1
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Bhaskara RM, Linker SM, Vögele M, Köfinger J, Hummer G. Carbon Nanotubes Mediate Fusion of Lipid Vesicles. ACS NANO 2017; 11:1273-1280. [PMID: 28103440 DOI: 10.1021/acsnano.6b05434] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The fusion of lipid membranes is opposed by high energetic barriers. In living organisms, complex protein machineries carry out this biologically essential process. Here we show that membrane-spanning carbon nanotubes (CNTs) can trigger spontaneous fusion of small lipid vesicles. In coarse-grained molecular dynamics simulations, we find that a CNT bridging between two vesicles locally perturbs their lipid structure. Their outer leaflets merge as the CNT pulls lipids out of the membranes, creating an hourglass-shaped fusion intermediate with still intact inner leaflets. As the CNT moves away from the symmetry axis connecting the vesicle centers, the inner leaflets merge, forming a pore that completes fusion. The distinct mechanism of CNT-mediated membrane fusion may be transferable, providing guidance in the development of fusion agents, e.g., for the targeted delivery of drugs or nucleic acids.
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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
| | - Stephanie M Linker
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Martin Vögele
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Jürgen Köfinger
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 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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2
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Mustafa G, Nandekar PP, Yu X, Wade RC. On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer. J Chem Phys 2015; 143:243139. [DOI: 10.1063/1.4936909] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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3
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Smeijers A, Markvoort A, Pieterse K, Hilbers P. Coarse-grained modelling of urea-adamantyl functionalised poly(propylene imine) dendrimers. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1096359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- A.F. Smeijers
- Computational Biology, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
| | - A.J. Markvoort
- Computational Biology, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
- Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
| | - K. Pieterse
- Computational Biology, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
- Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
| | - P.A.J. Hilbers
- Computational Biology, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
- Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
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4
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Posada IMD, Fantini J, Contreras FX, Barrantes F, Alonso A, Goñi FM. A cholesterol recognition motif in human phospholipid scramblase 1. Biophys J 2015; 107:1383-92. [PMID: 25229146 DOI: 10.1016/j.bpj.2014.07.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/28/2014] [Accepted: 07/22/2014] [Indexed: 11/26/2022] Open
Abstract
Human phospholipid scramblase 1 (SCR) catalyzes phospholipid transmembrane (flip-flop) motion. This protein is assumed to bind the membrane hydrophobic core through a transmembrane domain (TMD) as well as via covalently bound palmitoyl residues. Here, we explore the possible interaction of the SCR TMD with cholesterol by using a variety of experimental and computational biophysical approaches. Our findings indicate that SCR contains an amino acid segment at the C-terminal region that shows a remarkable affinity for cholesterol, although it lacks the CRAC sequence. Other 3-OH sterols, but not steroids lacking the 3-OH group, also bind this region of the protein. The newly identified cholesterol-binding region is located partly at the C-terminal portion of the TMD and partly in the first amino acid residues in the SCR C-terminal extracellular coil. This finding could be related to the previously described affinity of SCR for cholesterol-rich domains in membranes.
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Affiliation(s)
- Itziar M D Posada
- Unidad de Biofísica (CSIC, UPV/EHU), Departamento de Bioquímica y Biología Molecular, Bilbao, Spain
| | - Jacques Fantini
- Interactions Moléculaires et Systèmes Membranaires, EA-4674, Aix-Marseille Université, Marseille, France
| | - F Xabier Contreras
- Unidad de Biofísica (CSIC, UPV/EHU), Departamento de Bioquímica y Biología Molecular, Bilbao, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Francisco Barrantes
- Laboratory of Molecular Neurobiology, Faculty of Medical Sciences, Biomedical Research Institute (BIOMED) UCA-CONICET, Catholic University of Argentina, Buenos Aires, Argentina
| | - Alicia Alonso
- Unidad de Biofísica (CSIC, UPV/EHU), Departamento de Bioquímica y Biología Molecular, Bilbao, Spain
| | - Félix M Goñi
- Unidad de Biofísica (CSIC, UPV/EHU), Departamento de Bioquímica y Biología Molecular, Bilbao, Spain.
