1
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Jin J, Voth GA. Statistical Mechanical Design Principles for Coarse-Grained Interactions across Different Conformational Free Energy Surfaces. J Phys Chem Lett 2023; 14:1354-1362. [PMID: 36728761 PMCID: PMC9940719 DOI: 10.1021/acs.jpclett.2c03844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Systematic bottom-up coarse-graining (CG) of molecular systems provides a means to explore different coupled length and time scales while treating the molecular-scale physics at a reduced level. However, the configuration dependence of CG interactions often results in CG models with limited applicability for exploring the parametrized configurations. We propose a statistical mechanical theory to design CG interactions across different configurations and conditions. In order to span wide ranges of conformational space, distinct classical CG free energy surfaces for characteristic configurations are identified using molecular collective variables. The coupling interaction between different CG free energy surfaces can then be systematically determined by analogy to quantum mechanical approaches describing coupled states. The present theory can accurately capture the underlying many-body potentials of mean force in the CG variables for various order parameters applied to liquids, interfaces, and in principle proteins, uncovering the complex nature underlying the coupling interaction and imparting a new protocol for the design of predictive multiscale models.
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Affiliation(s)
| | - Gregory A. Voth
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
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2
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Jin R, Cao R, Baumgart T. Curvature dependence of BAR protein membrane association and dissociation kinetics. Sci Rep 2022; 12:7676. [PMID: 35538113 PMCID: PMC9091223 DOI: 10.1038/s41598-022-11221-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 04/18/2022] [Indexed: 11/09/2022] Open
Abstract
BAR (Bin/Amphiphysin/Rvs) domain containing proteins function as lipid bilayer benders and curvature sensors, and they contribute to membrane shaping involved in cell signaling and metabolism. The mechanism for their membrane shape sensing has been investigated by both equilibrium binding and kinetic studies. In prior research, stopped-flow spectroscopy has been used to deduce a positive dependence on membrane curvature for the binding rate constant, kon, of a BAR protein called endophilin. However, the impact of bulk diffusion of endophilin, on the kinetic binding parameters has not been thoroughly considered. Employing similar methods, and using lipid vesicles of multiple sizes, we obtained a linear dependence of kon on vesicle curvature. However, we found that the observed relation can be explained without considering the local curvature sensing ability of endophilin in the membrane association process. In contrast, the diffusion-independent unbinding rate constant (koff) obtained from stopped-flow measurements shows a negative dependence on membrane curvature, which is controlled/mediated by endophilin-membrane interactions. This latter dependency, in addition to protein-protein interactions on the membrane, explains the selective binding of BAR proteins to highly curved membranes in equilibrium binding experiments.
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Affiliation(s)
- Rui Jin
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Rui Cao
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.,Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA
| | - Tobias Baumgart
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.
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3
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Zhang L, Wang Y, Dong Y, Pant A, Liu Y, Masserman L, Xu Y, McLaughlin RN, Bai J. The endophilin curvature-sensitive motif requires electrostatic guidance to recycle synaptic vesicles in vivo. Dev Cell 2022; 57:750-766.e5. [PMID: 35303431 PMCID: PMC8969179 DOI: 10.1016/j.devcel.2022.02.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/21/2022] [Accepted: 02/22/2022] [Indexed: 12/29/2022]
Abstract
Curvature-sensing mechanisms assist proteins in executing particular actions on various membrane organelles. Here, we investigate the functional specificity of curvature-sensing amphipathic motifs in Caenorhabditis elegans through the study of endophilin, an endocytic protein for synaptic vesicle recycling. We generate chimeric endophilin proteins by replacing the endophilin amphipathic motif H0 with other curvature-sensing amphipathic motifs. We find that the role of amphipathic motifs cannot simply be extrapolated from the identity of their parental proteins. For example, the amphipathic motif of the nuclear pore complex protein NUP133 functionally replaces the synaptic role of endophilin H0. Interestingly, non-functional endophilin chimeras have similar defects-producing fewer synaptic vesicles but more endosomes-and this indicates that the curvature-sensing motifs in these chimeras have a common deficiency for reforming synaptic vesicles. Finally, we convert non-functional endophilin chimeras into functional proteins by changing the cationic property of amphipathic motifs, successfully reprogramming the functional specificity of curvature-sensing motifs in vivo.
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Affiliation(s)
- Lin Zhang
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Yu Wang
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, P.R. China; Fudan University, Shanghai 200433, P.R. China
| | - Yongming Dong
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Aaradhya Pant
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Yan Liu
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Laura Masserman
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ye Xu
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Jihong Bai
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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4
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Tanaka M, Ueno Y, Miyake T, Sakuma T, Okochi M. Enrichment of membrane curvature-sensing proteins from Escherichia coli using spherical supported lipid bilayers. J Biosci Bioeng 2021; 133:98-104. [PMID: 34776361 DOI: 10.1016/j.jbiosc.2021.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 10/19/2022]
Abstract
Bacteria display dynamically organized curved membrane structures, especially during cell division. The importance of membrane curvature-sensing (MCS) proteins for the recognition and regulation of biological membrane morphologies has predominately been investigated in eukaryotic cells. Recently, a technique for screening MCS proteins from solutions that contain peripheral membrane proteins was developed, and MCS protein candidates were identified from mammalian cells. The technique uses differently sized spherical supported lipid bilayers (SSLBs), which consist of spherical SiO2 particles covered with a lipid bilayer. To discriminate between proteins possessing the MCS property, SSLBs with the same surface area were used in a comparative sedimentation assay with shotgun proteome analysis. In this study, to prove that the technique could be applied to other samples, MCS proteins in Escherichia coli were investigated. Through a comparative proteomic study, 35 and 47 proteins were enriched as candidate MCS proteins preferentially bound to SSLBs of 100 nm and 1000 nm, respectively. Among the identified MCS candidate proteins, FtsZ and SecA were further examined for their MCS properties using the two SSLB sizes, which revealed a high binding affinity for the low membrane curvature (large SSLB). This is the first study to explore MCS proteins in prokaryotic cells and the MCS property of the SecA protein. The results demonstrate a method to enrich MCS proteins that could be utilized to better elucidate membrane dynamics and protein function expression on curved membrane structures in prokaryotic cells.
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Affiliation(s)
- Masayoshi Tanaka
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Yu Ueno
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Takahiro Miyake
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Takahiro Sakuma
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Mina Okochi
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan.
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5
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Phillips DA, Zacharoff LA, Hampton CM, Chong GW, Malanoski AP, Metskas LA, Xu S, Bird LJ, Eddie BJ, Miklos AE, Jensen GJ, Drummy LF, El-Naggar MY, Glaven SM. A bacterial membrane sculpting protein with BAR domain-like activity. eLife 2021; 10:60049. [PMID: 34643180 PMCID: PMC8687657 DOI: 10.7554/elife.60049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/12/2021] [Indexed: 11/13/2022] Open
Abstract
Bin/Amphiphysin/RVS (BAR) domain proteins belong to a superfamily of coiled-coil proteins influencing membrane curvature in eukaryotes and are associated with vesicle biogenesis, vesicle-mediated protein trafficking, and intracellular signaling. Here, we report a bacterial protein with BAR domain-like activity, BdpA, from Shewanella oneidensis MR-1, known to produce redox-active membrane vesicles and micrometer-scale outer membrane extensions (OMEs). BdpA is required for uniform size distribution of membrane vesicles and influences scaffolding of OMEs into a consistent diameter and curvature. Cryo-TEM reveals that a strain lacking BdpA produces lobed, disordered OMEs rather than membrane tubules or narrow chains produced by the wild-type strain. Overexpression of BdpA promotes OME formation during planktonic growth of S. oneidensis where they are not typically observed. Heterologous expression results in OME production in Marinobacter atlanticus and Escherichia coli. Based on the ability of BdpA to alter membrane architecture in vivo, we propose that BdpA and its homologs comprise a newly identified class of bacterial BAR domain-like proteins.
