- Email: [email protected]
Nonlamellar Lipid Membranes
572a
Wednesday, March 2, 2016
how their physical characteristics can forward membrane protein research. Small angle X-ray scattering and small angle neutron scattering were used to investigate the structure of micelles and bicelles, specifically binary mixtures of detergents and lipids. To determine the impact of membrane mimic structure on protein function, outer membrane phospholipase A1, the protease OmpT, and the lipid A palmitoyltransferase PagP were purified in detergent micelles with varying properties, and the overall protein activity was evaluated. Hypotheses based on the correlations between activity and micelle properties were tested using mixed micelles and bicelles with tunable properties. The information gained from these studies will determine the physical properties important in stabilizing membrane proteins and provide guiding principles for selecting membrane mimics. 2825-Pos Board B202 Detailed Investigation of Detergent Micelle Formation using Molecular Dynamics Simulations Sadegh Faramarzi1, Danielle Grodi2, Andrew Philpott2, Michael Block1, Madison Kukura1, Erica Harvey2, Blake Mertz1. 1 West Virginia University, Morgantown, WV, USA, 2Fairmont State University, Fairmont, WV, USA. Surfactants are amphiphilic molecules with the ability to self-assemble into micelles and are commonly used in membrane protein extraction and solvation. Recent studies have shown that detergent type and concentration have a direct impact on the degree of oligomerization and function of membrane proteins [1], further extending their usefulness as a tool for investigating the structure-function relationship of membrane proteins. Despite their widespread use, the biophysical properties of detergent micelles at the atomistic level are poorly understood. We have conducted a systematic study on the physical characteristics of surfactant micelles using all-atom and coarsegrained molecular dynamics (MD) simulations. The commonly used detergents n-dodecylphosphochiline (DPC) and n-dodecyl-b-D-maltoside (DDM) were chosen. Our results agree in general with small angle X-ray scattering (SAXS) experiments and provide valuable insights into the relationship between micelle shape and aggregation number. Cluster analysis of selfassembled micelles reveal a wide distribution of micellar size and shape. This is consistent with the large range of aggregation numbers for DPC and DDM that have been experimentally determined. The shape of DPC micelles was more spherical due to its lower aggregation number, whereas DDM micelles tended to be ellipsoidal. In addition, micelle shape strictly obeys behavior based on theoretical packing factor considerations [2] such that both DPC and DDM surfactants formed ellipsoid micelles and larger preformed micelles (up to 300 detergent molecules) deformed to a hexagonal shape. Our results allow us to more accurately estimate the number of molecules and the effective thickness of the detergent layer surrounding membrane proteins. These insights in turn add to our understanding of the relationship between detergent properties and membrane protein oligomerization. [1] Hussain, S. 2015 J. Mol. Biol. 427:1278. [2] Israelachvili. J. N. et. al., 2011 Academic Press, 3rd ed. 2826-Pos Board B203 Atomistic and Coarse-Grained Molecular Simulations of Mixed Lamellar/ Nonlamellar Lipid Membranes Wei Ding, Michail Palaiokostas, Wen Wang, Mario Orsi. Queen Mary University of London, London, United Kingdom. Biological membranes typically contain varying amounts of both lamellar and nonlamellar lipids, which are defined according to their inherent phase behavior: lamellar lipids are those who tend to self-assemble into lamellar phases when isolated into an aqueous environment, while nonlamellar lipids prefer nonlamellar structures such as micelles or hexagonal phases. In vivo, the relative compositions of membrane lipids are dynamically regulated, and substantial research attention has been devoted to how such regulations influence membrane properties, and hence membrane-related biological processes like protein folding and transmembrane permeation. However, nano-scale properties of biological membranes can be extremely hard to investigate by experimental means. In this work, we have employed allatom molecular dynamics simulations to quantify a range of membrane properties for a set of lamellar/nonlamellar mixed bilayers characterized by varying composition. In particular, we focused on transmembrane profiles of electron density, lateral pressure, electric field, and dipole potential. Moreover, we have developed a new ‘ultra coarse-grained’ lipid model aimed at capturing lamellar/nonlamellar membrane processes that are still beyond the capability of fully atomistic simulations. Our results show that the lamellar/nonlamellar composition variation greatly affects transmembrane mechanical and electrostatic properties, whereas structural features are not significantly altered. These effects could underlie non-specific mechanisms
