-bilayer construct harboring the specific lipid. We found that Ca2+-ATPase activity in a PC bilayer is comparable with that of SR vesicles and is suppressed in the other phospholipids, especially in PS. Ca2+ affinity at the high-affinity transport sites in PC was similar to that of SR vesicles, but 2-3-fold reduced in PE and PS. Ca2+ on- and off-rates in the non-phosphorylated ATPase were markedly reduced in PS. Rate-limiting phosphoenzyme (EP) conformational transition in 0.1 m KCl was as rapid in PC as in SR vesicles, but slowed in other phospholipids, especially in PS. Using kinetic plots of the logarithm of rate versus the square of mean activity coefficient of solutes in 0.1-1 m KCl, we noted that PC is optimal for the EP transition, but PG and especially PS had markedly unfavorable electrostatic effects, and PE exhibited a strong non-electrostatic restriction. Thus, the major SR membrane lipid PC is optimal for all steps and, unlike the other headgroups, contributes favorable electrostatics and non-electrostatic elements during the EP transition. Our analyses further revealed that the surface charge of the lipid bilayer directly modulates the transition rate.
Collapse
Affiliation(s)
- Kazuo Yamasaki
- Department of Biochemistry, Asahikawa Medical University, Midorigaoka-Higashi, Asahikawa 078-8510, Japan.
| | - Takashi Daiho
- Department of Biochemistry, Asahikawa Medical University, Midorigaoka-Higashi, Asahikawa 078-8510, Japan
| | - Stefania Danko
- Department of Biochemistry, Asahikawa Medical University, Midorigaoka-Higashi, Asahikawa 078-8510, Japan
| | - Satoshi Yasuda
- Department of Biochemistry, Asahikawa Medical University, Midorigaoka-Higashi, Asahikawa 078-8510, Japan
| | - Hiroshi Suzuki
- Department of Biochemistry, Asahikawa Medical University, Midorigaoka-Higashi, Asahikawa 078-8510, Japan
| |
Collapse
|