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Affiliation(s)
- Daniel A Phillips
- Oak Ridge Institute for Science and Education / US Army DEVCOM Chemical Biological Center, Aberdeen Proving Grounds, United States
| | - Lori A Zacharoff
- Department of Physics and Astronomy, University of Southern California, Los Angeles, United States
| | - Cheri M Hampton
- Materials and Manufacturing Directorate, Wright-Patterson Air Force Base, Dayton, United States
| | - Grace W Chong
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Anthony P Malanoski
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, United States
| | - Lauren Ann Metskas
- Biological Sciences, Chemistry, California Institute of Technology, Pasadena, United States
| | - Shuai Xu
- Department of Physics and Astronomy, University of Southern California, Los Angeles, United States
| | - Lina J Bird
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, United States
| | - Brian J Eddie
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, United States
| | - Aleksandr E Miklos
- BioSciences Division, BioChemistry Branch, US Army DEVCOM Chemical Biological Center, Aberdeen Proving Ground, United States
| | - Grant J Jensen
- Biology and Bioengineering, California Institute of Technology, Pasadena, United States
| | - Lawrence F Drummy
- Materials and Manufacturing Directorate, Wright-Patterson Air Force Base, Dayton, United States
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, Biological Sciences, and Chemistry, University of Southern California, Los Angeles, United States
| | - Sarah M Glaven
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, United States
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6
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Jarin Z, Newhouse J, Voth GA. Coarse-Grained Force Fields from the Perspective of Statistical Mechanics: Better Understanding of the Origins of a MARTINI Hangover. J Chem Theory Comput 2021; 17:1170-1180. [PMID: 33475352 PMCID: PMC7876797 DOI: 10.1021/acs.jctc.0c00638] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The popular MARTINI coarse-grained model is used as a test case to analyze the adherence of top-down coarse-grained molecular dynamics models (i.e., models primarily parametrized to match experimental results) to the known features of statistical mechanics for the underlying all-atom representations. Specifically, the temperature dependence of various pair distribution functions, and hence their underlying potentials of mean force via the reversible work theorem, are compared between MARTINI 2.0, Dry MARTINI, and all-atom simulations mapped onto equivalent coarse-grained sites for certain lipid bilayers. It is found that the MARTINI models do not completely capture the lipid structure seen in atomistic simulations as projected onto the coarse-grained mappings and that issues of accuracy and temperature transferability arise due to an incorrect enthalpy-entropy decomposition of these potentials of mean force. The potential of mean force for the association of two amphipathic helices in a lipid bilayer is also calculated, and especially at shorter ranges, the MARTINI and all-atom projection results differ substantially. The former is much less repulsive and hence will lead to a higher probability of MARTINI helix association in the MARTINI bilayer than occurs in the actual all-atom case. Additionally, the bilayer height fluctuation spectra are calculated for the MARTINI model, and compared to the all-atom results, it is found that the magnitude of thermally averaged amplitudes at intermediate length scales are quite different, pointing to a number of possible consequences for realistic modeling of membrane processes. Taken as a whole, the results presented here show disagreement in the enthalpic and entropic driving forces driving lateral structure in lipid bilayers as well as quantitative differences in association of embedded amphipathic helices, which can help direct future efforts to parametrize CG models with better agreement to the all-atom systems they aspire to represent.
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Affiliation(s)
- Zack Jarin
- Pritzker School for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - James Newhouse
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
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7
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Joseph JG, Osorio C, Yee V, Agrawal A, Liu AP. Complimentary action of structured and unstructured domains of epsin supports clathrin-mediated endocytosis at high tension. Commun Biol 2020; 3:743. [PMID: 33293652 PMCID: PMC7722716 DOI: 10.1038/s42003-020-01471-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 11/05/2020] [Indexed: 12/14/2022] Open
Abstract
Membrane tension plays an inhibitory role in clathrin-mediated endocytosis (CME) by impeding the transition of flat plasma membrane to hemispherical clathrin-coated structures (CCSs). Membrane tension also impedes the transition of hemispherical domes to omega-shaped CCSs. However, CME is not completely halted in cells under high tension conditions. Here we find that epsin, a membrane bending protein which inserts its N-terminus H0 helix into lipid bilayer, supports flat-to-dome transition of a CCS and stabilizes its curvature at high tension. This discovery is supported by molecular dynamic simulation of the epsin N-terminal homology (ENTH) domain that becomes more structured when embedded in a lipid bilayer. In addition, epsin has an intrinsically disordered protein (IDP) C-terminus domain which induces membrane curvature via steric repulsion. Insertion of H0 helix into lipid bilayer is not sufficient for stable epsin recruitment. Epsin's binding to adaptor protein 2 and clathrin is critical for epsin's association with CCSs under high tension conditions, supporting the importance of multivalent interactions in CCSs. Together, our results support a model where the ENTH and unstructured IDP region of epsin have complementary roles to ensure CME initiation and CCS maturation are unimpeded under high tension environments.
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Affiliation(s)
- Jophin G Joseph
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Carlos Osorio
- Department of Mechanical Engineering, University of Houston, Houston, TX, USA
| | - Vivian Yee
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Ashutosh Agrawal
- Department of Mechanical Engineering, University of Houston, Houston, TX, USA
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA.
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA.
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8
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Tanaka M, Komikawa T, Yanai K, Okochi M. Proteomic Exploration of Membrane Curvature Sensors Using a Series of Spherical Supported Lipid Bilayers. Anal Chem 2020; 92:16197-16203. [DOI: 10.1021/acs.analchem.0c04039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Masayoshi Tanaka
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Takumi Komikawa
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Kentaro Yanai
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Mina Okochi
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan
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9
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Nepal B, Sepehri A, Lazaridis T. Mechanisms of negative membrane curvature sensing and generation by ESCRT III subunit Snf7. Protein Sci 2020; 29:1473-1485. [PMID: 32142182 DOI: 10.1002/pro.3851] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 12/13/2022]
Abstract
Certain proteins have the propensity to bind to negatively curved membranes and generate negative membrane curvature. The mechanism of action of these proteins is much less studied and understood than those that sense and generate positive curvature. In this work, we use implicit membrane modeling to explore the mechanism of an important negative curvature sensing and generating protein: the main ESCRT III subunit Snf7. We find that Snf7 monomers alone can sense negative curvature and that curvature sensitivity increases for dimers and trimers. We have observed spontaneous bending of Snf7 oligomers into circular structures with preferred radius of ~20 nm. The preferred curvature of Snf7 filaments is further confirmed by the simulations of preformed spirals on a cylindrical membrane surface. Snf7 filaments cannot bind with the same interface to flat and curved membranes. We find that even when a filament has the preferred radius, it is always less stable on the flat membrane surface than on the interior cylindrical membrane surface. This provides an additional energy for membrane bending which has not been considered in the spiral spring model. Furthermore, the rings on the cylindrical spirals are bridged together by helix 4 and hence are extra stabilized compared to the spirals on the flat membrane surface.
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Affiliation(s)
- Binod Nepal
- Department of Chemistry, City College of New York, New York, New York, USA
| | - Aliasghar Sepehri
- Department of Chemistry, City College of New York, New York, New York, USA
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, New York, New York, USA.,Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, New York, New York, USA
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10
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Chan C, Pang X, Zhang Y, Niu T, Yang S, Zhao D, Li J, Lu L, Hsu VW, Zhou J, Sun F, Fan J. ACAP1 assembles into an unusual protein lattice for membrane deformation through multiple stages. PLoS Comput Biol 2019; 15:e1007081. [PMID: 31291238 PMCID: PMC6663034 DOI: 10.1371/journal.pcbi.1007081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/29/2019] [Accepted: 05/06/2019] [Indexed: 11/19/2022] Open
Abstract
Studies on the Bin-Amphiphysin-Rvs (BAR) domain have advanced a fundamental understanding of how proteins deform membrane. We previously showed that a BAR domain in tandem with a Pleckstrin Homology (PH domain) underlies the assembly of ACAP1 (Arfgap with Coil-coil, Ankryin repeat, and PH domain I) into an unusual lattice structure that also uncovers a new paradigm for how a BAR protein deforms membrane. Here, we initially pursued computation-based refinement of the ACAP1 lattice to identify its critical protein contacts. Simulation studies then revealed how ACAP1, which dimerizes into a symmetrical structure in solution, is recruited asymmetrically to the membrane through dynamic behavior. We also pursued electron microscopy (EM)-based structural studies, which shed further insight into the dynamic nature of the ACAP1 lattice assembly. As ACAP1 is an unconventional BAR protein, our findings broaden the understanding of the mechanistic spectrum by which proteins assemble into higher-ordered structures to achieve membrane deformation.
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Affiliation(s)
- Chun Chan
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
| | - Xiaoyun Pang
- National Laboratory of Biomacromolecules, CAS Center for excellence in biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yan Zhang
- National Laboratory of Biomacromolecules, CAS Center for excellence in biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Tongxin Niu
- National Laboratory of Biomacromolecules, CAS Center for excellence in biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shengjiang Yang
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Daohui Zhao
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Jian Li
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lanyuan Lu
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Victor W. Hsu
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, Guangdong, China
- * E-mail: (JZ); (FS); (JF)
| | - Fei Sun
- National Laboratory of Biomacromolecules, CAS Center for excellence in biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (JZ); (FS); (JF)
| | - Jun Fan
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Center for Advanced Nuclear Safety and Sustainable Development, City University of Hong Kong, Hong Kong, China
- * E-mail: (JZ); (FS); (JF)
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11
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Jarin Z, Tsai FC, Davtyan A, Pak AJ, Bassereau P, Voth GA. Unusual Organization of I-BAR Proteins on Tubular and Vesicular Membranes. Biophys J 2019; 117:553-562. [PMID: 31349990 PMCID: PMC6697384 DOI: 10.1016/j.bpj.2019.06.025] [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: 12/17/2018] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 12/26/2022] Open
Abstract
Protein-mediated membrane remodeling is a ubiquitous and critical process for proper cellular function. Inverse Bin/Amphiphysin/Rvs (I-BAR) domains drive local membrane deformation as a precursor to large-scale membrane remodeling. We employ a multiscale approach to provide the molecular mechanism of unusual I-BAR domain-driven membrane remodeling at a low protein surface concentration with near-atomistic detail. We generate a bottom-up coarse-grained model that demonstrates similar membrane-bound I-BAR domain aggregation behavior as our recent Mesoscopic Membrane with Explicit Proteins model. Together, these models bridge several length scales and reveal an aggregation behavior of I-BAR domains. We find that at low surface coverage (i.e., low bound protein density), I-BAR domains form transient, tip-to-tip strings on periodic flat membrane sheets. Inside of lipid bilayer tubules, we find linear aggregates parallel to the axis of the tubule. Finally, we find that I-BAR domains form tip-to-tip aggregates around the edges of membrane domes. These results are supported by in vitro experiments showing low curvature bulges surrounded by I-BAR domains on giant unilamellar vesicles. Overall, our models reveal new I-BAR domain aggregation behavior in membrane tubules and on the surface of vesicles at low surface concentration that add insight into how I-BAR domain proteins may contribute to certain aspects of membrane remodeling in cells.