of controlling membrane functions through the regulation of lamellar/nonlamellar lipids. 2827-Pos Board B204 Atomistic Simulations of Small Molecule Permeation Through Lamellar/ Nonlamellar Lipid Membranes Michail Palaiokostas, Wei Ding, Mario Orsi. School of Engineering and Materials Science, Queen Mary, University of London, London, United Kingdom. Passive permeation through biological membranes is an important mechanism for transporting molecules and regulating the cell’s content. In vivo membranes typically consist of mixtures of lamellar and nonlamellar lipids. Lamellar lipids are characterized by their tendency to form lamellar bilayer phases, which are predominant in biology. Nonlamellar lipids, when isolated, instead form nonbilayer structures such as inverse hexagonal phases. While mixed lamellar/nonlamellar lipid membranes tend to adopt the ubiquitous bilayer structure, the presence of nonlamellar lipids is known to have profound effects on key membrane properties, such as the lateral pressure profile and associated elastic constants. In this study, we examine the effect of changing the lamellar vs. nonlamellar lipid composition on the transmembrane passive permeation process. In particular, we investigate a series of small molecules including water, carbon dioxide, ammonia, and fluoromethane. We utilize atomistic molecular dynamics simulations and the z-constraint method, to obtain transfer free energy profiles, as well as the diffusion and permeation coefficients; these properties are not readily accessible by experiment. Our preliminary results indicate that the addition of nonlamellar lipids enhances the transfer of permeants through the interfacial lipid head region, while it hinders it in the hydrocarbon tails core.
Protein-Lipid Interactions III 2828-Pos Board B205 Memprotmd: Protein-Lipid Interactions of Phospholipid Biosynthetic Enzymes and Development of the Web Database Thomas D. Newport, Mark S.P. Sansom, Phillip J. Stansfeld. Department of Biochemistry, University of Oxford, Oxford, United Kingdom. Membrane bound proteins play an important role in many biological processes, therefore understanding their structure and function represents an important scientific challenge. Whilst improvements in experimental techniques are revealing high resolution structures for an increasing number of membrane proteins, these structures are rarely resolved in complex with membrane lipids. The MemProtMD pipeline uses Coarse-Grained molecular dynamics simulations to allow a lipid bilayer to self-assemble around a membrane protein, and can be used to study the structure and dynamics of membrane proteins and lipids at both Coarse-Grained and atomistic representations. A web database (http://sbcb.bioch.ox.ac.uk/memprotmd/beta/) has been developed to make data generated by the MemProtMD pipeline available to the scientific community. Simulations and the results of subsequent analysis can be viewed using a web browser, including interactive 3D visualisations of the assembled bilayer and 2D visualisations of membrane protein topology and lipid contact data. All files required to run further coarse-grained or atomistic simulations of proteins in the database are provided. Proteins may be searched using keywords or browsed using classification systems such as MPStruc or the Transporter Classification Database. Phospholipid biosynthetic enzymes catalyse reactions involving membrane lipids and often interact with membrane lipids in unusual ways. Many of these interactions are important to the biological function of the enzyme and can be identified using the MemProtMD pipeline. Tools provided through the MemProtMD web database were used to examine the properties of the phospholipid biosynthetic enzymes diacylglycerol kinase, phosphatidate cytidylyltransferase and acyl-CoA desaturase when simulated in a membrane environment. 2829-Pos Board B206 Lipophilicity is a Key Factor to Increase the Antiviral Activity of HIV Neutralizing Antibodies Marcelo T. Augusto1, Axel Hollmann1, Fulvia Troise2, Ana S. Veiga1, Antonello Pessi3, Nuno C. Santos1. 1 Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal, 2CEINGE Biotecnologie Avanzate, Napoli, Italy, 3 PeptiPharma, Rome, Italy. The HIV broadly neutralizing antibody 2F5 targets the transiently exposed epitope in the membrane proximal external region (MPER) of HIV-1 gp41 by a two-step mechanism involving the viral membrane and this viral
