51
|
Ludwig J, Maibaum L. Effect of alcohol on the phase separation in model membranes. Chem Phys Lipids 2020; 233:104986. [PMID: 33080278 DOI: 10.1016/j.chemphyslip.2020.104986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/20/2020] [Accepted: 09/28/2020] [Indexed: 12/20/2022]
Abstract
The discovery of coexisting liquid-ordered and liquid-disordered phases in multicomponent lipid bilayers has received widespread attention due to its potential relevance for biological systems. One of the many open questions is how the presence of additional components affects the nature of the coexisting phases. Of particular interest is the addition of alcohols because their anesthetic properties may arise from modulating bilayer behavior. We use coarse-grained Molecular Dynamics simulations to gain insight into the partitioning preferences of linear n-alcohols into ordered and disordered bilayers alongside their effects on local membrane structure. We find that alcohols cause only small changes to membrane composition alongside a lack of significant effects on membrane thickness and lipid tail order. Cholesterol and n-alcohol trans-bilayer motion is measured and found to be near or within the range of previous atomistic results. The cholesterol flip-flop rates increase with both n-alcohol length and concentration for octanol, dodecanol, and hexadecanol, indicating a decrease in lipid order. Umbrella sampling simulations of removing cholesterol from tertiary membranes find no significant difference with or without n-alcohols at various concentrations. Simulations of a phase-separated bilayer show that octanol preferentially partitions into the liquid-disordered phase in a ratio of approximately 3:1 over the liquid-ordered phase. Furthermore, partition coefficients of alcohol in single-phase membranes show a preference for longer alcohols (dodecanol and hexadecanol) to partition preferentially into the liquid-ordered phase, while decreasing the length of the alcohol reverses this trend. Our work tests experimental results while also investigating the ability for coarse-grained MARTINI simulations to capture minute differences in model membrane spatial arrangements on the nanoscale level.
Collapse
Affiliation(s)
- James Ludwig
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Lutz Maibaum
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States.
| |
Collapse
|
52
|
Newstead S, Barr F. Molecular basis for KDEL-mediated retrieval of escaped ER-resident proteins - SWEET talking the COPs. J Cell Sci 2020; 133:133/19/jcs250100. [PMID: 33037041 PMCID: PMC7561476 DOI: 10.1242/jcs.250100] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 07/30/2020] [Indexed: 12/11/2022] Open
Abstract
Protein localisation in the cell is controlled through the function of trafficking receptors, which recognise specific signal sequences and direct cargo proteins to different locations. The KDEL receptor (KDELR) was one of the first intracellular trafficking receptors identified and plays an essential role in maintaining the integrity of the early secretory pathway. The receptor recognises variants of a canonical C-terminal Lys-Asp-Glu-Leu (KDEL) signal sequence on ER-resident proteins when these escape to the Golgi, and targets these proteins to COPI- coated vesicles for retrograde transport back to the ER. The empty receptor is then recycled from the ER back to the Golgi by COPII-coated vesicles. Crystal structures of the KDELR show that it is structurally related to the PQ-loop family of transporters that are found in both pro- and eukaryotes, and shuttle sugars, amino acids and vitamins across cellular membranes. Furthermore, analogous to PQ-loop transporters, the KDELR undergoes a pH-dependent and ligand-regulated conformational cycle. Here, we propose that the striking structural similarity between the KDELR and PQ-loop transporters reveals a connection between transport and trafficking in the cell, with important implications for understanding trafficking receptor evolution and function. Summary: The structure of the KDEL receptor gives new insights into the close connection between trafficking and transport in the cell.
Collapse
Affiliation(s)
- Simon Newstead
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford OX1 3QU, UK
| | - Francis Barr
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford OX1 3QU, UK
| |
Collapse
|
53
|
de la Nuez Veulens A, Rodríguez Fernández RE, Álvarez Ginarte YM, Montero Cabrera LA. In silico strategy for detailing the binding modes of a novel family of peptides proven as ghrelin receptor agonists. J Mol Model 2020; 26:294. [PMID: 33015729 DOI: 10.1007/s00894-020-04553-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/17/2020] [Indexed: 11/26/2022]
Abstract
Ghrelin is a peptide hormone involved in multiple functions, including growth hormone release stimulation, food intake regulation, and metabolic and cytoprotective effect. A novel family of peptides with internal cycles was designed as ghrelin analogs and the biological activity of two of them (A228 and A233) was experimentally studied in-depth. In this work, an in silico strategy was developed for describing and assessing the binding modes of A228 and A233 to GHS-R1a (ghrelin receptor) comparing it with ghrelin and GHRP-6 peptides. Several reported structures of different G protein coupled receptors were used as templates, to obtain a good quality model of GHS-R1a. The best model was selected by preliminary molecular docking with ghrelin and GHRP-6. Docking was used to estimate peptide orientations in the binding site of the best model, observing a superposition of its N-terminal and its first aromatic residue. To test the complex stability in time, the C-terminal fragments of each peptide were added and the complexes were inserted a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membrane, performing a molecular dynamic simulation for 100 ns using the CHARMM36 force field. Despite of the structural differences, the studied peptides share a common binding mode; the N-terminal interacts with E124 and the aromatic residue close to it, with the aromatic cluster (F279, F309, and F312). A preliminary pharmacophore model, consisting in a positive charged amine and an aromatic ring at an approximate distance of 0.79 nm, can be proposed. The results here described could represent a step forward in the efficient search of new ghrelin analogs.
Collapse
Affiliation(s)
| | | | - Yoanna M Álvarez Ginarte
- Laboratory of Theoretical and Computational Chemistry, Faculty of Chemistry, University of Havana, Havana, Cuba
| | - Luis A Montero Cabrera
- Laboratory of Theoretical and Computational Chemistry, Faculty of Chemistry, University of Havana, Havana, Cuba.
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA.
| |
Collapse
|
54
|
Klesse G, Tucker SJ, Sansom MSP. Electric Field Induced Wetting of a Hydrophobic Gate in a Model Nanopore Based on the 5-HT 3 Receptor Channel. ACS NANO 2020; 14:10480-10491. [PMID: 32673478 PMCID: PMC7450702 DOI: 10.1021/acsnano.0c04387] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/16/2020] [Indexed: 05/14/2023]
Abstract
In this study we examined the influence of a transmembrane voltage on the hydrophobic gating of nanopores using molecular dynamics simulations. We observed electric field induced wetting of a hydrophobic gate in a biologically inspired model nanopore based on the 5-HT3 receptor in its closed state, with a field of at least ∼100 mV nm-1 (corresponding to a supra-physiological potential difference of ∼0.85 V across the membrane) required to hydrate the pore. We also found an unequal distribution of charged residues can generate an electric field intrinsic to the nanopore which, depending on its orientation, can alter the effect of the external field, thus making the wetting response asymmetric. This wetting response could be described by a simple model based on water surface tension, the volumetric energy contribution of the electric field, and the influence of charged amino acids lining the pore. Finally, the electric field response was used to determine time constants characterizing the phase transitions of water confined within the nanopore, revealing liquid-vapor oscillations on a time scale of ∼5 ns. This time scale was largely independent of the water model employed and was similar for different sized pores representative of the open and closed states of the pore. Furthermore, our finding that the threshold voltage required for hydrating a hydrophobic gate depends on the orientation of the electric field provides an attractive perspective for the design of rectifying artificial nanopores.
Collapse
Affiliation(s)
- Gianni Klesse
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Oxford OX1 3PU, United Kingdom
| | - Stephen J. Tucker
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Oxford OX1 3PU, United Kingdom
- OXION
Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Mark S. P. Sansom
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| |
Collapse
|
55
|
Dijkman PM, Muñoz-García JC, Lavington SR, Kumagai PS, dos Reis RI, Yin D, Stansfeld PJ, Costa-Filho AJ, Watts A. Conformational dynamics of a G protein-coupled receptor helix 8 in lipid membranes. SCIENCE ADVANCES 2020; 6:eaav8207. [PMID: 32851152 PMCID: PMC7428336 DOI: 10.1126/sciadv.aav8207] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 07/02/2020] [Indexed: 05/21/2023]
Abstract
G protein-coupled receptors (GPCRs) are the largest and pharmaceutically most important class of membrane proteins encoded in the human genome, characterized by a seven-transmembrane helix architecture and a C-terminal amphipathic helix 8 (H8). In a minority of GPCR structures solved to date, H8 either is absent or adopts an unusual conformation. The controversial existence of H8 of the class A GPCR neurotensin receptor 1 (NTS1) has been examined here for the nonthermostabilized receptor in a functionally supporting membrane environment using electron paramagnetic resonance, molecular dynamics simulations, and circular dichroism. Lipid-protein interactions with phosphatidylserine and phosphatidylethanolamine lipids, in particular, stabilize the residues 374 to 390 of NTS1 into forming a helix. Furthermore, introduction of a helix-breaking proline residue in H8 elicited an increase in ß-arrestin-NTS1 interactions observed in pull-down assays, suggesting that the structure and/or dynamics of H8 might play an important role in GPCR signaling.
Collapse
Affiliation(s)
- Patricia M. Dijkman
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Juan C. Muñoz-García
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Steven R. Lavington
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Patricia Suemy Kumagai
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-Carlense 400, C.P. 369, São Carlos SP 13560-970, Brazil
| | - Rosana I. dos Reis
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Daniel Yin
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Phillip J. Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Antonio José Costa-Filho
- Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto SP 14040-901, Brazil
| | - Anthony Watts
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Corresponding author.
| |
Collapse
|
56
|
Mechanisms of activation and desensitization of full-length glycine receptor in lipid nanodiscs. Nat Commun 2020; 11:3752. [PMID: 32719334 PMCID: PMC7385131 DOI: 10.1038/s41467-020-17364-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/25/2020] [Indexed: 12/31/2022] Open
Abstract
Glycinergic synapses play a central role in motor control and pain processing in the central nervous system. Glycine receptors (GlyRs) are key players in mediating fast inhibitory neurotransmission at these synapses. While previous high-resolution structures have provided insights into the molecular architecture of GlyR, several mechanistic questions pertaining to channel function are still unanswered. Here, we present Cryo-EM structures of the full-length GlyR protein complex reconstituted into lipid nanodiscs that are captured in the unliganded (closed), glycine-bound (open and desensitized), and allosteric modulator-bound conformations. A comparison of these states reveals global conformational changes underlying GlyR channel gating and modulation. The functional state assignments were validated by molecular dynamics simulations, and the observed permeation events are in agreement with the anion selectivity and conductance of GlyR. These studies provide the structural basis for gating, ion selectivity, and single-channel conductance properties of GlyR in a lipid environment. Glycinergic synapses play a central role in motor control and pain processing in the central nervous system. Here, authors present cryo-EM structures of the full-length glycine receptors (GlyRs) reconstituted into lipid nanodiscs in the unliganded, glycine-bound and allosteric modulator-bound conformations and reveal global conformational changes underlying GlyR channel gating and modulation.