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5
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van Hoof B, Markvoort AJ, van Santen RA, Hilbers PAJ. Molecular Simulation of Protein Encapsulation in Vesicle Formation. J Phys Chem B 2014; 118:3346-54. [DOI: 10.1021/jp410612k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Bram van Hoof
- Department of Biomedical Engineering, ‡Institute for Complex
Molecular
Systems, and §Department of Chemical Engineering and Chemistry, Eindhoven University of Technology,
P. O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Albert J. Markvoort
- Department of Biomedical Engineering, ‡Institute for Complex
Molecular
Systems, and §Department of Chemical Engineering and Chemistry, Eindhoven University of Technology,
P. O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Rutger A. van Santen
- Department of Biomedical Engineering, ‡Institute for Complex
Molecular
Systems, and §Department of Chemical Engineering and Chemistry, Eindhoven University of Technology,
P. O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Peter A. J. Hilbers
- Department of Biomedical Engineering, ‡Institute for Complex
Molecular
Systems, and §Department of Chemical Engineering and Chemistry, Eindhoven University of Technology,
P. O. Box 513, 5600 MB Eindhoven, The Netherlands
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6
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Langer M, Sah R, Veser A, Gütlich M, Langosch D. Structural properties of model phosphatidylcholine flippases. ACTA ACUST UNITED AC 2013; 20:63-72. [PMID: 23352140 DOI: 10.1016/j.chembiol.2012.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 11/13/2012] [Accepted: 11/20/2012] [Indexed: 11/28/2022]
Abstract
Lipid translocation from one lipid bilayer leaflet to the other, termed flip-flop, is required for the distribution of newly synthesized phospholipids during membrane biogenesis. However, a dedicated biogenic lipid flippase has not yet been identified. Here, we show that the efficiency by which model transmembrane peptides facilitate flip of reporter lipids with different headgroups critically depends on their content of helix-destabilizing residues, the charge state of polar flanking residues, and the composition of the host membrane. In particular, increased backbone dynamics of the transmembrane helix relates to its increased ability to flip lipids with phosphatidylcholine and phosphatidylserine headgroups, whereas a more rigid helix favors phosphatidylethanolamine flip. Further, the transmembrane domains of many SNARE protein subtypes share essential features with the dynamic model peptides. Indeed, recombinant SNAREs possess significant lipid flippase activity.
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Affiliation(s)
- Marcella Langer
- Lehrstuhl für Chemie der Biopolymere, Department für biowissenschaftliche Grundlagen, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising and Munich Center For Integrated Protein Science (CIPS(M)), Germany
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7
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Abstract
The time and length scales accessible by biomolecular simulations continue to increase. This is in part due to improvements in algorithms and computing performance, but is also the result of the emergence of coarse-grained (CG) potentials, which complement and extend the information obtainable from fully detailed models. CG methods have already proven successful for a range of applications that benefit from the ability to rapidly simulate spontaneous self-assembly within a lipid membrane environment, including the insertion and/or oligomerization of a range of "toy models," transmembrane peptides, and single- and multi-domain proteins. While these simplified approaches sacrifice atomistic level detail, it is now straightforward to "reverse map" from CG to atomistic descriptions, providing a strategy to assemble membrane proteins within a lipid environment, prior to all-atom simulation. Moreover, recent developments have been made in "dual resolution" techniques, allowing different molecules in the system to be modeled with atomistic or CG resolution simultaneously.