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Affiliation(s)
- Zack Jarin
- Pritzker School for Molecular Engineering, The University of Chicago, Chicago, Illinois
| | - Feng-Ching Tsai
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France; Sorbonne Universités, UPMC University Paris 06, Paris, France
| | - Aram Davtyan
- Department of Chemistry, Chicago Center for Theoretical Chemistry, The James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Alexander J Pak
- Department of Chemistry, Chicago Center for Theoretical Chemistry, The James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Patricia Bassereau
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France; Sorbonne Universités, UPMC University Paris 06, Paris, France
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, The James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois.
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12
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Bhaskara RM, Grumati P, Garcia-Pardo J, Kalayil S, Covarrubias-Pinto A, Chen W, Kudryashev M, Dikic I, Hummer G. Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy. Nat Commun 2019; 10:2370. [PMID: 31147549 PMCID: PMC6542808 DOI: 10.1038/s41467-019-10345-3] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 04/25/2019] [Indexed: 02/06/2023] Open
Abstract
FAM134B/RETREG1 is a selective ER-phagy receptor that regulates the size and shape of the endoplasmic reticulum. The structure of its reticulon-homology domain (RHD), an element shared with other ER-shaping proteins, and the mechanism of membrane shaping remain poorly understood. Using molecular modeling and molecular dynamics (MD) simulations, we assemble a structural model for the RHD of FAM134B. Through MD simulations of FAM134B in flat and curved membranes, we relate the dynamic RHD structure with its two wedge-shaped transmembrane helical hairpins and two amphipathic helices to FAM134B functions in membrane-curvature induction and curvature-mediated protein sorting. FAM134B clustering, as expected to occur in autophagic puncta, amplifies the membrane-shaping effects. Electron microscopy of in vitro liposome remodeling experiments support the membrane remodeling functions of the different RHD structural elements. Disruption of the RHD structure affects selective autophagy flux and leads to disease states. FAM134B/RETREG1 is a selective ER-phagy receptor that regulates the size and shape of the endoplasmic reticulum. Here authors use molecular modeling and molecular dynamics simulations to assemble a structural model for the reticulon-homology domain of FAM134B.
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Affiliation(s)
- Ramachandra M Bhaskara
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438, Frankfurt am Main, Germany
| | - Paolo Grumati
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Theoder-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Javier Garcia-Pardo
- Buchmann Institute of Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Straße 15, 60438, Frankfurt am Main, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology, Division for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Sissy Kalayil
- Buchmann Institute of Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Straße 15, 60438, Frankfurt am Main, Germany
| | - Adriana Covarrubias-Pinto
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Theoder-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Wenbo Chen
- Buchmann Institute of Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Straße 15, 60438, Frankfurt am Main, Germany.,Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438, Frankfurt am Main, Germany
| | - Mikhail Kudryashev
- Buchmann Institute of Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Straße 15, 60438, Frankfurt am Main, Germany.,Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438, Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Theoder-Stern-Kai 7, 60590, Frankfurt am Main, Germany. .,Buchmann Institute of Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Straße 15, 60438, Frankfurt am Main, Germany.
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438, Frankfurt am Main, Germany. .,Institute for Biophysics, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
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13
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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.
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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
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14
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Sharp ME, Vázquez FX, Wagner JW, Dannenhoffer-Lafage T, Voth GA. Multiconfigurational Coarse-Grained Molecular Dynamics. J Chem Theory Comput 2019; 15:3306-3315. [PMID: 30897328 PMCID: PMC6660024 DOI: 10.1021/acs.jctc.8b01133] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Standard low resolution
coarse-grained modeling techniques have difficulty capturing multiple
configurations of protein systems. Here, we present a method for creating
accurate coarse-grained (CG) models with multiple configurations using
a linear combination of functions or “states”. Individual
CG models are created to capture the individual states, and the approximate
coupling between the two states is determined from an all-atom potential
of mean force. We show that the resulting multiconfiguration coarse-graining
(MCCG) method accurately captures the transition state as well as
the free energy between the two states. We have tested this method
on the folding of dodecaalanine, as well as the amphipathic helix
of endophilin.
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Affiliation(s)
- Morris E Sharp
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Francisco X Vázquez
- Department of Chemistry , St. John's University , Queens , New York 11439 , United States
| | - Jacob W Wagner
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Thomas Dannenhoffer-Lafage
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
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15
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Monje-Galvan V, Warburton L, Klauda JB. Setting Up All-Atom Molecular Dynamics Simulations to Study the Interactions of Peripheral Membrane Proteins with Model Lipid Bilayers. Methods Mol Biol 2019; 1949:325-339. [PMID: 30790265 DOI: 10.1007/978-1-4939-9136-5_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
All-atom molecular dynamics (MD) simulations enable the study of biological systems at atomic detail, complement the understanding gained from experiment, and can also motivate experimental techniques to further examine a given biological process. This method is based on statistical mechanics; it predicts the trajectory of atoms over time by solving Newton's Laws of motion taking into account all forces. Here, we describe the use of this methodology to study the interaction between peripheral membrane proteins and a lipid bilayer. Specifically, we provide step-by-step instructions to set up MD simulations to study the binding and interaction of the amphipathic helix of Osh4, a lipid transport protein, and Thanatin, an antimicrobial peptide (AMP), with model lipid bilayers using both fully detailed lipid tails and the highly mobile membrane-mimetic (HMMM) method to enhance conformational sampling.
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Affiliation(s)
- Viviana Monje-Galvan
- Department of Chemistry, The University of Chicago, Chicago, IL, USA. .,Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA.
| | - Linnea Warburton
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA.,Biophysics Program, University of Maryland, College Park, MD, USA
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16
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Directed Supramolecular Organization of N-BAR Proteins through Regulation of H0 Membrane Immersion Depth. Sci Rep 2018; 8:16383. [PMID: 30401832 PMCID: PMC6219572 DOI: 10.1038/s41598-018-34273-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/11/2018] [Indexed: 11/12/2022] Open
Abstract
Many membrane remodeling events rely on the ability of curvature-generating N-BAR membrane proteins to organize into distinctive supramolecular configurations. Experiments have revealed a conformational switch in N-BAR proteins resulting in vesicular or tubular membrane shapes, with shallow membrane immersion of the H0 amphipathic helices of N-BAR proteins on vesicles but deep H0 immersion on tubes. We develop here a minimal elastic model of the local thinning of the lipid bilayer resulting from H0 immersion. Our model predicts that the observed conformational switch in N-BAR proteins produces a corresponding switch in the bilayer-mediated N-BAR interactions due to the H0 helices. In agreement with experiments, we find that bilayer-mediated H0 interactions oppose N-BAR multimerization for the shallow H0 membrane immersion depths measured on vesicles, but promote self-assembly of supramolecular N-BAR chains for the increased H0 membrane immersion depths measured on tubes. Finally, we consider the possibility that bilayer-mediated H0 interactions might contribute to the concerted structural reorganization of N-BAR proteins suggested by experiments. Our results indicate that the membrane immersion depth of amphipathic protein helices may provide a general molecular control parameter for membrane organization.
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17
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Monje-Galvan V, Klauda JB. Preferred Binding Mechanism of Osh4’s Amphipathic Lipid-Packing Sensor Motif, Insights from Molecular Dynamics. J Phys Chem B 2018; 122:9713-9723. [DOI: 10.1021/acs.jpcb.8b07067] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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18
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Pick H, Alves AC, Vogel H. Single-Vesicle Assays Using Liposomes and Cell-Derived Vesicles: From Modeling Complex Membrane Processes to Synthetic Biology and Biomedical Applications. Chem Rev 2018; 118:8598-8654. [PMID: 30153012 DOI: 10.1021/acs.chemrev.7b00777] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The plasma membrane is of central importance for defining the closed volume of cells in contradistinction to the extracellular environment. The plasma membrane not only serves as a boundary, but it also mediates the exchange of physical and chemical information between the cell and its environment in order to maintain intra- and intercellular functions. Artificial lipid- and cell-derived membrane vesicles have been used as closed-volume containers, representing the simplest cell model systems to study transmembrane processes and intracellular biochemistry. Classical examples are studies of membrane translocation processes in plasma membrane vesicles and proteoliposomes mediated by transport proteins and ion channels. Liposomes and native membrane vesicles are widely used as model membranes for investigating the binding and bilayer insertion of proteins, the structure and function of membrane proteins, the intramembrane composition and distribution of lipids and proteins, and the intermembrane interactions during exo- and endocytosis. In addition, natural cell-released microvesicles have gained importance for early detection of diseases and for their use as nanoreactors and minimal protocells. Yet, in most studies, ensembles of vesicles have been employed. More recently, new micro- and nanotechnological tools as well as novel developments in both optical and electron microscopy have allowed the isolation and investigation of individual (sub)micrometer-sized vesicles. Such single-vesicle experiments have revealed large heterogeneities in the structure and function of membrane components of single vesicles, which were hidden in ensemble studies. These results have opened enormous possibilities for bioanalysis and biotechnological applications involving unprecedented miniaturization at the nanometer and attoliter range. This review will cover important developments toward single-vesicle analysis and the central discoveries made in this exciting field of research.