Collapse
|
57
|
Buslaev P, Mustafin K, Gushchin I. Principal component analysis highlights the influence of temperature, curvature and cholesterol on conformational dynamics of lipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183253. [PMID: 32142820 DOI: 10.1016/j.bbamem.2020.183253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 02/14/2020] [Accepted: 02/27/2020] [Indexed: 01/06/2023]
Abstract
Membrane lipids are inherently highly dynamic molecules. Currently, it is difficult to probe the structures of individual lipids experimentally at the timescales corresponding to atomic motions, and consequently molecular dynamics simulations are used widely. In our previous work, we have introduced the principal component analysis (PCA) as a convenient framework for comprehensive quantitative description of lipid motions. Here, we present a newly developed open source script, PCAlipids, which automates the analysis and allows us to refine the approach and test its limitations. We use PCAlipids to determine the influence of temperature, cholesterol and curvature on individual lipids, and show that the most prominent lipid tail scissoring motion is strongly affected by these factors and allows tracking of phase transition. Addition of cholesterol affects the conformations and selectively changes the dynamics of lipid molecules, impacting the large-amplitude motions. Introduction of curvature biases the conformational ensembles towards more extended structures. We hope that the developed approach will be useful for understanding the molecular basis of different processes occurring in lipid membrane systems and will stimulate development of complementary experimental techniques probing the conformations of individual lipid molecules.
Collapse
Affiliation(s)
- P Buslaev
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
| | - K Mustafin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - I Gushchin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
| |
Collapse
|
58
|
Barros M, Houlihan WJ, Paresi CJ, Brendel M, Rynearson KD, Lee CW, Prikhodko O, Cregger C, Chang G, Wagner SL, Gilchrist ML, Li YM. γ-Secretase Partitioning into Lipid Bilayers Remodels Membrane Microdomains after Direct Insertion. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:6569-6579. [PMID: 32432881 PMCID: PMC7887708 DOI: 10.1021/acs.langmuir.0c01178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
γ-Secretase is a multisubunit complex that catalyzes intramembranous cleavage of transmembrane proteins. The lipid environment forms membrane microdomains that serve as spatio-temporal platforms for proteins to function properly. Despite substantial advances in the regulation of γ-secretase, the effect of the local membrane lipid microenvironment on the regulation of γ-secretase is poorly understood. Here, we characterized and quantified the partitioning of γ-secretase and its substrates, the amyloid precursor protein (APP) and Notch, into lipid bilayers using solid-supported model membranes. Notch substrate is preferentially localized in the liquid-disordered (Ld) lipid domains, whereas APP and γ-secretase partition as single or higher complex in both phases but highly favor the ordered phase, especially after recruiting lipids from the ordered phase, indicating that the activity and specificity of γ-secretase against these two substrates are modulated by membrane lateral organization. Moreover, time-elapse measurements reveal that γ-secretase can recruit specific membrane components from the cholesterol-rich Lo phase and thus creates a favorable lipid environment for substrate recognition and therefore activity. This work offers insight into how γ-secretase and lipid modulate each other and control its activity and specificity.
Collapse
Affiliation(s)
- Marilia Barros
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, United States
| | - William J Houlihan
- Department of Chemical Engineering and the Department of Biomedical Engineering, The City College of the City University of New York, New York, New York 10031, United States
| | - Chelsea J Paresi
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, United States
- Pharmacology Graduate Program, Weill Graduate School of Medical Sciences of Cornell University, New York, New York 10021, United States
| | - Matthew Brendel
- Molecular Cytology Core, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, United States
| | - Kevin D Rynearson
- Department of Neurosciences, University of California, San Diego, California 92093, United States
| | | | - Olga Prikhodko
- Department of Neurosciences, University of California, San Diego, California 92093, United States
| | - Cristina Cregger
- Department of Neurosciences, University of California, San Diego, California 92093, United States
| | | | - Steven L Wagner
- Department of Neurosciences, University of California, San Diego, California 92093, United States
- Research Biologist, VA San Diego Healthcare System, La Jolla, California 92161, United States
| | - M Lane Gilchrist
- Department of Chemical Engineering and the Department of Biomedical Engineering, The City College of the City University of New York, New York, New York 10031, United States
| | - Yue-Ming Li
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, United States
- Pharmacology Graduate Program, Weill Graduate School of Medical Sciences of Cornell University, New York, New York 10021, United States
| |
Collapse
|
59
|
Klesse G, Rao S, Tucker SJ, Sansom MS. Induced Polarization in Molecular Dynamics Simulations of the 5-HT 3 Receptor Channel. J Am Chem Soc 2020; 142:9415-9427. [PMID: 32336093 PMCID: PMC7243253 DOI: 10.1021/jacs.0c02394] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Indexed: 12/30/2022]
Abstract
Ion channel proteins form water-filled nanoscale pores within lipid bilayers, and their properties are dependent on the complex behavior of water in a nanoconfined environment. Using a simplified model of the pore of the 5-HT3 receptor (5HT3R) which restrains the backbone structure to that of the parent channel protein from which it is derived, we compare additive with polarizable models in describing the behavior of water in nanopores. Molecular dynamics simulations were performed with four conformations of the channel: two closed state structures, an intermediate state, and an open state, each embedded in a phosphatidylcholine bilayer. Water density profiles revealed that for all water models, the closed and intermediate states exhibited strong dewetting within the central hydrophobic gate region of the pore. However, the open state conformation exhibited varying degrees of hydration, ranging from partial wetting for the TIP4P/2005 water model to complete wetting for the polarizable AMOEBA14 model. Water dipole moments calculated using polarizable force fields also revealed that water molecules remaining within dewetted sections of the pore resemble gas phase water. Free energy profiles for Na+ and for Cl- ions within the open state pore revealed more rugged energy landscapes using polarizable force fields, and the hydration number profiles of these ions were also sensitive to induced polarization resulting in a substantive reduction of the number of waters within the first hydration shell of Cl- while it permeates the pore. These results demonstrate that induced polarization can influence the complex behavior of water and ions within nanoscale pores and provides important new insights into their chemical properties.
Collapse
Affiliation(s)
- Gianni Klesse
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K.
- Clarendon
Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, U.K.
| | - Shanlin Rao
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K.
| | - Stephen J. Tucker
- Clarendon
Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, U.K.
- OXION
Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PT, U.K.
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K.
| |
Collapse
|
60
|
Farkas B, Csizmadia G, Katona E, Tusnády GE, Hegedűs T. MemBlob database and server for identifying transmembrane regions using cryo-EM maps. Bioinformatics 2020; 36:2595-2598. [PMID: 31290936 PMCID: PMC7178402 DOI: 10.1093/bioinformatics/btz539] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/31/2019] [Accepted: 07/09/2019] [Indexed: 11/14/2022] Open
Abstract
SUMMARY The identification of transmembrane helices in transmembrane proteins is crucial, not only to understand their mechanism of action but also to develop new therapies. While experimental data on the boundaries of membrane-embedded regions are sparse, this information is present in cryo-electron microscopy (cryo-EM) density maps and it has not been utilized yet for determining membrane regions. We developed a computational pipeline, where the inputs of a cryo-EM map, the corresponding atomistic structure, and the potential bilayer orientation determined by TMDET algorithm of a given protein result in an output defining the residues assigned to the bulk water phase, lipid interface and the lipid hydrophobic core. Based on this method, we built a database involving published cryo-EM protein structures and a server to be able to compute this data for newly obtained structures. AVAILABILITY AND IMPLEMENTATION http://memblob.hegelab.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Bianka Farkas
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest 1094, Hungary.,MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Budapest 1094, Hungary.,Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest 1083, Hungary
| | - Georgina Csizmadia
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest 1094, Hungary.,MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Budapest 1094, Hungary
| | - Eszter Katona
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest 1094, Hungary.,Faculty of Brain Sciences, University College London, London W1T 7NF, UK
| | - Gábor E Tusnády
- 'Momentum' Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 1117 Budapest, Hungary
| | - Tamás Hegedűs
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest 1094, Hungary.,MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Budapest 1094, Hungary
| |
Collapse
|
61
|
Membrane mediated toppling mechanism of the folate energy coupling factor transporter. Nat Commun 2020; 11:1763. [PMID: 32273501 PMCID: PMC7145868 DOI: 10.1038/s41467-020-15554-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 03/13/2020] [Indexed: 01/12/2023] Open
Abstract
Energy coupling factor (ECF) transporters are responsible for the uptake of micronutrients in bacteria and archaea. They consist of an integral membrane unit, the S-component, and a tripartite ECF module. It has been proposed that the S-component mediates the substrate transport by toppling over in the membrane when docking onto an ECF module. Here, we present multi-scale molecular dynamics simulations and in vitro experiments to study the molecular toppling mechanism of the S-component of a folate-specific ECF transporter. Simulations reveal a strong bending of the membrane around the ECF module that provides a driving force for toppling of the S-component. The stability of the toppled state depends on the presence of non-bilayer forming lipids, as confirmed by folate transport activity measurements. Together, our data provide evidence for a lipid-dependent toppling-based mechanism for the folate-specific ECF transporter, a mechanism that might apply to other ECF transporters.
Collapse
|
62
|
Rao S, Bates GT, Matthews CR, Newport TD, Vickery ON, Stansfeld PJ. Characterizing Membrane Association and Periplasmic Transfer of Bacterial Lipoproteins through Molecular Dynamics Simulations. Structure 2020; 28:475-487.e3. [PMID: 32053772 PMCID: PMC7139219 DOI: 10.1016/j.str.2020.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 11/22/2019] [Accepted: 01/24/2020] [Indexed: 01/09/2023]
Abstract
Escherichia coli lipoprotein precursors at the inner membrane undergo three maturation stages before transport by the Lol system to the outer membrane. Here, we develop a pipeline to simulate the membrane association of bacterial lipoproteins in their four maturation states. This has enabled us to model and simulate 81 of the predicted 114 E. coli lipoproteins and reveal their interactions with the host lipid membrane. As part of this set we characterize the membrane contacts of LolB, the lipoprotein involved in periplasmic translocation. We also consider the means and bioenergetics for lipoprotein localization. Our calculations uncover a preference for LolB over LolA and therefore indicate how a lipoprotein may be favorably transferred from the inner to outer membrane. Finally, we reveal that LolC has a role in membrane destabilization, thereby promoting lipoprotein transfer to LolA.