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Affiliation(s)
- Syma Khalid
- School of Chemistry, University of Southampton, Southampton, UK
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8
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van Hoof B, Markvoort AJ, van Santen RA, Hilbers PAJ. On protein crowding and bilayer bulging in spontaneous vesicle formation. J Phys Chem B 2012; 116:12677-83. [PMID: 23025534 DOI: 10.1021/jp3062306] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Spontaneous aggregation of lipids into bilayers and vesicles is a key property for the formation of biological membranes. Understanding the compartmentalization achieved by vesicle formation is an important step toward understanding the origin of life, and is crucial in current efforts to develop artificial life. Spontaneously formed vesicles may be applied as artificial cells if they can efficiently encapsulate biomacromolecules. Recent studies report an enhanced concentration of encapsulated proteins during vesicle formation. In order to obtain more insight into this encapsulation process, here we simulate the spontaneous transition of flat bilayers to vesicles in the presence of solvated model proteins using molecular dynamics simulations. In the bilayer-vesicle transition, which is found to be unaffected by the presence of the solvated proteins, the bilayer edge remains at almost the same height, while the center of the membrane bulges out, a molecular pathway we denominate "bilayer bulging". This bulging results in an interior protein concentration that is significantly lower than that of the solution. By means of an increased protein-membrane interaction, enhanced encapsulation of proteins inside the vesicles could be achieved in our simulations.
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Affiliation(s)
- Bram van Hoof
- Department of Biomedical Engineering, Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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9
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Muhle-Goll C, Hoffmann S, Afonin S, Grage SL, Polyansky AA, Windisch D, Zeitler M, Bürck J, Ulrich AS. Hydrophobic matching controls the tilt and stability of the dimeric platelet-derived growth factor receptor (PDGFR) β transmembrane segment. J Biol Chem 2012; 287:26178-86. [PMID: 22619173 DOI: 10.1074/jbc.m111.325555] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The platelet-derived growth factor receptor β is a member of the cell surface receptor tyrosine kinase family and dimerizes upon activation. We determined the structure of the transmembrane segment in dodecylphosphocholine micelles by liquid-state NMR and found that it forms a stable left-handed helical dimer. Solid-state NMR and oriented circular dichroism were used to measure the tilt angle of the helical segments in macroscopically aligned model membranes with different acyl chain lengths. Both methods showed that decreasing bilayer thickness (DEPC-POPC-DMPC) led to an increase in the helix tilt angle from 10° to 30° with respect to the bilayer normal. At the same time, reconstitution of the comparatively long hydrophobic segment became less effective, eventually resulting in complete protein aggregation in the short-chain lipid DLPC. Unrestrained molecular dynamics simulations of the dimer were carried out in explicit lipid bilayers (DEPC, POPC, DMPC, sphingomyelin), confirming the observed dependence of the helix tilt angle on bilayer thickness. Notably, molecular dynamics revealed that the left-handed dimer gets tilted en bloc, whereas conformational transitions to alternative (e.g. right-handed dimeric) states were not supported. The experimental data along with the simulation results demonstrate a pronounced interplay between the platelet-directed growth factor receptor β transmembrane segment and the bilayer thickness. The effect of hydrophobic mismatch might play a key role in the redistribution and activation of the receptor within different lipid microdomains of the plasma membrane in vivo.
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Affiliation(s)
- Claudia Muhle-Goll
- Institute for Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P. O. Box 3640, 76021 Karlsruhe, Germany
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10
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Structural modelling and dynamics of proteins for insights into drug interactions. Adv Drug Deliv Rev 2012; 64:323-43. [PMID: 22155026 DOI: 10.1016/j.addr.2011.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 11/17/2011] [Accepted: 11/24/2011] [Indexed: 12/27/2022]
Abstract
Proteins are the workhorses of biomolecules and their function is affected by their structure and their structural rearrangements during ligand entry, ligand binding and protein-protein interactions. Hence, the knowledge of protein structure and, importantly, the dynamic behaviour of the structure are critical for understanding how the protein performs its function. The predictions of the structure and the dynamic behaviour can be performed by combinations of structure modelling and molecular dynamics simulations. The simulations also need to be sensitive to the constraints of the environment in which the protein resides. Standard computational methods now exist in this field to support the experimental effort of solving protein structures. This review presents a comprehensive overview of the basis of the calculations and the well-established computational methods used to generate and understand protein structure and function and the study of their dynamic behaviour with the reference to lung-related targets.