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Affiliation(s)
- Horst Pick
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Ana Catarina Alves
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Horst Vogel
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
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19
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Membrane re-modelling by BAR domain superfamily proteins via molecular and non-molecular factors. Biochem Soc Trans 2018. [PMID: 29540508 DOI: 10.1042/bst20170322] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lipid membranes are structural components of cell surfaces and intracellular organelles. Alterations in lipid membrane shape are accompanied by numerous cellular functions, including endocytosis, intracellular transport, and cell migration. Proteins containing Bin-Amphiphysin-Rvs (BAR) domains (BAR proteins) are unique, because their structures correspond to the membrane curvature, that is, the shape of the lipid membrane. BAR proteins present at high concentration determine the shape of the membrane, because BAR domain oligomers function as scaffolds that mould the membrane. BAR proteins co-operate with various molecular and non-molecular factors. The molecular factors include cytoskeletal proteins such as the regulators of actin filaments and the membrane scission protein dynamin. Lipid composition, including saturated or unsaturated fatty acid tails of phospholipids, also affects the ability of BAR proteins to mould the membrane. Non-molecular factors include the external physical forces applied to the membrane, such as tension and friction. In this mini-review, we will discuss how the BAR proteins orchestrate membrane dynamics together with various molecular and non-molecular factors.
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20
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Simunovic M, Šarić A, Henderson JM, Lee KYC, Voth GA. Long-Range Organization of Membrane-Curving Proteins. ACS CENTRAL SCIENCE 2017; 3:1246-1253. [PMID: 29296664 PMCID: PMC5746856 DOI: 10.1021/acscentsci.7b00392] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Indexed: 05/02/2023]
Abstract
Biological membranes have a central role in mediating the organization of membrane-curving proteins, a dynamic process that has proven to be challenging to probe experimentally. Using atomic force microscopy, we capture the hierarchically organized assemblies of Bin/amphiphysin/Rvs (BAR) proteins on supported lipid membranes. Their structure reveals distinct long linear aggregates of proteins, regularly spaced by up to 300 nm. Employing accurate free-energy calculations from large-scale coarse-grained computer simulations, we found that the membrane mediates the interaction among protein filaments as a combination of short- and long-ranged interactions. The long-ranged component acts at strikingly long distances, giving rise to a variety of micron-sized ordered patterns. This mechanism may contribute to the long-ranged spatiotemporal control of membrane remodeling by proteins in the cell.
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Affiliation(s)
- Mijo Simunovic
- Department
of Chemistry, Institute for Biophysical Dynamics, and James Franck
Institute, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Anđela Šarić
- Department
of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, Gower Street, London, WC1E 6BT, U.K.
| | - J. Michael Henderson
- Department
of Chemistry, Institute for Biophysical Dynamics, and James Franck
Institute, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Ka Yee C. Lee
- Department
of Chemistry, Institute for Biophysical Dynamics, and James Franck
Institute, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department
of Chemistry, Institute for Biophysical Dynamics, and James Franck
Institute, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
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21
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Takemura K, Hanawa-Suetsugu K, Suetsugu S, Kitao A. Salt Bridge Formation between the I-BAR Domain and Lipids Increases Lipid Density and Membrane Curvature. Sci Rep 2017; 7:6808. [PMID: 28754893 PMCID: PMC5533756 DOI: 10.1038/s41598-017-06334-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/12/2017] [Indexed: 11/17/2022] Open
Abstract
The BAR domain superfamily proteins sense or induce curvature in membranes. The inverse-BAR domain (I-BAR) is a BAR domain that forms a straight “zeppelin-shaped” dimer. The mechanisms by which IRSp53 I-BAR binds to and deforms a lipid membrane are investigated here by all-atom molecular dynamics simulation (MD), binding energy analysis, and the effects of mutation experiments on filopodia on HeLa cells. I-BAR adopts a curved structure when crystallized, but adopts a flatter shape in MD. The binding of I-BAR to membrane was stabilized by ~30 salt bridges, consistent with experiments showing that point mutations of the interface residues have little effect on the binding affinity whereas multiple mutations have considerable effect. Salt bridge formation increases the local density of lipids and deforms the membrane into a concave shape. In addition, the point mutations that break key intra-molecular salt bridges within I-BAR reduce the binding affinity; this was confirmed by expressing these mutants in HeLa cells and observing their effects. The results indicate that the stiffness of I-BAR is important for membrane deformation, although I-BAR does not act as a completely rigid template.
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Affiliation(s)
- Kazuhiro Takemura
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-0032, Japan
| | - Kyoko Hanawa-Suetsugu
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Shiro Suetsugu
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Akio Kitao
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-0032, Japan.
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22
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Mahata P, Das SL. Generation of wavy structure on lipid membrane by peripheral proteins: a linear elastic analysis. FEBS Lett 2017; 591:1333-1348. [DOI: 10.1002/1873-3468.12661] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/11/2017] [Accepted: 04/12/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Paritosh Mahata
- Department of Mechanical Engineering; Birla Institute of Technology Mesra; Ranchi India
| | - Sovan Lal Das
- Department of Mechanical Engineering; Indian Institute of Technology Kharagpur; India
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23
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Abstract
Membrane deformation by proteins is a universal phenomenon that has been studied extensively in eukaryotes but much less in prokaryotes. In this study, we discovered a membrane-deforming activity of the phospholipid N-methyltransferase PmtA from the plant-pathogenic bacterium Agrobacterium tumefaciens PmtA catalyzes the successive three-step N-methylation of phosphatidylethanolamine to phosphatidylcholine. Here, we defined the lipid and protein requirements for the membrane-remodeling activity of PmtA by a combination of transmission electron microscopy and liposome interaction studies. Dependent on the lipid composition, PmtA changes the shape of spherical liposomes either into filaments or small vesicles. Upon overproduction of PmtA in A. tumefaciens, vesicle-like structures occur in the cytoplasm, dependent on the presence of the anionic lipid cardiolipin. The N-terminal lipid-binding α-helix (αA) is involved in membrane deformation by PmtA. Two functionally distinct and spatially separated regions in αA can be distinguished. Anionic interactions by positively charged amino acids on one face of the helix are responsible for membrane recruitment of the enzyme. The opposite hydrophobic face of the helix is required for membrane remodeling, presumably by shallow insertion into the lipid bilayer.IMPORTANCE The ability to alter the morphology of biological membranes is known for a small number of some bacterial proteins. Our study adds the phospholipid N-methyltransferase PmtA as a new member to the category of bacterial membrane-remodeling proteins. A combination of in vivo and in vitro methods reveals the molecular requirements for membrane deformation at the protein and phospholipid level. The dual functionality of PmtA suggests a contribution of membrane biosynthesis enzymes to the complex morphology of bacterial membranes.
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24
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Chen Z, Zhu C, Kuo CJ, Robustelli J, Baumgart T. The N-Terminal Amphipathic Helix of Endophilin Does Not Contribute to Its Molecular Curvature Generation Capacity. J Am Chem Soc 2016; 138:14616-14622. [PMID: 27755867 PMCID: PMC5562367 DOI: 10.1021/jacs.6b06820] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N-BAR proteins such as endophilin are thought to bend lipid membranes via scaffolding (the molding of membranes through the crescent protein shape) and membrane insertion (also called wedging) of amphipathic helices. However, the contributions from these distinct mechanisms to membrane curvature generation and sensing have remained controversial. Here we quantitatively demonstrate that the amphipathic N-terminal H0 helix of endophilin is important for recruiting this protein to the membrane, but does not contribute significantly to its intrinsic membrane curvature generation capacity. These observations elevate the importance of the scaffolding mechanism, rather than H0 insertion, for the membrane curvature generation by N-BAR domains. Furthermore, consistent with the thermodynamically required coupling between curvature generation and sensing, we observed that the H0-truncated N-BAR domain is capable of sensing membrane curvature. Overall, our contribution clarifies an important mechanistic controversy in the function of N-BAR domain proteins.