Collapse
Affiliation(s)
- Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - George T Bates
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Callum R Matthews
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Thomas D Newport
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Owen N Vickery
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; School of Life Sciences & Department of Chemistry, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; School of Life Sciences & Department of Chemistry, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK.
| |
Collapse
|
63
|
Koukos P, Bonvin A. Integrative Modelling of Biomolecular Complexes. J Mol Biol 2020; 432:2861-2881. [DOI: 10.1016/j.jmb.2019.11.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022]
|
64
|
Umeda R, Satouh Y, Takemoto M, Nakada-Nakura Y, Liu K, Yokoyama T, Shirouzu M, Iwata S, Nomura N, Sato K, Ikawa M, Nishizawa T, Nureki O. Structural insights into tetraspanin CD9 function. Nat Commun 2020; 11:1606. [PMID: 32231207 PMCID: PMC7105497 DOI: 10.1038/s41467-020-15459-7] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 03/06/2020] [Indexed: 01/16/2023] Open
Abstract
Tetraspanins play critical roles in various physiological processes, ranging from cell adhesion to virus infection. The members of the tetraspanin family have four membrane-spanning domains and short and large extracellular loops, and associate with a broad range of other functional proteins to exert cellular functions. Here we report the crystal structure of CD9 and the cryo-electron microscopic structure of CD9 in complex with its single membrane-spanning partner protein, EWI-2. The reversed cone-like molecular shape of CD9 generates membrane curvature in the crystalline lipid layers, which explains the CD9 localization in regions with high membrane curvature and its implications in membrane remodeling. The molecular interaction between CD9 and EWI-2 is mainly mediated through the small residues in the transmembrane region and protein/lipid interactions, whereas the fertilization assay revealed the critical involvement of the LEL region in the sperm-egg fusion, indicating the different dependency of each binding domain for other partner proteins. Tetraspanins play critical roles in various physiological processes, ranging from cell adhesion to virus infection. Here authors report the crystal structure of CD9 and the cryo-electron microscopic structure of CD9 in complex with its single membrane-spanning partner protein, EWI-2.
Collapse
Affiliation(s)
- Rie Umeda
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Yuhkoh Satouh
- Laboratory of Molecular Traffic, Institute for Molecular and Cellular Regulation (IMCR), Gunma University, Maebashi, 371-8512, Japan.,Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, Japan
| | - Mizuki Takemoto
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.,Preferred Networks, Inc., Bunkyo-ku, Tokyo, Japan
| | - Yoshiko Nakada-Nakura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kehong Liu
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takeshi Yokoyama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, Japan
| | - Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ken Sato
- Laboratory of Molecular Traffic, Institute for Molecular and Cellular Regulation (IMCR), Gunma University, Maebashi, 371-8512, Japan.,Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi, 371-8512, Japan
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan. .,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology, Bunkyo-ku, Tokyo, Japan.
| | - Osamu Nureki
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
| |
Collapse
|
65
|
Lei X, Cai X, Yang Y. Genetic engineering strategies for construction of multivalent chimeric VLPs vaccines. Expert Rev Vaccines 2020; 19:235-246. [PMID: 32133886 DOI: 10.1080/14760584.2020.1738227] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction: Over the past two decades, virus-like particles (VLPs) have been developed as a new generation of vaccines against viral infections. Based on VLPs, chimeric VLPs (chi-VLPs) have been generated through genetic modifications or chemical couplings. For construction of multivalent chi-VLPs vaccines, multiple genetic engineering strategies are continuously being developed. Thus, it is important to provide a summary as reference for researchers in this field.Areas covered: The representative studies on the genetic engineered multivalent chi-VLPs are summarized and mainly focused on chimeric capsid VLPs and chimeric enveloped VLPs. The advantages and limitations of each strategy are also discussed at last, as well as opinions on platform choice and future directions of eVLPs vaccines.Expert opinion: The design of multivalent chi-VLPs vaccines needs to meet the following specifications: 1) the incorporated antigens are suggested to display on the exposed surface of chi-VLPs and do not have excessive adverse effects on the stability of chi-VLPs; 2) the chi-VLPs should elicit protective antibodies against the incorporated antigen as well as the source virus of VLPs. However, there is no requirement of retaining the antigenicity of VLPs when using VLPs solely as carriers for antigens display or drug delivery.
Collapse
Affiliation(s)
- Xinnuo Lei
- Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Research Center of Reverse Vaccinology (RCRV), Hunan Agricultural University, Changsha, Hunan, China.,Laboratory of Functional Proteomics (LFP), College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, China
| | - Xiong Cai
- Institute of Innovation and Applied Research in Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Yi Yang
- Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Research Center of Reverse Vaccinology (RCRV), Hunan Agricultural University, Changsha, Hunan, China.,Laboratory of Functional Proteomics (LFP), College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, China
| |
Collapse
|
66
|
Banavali NK. The Mechanism of Cholesterol Modification of Hedgehog Ligand. J Comput Chem 2020; 41:520-527. [PMID: 31823413 DOI: 10.1002/jcc.26097] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/06/2019] [Accepted: 10/14/2019] [Indexed: 12/21/2022]
Abstract
Hedgehog (Hh) proteins are important components of signal transduction pathways involved in animal development, and their defects are implicated in carcinogenesis. Their N-terminal domain (HhN) acts as a signaling ligand, and their C-terminal domain (HhC) performs an autocatalytic function of cleaving itself away, while adding a cholesterol moiety to HhN. HhC has two sub-domains: a hedgehog/intein (hint) domain that primarily performs the autocatalytic activity, and a sterol-recognition region (SRR) that binds to cholesterol and properly positions it with respect to HhN. The three-dimensional details of this autocatalytic mechanism remain unknown, as does the structure of the precursor Hh protein. In this study, a complete cholesterol-bound precursor form of the drosophila Hh precursor is modeled using known crystal structures of HhN and the hint domain, and a hypothesized similarity of SRR to an unrelated but similar-sized cholesterol binding protein. The restrained geometries and topology switching (RGATS) strategy is then used to predict atomic-detail pathways for the full autocatalytic reaction starting from the precursor and ending in a cholesterol-linked HhN domain and a cleaved HhC domain. The RGATS explicit solvent simulations indicate the roles of individual HhC residues in facilitating the reaction, which can be confirmed through mutational experiments. These simulations also provide plausible structural models for the N/S acyl transfer intermediate and the product states of this reaction. This study thus provides a good framework for future computational and experimental studies to develop a full structural and dynamic understanding of Hh autoprocessing. © 2019 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Nilesh K Banavali
- Laboratory of Cellular and Molecular Basis of Diseases, Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| |
Collapse
|
67
|
Khelashvili G, Cheng X, Falzone ME, Doktorova M, Accardi A, Weinstein H. Membrane lipids are both the substrates and a mechanistically responsive environment of TMEM16 scramblase proteins. J Comput Chem 2020; 41:538-551. [PMID: 31750558 PMCID: PMC7261202 DOI: 10.1002/jcc.26105] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/04/2019] [Accepted: 10/17/2019] [Indexed: 12/21/2022]
Abstract
Recent discoveries about functional mechanisms of proteins in the TMEM16 family of phospholipid scramblases have illuminated the dual role of the membrane as both the substrate and a mechanistically responsive environment in the wide range of physiological processes and genetic disorders in which they are implicated. This is highlighted in the review of recent findings from our collaborative investigations of molecular mechanisms of TMEM16 scramblases that emerged from iterative functional, structural, and computational experimentation. In the context of this review, we present new MD simulations and trajectory analyses motivated by the fact that new structural information about the TMEM16 scramblases is emerging from cryo-EM determinations in lipid nanodiscs. Because the functional environment of these proteins in in vivo and in in vitro is closer to flat membranes, we studied comparatively the responses of the membrane to the TMEM16 proteins in flat membranes and nanodiscs. We find that bilayer shapes in the nanodiscs are very different from those observed in the flat membrane systems, but the function-related slanting of the membrane observed at the nhTMEM16 boundary with the protein is similar in the nanodiscs and in the flat bilayers. This changes, however, in the bilayer composed of longer-tail lipids, which is thicker near the phospholipid translocation pathway, which may reflect an enhanced tendency of the long tails to penetrate the pathway and create, as shown previously, a nonconductive environment. These findings support the correspondence between the mechanistic involvement of the lipid environment in the flat membranes, and the nanodiscs. © 2019 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York, 10065
- Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York, 10065
| | - Xiaolu Cheng
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York, 10065
| | - Maria E Falzone
- Department of Biochemistry, Weill Cornell Medical College of Cornell University, New York, New York, 10065
| | - Milka Doktorova
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas, 77030
| | - Alessio Accardi
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York, 10065
- Department of Biochemistry, Weill Cornell Medical College of Cornell University, New York, New York, 10065
- Department of Anesthesiology, Weill Cornell Medical College of Cornell University, New York, New York, 10065
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York, 10065
- Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York, 10065
| |
Collapse
|
68
|
Nakao H, Sugimoto Y, Ikeda K, Saito H, Nakano M. Structural Feature of Lipid Scrambling Model Transmembrane Peptides: Same-Side Positioning of Hydrophilic Residues and Their Deeper Position. J Phys Chem Lett 2020; 11:1662-1667. [PMID: 32058725 DOI: 10.1021/acs.jpclett.0c00175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Phospholipid scramblases that catalyze lipid transbilayer movement are associated with intercellular signaling and lipid homeostasis. Although several studies have shown that the hydrophilic residue-rich groove of the proteins mediates lipid scrambling, the interactions between the groove and the lipid bilayers remain poorly understood. Here we have revealed the structural features of model transmembrane peptides that conduct lipid scrambling as well as the interactions between the peptides and the surrounding lipids by means of experimental and simulation techniques. Peptides with two strongly hydrophilic residues located on the same side of the helices and at a deeper position in the membrane exhibited high scramblase activities. All-atom molecular dynamics simulations showed that the interactions between the hydrophilic residues and lipid head groups regulate the membrane thinning and disorder near the peptides in an order that correlates with the scramblase activity of the peptides. These results provide a basis for understanding the lipid scrambling mechanisms by transmembrane regions.