Wednesday, March 2, 2016
how their physical characteristics can forward membrane protein research. Small angle X-ray scattering and small angle neutron scattering were used to investigate the structure of micelles and bicelles, specifically binary mixtures of detergents and lipids. To determine the impact of membrane mimic structure on protein function, outer membrane phospholipase A1, the protease OmpT, and the lipid A palmitoyltransferase PagP were purified in detergent micelles with varying properties, and the overall protein activity was evaluated. Hypotheses based on the correlations between activity and micelle properties were tested using mixed micelles and bicelles with tunable properties. The information gained from these studies will determine the physical properties important in stabilizing membrane proteins and provide guiding principles for selecting membrane mimics. 2825-Pos Board B202 Detailed Investigation of Detergent Micelle Formation using Molecular Dynamics Simulations Sadegh Faramarzi1, Danielle Grodi2, Andrew Philpott2, Michael Block1, Madison Kukura1, Erica Harvey2, Blake Mertz1. 1 West Virginia University, Morgantown, WV, USA, 2Fairmont State University, Fairmont, WV, USA. Surfactants are amphiphilic molecules with the ability to self-assemble into micelles and are commonly used in membrane protein extraction and solvation. Recent studies have shown that detergent type and concentration have a direct impact on the degree of oligomerization and function of membrane proteins [1], further extending their usefulness as a tool for investigating the structure-function relationship of membrane proteins. Despite their widespread use, the biophysical properties of detergent micelles at the atomistic level are poorly understood. We have conducted a systematic study on the physical characteristics of surfactant micelles using all-atom and coarsegrained molecular dynamics (MD) simulations. The commonly used detergents n-dodecylphosphochiline (DPC) and n-dodecyl-b-D-maltoside (DDM) were chosen. Our results agree in general with small angle X-ray scattering (SAXS) experiments and provide valuable insights into the relationship between micelle shape and aggregation number. Cluster analysis of selfassembled micelles reveal a wide distribution of micellar size and shape. This is consistent with the large range of aggregation numbers for DPC and DDM that have been experimentally determined. The shape of DPC micelles was more spherical due to its lower aggregation number, whereas DDM micelles tended to be ellipsoidal. In addition, micelle shape strictly obeys behavior based on theoretical packing factor considerations [2] such that both DPC and DDM surfactants formed ellipsoid micelles and larger preformed micelles (up to 300 detergent molecules) deformed to a hexagonal shape. Our results allow us to more accurately estimate the number of molecules and the effective thickness of the detergent layer surrounding membrane proteins. These insights in turn add to our understanding of the relationship between detergent properties and membrane protein oligomerization. [1] Hussain, S. 2015 J. Mol. Biol. 427:1278. [2] Israelachvili. J. N. et. al., 2011 Academic Press, 3rd ed. 2826-Pos Board B203 Atomistic and Coarse-Grained Molecular Simulations of Mixed Lamellar/ Nonlamellar Lipid Membranes Wei Ding, Michail Palaiokostas, Wen Wang, Mario Orsi. Queen Mary University of London, London, United Kingdom. Biological membranes typically contain varying amounts of both lamellar and nonlamellar lipids, which are defined according to their inherent phase behavior: lamellar lipids are those who tend to self-assemble into lamellar phases when isolated into an aqueous environment, while nonlamellar lipids prefer nonlamellar structures such as micelles or hexagonal phases. In vivo, the relative compositions of membrane lipids are dynamically regulated, and substantial research attention has been devoted to how such regulations influence membrane properties, and hence membrane-related biological processes like protein folding and transmembrane permeation. However, nano-scale properties of biological membranes can be extremely hard to investigate by experimental means. In this work, we have employed allatom molecular dynamics simulations to quantify a range of membrane properties for a set of lamellar/nonlamellar mixed bilayers characterized by varying composition. In particular, we focused on transmembrane profiles of electron density, lateral pressure, electric field, and dipole potential. Moreover, we have developed a new ‘ultra coarse-grained’ lipid model aimed at capturing lamellar/nonlamellar membrane processes that are still beyond the capability of fully atomistic simulations. Our results show that the lamellar/nonlamellar composition variation greatly affects transmembrane mechanical and electrostatic properties, whereas structural features are not significantly altered. These effects could underlie non-specific mechanisms
