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Science & Technology Multiscale Modeling of Lipid Bilayer Interactions with Solid Substrates David R. Heine, Aravind R. Rammohan, and Jitendra Balakrishnan October 23rd, 2008 RPI High Performance Computing Conference Outline • Background – structure of lipid bilayers – applications of supported lipid bilayers • • • • • Modeling challenges Atomistic modeling Mesoscale modeling Experimental work Conclusions Science & Technology 2 Lipids and Bilayers Science & Technology 3 Technological Relevance of Supported Lipid Bilayers • SLBs are important for various biotech applications – Biological research • • • • Model systems to study the properties of cell membranes Stable, immobilized base for research on membrane moieties Biosensors for the activity of various biological species Cell attachment surfaces – Pharmaceutical research • Investigation of membrane receptor drug targets • Membrane microarrays: High throughput screening for drug discovery – How does bilayer-substrate interaction affect bilayer behavior? Science & Technology 4 Supported Lipid Bilayers at Corning • Applications: Membrane-protein microarrays for pharmaceutical drug discovery • Substrate texture is important in the adhesion and conformation of bilayers on the surface – Crucial for the biological functionality of bilayers • Objective: Quantify the effect of substrate topography and chemical composition on bilayer conformation and dynamics Science & Technology 5 Bilayer Length & Time Scales • Bilayer dynamics vary over large length and time scales, suggesting a multiscale approach. Time Scales Length Scales Bond Vibrations: fs Stokes Radius: 2.4 nm Lateral Diffusion Time: 4 ps Bilayer Thickness: 4 nm Area per lipid: 60 +/- 2 Å2 Undulations: 4 Å – 0.25 mm Peristaltic Modes: 1-10 ns Undulatory Modes 0.1 ns – 0.1 ms Membrane Fusion: 1-10 s Science & Technology 6 Multiscale Approach • Atomistic model – capture local structure and short term dynamics • Mesoscale model – capture longer length and time scales – sufficient to look at interaction with rough surfaces Science & Technology 7 Atomistic Model • The bilayer is composed of 72 DPPC lipid molecules described in full atomistic detail using the CHARMM potential • Water uses the flexible SPC model to allow for bond angle variations near the substrate • The substrate is the [100] face of aquartz with lateral dimensions of 49 x 49 Å described by the ClayFF potential R 12 R 6 e2 o ,ij o ,ij Enonbond Do ,ij 2 r r i j ij 40 ij Science & Technology i j lipid water substrate qi q j rij 8 Simulation Technique • System is periodic in x and y directions with a repulsive wall above the water surface in the z direction Water • NVT ensemble must be used since pressure control is prohibited by the solid substrate Upper leaflet • Temperature is maintained at 323K with a Nose-Hoover thermostat • Total energy and force on the bilayer are extracted during the simulation. Heine et al. Molecular Simulations, 2007, 33(4-5), pp.391-397. Science & Technology Lower leaflet Bilayer Lipids Water Substrate 9 Simulation Technique • System is periodic in x and y directions with a repulsive wall above the water surface in the z direction • NVT ensemble must be used since pressure control is prohibited by the solid substrate • Temperature is maintained at 323K with a Nose-Hoover thermostat • Total energy and force on the bilayer are extracted during the simulation. Heine et al. Molecular Simulations, 2007, 33(4-5), pp.391-397. Science & Technology 10 Comparison with Experimental Measurements Bilayer-Substrate Interaction Energy from Simulations Simulations show an energy minimum at a separation of 3 to 3.5 nm SFA Measurements Between Substrate and Bilayer Experimental measurements show a repulsion starting around 4 nm and pullout at 3 nm separations courtesy J. Israelachvili, UCSB Science & Technology 11 Bilayer structure near the substrate • Lower monolayer is compressed in the vicinity of substrate • Upper monolayer seems relatively unaffected Science & Technology 12 Effect of substrate on lateral