Collapse
Affiliation(s)
- Hiroyuki Nakao
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yuta Sugimoto
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Keisuke Ikeda
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Hiroaki Saito
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, 6-2-4 Furuedai, Suita, Osaka 565-0874, Japan
| | - Minoru Nakano
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| |
Collapse
|
69
|
Corey RA, Stansfeld PJ, Sansom MS. The energetics of protein-lipid interactions as viewed by molecular simulations. Biochem Soc Trans 2020; 48:25-37. [PMID: 31872229 PMCID: PMC7054751 DOI: 10.1042/bst20190149] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/06/2019] [Accepted: 12/10/2019] [Indexed: 12/20/2022]
Abstract
Membranes are formed from a bilayer containing diverse lipid species with which membrane proteins interact. Integral, membrane proteins are embedded in this bilayer, where they interact with lipids from their surroundings, whilst peripheral membrane proteins bind to lipids at the surface of membranes. Lipid interactions can influence the function of membrane proteins, either directly or allosterically. Both experimental (structural) and computational approaches can reveal lipid binding sites on membrane proteins. It is, therefore, important to understand the free energies of these interactions. This affords a more complete view of the engagement of a particular protein with the biological membrane surrounding it. Here, we describe many computational approaches currently in use for this purpose, including recent advances using both free energy and unbiased simulation methods. In particular, we focus on interactions of integral membrane proteins with cholesterol, and with anionic lipids such as phosphatidylinositol 4,5-bis-phosphate and cardiolipin. Peripheral membrane proteins are exemplified via interactions of PH domains with phosphoinositide-containing membranes. We summarise the current state of the field and provide an outlook on likely future directions of investigation.
Collapse
Affiliation(s)
- Robin A. Corey
- 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
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Mark S.P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| |
Collapse
|
70
|
Jefferies D, Khalid S. Atomistic and coarse-grained simulations of membrane proteins: A practical guide. Methods 2020; 185:15-27. [PMID: 32084518 DOI: 10.1016/j.ymeth.2020.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 02/07/2020] [Accepted: 02/14/2020] [Indexed: 12/12/2022] Open
Abstract
Membrane proteins are amphipathic macromolecules whose exposed hydrophobic surfaces promote interactions with lipid membranes. Membrane proteins are remarkably diverse in terms of chemical composition and correspondingly, their biological functions and general biophysical behavior. Conventional experimental techniques provide an approach to study specific properties of membrane proteins e.g. their surface features, the nature and abundance of stabilizing intramolecular forces, preferred bilayer orientation, and the characteristics of their annular lipid shells. Molecular modeling software-and in particular, the suite of molecular dynamics algorithms-enables a more comprehensive exploration of dynamic membrane protein behavior. Molecular dynamics methods enable users to produce stepwise trajectories of proteins on arbitrary spatiotemporal scales that enable the easy identification of dynamic interactions that are beyond the scope of conventional analytical techniques. This article explains the molecular dynamics theoretical framework and popular step-by-step approaches for simulating membrane proteins in planar, and to a lesser extent, nonplanar lipid geometries. We detail popular procedures and computational tools that produce well-packed configurations of lipids and proteins and additionally, the efficient molecular dynamics simulation algorithms that reproduce their dynamic interactions.
Collapse
Affiliation(s)
- Damien Jefferies
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK.
| |
Collapse
|
71
|
Using MemBlob to Analyze Transmembrane Regions Based on Cryo-EM Maps. Methods Mol Biol 2020. [PMID: 32006282 DOI: 10.1007/978-1-0716-0270-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Transmembrane proteins include membrane channels, pores, and receptors and, as such, comprise an important part of the proteome, yet our knowledge about them is much less complete than about soluble, globular proteins. An important aspect of transmembrane protein structure is their exact position within the lipid bilayer, a feature hard to investigate experimentally at the atomic level. Here we describe MemBlob, a novel approach utilizing difference electron density maps obtained by cryo-EM studies of transmembrane proteins. The idea behind is that the nonprotein part of such maps carries information on the exact localization of the membrane mimetics used in the experiment and can be used to extract the positional information of the protein within the membrane. MemBlob uses a structural model of the protein and an experimental electron density map to provide an estimation of the surface residues interacting with the membrane.
Collapse
|
72
|
Tascón I, Sousa JS, Corey RA, Mills DJ, Griwatz D, Aumüller N, Mikusevic V, Stansfeld PJ, Vonck J, Hänelt I. Structural basis of proton-coupled potassium transport in the KUP family. Nat Commun 2020; 11:626. [PMID: 32005818 PMCID: PMC6994465 DOI: 10.1038/s41467-020-14441-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/10/2020] [Indexed: 12/05/2022] Open
Abstract
Potassium homeostasis is vital for all organisms, but is challenging in single-celled organisms like bacteria and yeast and immobile organisms like plants that constantly need to adapt to changing external conditions. KUP transporters facilitate potassium uptake by the co-transport of protons. Here, we uncover the molecular basis for transport in this widely distributed family. We identify the potassium importer KimA from Bacillus subtilis as a member of the KUP family, demonstrate that it functions as a K+/H+ symporter and report a 3.7 Å cryo-EM structure of the KimA homodimer in an inward-occluded, trans-inhibited conformation. By introducing point mutations, we identify key residues for potassium and proton binding, which are conserved among other KUP proteins. KUP transporters facilitate potassium uptake by the co-transport of protons and are key players in potassium homeostasis. Here authors identify the potassium importer KimA from Bacillus subtilis as a new member of the KUP transporter family and show the cryo-EM structure of KimA in an inward-occluded, trans-inhibited conformation.
Collapse
Affiliation(s)
- Igor Tascón
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Joana S Sousa
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Deryck J Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - David Griwatz
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Nadine Aumüller
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Vedrana Mikusevic
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, Oxford, UK.,School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
| | - Inga Hänelt
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
| |
Collapse
|
73
|
Structure and assembly of calcium homeostasis modulator proteins. Nat Struct Mol Biol 2020; 27:150-159. [PMID: 31988524 PMCID: PMC7015811 DOI: 10.1038/s41594-019-0369-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 12/23/2019] [Indexed: 01/17/2023]
Abstract
The biological membranes of many cell types contain large-pore channels through which a wide variety of ions and metabolites permeate. Examples include connexin, innexin and pannexin, which form gap junctions and/or bona fide cell surface channels. The most recently identified large-pore channels are the calcium homeostasis modulators (CALHMs), through which ions and ATP permeate in a voltage-dependent manner to control neuronal excitability, taste signaling and pathologies of depression and Alzheimer's disease. Despite such critical biological roles, the structures and patterns of their oligomeric assembly remain unclear. Here, we reveal the structures of two CALHMs, chicken CALHM1 and human CALHM2, by single-particle cryo-electron microscopy (cryo-EM), which show novel assembly of the four transmembrane helices into channels of octamers and undecamers, respectively. Furthermore, molecular dynamics simulations suggest that lipids can favorably assemble into a bilayer within the larger CALHM2 pore, but not within CALHM1, demonstrating the potential correlation between pore size, lipid accommodation and channel activity.
Collapse
|
74
|
Chan J, Zou J, Ortiz CL, Chang Chien CH, Pan RL, Yang LW. DR-SIP: protocols for higher order structure modeling with distance restraints- and cyclic symmetry-imposed packing. Bioinformatics 2020; 36:449-461. [PMID: 31347658 DOI: 10.1093/bioinformatics/btz579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 07/05/2019] [Accepted: 07/18/2019] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Quaternary structure determination for transmembrane/soluble proteins requires a reliable computational protocol that leverages observed distance restraints and/or cyclic symmetry (Cn symmetry) found in most homo-oligomeric transmembrane proteins. RESULTS We survey 118 X-ray crystallographically solved structures of homo-oligomeric transmembrane proteins (HoTPs) and find that ∼97% are Cn symmetric. Given the prevalence of Cn symmetric HoTPs and the benefits of incorporating geometry restraints in aiding quaternary structure determination, we introduce two new filters, the distance-restraints (DR) and the Symmetry-Imposed Packing (SIP) filters. SIP relies on a new method that can rebuild the closest ideal Cn symmetric complex from docking poses containing a homo-dimer without prior knowledge of the number (n) of monomers. Using only the geometrical filter, SIP, near-native poses of 7 HoTPs in their monomeric states can be correctly identified in the top-10 for 71% of all cases, or 29% among 31 HoTP structures obtained through homology modeling, while ZDOCK alone returns 14 and 3%, respectively. When the n is given, the optional n-mer filter is applied with SIP and returns the near-native poses for 76% of the test set within the top-10, outperforming M-ZDOCK's 55% and Sam's 47%. While applying only SIP to three HoTPs that comes with distance restraints, we found the near-native poses were ranked 1st, 1st and 10th among 54 000 possible decoys. The results are further improved to 1st, 1st and 3rd when both DR and SIP filters are used. By applying only DR, a soluble system with distance restraints is recovered at the 1st-ranked pose. AVAILABILITY AND IMPLEMENTATION https://github.com/capslockwizard/drsip. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Justin Chan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.,Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Sciences, Academia Sinica, Taipei, Taiwan
| | - Jinhao Zou
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.,UTHealth Graduate School of Biomedical Science, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Chi-Hong Chang Chien
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Rong-Long Pan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Lee-Wei Yang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.,Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Sciences, Academia Sinica, Taipei, Taiwan.,Physics Division, National Center for Theoretical Sciences, National Tsing Hua University, Hsinchu, Taiwan
| |
Collapse
|
75
|
Juračka J, Šrejber M, Melíková M, Bazgier V, Berka K. MolMeDB: Molecules on Membranes Database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5523873. [PMID: 31250015 PMCID: PMC6597476 DOI: 10.1093/database/baz078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 12/16/2022]
Abstract
Biological membranes act as barriers or reservoirs for many compounds within the human body. As such, they play an important role in pharmacokinetics and pharmacodynamics of drugs and other molecular species. Until now, most membrane/drug interactions have been inferred from simple partitioning between octanol and water phases. However, the observed variability in membrane composition and among compounds themselves stretches beyond such simplification as there are multiple drug–membrane interactions. Numerous experimental and theoretical approaches are used to determine the molecule–membrane interactions with variable accuracy, but there is no open resource for their critical comparison. For this reason, we have built Molecules on Membranes Database (MolMeDB), which gathers data about over 3600 compound–membrane interactions including partitioning, penetration and positioning. The data have been collected from scientific articles published in peer-reviewed journals and complemented by in-house calculations from high-throughput COSMOmic approach to set up a baseline for further comparison. The data in MolMeDB are fully searchable and browsable by means of name, SMILES, membrane, method or dataset and we offer the collected data openly for further reuse and we are open to further additions. MolMeDB can be a powerful tool that could help researchers better understand the role of membranes and to compare individual approaches used for the study of molecule/membrane interactions.