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11
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Wan CK, Han W, Wu YD. Parameterization of PACE Force Field for Membrane Environment and Simulation of Helical Peptides and Helix–Helix Association. J Chem Theory Comput 2011; 8:300-13. [DOI: 10.1021/ct2004275] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Cheuk-Kin Wan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Wei Han
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yun-Dong Wu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- School of Chemical Biology and Biotechnology, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- College of Chemistry, Peking University, Beijing, 100871, China
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12
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Is lipid flippase activity of SNARE transmembrane domains required for membrane fusion? FEBS Lett 2011; 585:1021-4. [PMID: 21362418 DOI: 10.1016/j.febslet.2011.02.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 02/23/2011] [Accepted: 02/23/2011] [Indexed: 11/22/2022]
Abstract
It has been suggested that lipids translocate between the outer and inner leaflets of fusing membranes, or flip-flop, to facilitate changes in bilayer leaflet areas at various stages of fusion. Here, we investigated the lipid flip activity of synthetic peptides that mimic SNARE transmembrane domains (TMDs). These peptides indeed induce flip of marker lipids. However, mutations that reduce flip activity do not diminish fusogenicity and cholesterol blocks flip much more efficiently than fusion. Therefore, our data do not support a role for flip in membrane fusion. On the other hand, the ability of SNARE TMDs to catalyze flip is consistent with a role of SNAREs in biogenic lipid flip.
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13
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Markvoort AJ, Marrink SJ. Lipid acrobatics in the membrane fusion arena. CURRENT TOPICS IN MEMBRANES 2011; 68:259-94. [PMID: 21771503 DOI: 10.1016/b978-0-12-385891-7.00011-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Albert J Markvoort
- Institute for Complex Molecular Systems & Biomodeling and Bioinformatics Group, Eindhoven University of Technology, Eindhoven, The Netherlands
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14
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Baoukina S, Tieleman DP. Direct simulation of protein-mediated vesicle fusion: lung surfactant protein B. Biophys J 2010; 99:2134-42. [PMID: 20923647 PMCID: PMC3042587 DOI: 10.1016/j.bpj.2010.07.049] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 07/22/2010] [Accepted: 07/23/2010] [Indexed: 10/19/2022] Open
Abstract
We simulated spontaneous fusion of small unilamellar vesicles mediated by lung surfactant protein B (SP-B) using the MARTINI force field. An SP-B monomer triggers fusion events by anchoring two vesicles and facilitating the formation of a lipid bridge between the proximal leaflets. Once a lipid bridge is formed, fusion proceeds via a previously described stalk - hemifusion diaphragm - pore-opening pathway. In the absence of protein, fusion of vesicles was not observed in either unbiased simulations or upon application of a restraining potential to maintain the vesicles in close proximity. The shape of SP-B appears to enable it to bind to two vesicles at once, forcing their proximity, and to facilitate the initial transfer of lipids to form a high-energy hemifusion intermediate. Our results may provide insight into more general mechanisms of protein-mediated membrane fusion, and a possible role of SP-B in the secretory pathway and transfer of lung surfactant to the gas exchange interface.