of controlling membrane functions through the regulation of lamellar/nonlamellar lipids. 2827-Pos Board B204 Atomistic Simulations of Small Molecule Permeation Through Lamellar/ Nonlamellar Lipid Membranes Michail Palaiokostas, Wei Ding, Mario Orsi. School of Engineering and Materials Science, Queen Mary, University of London, London, United Kingdom. Passive permeation through biological membranes is an important mechanism for transporting molecules and regulating the cell’s content. In vivo membranes typically consist of mixtures of lamellar and nonlamellar lipids. Lamellar lipids are characterized by their tendency to form lamellar bilayer phases, which are predominant in biology. Nonlamellar lipids, when isolated, instead form nonbilayer structures such as inverse hexagonal phases. While mixed lamellar/nonlamellar lipid membranes tend to adopt the ubiquitous bilayer structure, the presence of nonlamellar lipids is known to have profound effects on key membrane properties, such as the lateral pressure profile and associated elastic constants. In this study, we examine the effect of changing the lamellar vs. nonlamellar lipid composition on the transmembrane passive permeation process. In particular, we investigate a series of small molecules including water, carbon dioxide, ammonia, and fluoromethane. We utilize atomistic molecular dynamics simulations and the z-constraint method, to obtain transfer free energy profiles, as well as the diffusion and permeation coefficients; these properties are not readily accessible by experiment. Our preliminary results indicate that the addition of nonlamellar lipids enhances the transfer of permeants through the interfacial lipid head region, while it hinders it in the hydrocarbon tails core.
Protein-Lipid Interactions III 2828-Pos Board B205 Memprotmd: Protein-Lipid Interactions of Phospholipid Biosynthetic Enzymes and Development of the Web Database Thomas D. Newport, Mark S.P. Sansom, Phillip J. Stansfeld. Department of Biochemistry, University of Oxford, Oxford, United Kingdom. Membrane bound proteins play an important role in many biological processes, therefore understanding their structure and function represents an important scientific challenge. Whilst improvements in experimental techniques are revealing high resolution structures for an increasing number of membrane proteins, these structures are rarely resolved in complex with membrane lipids. The MemProtMD pipeline uses Coarse-Grained molecular dynamics simulations to allow a lipid bilayer to self-assemble around a membrane protein, and can be used to study the structure and dynamics of membrane proteins and lipids at both Coarse-Grained and atomistic representations. A web database (http://sbcb.bioch.ox.ac.uk/memprotmd/beta/) has been developed to make data generated by the MemProtMD pipeline available to the scientific community. Simulations and the results of subsequent analysis can be viewed using a web browser, including interactive 3D visualisations of the assembled bilayer and 2D visualisations of membrane protein topology and lipid contact data. All files required to run further coarse-grained or atomistic simulations of proteins in the database are provided. Proteins may be searched using keywords or browsed using classification systems such as MPStruc or the Transporter Classification Database. Phospholipid biosynthetic enzymes catalyse reactions involving membrane lipids and often interact with membrane lipids in unusual ways. Many of these interactions are important to the biological function of the enzyme and can be identified using the MemProtMD pipeline. Tools provided through the MemProtMD web database were used to examine the properties of the phospholipid biosynthetic enzymes diacylglycerol kinase, phosphatidate cytidylyltransferase and acyl-CoA desaturase when simulated in a membrane environment. 2829-Pos Board B206 Lipophilicity is a Key Factor to Increase the Antiviral Activity of HIV Neutralizing Antibodies Marcelo T. Augusto1, Axel Hollmann1, Fulvia Troise2, Ana S. Veiga1, Antonello Pessi3, Nuno C. Santos1. 1 Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal, 2CEINGE Biotecnologie Avanzate, Napoli, Italy, 3 PeptiPharma, Rome, Italy. The HIV broadly neutralizing antibody 2F5 targets the transiently exposed epitope in the membrane proximal external region (MPER) of HIV-1 gp41 by a two-step mechanism involving the viral membrane and this viral