Collapse
Affiliation(s)
- Jakub Juračka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Tř. 17, listopadu 12, 771 46 Olomouc, Czech Republic
| | - Martin Šrejber
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Tř. 17, listopadu 12, 771 46 Olomouc, Czech Republic
| | - Michaela Melíková
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Tř. 17, listopadu 12, 771 46 Olomouc, Czech Republic
| | - Václav Bazgier
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Tř. 17, listopadu 12, 771 46 Olomouc, Czech Republic
| | - Karel Berka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Tř. 17, listopadu 12, 771 46 Olomouc, Czech Republic
| |
Collapse
|
76
|
Wang Q, Corey RA, Hedger G, Aryal P, Grieben M, Nasrallah C, Baronina A, Pike ACW, Shi J, Carpenter EP, Sansom MSP. Lipid Interactions of a Ciliary Membrane TRP Channel: Simulation and Structural Studies of Polycystin-2. Structure 2019; 28:169-184.e5. [PMID: 31806353 PMCID: PMC7001106 DOI: 10.1016/j.str.2019.11.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/04/2019] [Accepted: 11/08/2019] [Indexed: 01/08/2023]
Abstract
Polycystin-2 (PC2) is a transient receptor potential (TRP) channel present in ciliary membranes of the kidney. PC2 shares a transmembrane fold with other TRP channels, in addition to an extracellular domain found in TRPP and TRPML channels. Using molecular dynamics (MD) simulations and cryoelectron microscopy we identify and characterize PIP2 and cholesterol interactions with PC2. PC2 is revealed to have a PIP binding site close to the equivalent vanilloid/lipid binding site in the TRPV1 channel. A 3.0-Å structure reveals a binding site for cholesterol on PC2. Cholesterol interactions with the channel at this site are characterized by MD simulations. The two classes of lipid binding sites are compared with sites observed in other TRPs and in Kv channels. These findings suggest PC2, in common with other ion channels, may be modulated by both PIPs and cholesterol, and position PC2 within an emerging model of the roles of lipids in the regulation and organization of ciliary membranes. Lipid interactions of PC2 channels have been explored by MD simulation and cryo-EM PIP2 binds to a site corresponding to the vanilloid/lipid binding site of TRPV1 Cholesterol binds between the S3 and S4 helices and S6 of the adjacent subunit PC2, in common with other channels, may be modulated by PIPs and cholesterol
Collapse
Affiliation(s)
- Qinrui Wang
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - George Hedger
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Prafulla Aryal
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mariana Grieben
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Chady Nasrallah
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Agnese Baronina
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Ashley C W Pike
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Jiye Shi
- UCB Pharma, 208 Bath Road, Slough SL1 3WE, UK
| | - Elisabeth P Carpenter
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK.
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| |
Collapse
|
77
|
Khelashvili G, Falzone ME, Cheng X, Lee BC, Accardi A, Weinstein H. Dynamic modulation of the lipid translocation groove generates a conductive ion channel in Ca 2+-bound nhTMEM16. Nat Commun 2019; 10:4972. [PMID: 31672969 PMCID: PMC6823365 DOI: 10.1038/s41467-019-12865-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 10/01/2019] [Indexed: 12/05/2022] Open
Abstract
Both lipid and ion translocation by Ca2+-regulated TMEM16 transmembrane proteins utilizes a membrane-exposed hydrophilic groove. Several conformations of the groove are observed in TMEM16 protein structures, but how these conformations form, and what functions they support, remains unknown. From analyses of atomistic molecular dynamics simulations of Ca2+-bound nhTMEM16 we find that the mechanism of a conformational transition of the groove from membrane-exposed to occluded from the membrane involves the repositioning of transmembrane helix 4 (TM4) following its disengagement from a TM3/TM4 interaction interface. Residue L302 is a key element in the hydrophobic TM3/TM4 interaction patch that braces the open-groove conformation, which should be changed by an L302A mutation. The structure of the L302A mutant determined by cryogenic electron microscopy (cryo-EM) reveals a partially closed groove that could translocate ions, but not lipids. This is corroborated with functional assays showing severely impaired lipid scrambling, but robust channel activity by L302A. A membrane-exposed groove in Ca2+-gated TMEM16 scramblases forms the translocation pathway for ions and lipids. Here authors combine molecular dynamics with cryo-EM and functional assays to uncover the conformational transitions of the groove leading to a non-selective ion channel pore.
Collapse
Affiliation(s)
- George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA. .,Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA.
| | - Maria E Falzone
- Department of Biochemistry, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA
| | - Xiaolu Cheng
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA
| | - Byoung-Cheol Lee
- Research Group for the Neurovascular Unit, Korea Brain Research Institute, Daegu, Republic of Korea.,Department of Anesthesiology, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA
| | - Alessio Accardi
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA. .,Department of Biochemistry, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA. .,Department of Anesthesiology, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA.
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA. .,Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA.
| |
Collapse
|
78
|
Siggel M, Bhaskara RM, Hummer G. Phospholipid Scramblases Remodel the Shape of Asymmetric Membranes. J Phys Chem Lett 2019; 10:6351-6354. [PMID: 31566982 DOI: 10.1021/acs.jpclett.9b02531] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The cell membrane and many organellar membranes are asymmetric and highly curved. In experiments, it is challenging to reconstitute and characterize membranes that differ in the lipid composition of their leaflets. Here we use molecular dynamics simulations to study the large-scale membrane shape changes associated with lipid shuttling between asymmetric leaflets. We exploit leaflet asymmetry to create a stable, near-spherical vesicle bud connected to a flat bilayer under periodic boundary conditions. Then we demonstrate how the lipid scramblase nhTMEM16 relaxes the lipid-number asymmetry. By mediating the flipping of lipids, this transmembrane protein dissipates the mechanochemical gradient between the leaflets and drives a large-scale membrane reorganization, converting the vesicle bud into a flat membrane. Our procedure to exploit bilayer asymmetry for simulations of highly curved membranes can be used to study the function of other lipid transporters and membrane-shaping proteins.
Collapse
Affiliation(s)
- Marc Siggel
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Str. 3 , 60438 Frankfurt am Main , Germany
| | - Ramachandra M Bhaskara
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Str. 3 , 60438 Frankfurt am Main , Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Str. 3 , 60438 Frankfurt am Main , Germany
- Institute of Biophysics , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
| |
Collapse
|
79
|
Abraham M, Apostolov R, Barnoud J, Bauer P, Blau C, Bonvin AMJJ, Chavent M, Chodera J, Čondić-Jurkić K, Delemotte L, Grubmüller H, Howard RJ, Jordan EJ, Lindahl E, Ollila OHS, Selent J, Smith DGA, Stansfeld PJ, Tiemann JKS, Trellet M, Woods C, Zhmurov A. Sharing Data from Molecular Simulations. J Chem Inf Model 2019; 59:4093-4099. [PMID: 31525920 DOI: 10.1021/acs.jcim.9b00665] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Given the need for modern researchers to produce open, reproducible scientific output, the lack of standards and best practices for sharing data and workflows used to produce and analyze molecular dynamics (MD) simulations has become an important issue in the field. There are now multiple well-established packages to perform molecular dynamics simulations, often highly tuned for exploiting specific classes of hardware, each with strong communities surrounding them, but with very limited interoperability/transferability options. Thus, the choice of the software package often dictates the workflow for both simulation production and analysis. The level of detail in documenting the workflows and analysis code varies greatly in published work, hindering reproducibility of the reported results and the ability for other researchers to build on these studies. An increasing number of researchers are motivated to make their data available, but many challenges remain in order to effectively share and reuse simulation data. To discuss these and other issues related to best practices in the field in general, we organized a workshop in November 2018 ( https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/ ). Here, we present a brief overview of this workshop and topics discussed. We hope this effort will spark further conversation in the MD community to pave the way toward more open, interoperable, and reproducible outputs coming from research studies using MD simulations.