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Affiliation(s)
| | - D. Peter Tieleman
- Department of Biological Sciences, University of Calgary, Calgary, Canada
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15
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Coarse grained molecular dynamics simulations of transmembrane protein-lipid systems. Int J Mol Sci 2010; 11:2393-420. [PMID: 20640160 PMCID: PMC2904924 DOI: 10.3390/ijms11062393] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 05/16/2010] [Accepted: 05/30/2010] [Indexed: 12/24/2022] Open
Abstract
Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG) can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity. In this paper the first version of a coarse grained model for transmembrane proteins is presented. This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. These new potentials are used to stabilize the backbone. The model has been validated by investigating the adaptation of the hydrophobic mismatch induced by the insertion of WALP-peptides into a lipid membrane, showing that the first step in the adaptation is an increase in the membrane thickness, followed by a tilting of the peptide.
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16
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Nguyen THT, Rao NZ, Schroeder WM, Moore PB. Coarse-grained molecular dynamics of tetrameric transmembrane peptide bundles within a lipid bilayer. Chem Phys Lipids 2010; 163:530-7. [PMID: 20433819 DOI: 10.1016/j.chemphyslip.2010.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 03/05/2010] [Accepted: 04/19/2010] [Indexed: 01/17/2023]
Abstract
The conformations of model transmembrane peptides are studied to understand the structural and dynamical aspects of tetrameric bundles using a series of coarse grain (CG) molecular dynamics (MD) simulations since membrane proteins play a crucial role in cell function. In this work, two different amphipathic models have been constructed using similar hydrophobic/hydrophilic characteristics with two structurally distinct morphologies to evaluate the effect of roughness and hydrophilic topology on the structure of tetrameric bundles, one class that forms an ion-channel and one class that does not. Free energy calculations of typical amphipathic peptide topologies show that using a relatively smooth surface morphology allows for a stable conformation of the tetramer bundle in a diamond formation. However, the model with side chains attached to the core in order to roughen the surface has a stable square tetramer bundle which is consistent with experimental data and all-atom (AA) MD simulations. Comparisons of the CG simulations with AA MD simulations are in reasonable agreement with the formation of tetrameric homo-oligomers, partitioning within the lipid bilayer and tilt angle with respect to the bilayer normal. We concluded that a square or diamond shape tetrameric homo-oligomers could be stabilized by rational design of the peptide morphology and topology of the surface, thus allowing us to tune the permeability of the bundle or channel.
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Affiliation(s)
- Thuy Hien T Nguyen
- Department of Chemistry & Biochemistry and the West Center for Computational Chemistry and Drug Design, University of the Sciences in Philadelphia, 600 South 43rd Street, Philadelphia, PA 19104-4495, United States
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17
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Peptide nanopores and lipid bilayers: interactions by coarse-grained molecular-dynamics simulations. Biophys J 2009; 96:3519-28. [PMID: 19413958 DOI: 10.1016/j.bpj.2009.01.046] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Revised: 01/13/2009] [Accepted: 01/13/2009] [Indexed: 11/20/2022] Open
Abstract
A set of 49 protein nanopore-lipid bilayer systems was explored by means of coarse-grained molecular-dynamics simulations to study the interactions between nanopores and the lipid bilayers in which they are embedded. The seven nanopore species investigated represent the two main structural classes of membrane proteins (alpha-helical and beta-barrel), and the seven different bilayer systems range in thickness from approximately 28 to approximately 43 A. The study focuses on the local effects of hydrophobic mismatch between the nanopore and the lipid bilayer. The effects of nanopore insertion on lipid bilayer thickness, the dependence between hydrophobic thickness and the observed nanopore tilt angle, and the local distribution of lipid types around a nanopore in mixed-lipid bilayers are all analyzed. Different behavior for nanopores of similar hydrophobic length but different geometry is observed. The local lipid bilayer perturbation caused by the inserted nanopores suggests possible mechanisms for both lipid bilayer-induced protein sorting and protein-induced lipid sorting. A correlation between smaller lipid bilayer thickness (larger hydrophobic mismatch) and larger nanopore tilt angle is observed and, in the case of larger hydrophobic mismatches, the simulated tilt angle distribution seems to broaden. Furthermore, both nanopore size and key residue types (e.g., tryptophan) seem to influence the level of protein tilt, emphasizing the reciprocal nature of nanopore-lipid bilayer interactions.