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Affiliation(s)
- Zhiming Chen
- Department of Chemistry, University of Pennsylvania, Philadelphia, USA
| | - Chen Zhu
- Department of Chemistry, University of Pennsylvania, Philadelphia, USA
| | - Curtis J. Kuo
- Department of Chemistry, University of Pennsylvania, Philadelphia, USA
| | - Jaclyn Robustelli
- Department of Chemistry, University of Pennsylvania, Philadelphia, USA
| | - Tobias Baumgart
- Department of Chemistry, University of Pennsylvania, Philadelphia, USA
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25
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Sapp K, Maibaum L. Suppressing membrane height fluctuations leads to a membrane-mediated interaction among proteins. Phys Rev E 2016; 94:052414. [PMID: 27967200 PMCID: PMC5376292 DOI: 10.1103/physreve.94.052414] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Indexed: 01/27/2023]
Abstract
Membrane-induced interactions can play a significant role in the spatial distribution of membrane-bound proteins. We develop a model that combines a continuum description of lipid bilayers with a discrete particle model of proteins to probe the emerging structure of the combined membrane-protein system. Our model takes into account the membrane's elastic behavior, the steric repulsion between proteins, and the quenching of membrane shape fluctuations due to the presence of the proteins. We employ coupled Langevin equations to describe the dynamics of the system. We show that coupling to the membrane induces an attractive interaction among proteins, which may contribute to the clustering of proteins in biological membranes. We investigate the lateral protein diffusion and find that it is reduced due to transient fluctuations in membrane shape.
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Affiliation(s)
- Kayla Sapp
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Lutz Maibaum
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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26
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Stanishneva-Konovalova T, Derkacheva N, Polevova S, Sokolova O. The Role of BAR Domain Proteins in the Regulation of Membrane Dynamics. Acta Naturae 2016; 8:60-69. [PMID: 28050267 PMCID: PMC5199207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Indexed: 11/09/2022] Open
Abstract
Many cellular processes are associated with membrane remodeling. The BAR domain protein family plays a key role in the formation and detection of local membrane curvatures and in attracting other proteins, including the regulators of actin dynamics. Based on their structural and phylogenetic properties, BAR domains are divided into several groups which affect membrane in various ways and perform different functions in cells. However, recent studies have uncovered evidence of functional differences even within the same group. This review discusses the principles underlying the interactions of different groups of BAR domains, and their individual representatives ,with membranes.
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Affiliation(s)
| | - N.I. Derkacheva
- A.I. Evdokimov Moscow State University of Medicine and Dentistry, Department of Biochemistry, Delegatskaya Str. 20, Bld 1, Moscow, 127473, Russia
| | - S.V. Polevova
- Lomonosov Moscow State University, Faculty of Biology, Leninskie Gory 1, Bld 12, Moscow, 119234 , Russia
| | - O.S. Sokolova
- Lomonosov Moscow State University, Faculty of Biology, Leninskie Gory 1, Bld 12, Moscow, 119234 , Russia
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27
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How curvature-generating proteins build scaffolds on membrane nanotubes. Proc Natl Acad Sci U S A 2016; 113:11226-11231. [PMID: 27655892 DOI: 10.1073/pnas.1606943113] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bin/Amphiphysin/Rvs (BAR) domain proteins control the curvature of lipid membranes in endocytosis, trafficking, cell motility, the formation of complex subcellular structures, and many other cellular phenomena. They form 3D assemblies that act as molecular scaffolds to reshape the membrane and alter its mechanical properties. It is unknown, however, how a protein scaffold forms and how BAR domains interact in these assemblies at protein densities relevant for a cell. In this work, we use various experimental, theoretical, and simulation approaches to explore how BAR proteins organize to form a scaffold on a membrane nanotube. By combining quantitative microscopy with analytical modeling, we demonstrate that a highly curving BAR protein endophilin nucleates its scaffolds at the ends of a membrane tube, contrary to a weaker curving protein centaurin, which binds evenly along the tube's length. Our work implies that the nature of local protein-membrane interactions can affect the specific localization of proteins on membrane-remodeling sites. Furthermore, we show that amphipathic helices are dispensable in forming protein scaffolds. Finally, we explore a possible molecular structure of a BAR-domain scaffold using coarse-grained molecular dynamics simulations. Together with fluorescence microscopy, the simulations show that proteins need only to cover 30-40% of a tube's surface to form a rigid assembly. Our work provides mechanical and structural insights into the way BAR proteins may sculpt the membrane as a high-order cooperative assembly in important biological processes.
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28
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McCullagh P, Lake PT, McCullagh M. Deriving Coarse-Grained Charges from All-Atom Systems: An Analytic Solution. J Chem Theory Comput 2016; 12:4390-9. [DOI: 10.1021/acs.jctc.6b00507] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter McCullagh
- Department
of Statistics, University of Chicago, Chicago, Illinois 60637, United States
| | - Peter T. Lake
- Department
of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Martin McCullagh
- Department
of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
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29
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Curvature-undulation coupling as a basis for curvature sensing and generation in bilayer membranes. Proc Natl Acad Sci U S A 2016; 113:E5117-24. [PMID: 27531962 DOI: 10.1073/pnas.1605259113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present coarse-grained molecular dynamics simulations of the epsin N-terminal homology domain interacting with a lipid bilayer and demonstrate a rigorous theoretical formalism and analysis method for computing the induced curvature field in varying concentrations of the protein in the dilute limit. Our theory is based on the description of the height-height undulation spectrum in the presence of a curvature field. We formulated an objective function to compare the acquired undulation spectrum from the simulations to that of the theory. We recover the curvature field parameters by minimizing the objective function even in the limit where the protein-induced membrane curvature is of the same order as the amplitude due to thermal undulations. The coupling between curvature and undulations leads to significant predictions: (i) Under dilute conditions, the proteins can sense a site of spontaneous curvature at distances much larger than their size; (ii) as the density of proteins increases the coupling focuses and stabilizes the curvature field to the site of the proteins; and (iii) the mapping of the protein localization and the induction of a stable curvature is a cooperative process that can be described through a Hill function.
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30
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West A, Brummel BE, Braun AR, Rhoades E, Sachs JN. Membrane remodeling and mechanics: Experiments and simulations of α-Synuclein. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1858:1594-609. [PMID: 26972046 PMCID: PMC5081225 DOI: 10.1016/j.bbamem.2016.03.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 03/05/2016] [Accepted: 03/07/2016] [Indexed: 01/24/2023]
Abstract
We review experimental and simulation approaches that have been used to determine curvature generation and remodeling of lipid bilayers by membrane-bending proteins. Particular emphasis is placed on the complementary approaches used to study α-Synuclein (αSyn), a major protein involved in Parkinson's disease (PD). Recent cellular and biophysical experiments have shown that the protein 1) deforms the native structure of mitochondrial and model membranes; and 2) inhibits vesicular fusion. Today's advanced experimental and computational technology has made it possible to quantify these protein-induced changes in membrane shape and material properties. Collectively, experiments, theory and multi-scale simulation techniques have established the key physical determinants of membrane remodeling and rigidity: protein binding energy, protein partition depth, protein density, and membrane tension. Despite the exciting and significant progress made in recent years in these areas, challenges remain in connecting biophysical insights to the cellular processes that lead to disease. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Ana West
- Department of Biomedical Engineering, University of Minnesota, 312 Church St. SE, Minneapolis, MN 55455, USA
| | - Benjamin E Brummel
- Department of Biomedical Engineering, University of Minnesota, 312 Church St. SE, Minneapolis, MN 55455, USA
| | - Anthony R Braun
- Department of Neuroscience, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, 231 S 34th St., Philadelphia, PA 19104, USA
| | - Jonathan N Sachs
- Department of Biomedical Engineering, University of Minnesota, 312 Church St. SE, Minneapolis, MN 55455, USA.
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31
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Multiscale simulations of protein-facilitated membrane remodeling. J Struct Biol 2016; 196:57-63. [PMID: 27327264 DOI: 10.1016/j.jsb.2016.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Abstract
Protein-facilitated shape and topology changes of cell membranes are crucial for many biological processes, such as cell division, protein trafficking, and cell signaling. However, the inherently multiscale nature of membrane remodeling presents a considerable challenge for understanding the mechanisms and physics that drive this process. To address this problem, a multiscale approach that makes use of a diverse set of computational and experimental techniques is required. The atomistic simulations provide high-resolution information on protein-membrane interactions. Experimental techniques, like electron microscopy, on the other hand, resolve high-order organization of proteins on the membrane. Coarse-grained (CG) and mesoscale computational techniques provide the intermediate link between the two scales and can give new insights into the underlying mechanisms. In this Review, we present the recent advances in multiscale computational approaches established in our group. We discuss various CG and mesoscale approaches in studying the protein-mediated large-scale membrane remodeling.