Collapse
Affiliation(s)
- Mark Abraham
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , Box 1031, SE-171 21 Solna , Sweden
| | - Rossen Apostolov
- PDC Center for High Performance Computing, School of Electrical Engineering and Computer Science , KTH Royal Institute of Technology , 114 28 Stockholm , Sweden
| | | | - Paul Bauer
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , Box 1031, SE-171 21 Solna , Sweden
| | - Christian Blau
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , Box 1031, SE-171 21 Solna , Sweden
| | | | | | - John Chodera
- Computational and Systems Biology Program , Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States
| | - Karmen Čondić-Jurkić
- Computational and Systems Biology Program , Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Open Force Field Consortium , https://openforcefield.org/consortium/
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , Box 1031, SE-171 21 Solna , Sweden
| | - Helmut Grubmüller
- Max Planck Institute for Biophysical Chemistry , 37077 Goettingen , Germany
| | - Rebecca J Howard
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , Box 1031, SE-171 21 Solna , Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics , Stockholm University , Box 1031, SE-171 21 Solna , Sweden
| | - E Joseph Jordan
- Science for Life Laboratory, Department of Biochemistry and Biophysics , Stockholm University , Box 1031, SE-171 21 Solna , Sweden
| | - Erik Lindahl
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , Box 1031, SE-171 21 Solna , Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics , Stockholm University , Box 1031, SE-171 21 Solna , Sweden
| | - O H Samuli Ollila
- Institute of Biotechnology , University of Helsinki , 00100 Helsinki , Finland
| | - Jana Selent
- Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute (IMIM) & Department of Experimental and Health Sciences , Pompeu Fabra University , 08002 Barcelona , Spain
| | - Daniel G A Smith
- The Molecular Sciences Software Institute , Blacksburg , Virginia 24060 , United States
| | | | - Johanna K S Tiemann
- Institute of Medical Physics and Biophysics, Faculty of Medicine , University Leipzig , Leipzig 04107 , Germany
| | - Mikael Trellet
- Faculty of Science , Utrecht University , Bijvoet Center, Utrecht , The Netherlands
| | | | - Artem Zhmurov
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , Box 1031, SE-171 21 Solna , Sweden
| |
Collapse
|
80
|
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
|
81
|
Bushell SR, Pike ACW, Falzone ME, Rorsman NJG, Ta CM, Corey RA, Newport TD, Christianson JC, Scofano LF, Shintre CA, Tessitore A, Chu A, Wang Q, Shrestha L, Mukhopadhyay SMM, Love JD, Burgess-Brown NA, Sitsapesan R, Stansfeld PJ, Huiskonen JT, Tammaro P, Accardi A, Carpenter EP. The structural basis of lipid scrambling and inactivation in the endoplasmic reticulum scramblase TMEM16K. Nat Commun 2019; 10:3956. [PMID: 31477691 PMCID: PMC6718402 DOI: 10.1038/s41467-019-11753-1] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 08/01/2019] [Indexed: 11/20/2022] Open
Abstract
Membranes in cells have defined distributions of lipids in each leaflet, controlled by lipid scramblases and flip/floppases. However, for some intracellular membranes such as the endoplasmic reticulum (ER) the scramblases have not been identified. Members of the TMEM16 family have either lipid scramblase or chloride channel activity. Although TMEM16K is widely distributed and associated with the neurological disorder autosomal recessive spinocerebellar ataxia type 10 (SCAR10), its location in cells, function and structure are largely uncharacterised. Here we show that TMEM16K is an ER-resident lipid scramblase with a requirement for short chain lipids and calcium for robust activity. Crystal structures of TMEM16K show a scramblase fold, with an open lipid transporting groove. Additional cryo-EM structures reveal extensive conformational changes from the cytoplasmic to the ER side of the membrane, giving a state with a closed lipid permeation pathway. Molecular dynamics simulations showed that the open-groove conformation is necessary for scramblase activity. TMEM16K is a member of the TMEM16 family of integral membrane proteins that are either lipid scramblases or chloride channels. Here the authors combine cell biology, electrophysiology measurements, X-ray crystallography, cryo-EM and MD simulations to structurally characterize TMEM16K and show that it is an ER-resident lipid scramblase.
Collapse
Affiliation(s)
- Simon R Bushell
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Ashley C W Pike
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Maria E Falzone
- Department of Biochemistry, Weill Cornell Medical School, 1300 York Avenue, New York, NY, 10065, USA
| | - Nils J G Rorsman
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.,OxSyBio, Atlas Building, Harwell Campus, Didcot, Oxfordshire, OX11 0QX, UK
| | - Chau M Ta
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.,Department of Cardiology, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QT, UK
| | - Thomas D Newport
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QT, UK.,Oxford Nanopore Technologies, Oxford Science Park, Oxford, OX4 4DQ, UK
| | - John C Christianson
- Nuffield Department of Rheumatology, Orthopaedics and Musculoskeletal Sciences, University of Oxford, Windmill Road, Oxford, OX3 7LD, UK
| | - Lara F Scofano
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Chitra A Shintre
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.,Vertex Pharmaceuticals Ltd, Milton Park, Oxfordshire, OX14 4RW, UK
| | - Annamaria Tessitore
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.,Nuffield Division of Clinical Laboratory Sciences, Oxford University, Oxford, OX3 9DU, UK
| | - Amy Chu
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.,Department of Biochemistry, Oxford University, Oxford, OX1 3QT, UK
| | - Qinrui Wang
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QT, UK
| | - Leela Shrestha
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Shubhashish M M Mukhopadhyay
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - James D Love
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461-1602, USA.,Novo Nordisk A/S, Novo Nordisk Park, 2760, Måløv, Denmark
| | - Nicola A Burgess-Brown
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Rebecca Sitsapesan
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QT, UK
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Paolo Tammaro
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Alessio Accardi
- Department of Biochemistry, Weill Cornell Medical School, 1300 York Avenue, New York, NY, 10065, USA.,Department of Anesthesiology, Weill Cornell Medical School, 25 East 68th Street, New York, NY, 10065, USA.,Department of Physiology and Biophysics, Weill Cornell Medical School, 1300 York Avenue, New York, NY, 10065, USA
| | - Elisabeth P Carpenter
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.
| |
Collapse
|
82
|
Situ AJ, Ulmer TS. Universal principles of membrane protein assembly, composition and evolution. PLoS One 2019; 14:e0221372. [PMID: 31415673 PMCID: PMC6695178 DOI: 10.1371/journal.pone.0221372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/05/2019] [Indexed: 11/18/2022] Open
Abstract
Structural diversity in α-helical membrane proteins (MP) arises from variations in helix-helix crossings and contacts that may bias amino acid usage. Here, we reveal systematic changes in transmembrane amino acid frequencies (f) as a function of the number of helices (n). For eukarya, breaks in f(n) trends of packing (Ala, Gly and Pro), polar, and hydrophobic residues identify different MP assembly principles for 2≤n≤7, 8≤n≤12 and n≥13. In bacteria, the first f break already occurs after n = 6 in correlation to an earlier n peak in MP size distribution and dominance of packing over polar interactions. In contrast to the later n brackets, the integration levels of helix bundles continuously increased in the first, most populous brackets indicating the formation of single structural units (domains). The larger first bracket of eukarya relates to a balance of polar and packing interactions that enlarges helix-helix combinatorial possibilities (MP diversity). Between the evolutionary old, packing and new, polar residues f anti-correlations extend over all biological taxa, broadly ordering them according to evolutionary history and allowing f estimates for the earliest forms of life. Next to evolutionary history, the amino acid composition of MP is determined by size (n), proteome diversity, and effective amino acid cost.
Collapse
Affiliation(s)
- Alan J. Situ
- Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Tobias S. Ulmer
- Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
- * E-mail:
| |
Collapse
|
83
|
Campaña MB, Irudayanathan FJ, Davis TR, McGovern-Gooch KR, Loftus R, Ashkar M, Escoffery N, Navarro M, Sieburg MA, Nangia S, Hougland JL. The ghrelin O-acyltransferase structure reveals a catalytic channel for transmembrane hormone acylation. J Biol Chem 2019; 294:14166-14174. [PMID: 31413115 DOI: 10.1074/jbc.ac119.009749] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/12/2019] [Indexed: 01/17/2023] Open
Abstract
Integral membrane proteins represent a large and diverse portion of the proteome and are often recalcitrant to purification, impeding studies essential for understanding protein structure and function. By combining co-evolutionary constraints and computational modeling with biochemical validation through site-directed mutagenesis and enzyme activity assays, we demonstrate here a synergistic approach to structurally model purification-resistant topologically complex integral membrane proteins. We report the first structural model of a eukaryotic membrane-bound O-acyltransferase (MBOAT), ghrelin O-acyltransferase (GOAT), which modifies the metabolism-regulating hormone ghrelin. Our structure, generated in the absence of any experimental structural data, revealed an unanticipated strategy for transmembrane protein acylation with catalysis occurring in an internal channel connecting the endoplasmic reticulum lumen and cytoplasm. This finding validated the power of our approach to generate predictive structural models for other experimentally challenging integral membrane proteins. Our results illuminate novel aspects of membrane protein function and represent key steps for advancing structure-guided inhibitor design to target therapeutically important but experimentally intractable membrane proteins.
Collapse
Affiliation(s)
- Maria B Campaña
- Department of Chemistry, Syracuse University, Syracuse, New York 13244
| | | | - Tasha R Davis
- Department of Chemistry, Syracuse University, Syracuse, New York 13244
| | | | - Rosemary Loftus
- Department of Chemistry, Syracuse University, Syracuse, New York 13244
| | - Mohammad Ashkar
- Department of Chemistry, Syracuse University, Syracuse, New York 13244
| | - Najae Escoffery
- Department of Chemistry, Syracuse University, Syracuse, New York 13244
| | - Melissa Navarro
- Department of Chemistry, Syracuse University, Syracuse, New York 13244
| | | | - Shikha Nangia
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244 .,Syracuse Biomaterials Institute, Syracuse University, Syracuse, New York 13244
| | - James L Hougland
- Department of Chemistry, Syracuse University, Syracuse, New York 13244 .,Syracuse Biomaterials Institute, Syracuse University, Syracuse, New York 13244
| |
Collapse
|
84
|
Structure of the Mechanosensitive Channel MscS Embedded in the Membrane Bilayer. J Mol Biol 2019; 431:3081-3090. [DOI: 10.1016/j.jmb.2019.07.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/12/2019] [Accepted: 07/01/2019] [Indexed: 12/29/2022]
|
85
|
Storek KM, Chan J, Vij R, Chiang N, Lin Z, Bevers J, Koth CM, Vernes JM, Meng YG, Yin J, Wallweber H, Dalmas O, Shriver S, Tam C, Schneider K, Seshasayee D, Nakamura G, Smith PA, Payandeh J, Koerber JT, Comps-Agrar L, Rutherford ST. Massive antibody discovery used to probe structure-function relationships of the essential outer membrane protein LptD. eLife 2019; 8:46258. [PMID: 31237236 PMCID: PMC6592684 DOI: 10.7554/elife.46258] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/17/2019] [Indexed: 12/17/2022] Open
Abstract
Outer membrane proteins (OMPs) in Gram-negative bacteria dictate permeability of metabolites, antibiotics, and toxins. Elucidating the structure-function relationships governing OMPs within native membrane environments remains challenging. We constructed a diverse library of >3000 monoclonal antibodies to assess the roles of extracellular loops (ECLs) in LptD, an essential OMP that inserts lipopolysaccharide into the outer membrane of Escherichia coli. Epitope binning and mapping experiments with LptD-loop-deletion mutants demonstrated that 7 of the 13 ECLs are targeted by antibodies. Only ECLs inaccessible to antibodies were required for the structure or function of LptD. Our results suggest that antibody-accessible loops evolved to protect key extracellular regions of LptD, but are themselves dispensable. Supporting this hypothesis, no α-LptD antibody interfered with essential functions of LptD. Our experimental workflow enables structure-function studies of OMPs in native cellular environments, provides unexpected insight into LptD, and presents a method to assess the therapeutic potential of antibody targeting. The overuse and misuse of antibiotics has led to the rise of multi-drug resistant bacteria which threaten global public health. Antibiotics interfere with essential processes in bacteria so they are unable to divide or survive, but over time, the microbes have found ways to become immune to the drugs. New antibiotics are now desperately needed. Gram-negative bacteria are wrapped in an outer membrane made of large molecules called lipopolysaccharides. This structure is an extra barrier to molecules (such as drugs) that try to enter the cell, but it could also hold new targets for antibiotics to exploit. A protein called LptD is embedded in the outer membrane, where it inserts new lipopolysaccharides. It is critical for bacteria to grow and survive, and is a relatively new potential target for antibiotic development. The protein has a number of ‘extracellular loops’ that extend into the environment, but their roles in the structure and the activity of LptD are still largely unknown. This is partly due to a lack of tools to investigate these elements. In response, Storek et al. built a library of over 3,000 custom antibodies, which are small Y-shaped proteins that can each recognise a specific portion in one of the extracellular loops and potentially incapacitate LptD. The antibodies were used to target LptD in its native environment, when it is embedded in the bacteria. In parallel, mutant bacteria were created in which the loops were genetically removed one by one to assess their importance for LptD activity. The experiments revealed that although the antibodies could target most extracellular loops, they could not target the few loops that were essential for LptD to work properly. This suggests that antibody-accessible loops are expendable and that these structures could serve to shield other regions of LptD which are critical for survival. The findings will help to prioritise research that develops other approaches to inhibit LptD. Finally, the antibody workflow designed by Storek et al. can serve as a road map to study other membrane proteins in their native cellular environment.