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18
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West B, Brown FLH, Schmid F. Membrane-protein interactions in a generic coarse-grained model for lipid bilayers. Biophys J 2009; 96:101-15. [PMID: 18835907 PMCID: PMC2710048 DOI: 10.1529/biophysj.108.138677] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Accepted: 09/04/2008] [Indexed: 11/18/2022] Open
Abstract
We study membrane-protein interactions and membrane-mediated protein-protein interactions by Monte Carlo simulations of a generic coarse-grained model for lipid bilayers with cylindrical hydrophobic inclusions. The strength of the hydrophobic force and the hydrophobic thickness of the proteins are systematically varied. The results are compared with analytical predictions of two popular analytical theories: The Landau-de Gennes theory and the elastic theory. The elastic theory provides an excellent description of the fluctuation spectra of pure membranes and successfully reproduces the deformation profiles of membranes around single proteins. However, its prediction for the potential of mean force between proteins is not compatible with the simulation data for large distances. The simulations show that the lipid-mediated interactions are governed by five competing factors: direct interactions; lipid-induced depletion interactions; lipid bridging; lipid packing; and a smooth long-range contribution. The mechanisms leading to hydrophobic mismatch interactions are critically analyzed.
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Affiliation(s)
- Beate West
- Fakultät für Physik, Universität Bielefeld, Bielefeld, Germany.
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19
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Hwang H, Schatz GC, Ratner MA. Coarse-Grained Molecular Dynamics Study of Cyclic Peptide Nanotube Insertion into a Lipid Bilayer. J Phys Chem A 2008; 113:4780-7. [DOI: 10.1021/jp8080657] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hyonseok Hwang
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon, Kangwon 200-701, Republic of Korea
| | - George C. Schatz
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113
| | - Mark A. Ratner
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113
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20
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Marrink SJ, de Vries AH, Tieleman DP. Lipids on the move: simulations of membrane pores, domains, stalks and curves. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1788:149-68. [PMID: 19013128 DOI: 10.1016/j.bbamem.2008.10.006] [Citation(s) in RCA: 369] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2008] [Revised: 10/13/2008] [Accepted: 10/14/2008] [Indexed: 11/16/2022]
Abstract
In this review we describe the state-of-the-art of computer simulation studies of lipid membranes. We focus on collective lipid-lipid and lipid-protein interactions that trigger deformations of the natural lamellar membrane state, showing that many important biological processes including self-aggregation of membrane components into domains, the formation of non-lamellar phases, and membrane poration and curving, are now amenable to detailed simulation studies.
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Affiliation(s)
- Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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21
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Peptide aggregation and pore formation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study. Biophys J 2008; 95:4337-47. [PMID: 18676652 DOI: 10.1529/biophysj.108.133330] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a simulation study where different resolutions, namely coarse-grained (CG) and all-atom (AA) molecular dynamics simulations, are used sequentially to combine the long timescale reachable by CG simulations with the high resolution of AA simulations, to describe the complete processes of peptide aggregation and pore formation by alamethicin peptides in a hydrated lipid bilayer. In the 1-micros CG simulations the peptides spontaneously aggregate in the lipid bilayer and exhibit occasional transitions between the membrane-spanning and the surface-bound configurations. One of the CG systems at t = 1 micros is reverted to an AA representation and subjected to AA simulation for 50 ns, during which water molecules penetrate the lipid bilayer through interactions with the peptide aggregates, and the membrane starts leaking water. During the AA simulation significant deviations from the alpha-helical structure of the peptides are observed, however, the size and arrangement of the clusters are not affected within the studied time frame. Solid-state NMR experiments designed to match closely the setup used in the molecular dynamics simulations provide strong support for our finding that alamethicin peptides adopt a diverse set of configurations in a lipid bilayer, which is in sharp contrast to the prevailing view of alamethicin oligomers formed by perfectly aligned helical alamethicin peptides in a lipid bilayer.