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32
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Poudel KR, Dong Y, Yu H, Su A, Ho T, Liu Y, Schulten K, Bai J. A time course of orchestrated endophilin action in sensing, bending, and stabilizing curved membranes. Mol Biol Cell 2016; 27:2119-32. [PMID: 27170174 PMCID: PMC4927284 DOI: 10.1091/mbc.e16-04-0264] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 05/06/2016] [Indexed: 11/11/2022] Open
Abstract
Endophilin is a founding member of the membrane-bending protein family. It promotes rapid endocytosis on a milliseconds-to-seconds time scale. The short duration of rapid endocytosis requires endophilin to act quickly. High-resolution kinetic measurements show the sequential action that endophilin takes to quickly deform membranes. Numerous proteins act in concert to sculpt membrane compartments for cell signaling and metabolism. These proteins may act as curvature sensors, membrane benders, and scaffolding molecules. Here we show that endophilin, a critical protein for rapid endocytosis, quickly transforms from a curvature sensor into an active bender upon membrane association. We find that local membrane deformation does not occur until endophilin inserts its amphipathic helices into lipid bilayers, supporting an active bending mechanism through wedging. Our time-course studies show that endophilin continues to drive membrane changes on a seconds-to-minutes time scale, indicating that the duration of endocytosis events constrains the mode of endophilin action. Finally, we find a requirement of coordinated activities between wedging and scaffolding for endophilin to produce stable membrane tubules in vitro and to promote synaptic activity in vivo. Together these data demonstrate that endophilin is a multifaceted molecule that precisely integrates activities of sensing, bending, and stabilizing curvature to sculpt membranes with speed.
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Affiliation(s)
- Kumud R Poudel
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Yongming Dong
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Hang Yu
- Beckman Institute, University of Illinois, Urbana, IL 61801
| | - Allen Su
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Thuong Ho
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Yan Liu
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Klaus Schulten
- Beckman Institute, University of Illinois, Urbana, IL 61801 Department of Physics, University of Illinois, Urbana, IL 61801
| | - Jihong Bai
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 Department of Biochemistry, University of Washington, Seattle, WA 98195
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33
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Li ZL, Ding HM, Ma YQ. Interaction of peptides with cell membranes: insights from molecular modeling. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:083001. [PMID: 26828575 DOI: 10.1088/0953-8984/28/8/083001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The investigation of the interaction of peptides with cell membranes is the focus of active research. It can enhance the understanding of basic membrane functions such as membrane transport, fusion, and signaling processes, and it may shed light on potential applications of peptides in biomedicine. In this review, we will present current advances in computational studies on the interaction of different types of peptides with the cell membrane. Depending on the properties of the peptide, membrane, and external environment, the peptide-membrane interaction shows a variety of different forms. Here, on the basis of recent computational progress, we will discuss how different peptides could initiate membrane pores, translocate across the membrane, induce membrane endocytosis, produce membrane curvature, form fibrils on the membrane surface, as well as interact with functional membrane proteins. Finally, we will present a conclusion summarizing recent progress and providing some specific insights into future developments in this field.
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Affiliation(s)
- Zhen-lu Li
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, People's Republic of China
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Structural insights into the cooperative remodeling of membranes by amphiphysin/BIN1. Sci Rep 2015; 5:15452. [PMID: 26487375 PMCID: PMC4614383 DOI: 10.1038/srep15452] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/24/2015] [Indexed: 01/08/2023] Open
Abstract
Amphiphysin2/BIN1 is a crescent-shaped N-BAR protein playing a key role in forming deeply invaginated tubes in muscle T-tubules. Amphiphysin2/BIN1 structurally stabilizes tubular formations in contrast to other N-BAR proteins involved in dynamic membrane scission processes; however, the molecular mechanism of the stabilizing effect is poorly understood. Using cryo-EM, we investigated the assembly of the amphiphysin/BIN1 on a membrane tube. We found that the N-BAR domains self-assemble on the membrane surface in a highly cooperative manner. Our biochemical assays and 3D reconstructions indicate that the N-terminal amphipathic helix H0 plays an important role in the initiation of the tube assembly and further in organizing BAR-mediated polymerization by locking adjacent N-BAR domains. Mutants that lack H0 or the tip portion, which is also involved in interactions of the neighboring BAR unit, lead to a disruption of the polymer organization, even though tubulation can still be observed. The regulatory region of amphiphysin/BIN1 including an SH3 domain does not have any apparent involvement in the polymer lattice. Our study indicates that the H0 helix and the BAR tip are necessary for efficient and organized self-assembly of amphiphysin/N-BAR.
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35
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Tourdot RW, Ramakrishnan N, Baumgart T, Radhakrishnan R. Application of a free-energy-landscape approach to study tension-dependent bilayer tubulation mediated by curvature-inducing proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:042715. [PMID: 26565280 PMCID: PMC4794322 DOI: 10.1103/physreve.92.042715] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Indexed: 05/26/2023]
Abstract
We investigate the phenomenon of protein-induced tubulation of lipid bilayer membranes within a continuum framework using Monte Carlo simulations coupled with the Widom insertion technique to compute excess chemical potentials. Tubular morphologies are spontaneously formed when the density and the curvature-field strength of the membrane-bound proteins exceed their respective thresholds and this transition is marked by a sharp drop in the excess chemical potential. We find that the planar to tubular transition can be described by a micellar model and that the corresponding free-energy barrier increases with an increase in the curvature-field strength (i.e., of protein-membrane interactions) and also with an increase in membrane tension.
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Affiliation(s)
- Richard W Tourdot
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - N Ramakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Tobias Baumgart
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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36
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Kegulian NC, Sankhagowit S, Apostolidou M, Jayasinghe SA, Malmstadt N, Butler PC, Langen R. Membrane Curvature-sensing and Curvature-inducing Activity of Islet Amyloid Polypeptide and Its Implications for Membrane Disruption. J Biol Chem 2015; 290:25782-93. [PMID: 26283787 DOI: 10.1074/jbc.m115.659797] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Indexed: 11/06/2022] Open
Abstract
Islet amyloid polypeptide (IAPP) is a 37-amino acid amyloid protein intimately associated with pancreatic islet β-cell dysfunction and death in type II diabetes. In this study, we combine spectroscopic methods and microscopy to investigate α-helical IAPP-membrane interactions. Using light scattering and fluorescence microscopy, we observe that larger vesicles become smaller upon treatment with human or rat IAPP. Electron microscopy shows the formation of various highly curved structures such as tubules or smaller vesicles in a membrane-remodeling process, and spectrofluorometric detection of vesicle leakage shows disruption of membrane integrity. This effect is stronger for human IAPP than for the less toxic rat IAPP. From CD spectra in the presence of different-sized vesicles, we also uncover the membrane curvature-sensing ability of IAPP and find that it transitions from inducing to sensing membrane curvature when lipid negative charge is decreased. Our in vivo EM images of immunogold-labeled rat IAPP and human IAPP show both forms to localize to mitochondrial cristae, which contain not only locally curved membranes but also phosphatidylethanolamine and cardiolipin, lipids with high spontaneous negative curvature. Disruption of membrane integrity by induction of membrane curvature could apply more broadly to other amyloid proteins and be responsible for membrane damage observed in other amyloid diseases as well.
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Affiliation(s)
- Natalie C Kegulian
- From the Department of Biochemistry and Molecular Biology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California 90033
| | - Shalene Sankhagowit
- the Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, and
| | - Melania Apostolidou
- From the Department of Biochemistry and Molecular Biology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California 90033
| | - Sajith A Jayasinghe
- From the Department of Biochemistry and Molecular Biology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California 90033
| | - Noah Malmstadt
- the Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, and
| | - Peter C Butler
- the Larry Hillblom Islet Research Center, David Geffen School of Medicine at UCLA, Los Angeles, California 90095
| | - Ralf Langen
- From the Department of Biochemistry and Molecular Biology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California 90033,
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37
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Tubulation by amphiphysin requires concentration-dependent switching from wedging to scaffolding. Structure 2015; 23:873-881. [PMID: 25865245 DOI: 10.1016/j.str.2015.02.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/09/2015] [Accepted: 02/24/2015] [Indexed: 02/08/2023]
Abstract
BAR proteins are involved in a variety of membrane remodeling events but how they can mold membranes into different shapes remains poorly understood. Using electron paramagnetic resonance, we find that vesicle binding of the N-BAR protein amphiphysin is predominantly mediated by the shallow insertion of amphipathic N-terminal helices. In contrast, the interaction with tubes involves deeply inserted N-terminal helices together with the concave surface of the BAR domain, which acts as a scaffold. Combined with the observed concentration dependence of tubulation and BAR domain scaffolding, the data indicate that initial membrane deformations and vesicle binding are mediated by insertion of amphipathic helical wedges, while tubulation requires high protein densities at which oligomeric BAR domain scaffolds form. In addition, we identify a pocket of residues on the concave surface of the BAR domain that insert deeply into tube membrane. Interestingly, this pocket harbors a number of disease mutants in the homologous amphiphysin 2.