Collapse
Affiliation(s)
- Kelly M Storek
- Department of Infectious Diseases, Genentech, Inc, South San Francisco, United States
| | - Joyce Chan
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc, South San Francisco, United States
| | - Rajesh Vij
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Nancy Chiang
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Zhonghua Lin
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Jack Bevers
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Christopher M Koth
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - Jean-Michel Vernes
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc, South San Francisco, United States
| | - Y Gloria Meng
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc, South San Francisco, United States
| | - JianPing Yin
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - Heidi Wallweber
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - Olivier Dalmas
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - Stephanie Shriver
- Department of Biomolecular Resources, Genentech, Inc, South San Francisco, United States
| | - Christine Tam
- Department of Biomolecular Resources, Genentech, Inc, South San Francisco, United States
| | - Kellen Schneider
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Dhaya Seshasayee
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Gerald Nakamura
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Peter A Smith
- Department of Infectious Diseases, Genentech, Inc, South San Francisco, United States
| | - Jian Payandeh
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - James T Koerber
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Laetitia Comps-Agrar
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc, South San Francisco, United States
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech, Inc, South San Francisco, United States
| |
Collapse
|
86
|
A heuristic derived from analysis of the ion channel structural proteome permits the rapid identification of hydrophobic gates. Proc Natl Acad Sci U S A 2019; 116:13989-13995. [PMID: 31235590 PMCID: PMC6628796 DOI: 10.1073/pnas.1902702116] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ion channels are nanoscale protein pores in cell membranes. An exponentially increasing number of structures for channels means that computational methods for predicting their functional state are needed. Hydrophobic gates in ion channels result in local dewetting of pores, which functionally closes them to water and ion permeation. We use simulations of water behavior within nearly 200 different ion channel structures to explore how the radius and hydrophobicity of pores determine their hydration vs. dewetting behavior. Machine learning-assisted analysis of these simulations allowed us to propose a simple model for this relationship and present an easy method for rapidly predicting the functional state of new channel structures as they emerge. Ion channel proteins control ionic flux across biological membranes through conformational changes in their transmembrane pores. An exponentially increasing number of channel structures captured in different conformational states are now being determined; however, these newly resolved structures are commonly classified as either open or closed based solely on the physical dimensions of their pore, and it is now known that more accurate annotation of their conductive state requires additional assessment of the effect of pore hydrophobicity. A narrow hydrophobic gate region may disfavor liquid-phase water, leading to local dewetting, which will form an energetic barrier to water and ion permeation without steric occlusion of the pore. Here we quantify the combined influence of radius and hydrophobicity on pore dewetting by applying molecular dynamics simulations and machine learning to nearly 200 ion channel structures. This allows us to propose a simple simulation-free heuristic model that rapidly and accurately predicts the presence of hydrophobic gates. This not only enables the functional annotation of new channel structures as soon as they are determined, but also may facilitate the design of novel nanopores controlled by hydrophobic gates.
Collapse
|
87
|
Greene D, Qi R, Nguyen R, Qiu T, Luo R. Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies. J Chem Inf Model 2019; 59:3041-3056. [PMID: 31145610 PMCID: PMC7197397 DOI: 10.1021/acs.jcim.9b00363] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Membrane-bound protein receptors are a primary biological drug target, but the computational analysis of membrane proteins has been limited. In order to improve molecular mechanics Poisson-Boltzmann surface area (MMPBSA) binding free energy calculations for membrane protein-ligand systems, we have optimized a new heterogeneous dielectric implicit membrane model, with respect to free energy simulations in explicit membrane and explicit water, and implemented it into the Amber software suite. This new model supersedes our previous uniform, single dielectric implicit membrane model by allowing the dielectric constant to vary with depth within the membrane. We calculated MMPBSA binding free energies for the human purinergic platelet receptor (P2Y12R) and two of the muscarinic acetylcholine receptors (M2R and M3R) bound to various antagonist ligands using both membrane models, and we found that the heterogeneous dielectric membrane model has a stronger correlation with experimental binding affinities compared to the older model under otherwise identical conditions. This improved membrane model increases the utility of MMPBSA calculations for the rational design and improvement of future drug candidates.
Collapse
|
88
|
Saotome K, Teng B, Tsui CCA, Lee WH, Tu YH, Kaplan JP, Sansom MSP, Liman ER, Ward AB. Structures of the otopetrin proton channels Otop1 and Otop3. Nat Struct Mol Biol 2019; 26:518-525. [PMID: 31160780 PMCID: PMC6564688 DOI: 10.1038/s41594-019-0235-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/26/2019] [Indexed: 01/08/2023]
Abstract
Otopetrins (Otop1-Otop3) comprise one of two known eukaryotic proton-selective channel families. Otop1 is required for otoconia formation and a candidate mammalian sour taste receptor. Here we report cryo-EM structures of zebrafish Otop1 and chicken Otop3 in lipid nanodiscs. The structures reveal a dimeric architecture, with each subunit forming 12 transmembrane helices divided into structurally similar amino (N) and carboxy (C) domains. Cholesterol-like molecules occupy various sites in Otop1 and Otop3 and occlude a central tunnel. In molecular dynamics simulations, hydrophilic vestibules formed by the N and C domains and in the intrasubunit interface between N and C domains form conduits for water entry into the membrane core, suggesting three potential proton conduction pathways. By mutagenesis, we tested the roles of charged residues in each putative permeation pathway. Our results provide a structural basis for understanding selective proton permeation and gating of this conserved family of proton channels.
Collapse
Affiliation(s)
- Kei Saotome
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Bochuan Teng
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Che Chun Alex Tsui
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Yu-Hsiang Tu
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Joshua P Kaplan
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Emily R Liman
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| |
Collapse
|
89
|
Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 410] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
Collapse
Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| |
Collapse
|
90
|
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: 133] [Impact Index Per Article: 26.6] [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
|
91
|
Visualizing Biological Membrane Organization and Dynamics. J Mol Biol 2019; 431:1889-1919. [DOI: 10.1016/j.jmb.2019.02.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/02/2019] [Accepted: 02/13/2019] [Indexed: 11/22/2022]
|
92
|
Dämgen MA, Biggin PC. Computational methods to examine conformational changes and ligand-binding properties: Examples in neurobiology. Neurosci Lett 2019. [DOI: 10.1016/j.neulet.2018.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
93
|
Structure and Dynamics of the Central Lipid Pool and Proteins of the Bacterial Holo-Translocon. Biophys J 2019; 116:1931-1940. [PMID: 31053257 PMCID: PMC6531790 DOI: 10.1016/j.bpj.2019.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/11/2019] [Accepted: 04/02/2019] [Indexed: 01/01/2023] Open
Abstract
The bacterial Sec translocon, SecYEG, associates with accessory proteins YidC and the SecDF-YajC subcomplex to form the bacterial holo-translocon (HTL). The HTL is a dynamic and flexible protein transport machine capable of coordinating protein secretion across the membrane and efficient lateral insertion of nascent membrane proteins. It has been hypothesized that a central lipid core facilitates the controlled passage of membrane proteins into the bilayer, ensuring the efficient formation of their native state. By performing small-angle neutron scattering on protein solubilized in “match-out” deuterated detergent, we have been able to interrogate a “naked” HTL complex, with the scattering contribution of the surrounding detergent micelle rendered invisible. Such an approach has allowed the confirmation of a lipid core within the HTL, which accommodates between 8 and 29 lipids. Coarse-grained molecular dynamics simulations of the HTL also demonstrate a dynamic, central pool of lipids. An opening at this lipid-rich region between YidC and the SecY lateral gate may provide an exit gateway for newly synthesized, correctly oriented, membrane protein helices, or even small bundles of helices, to emerge from the HTL.
Collapse
|
94
|
Song C, de Groot BL, Sansom MSP. Lipid Bilayer Composition Influences the Activity of the Antimicrobial Peptide Dermcidin Channel. Biophys J 2019; 116:1658-1666. [PMID: 31010668 DOI: 10.1016/j.bpj.2019.03.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 03/23/2019] [Accepted: 03/28/2019] [Indexed: 10/27/2022] Open
Abstract
Antimicrobial peptides (AMPs) carry great potential as new antibiotics against "superbugs." Dermcidin (DCD), a broad-spectrum AMP in human sweat, has been recently crystallized in its oligomeric state and showed channel-like properties. In this work, we performed multiscale molecular dynamics simulations to study how the membrane composition influences the behavior of a transmembrane pore formed by the DCD oligomer in the hope of revealing the origin of the membrane selectivity of this AMP toward bacteria. Our results indicate that bilayers composed of various lipids (DMPC, DPPC, and DSPC) with different thicknesses result in different orientations of the DCD oligomer when embedded in lipid bilayers. The thicker the bilayer, the less tilted the channel. Cholesterol makes the bilayers more rigid and thicker, which also affects the orientation of the channel. Furthermore, we observed that the predicted conductance of the channel from computational electrophysiology simulations is related to its orientation in the lipid bilayer: the larger the tilt, the larger the conductance. Our results indicate that the membrane composition has a significant influence on the activity of the DCD channel, with thicker, cholesterol-rich membranes showing lower conductance than that of thinner membranes.