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Abstract
Recent experimental results revealed that lipid-mediated interactions due to hydrophobic forces may be important in determining the protein topology after insertion in the membrane, in regulating the protein activity, in protein aggregation and in signal transduction. To gain insight into the lipid-mediated interactions between two intrinsic membrane proteins, we developed a mesoscopic model of a lipid bilayer with embedded proteins, which we studied with dissipative particle dynamics. Our calculations of the potential of mean force between transmembrane proteins show that hydrophobic forces drive long-range protein-protein interactions and that the nature of these interactions depends on the length of the protein hydrophobic segment, on the three-dimensional structure of the protein and on the properties of the lipid bilayer. To understand the nature of the computed potentials of mean force, the concept of hydrophilic shielding is introduced. The observed protein interactions are interpreted as resulting from the dynamic reorganization of the system to maintain an optimal hydrophilic shielding of the protein and lipid hydrophobic parts, within the constraint of the flexibility of the components. Our results could lead to a better understanding of several membrane processes in which protein interactions are involved.
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Monticelli L, Kandasamy SK, Periole X, Larson RG, Tieleman DP, Marrink SJ. The MARTINI Coarse-Grained Force Field: Extension to Proteins. J Chem Theory Comput 2008; 4:819-34. [DOI: 10.1021/ct700324x] [Citation(s) in RCA: 1835] [Impact Index Per Article: 114.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luca Monticelli
- Dept of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada, Chemical Engineering Department, The University of Michigan, 2300 Hayward Street, Ann Arbor, Michigan 48109, and Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Senthil K. Kandasamy
- Dept of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada, Chemical Engineering Department, The University of Michigan, 2300 Hayward Street, Ann Arbor, Michigan 48109, and Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Xavier Periole
- Dept of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada, Chemical Engineering Department, The University of Michigan, 2300 Hayward Street, Ann Arbor, Michigan 48109, and Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ronald G. Larson
- Dept of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada, Chemical Engineering Department, The University of Michigan, 2300 Hayward Street, Ann Arbor, Michigan 48109, and Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - D. Peter Tieleman
- Dept of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada, Chemical Engineering Department, The University of Michigan, 2300 Hayward Street, Ann Arbor, Michigan 48109, and Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Siewert-Jan Marrink
- Dept of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada, Chemical Engineering Department, The University of Michigan, 2300 Hayward Street, Ann Arbor, Michigan 48109, and Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Aksimentiev A, Brunner R, Cohen J, Comer J, Cruz-Chu E, Hardy D, Rajan A, Shih A, Sigalov G, Yin Y, Schulten K. Computer modeling in biotechnology: a partner in development. Methods Mol Biol 2008; 474:181-234. [PMID: 19031067 DOI: 10.1007/978-1-59745-480-3_11] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Computational modeling can be a useful partner in biotechnology, in particular, in nanodevice engineering. Such modeling guides development through nanoscale views of biomolecules and devices not available through experimental imaging methods. We illustrate the role of computational modeling, mainly of molecular dynamics, through four case studies: development of silicon bionanodevices for single molecule electrical recording, development of carbon nano-tube-biomolecular systems as in vivo sensors, development of lipoprotein nanodiscs for assays of single membrane proteins, and engineering of oxygen tolerance into the enzyme hydrogenase for photosynthetic hydrogen gas production. The four case studies show how molecular dynamics approaches were adapted to the specific technical uses through (i) multi-scale extensions, (ii) fast quantum chemical force field evaluation, (iii) coarse graining, and (iv) novel sampling methods. The adapted molecular dynamics simulations provided key information on device behavior and revealed development opportunities, arguing that the "computational microscope" is an indispensable nanoengineering tool.
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Affiliation(s)
- Aleksei Aksimentiev
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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