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38
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Božič B, Das SL, Svetina S. Sorting of integral membrane proteins mediated by curvature-dependent protein-lipid bilayer interaction. SOFT MATTER 2015; 11:2479-2487. [PMID: 25675862 DOI: 10.1039/c4sm02289k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Cell membrane proteins, both bound and integral, are known to preferentially accumulate at membrane locations with curvatures favorable to their shape. This is mainly due to the curvature dependent interaction between membrane proteins and their lipid environment. Here, we analyze the effects of the protein-lipid bilayer interaction energy due to mismatch between the protein shape and the principal curvatures of the surrounding bilayer. The role of different macroscopic parameters that define the interaction energy term is elucidated in relation to recent experiment in which the lateral distribution of a membrane embedded protein potassium channel KvAP is measured on a giant unilamellar lipid vesicle (reservoir) and a narrow tubular extension - a tether - kept at constant length. The dependence of the sorting ratio, defined as the ratio between the areal density of the protein on the tether and on the vesicle, on the inverse tether radius is influenced by the strength of the interaction, the intrinsic shape of the membrane embedded protein, and its abundance in the reservoir. It is described how the values of these constants can be extracted from experiments. The intrinsic principal curvatures of a protein are related to the tether radius at which the sorting ratio attains its maximum value. The estimate of the principal intrinsic curvature of the protein KvAP, obtained by comparing the experimental and theoretical sorting behavior, is consistent with the available information on its structure.
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Affiliation(s)
- Bojan Božič
- Institute of Biophysics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
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39
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Fernandes F, Coutinho A, Prieto M, Loura LMS. Electrostatically driven lipid-protein interaction: Answers from FRET. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1837-48. [PMID: 25769805 DOI: 10.1016/j.bbamem.2015.02.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 02/23/2015] [Indexed: 12/13/2022]
Abstract
Electrostatics govern the association of a large number of proteins with cellular membranes. In some cases, these proteins present specialized lipid-binding modules or membrane targeting domains while in other cases association is achieved through nonspecific interaction of unstructured clusters of basic residues with negatively charged lipids. Given its spatial resolution in the nanometer range, Förster resonance energy transfer (FRET) is a powerful tool to give insight into protein-lipid interactions and provide molecular level information which is difficult to retrieve with other spectroscopic techniques. In this review we present and discuss the basic formalisms of both hetero- and homo-FRET pertinent to the most commonly encountered problems in lipid-protein interaction studies and highlight some examples of implementations of different FRET methodologies to characterize lipid/protein systems in which electrostatic interactions play a crucial role. This article is part of a Special Issue entitled: Lipid-protein interactions.
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Affiliation(s)
- Fábio Fernandes
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Ana Coutinho
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Dep. Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Manuel Prieto
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Luís M S Loura
- Faculdade de Farmácia, Universidade de Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal; Centro de Química de Coimbra, Largo D. Dinis, Rua Larga, 3004-535 Coimbra, Portugal.
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40
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Czogalla A, Kauert DJ, Seidel R, Schwille P, Petrov EP. DNA origami nanoneedles on freestanding lipid membranes as a tool to observe isotropic-nematic transition in two dimensions. NANO LETTERS 2015; 15:649-55. [PMID: 25467421 DOI: 10.1021/nl504158h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We introduce a simple experimental system to study dynamics of needle-like nanoobjects in two dimensions (2D) as a function of their surface density close to the isotropic-nematic transition. Using fluorescence correlation spectroscopy, we find that translational and rotational diffusion of rigid DNA origami nanoneedles bound to freestanding lipid membranes is strongly suppressed upon an increase in the surface particle density. Our experimental observations show a good agreement with results of Monte Carlo simulations of Brownian hard needles in 2D.
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Affiliation(s)
- Aleksander Czogalla
- Laboratory of Membrane Biochemistry, Paul Langerhans Institute, Technische Universität Dresden , Fetscherstraße 74, 01307 Dresden, Germany
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41
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Shi Z, Baumgart T. Membrane tension and peripheral protein density mediate membrane shape transitions. Nat Commun 2015; 6:5974. [PMID: 25569184 PMCID: PMC4353700 DOI: 10.1038/ncomms6974] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 11/28/2014] [Indexed: 01/21/2023] Open
Abstract
Endocytosis is a ubiquitous eukaryotic membrane budding, vesiculation and internalization process fulfilling numerous roles including compensation of membrane area increase after bursts of exocytosis. The mechanism of the coupling between these two processes to enable homeostasis is not well understood. Recently, an ultrafast endocytosis (UFE) pathway was revealed with a speed significantly exceeding classical clathrin-mediated endocytosis (CME). Membrane tension reduction is a potential mechanism by which endocytosis can be rapidly activated at remote sites. Here, we provide experimental evidence for a mechanism whereby membrane tension reduction initiates membrane budding and tubulation mediated by endocytic proteins, such as endophilin A1. We find that shape instabilities occur at well-defined membrane tensions and surface densities of endophilin. From our data, we obtain a membrane shape stability diagram that shows remarkable consistency with a quantitative model. This model applies to all laterally diffusive curvature-coupling proteins and therefore a wide range of endocytic proteins.
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Affiliation(s)
- Zheng Shi
- Department of Chemistry, University of Pennsylvania, 231 S. 34th St., Philadelphia, PA 19104, USA
| | - Tobias Baumgart
- Department of Chemistry, University of Pennsylvania, 231 S. 34th St., Philadelphia, PA 19104, USA
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42
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Ramakrishnan N, Radhakrishnan R. Phenomenology based multiscale models as tools to understand cell membrane and organelle morphologies. ACTA ACUST UNITED AC 2015; 22:129-175. [PMID: 27087801 DOI: 10.1016/bs.adplan.2015.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An intriguing question in cell biology is "how do cells regulate their shape?" It is commonly believed that the observed cellular morphologies are a result of the complex interaction among the lipid molecules (constituting the cell membrane), and with a number of other macromolecules, such as proteins. It is also believed that the common biophysical processes essential for the functioning of a cell also play an important role in cellular morphogenesis. At the cellular scale-where typical dimensions are in the order of micrometers-the effects arising from the molecular scale can either be modeled as equilibrium or non-equilibrium processes. In this chapter, we discuss the dynamically triangulated Monte Carlo technique to model and simulate membrane morphologies at the cellular scale, which in turn can be used to investigate several questions related to shape regulation in cells. In particular, we focus on two specific problems within the framework of isotropic and anisotropic elasticity theories: namely, (i) the origin of complex, physiologically relevant, membrane shapes due to the interaction of the membrane with curvature remodeling proteins, and (ii) the genesis of steady state cellular shapes due to the action of non-equilibrium forces that are generated by the fission and fusion of transport vesicles and by the binding and unbinding of proteins from the parent membrane.
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Affiliation(s)
- N Ramakrishnan
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA-19104
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA-19104
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43
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Beales PA, Ciani B, Cleasby AJ. Nature's lessons in design: nanomachines to scaffold, remodel and shape membrane compartments. Phys Chem Chem Phys 2015; 17:15489-507. [DOI: 10.1039/c5cp00480b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Our understanding of the membrane sculpting capabilities of proteins from experimental model systems could be used to construct functional compartmentalised architectures for the engineering of synthetic cells.
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Affiliation(s)
- Paul A. Beales
- School of Chemistry and Astbury Centre for Structural Molecular Biology
- University of Leeds
- Leeds LS2 9JT
- UK
| | - Barbara Ciani
- Centre for Membrane Interaction and Dynamics
- Department of Chemistry
- University of Sheffield
- Sheffield S3 7HF
- UK
| | - Alexa J. Cleasby
- Centre for Membrane Interaction and Dynamics
- Department of Chemistry
- University of Sheffield
- Sheffield S3 7HF
- UK
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44
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Practical Considerations in Virtual Screening and Molecular Docking. EMERGING TRENDS IN COMPUTATIONAL BIOLOGY, BIOINFORMATICS, AND SYSTEMS BIOLOGY 2015. [PMCID: PMC7173576 DOI: 10.1016/b978-0-12-802508-6.00027-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Molecular docking has become an important common component of the drug discovery toolbox, and its relative low-cost implications and perceived simplicity of use has stimulated an everincreasing popularity within academic communities. The inherent “garbage-in-garbage-out” defect of molecular docking, however, leads a lot of researchers to dedicate countless hours to the identification of hit compounds that later prove to be inactive. Several considerations that can greatly improve the success and enrichment of true bioactive hit compounds are commonly overlooked at the initial stages of a molecular docking study. This chapter will cover several of these considerations, including protonation states, active site waters, separating actives from decoys, consensus docking and molecular mechanics generalized-Born/surface area (MM-GBSA) rescoring, and incorporation of pharmacophoric constraints, in an attempt to clarify what is, in fact, very complicated and inherent difficulties of a structure-based drug design study.
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45
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Petoukhov MV, Weissenhorn W, Svergun DI. Endophilin-A1 BAR domain interaction with arachidonyl CoA. Front Mol Biosci 2014; 1:20. [PMID: 25988161 PMCID: PMC4428356 DOI: 10.3389/fmolb.2014.00020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/08/2014] [Indexed: 11/13/2022] Open
Abstract
Endophilin-A1 belongs to the family of BAR domain containing proteins that catalyze membrane remodeling processes via sensing, inducing and stabilizing membrane curvature. We show that the BAR domain of endophilin-A1 binds arachidonic acid and molds its coenzyme A (CoA) activated form, arachidonyl-CoA into a defined structure. We studied low resolution structures of endophilin-A1-BAR and its complex with arachidonyl-CoA in solution using synchrotron small-angle X-ray scattering (SAXS). The free endophilin-A1-BAR domain is shown to be dimeric at lower concentrations but builds tetramers and higher order complexes with increasing concentrations. Extensive titration SAXS studies revealed that the BAR domain produces a homogenous complex with the lipid micelles. The structural model of the complexes revealed two arachidonyl-CoA micelles bound to the distal arms of an endophilin-A1-BAR dimer. Intriguingly, the radius of the bound micelles significantly decreases compared to that of the free micelles, and this structural result may provide hints on the potential biological relevance of the endophilin-A1-BAR interaction with arachidonyl CoA.