Collapse
Affiliation(s)
- Chen Song
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China; Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
| | - Bert L de Groot
- Department of Theoretical and Computational Biophysics, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
95
|
Schmidt A, Alsop RJ, Rimal R, Lenzig P, Joussen S, Gervasi NN, Khondker A, Gründer S, Rheinstädter MC, Wiemuth D. Modulation of DEG/ENaCs by Amphiphiles Suggests Sensitivity to Membrane Alterations. Biophys J 2019; 114:1321-1335. [PMID: 29590590 DOI: 10.1016/j.bpj.2018.01.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 01/22/2018] [Accepted: 01/26/2018] [Indexed: 12/25/2022] Open
Abstract
The bile acid-sensitive ion channel is activated by amphiphilic substances such as bile acids or artificial detergents via membrane alterations; however, the mechanism of membrane sensitivity of the bile acid-sensitive ion channel is not known. It has also not been systematically investigated whether other members of the degenerin/epithelial Na+ channel (DEG/ENaC) gene family are affected by amphiphilic compounds. Here, we show that DEG/ENaCs ASIC1a, ASIC3, ENaC, and the purinergic receptor P2X2 are modulated by a large number of different, structurally unrelated amphiphilic substances, namely the detergents N-lauroylsarcosine, Triton X-100, and β-octylglucoside; the fenamate flufenamic acid; the antipsychotic drug chlorpromazine; the natural phenol resveratrol; the chili pepper compound capsaicin; the loop diuretic furosemide; and the antiarrythmic agent verapamil. We determined the modification of membrane properties using large-angle x-ray diffraction experiments on model lipid bilayers, revealing that the amphiphilic compounds are positioned in a characteristic fashion either in the lipid tail group region or in the lipid head group region, demonstrating that they perturbed the membrane structure. Collectively, our results show that DEG/ENaCs and structurally related P2X receptors are modulated by diverse amphiphilic molecules. Furthermore, they suggest alterations of membrane properties by amphiphilic compounds as a mechanism contributing to modulation.
Collapse
Affiliation(s)
- Axel Schmidt
- Institute of Physiology, RWTH Aachen University, Aachen, Germany
| | - Rick J Alsop
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada
| | - Rahul Rimal
- Institute of Physiology, RWTH Aachen University, Aachen, Germany
| | - Pia Lenzig
- Institute of Physiology, RWTH Aachen University, Aachen, Germany
| | - Sylvia Joussen
- Institute of Physiology, RWTH Aachen University, Aachen, Germany
| | - Natalie N Gervasi
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada
| | - Adree Khondker
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada
| | - Stefan Gründer
- Institute of Physiology, RWTH Aachen University, Aachen, Germany
| | | | - Dominik Wiemuth
- Institute of Physiology, RWTH Aachen University, Aachen, Germany.
| |
Collapse
|
96
|
Lee AG. Interfacial Binding Sites for Cholesterol on G Protein-Coupled Receptors. Biophys J 2019; 116:1586-1597. [PMID: 31010663 DOI: 10.1016/j.bpj.2019.03.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/04/2019] [Accepted: 03/25/2019] [Indexed: 01/13/2023] Open
Abstract
A docking procedure is described that allows the transmembrane surface of a G protein-coupled receptor (GPCR) to be swept rapidly for potential binding sites for cholesterol at the bilayer interfaces on the two sides of the membrane. The procedure matches 89% of the cholesterols resolved in published GPCR crystal structures, when cholesterols likely to be crystal packing artifacts are excluded. Docking poses are shown to form distinct clusters on the protein surface, the clusters corresponding to "greasy hollows" between protein ridges. Docking poses depend on the angle of tilt of the GPCR in the surrounding lipid bilayer. It is suggested that thermal motion could alter the optimal binding pose for a cholesterol molecule, with the range of binding poses within a cluster providing a guide to the range of thermal motions likely for a cholesterol within a binding site.
Collapse
Affiliation(s)
- Anthony G Lee
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom.
| |
Collapse
|
97
|
Shearer J, Jefferies D, Khalid S. Outer Membrane Proteins OmpA, FhuA, OmpF, EstA, BtuB, and OmpX Have Unique Lipopolysaccharide Fingerprints. J Chem Theory Comput 2019; 15:2608-2619. [PMID: 30848905 DOI: 10.1021/acs.jctc.8b01059] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The outer membrane of Gram-negative bacteria has a highly complex asymmetrical architecture, containing a mixture of phospholipids in the inner leaflet and almost exclusively lipopolysaccharide (LPS) molecules in the outer leaflet. In E. coli, the outer membrane contains a wide range of proteins with a β barrel architecture, that vary in size from the smallest having eight strands to larger barrels composed of 22 strands. Here we report coarse-grained molecular dynamics simulations of six proteins from the E. coli outer membrane OmpA, OmpX, BtuB, FhuA, OmpF, and EstA in a range of membrane environments, which are representative of the in vivo conditions for different strains of E. coli. We show that each protein has a unique pattern of interaction with the surrounding membrane, which is influenced by the composition of the protein, the level of LPS in the outer leaflet, and the differing mobilities of the lipids in the two leaflets of the membrane. Overall we present analyses from over 200 μs of simulation for each protein.
Collapse
Affiliation(s)
- Jonathan Shearer
- School of Chemistry , University of Southampton, Highfield , Southampton , SO17 1BJ United Kingdom
| | - Damien Jefferies
- School of Chemistry , University of Southampton, Highfield , Southampton , SO17 1BJ United Kingdom
| | - Syma Khalid
- School of Chemistry , University of Southampton, Highfield , Southampton , SO17 1BJ United Kingdom
| |
Collapse
|
98
|
Kalienkova V, Clerico Mosina V, Bryner L, Oostergetel GT, Dutzler R, Paulino C. Stepwise activation mechanism of the scramblase nhTMEM16 revealed by cryo-EM. eLife 2019; 8:44364. [PMID: 30785398 PMCID: PMC6414200 DOI: 10.7554/elife.44364] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/08/2019] [Indexed: 12/26/2022] Open
Abstract
Scramblases catalyze the movement of lipids between both leaflets of a bilayer. Whereas the X-ray structure of the protein nhTMEM16 has previously revealed the architecture of a Ca2+-dependent lipid scramblase, its regulation mechanism has remained elusive. Here, we have used cryo-electron microscopy and functional assays to address this question. Ca2+-bound and Ca2+-free conformations of nhTMEM16 in detergent and lipid nanodiscs illustrate the interactions with its environment and they reveal the conformational changes underlying its activation. In this process, Ca2+ binding induces a stepwise transition of the catalytic subunit cavity, converting a closed cavity that is shielded from the membrane in the absence of ligand, into a polar furrow that becomes accessible to lipid headgroups in the Ca2+-bound state. Additionally, our structures demonstrate how nhTMEM16 distorts the membrane at both entrances of the subunit cavity, thereby decreasing the energy barrier for lipid movement.
Collapse
Affiliation(s)
| | - Vanessa Clerico Mosina
- Department of Structural Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Laura Bryner
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Gert T Oostergetel
- Department of Structural Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Raimund Dutzler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Cristina Paulino
- Department of Structural Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| |
Collapse
|
99
|
Alvadia C, Lim NK, Clerico Mosina V, Oostergetel GT, Dutzler R, Paulino C. Cryo-EM structures and functional characterization of the murine lipid scramblase TMEM16F. eLife 2019; 8:44365. [PMID: 30785399 PMCID: PMC6414204 DOI: 10.7554/elife.44365] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/19/2019] [Indexed: 12/13/2022] Open
Abstract
The lipid scramblase TMEM16F initiates blood coagulation by catalyzing the exposure of phosphatidylserine in platelets. The protein is part of a family of membrane proteins, which encompasses calcium-activated channels for ions and lipids. Here, we reveal features of murine TMEM16F (mTMEM16F) that underlie its function as a lipid scramblase and an ion channel. The cryo-EM data of mTMEM16F in absence and presence of Ca2+ define the ligand-free closed conformation of the protein and the structure of a Ca2+-bound intermediate. Both conformations resemble their counterparts of the scrambling-incompetent anion channel mTMEM16A, yet with distinct differences in the region of ion and lipid permeation. In conjunction with functional data, we demonstrate the relationship between ion conduction and lipid scrambling. Although activated by a common mechanism, both functions appear to be mediated by alternate protein conformations that are at equilibrium in the ligand-bound state.
Collapse
Affiliation(s)
- Carolina Alvadia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Novandy K Lim
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Vanessa Clerico Mosina
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Gert T Oostergetel
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Raimund Dutzler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Cristina Paulino
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| |
Collapse
|
100
|
Caffalette CA, Corey RA, Sansom MSP, Stansfeld PJ, Zimmer J. A lipid gating mechanism for the channel-forming O antigen ABC transporter. Nat Commun 2019; 10:824. [PMID: 30778065 PMCID: PMC6379404 DOI: 10.1038/s41467-019-08646-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/23/2019] [Indexed: 12/15/2022] Open
Abstract
Extracellular glycan biosynthesis is a widespread microbial protection mechanism. In Gram-negative bacteria, the O antigen polysaccharide represents the variable region of outer membrane lipopolysaccharides. Fully assembled lipid-linked O antigens are translocated across the inner membrane by the WzmWzt ABC transporter for ligation to the lipopolysaccharide core, with the transporter forming a continuous transmembrane channel in a nucleotide-free state. Here, we report its structure in an ATP-bound conformation. Large structural changes within the nucleotide-binding and transmembrane regions push conserved hydrophobic residues at the substrate entry site towards the periplasm and provide a model for polysaccharide translocation. With ATP bound, the transporter forms a large transmembrane channel with openings toward the membrane and periplasm. The channel's periplasmic exit is sealed by detergent molecules that block solvent permeation. Molecular dynamics simulation data suggest that, in a biological membrane, lipid molecules occupy this periplasmic exit and prevent water flux in the transporter's resting state.
Collapse
Affiliation(s)
- Christopher A Caffalette
- Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | | | - Jochen Zimmer
- Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
| |
Collapse
|