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Affiliation(s)
- Maxim V. Petoukhov
- Hamburg Unit, European Molecular Biology Laboratory c/o DESYHamburg, Germany
| | - Winfried Weissenhorn
- Unit of Virus Host Cell Interactions, University Grenoble AlpesGrenoble, France
- Unit of Virus Host Cell Interactions, Centre National de la Recherche ScientifiqueGrenoble, France
| | - Dmitri I. Svergun
- Hamburg Unit, European Molecular Biology Laboratory c/o DESYHamburg, Germany
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Tourdot RW, Bradley RP, Ramakrishnan N, Radhakrishnan R. Multiscale computational models in physical systems biology of intracellular trafficking. IET Syst Biol 2014; 8:198-213. [PMID: 25257021 PMCID: PMC4336166 DOI: 10.1049/iet-syb.2013.0057] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 07/03/2014] [Accepted: 08/08/2014] [Indexed: 01/19/2023] Open
Abstract
In intracellular trafficking, a definitive understanding of the interplay between protein binding and membrane morphology remains incomplete. The authors describe a computational approach by integrating coarse-grained molecular dynamics (CGMD) simulations with continuum Monte Carlo (CM) simulations of the membrane to study protein-membrane interactions and the ensuing membrane curvature. They relate the curvature field strength discerned from the molecular level to its effect at the cellular length-scale. They perform thermodynamic integration on the CM model to describe the free energy landscape of vesiculation in clathrin-mediated endocytosis. The method presented here delineates membrane morphologies and maps out the free energy changes associated with membrane remodeling due to varying coat sizes, coat curvature strengths, membrane bending rigidities, and tensions; furthermore several constraints on mechanisms underlying clathrin-mediated endocytosis have also been identified, Their CGMD simulations have revealed the importance of PIP2 for stable binding of proteins essential for curvature induction in the bilayer and have provided a molecular basis for the positive curvature induction by the epsin N-terminal homology (EIMTH) domain. Calculation of the free energy landscape for vesicle budding has identified the critical size and curvature strength of a clathrin coat required for nucleation and stabilisation of a mature vesicle.
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Affiliation(s)
- Richard W Tourdot
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ryan P Bradley
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Natesan Ramakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ravi Radhakrishnan
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Fluorescent quantification of size and lamellarity of membrane nanotubes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 43:595-602. [PMID: 25256431 DOI: 10.1007/s00249-014-0989-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/28/2014] [Accepted: 09/08/2014] [Indexed: 12/31/2022]
Abstract
Membrane nanotubes, ubiquitous in cellular systems, adopt a spectrum of curvatures and shapes that are dictated by their intrinsic physical characteristics as well as their interactions with the local cellular environment. A high bending flexibility is needed in the crowded cytoplasm where tubes often need to bend significantly in the axial direction at sub-micron length scales. We find the stiffness of spontaneously formed membrane nanotubes by measuring the persistence length of reconstituted membrane nanotubes freely suspended in solution and imaged by fluorescence microscopy. By quantifying the tube diameter we demonstrate for the first time that the persistence length scales linearly with radius. Although most tubes are uni-lamellar, the predicted linear scaling between tube radius and persistence length allows us to identify tubes that spontaneously form as multilamellar structures upon hydration. We provide the first experimental evidence that illumination of lipid fluorophores can have a profound effect on the lipid bilayer which we sensitively detect as a continuous change in the tube persistence length with time. The novel assay and methodology here presented has potential for quantification of the structural reinforcement of membrane tubes by scaffolding proteins.
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Srivastava A, Voth GA. Solvent-Free, Highly Coarse-Grained Models for Charged Lipid Systems. J Chem Theory Comput 2014; 10:4730-4744. [PMID: 25328498 PMCID: PMC4196741 DOI: 10.1021/ct500474a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Indexed: 12/13/2022]
Abstract
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We
present a methodology to develop coarse-grained lipid models
such that electrostatic interactions between the coarse-grained sites
can be derived accurately from an all-atom molecular dynamics trajectory
and expressed as an effective pairwise electrostatic potential with
appropriate screening functions. The reference nonbonded forces from
the all-atom trajectory are decomposed into separate electrostatic
and van der Waals (vdW) forces, based on the multiscale coarse-graining
method. The coarse-grained electrostatic potential is assumed to be
a general function of unknown variables and the final site–site
interactions are obtained variationally, where the residual of the
electrostatic forces from the assumed field is minimized. The resulting
electrostatic interactions are fitted to screened electrostatics functions,
with a special treatment for distance-dependent dielectrics and screened
dipole–dipole interactions. The vdW interactions are derived
separately. The resulting charged hybrid coarse-graining method is
applied to various solvent-free three-site models of anionic lipid
systems.
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Affiliation(s)
- Anand Srivastava
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, The University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Gregory A Voth
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, The University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
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Tourdot RW, Ramakrishnan N, Radhakrishnan R. Defining the free-energy landscape of curvature-inducing proteins on membrane bilayers. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:022717. [PMID: 25215768 PMCID: PMC4336182 DOI: 10.1103/physreve.90.022717] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Indexed: 05/08/2023]
Abstract
Curvature-sensing and curvature-remodeling proteins, such as Amphiphysin, Epsin, and Exo70, are known to reshape cell membranes, and this remodeling event is essential for key biophysical processes such as tubulation, exocytosis, and endocytosis. Curvature-inducing proteins can act as curvature sensors; they aggregate to membrane regions matching their intrinsic curvature; as well as induce curvature in cell membranes to stabilize emergent high curvature, nonspherical, structures such as tubules, discs, and caveolae. A definitive understanding of the interplay between protein recruitment and migration, the evolution of membrane curvature, and membrane morphological transitions is emerging but remains incomplete. Here, within a continuum framework and using the machinery of Monte Carlo simulations, we introduce and compare three free-energy methods to delineate the free-energy landscape of curvature-inducing proteins on bilayer membranes. We demonstrate the utility of the Widom test particle (or field) insertion methodology in computing the excess chemical potentials associated with curvature-inducing proteins on the membrane-in particular, we use this method to track the onset of morphological transitions in the membrane at elevated protein densities. We validate this approach by comparing the results from the Widom method with those of thermodynamic integration and Bennett acceptance ratio methods. Furthermore, the predictions from the Widom method have been tested against analytical calculations of the excess chemical potential at infinite dilution. Our results are useful in precisely quantifying the free-energy landscape, and also in determining the phase boundaries associated with curvature-induction, curvature-sensing, and morphological transitions. This approach can be extended to studies exploring the role of thermal fluctuations and other external (control) variables, such as membrane excess area, in shaping curvature-mediated interactions on bilayer membranes.
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Affiliation(s)
- Richard W. Tourdot
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - N. Ramakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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50
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Braun AR, Lacy MM, Ducas VC, Rhoades E, Sachs JN. α-Synuclein-induced membrane remodeling is driven by binding affinity, partition depth, and interleaflet order asymmetry. J Am Chem Soc 2014; 136:9962-72. [PMID: 24960410 PMCID: PMC4105054 DOI: 10.1021/ja5016958] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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We have investigated
the membrane remodeling capacity of the N-terminal
membrane-binding domain of α-synuclein (α-Syn100). Using fluorescence correlation spectroscopy and vesicle clearance
assays, we show that α-Syn100 fully tubulates POPG
vesicles, the first demonstration that the amphipathic helix on its
own is capable of this effect. We also show that at equal density
of membrane-bound protein, α-Syn has dramatically reduced affinity
for, and does not tubulate, vesicles composed of a 1:1 POPG:POPC mixture.
Coarse-grained molecular dynamics simulations suggested that the difference
between the pure POPG and mixture results may be attributed to differences
in the protein’s partition depth, the membrane’s hydrophobic
thickness, and disruption of acyl chain order. To explore the importance
of these attributes compared with the role of the reduced binding
energy, we created an α-Syn100 variant in which we
removed the hydrophobic core of the non-amyloid component (NAC) domain
and tested its impact on pure POPG vesicles. We observed a substantial
reduction in binding affinity and tubulation, and simulations of the
NAC-null protein suggested that the reduced binding energy increases
the protein mobility on the bilayer surface, likely impacting the
protein’s ability to assemble into organized pretubule structures.
We also used simulations to explore a potential role for interleaflet
coupling as an additional driving force for tubulation. We conclude
that symmetry across the leaflets in the tubulated state maximizes
the interaction energy of the two leaflets and relieves the strain
induced by the hydrophobic void beneath the amphipathic helix.
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Affiliation(s)
- Anthony R Braun
- Department of Biomedical Engineering, University of Minnesota , Minneapolis, Minnesota 55455, United States
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