lipid diffusion • Reduction in lateral diffusivity observed, compared to free bilayers – Bulk simulations match diffusivity of free bilayers • Suppression of transverse fluctuations near substrate inhibit a key mechanism for lateral diffusion Science & Technology Transverse lipid motion enables lateral diffusion Substrate reduces transverse motion & Experimental value For free bilayers reduces diffusivity 13 Atomistic Simulation Results • MD simulations show bilayer-substrate equilibrium separation of 3 – 3.5 nm, in agreement with SFA experiments • Lateral diffusion of the lipid head groups decreases as the bilayer approaches the substrate • Suppression of transverse fluctuations may be responsible for reduced lateral diffusion Science & Technology 14 Mesoscopic Model dv m FDISSIPATIV E FRANDOM FCONSERVATI VE dt • Dissipative force – Formulation based on Newtonian solvent viscosity FDISSIPATIV E 6water aij v • Random force – Formulation based on fluctuation-dissipation theorem FRANDOM 3 2 Dt (t t ' ) D k BT 6water rij Science & Technology • Conservative force – Elastic stretching of bilayer – Bending modes of bilayer – Surface interactions – Other (electrostatic, etc.) Membrane Continuum solvent Substrate 15 Mesoscopic Modeling of Supported Lipid Bilayers • Continuum representation to study large length and time scales – 1 m2, 1 ms • Allows study of bilayer behavior on textured substrates • Dynamic model that includes effect of solvent and environment Science & Technology All dimensions in nanometers z axis not to scale 16 Mesoscopic Model Results z: 2 2.5 3 3.5 4 4.5 5 5.5 6 6.5 7 7.5 8 z: 75 75 y 100 y 100 50 25 0 6 6.5 7 7.5 8 8.5 9 9.5 10 10.5 11 11.5 12 50 25 0 25 50 75 x Substrate topography contours Science & Technology 100 0 0 25 50 75 100 x Membrane topography contours 17 Mesoscopic Model Results Maximum and Minimum Separation Separations in nm 9 Membrane Coating 8 7 Min_Sep Max_Sep Membrane spanning 6 Maximum Separation 5 4 3 Minimum Separation 2 1 0 -1 0 Science & Technology 3 6 9 Roughness in nm 12 15 18 Mesoscopic Model Results • Allows study of bilayer on micron and microsecond scales • Minimum surface roughness of 4-5 nm required for membrane spanning conformation • Spanning configuration important for maintaining bilayer mobility Science & Technology 19 AFM measurements Spreading of Bilayer on Synthetic Substrates AFM image & measurements courtesy Sergiy Minko, Clarkson University Ref: Nanoletters, 2008, 8(3), 941-944 Science & Technology 20 AFM measurements Smoothening of membrane on rough substrates AFM image & measurements courtesy Sergiy Minko, Clarkson University Science & Technology 21 Lipid membrane conformation Numerical and Experimental Results Macroscopic model predictions AFM images courtesy Sergiy Minko, Clarkson U. Membrane conformation vs.substrate roughness Separation from substrate (nm) 10 BILAYER Minimum Separation Maximum Separation 8 6 Maximum Separation 4 ~ 5 nm Minimum Separation 2 0 SUBSTRATE 0 2 4 6 8 10 12 Substrate roughness (nm) 14 Roiter et al. Nanoletters 8, 941 (2008) • Model shows membrane coating up to about 4-5 nm • AFM images show membrane coating 5 nm particles Science & Technology 22 Conclusions • MD simulations show bilayer-substrate separation of 3 – 3.5 nm, in agreement with SFA experiments • MD simulations show reduced lateral diffusion in lipids as the bilayer approaches the substrate • Mesoscopic model shows membranes coat particles up to 4 – 5 nm in diameter, in agreement with AFM observations • Larger surface features are needed to achieve separation between bilayer and substrate • High-performance computing has opened up new approaches for understanding biomolecule-substrate interactions, which aids design • There is still plenty of room to grow as these models are still restricted in terms of size, timescale, and complexity Science & Technology 23 Acknowledgements • Professor Sergiy Minko & his group at Clarkson U. • Professor Jacob Israelachvili & his group at U. C. Santa Barbara Science & Technology 24 Lipid Behavior on Nanoparticles • Bilayer conforms to Nanoparticles < 1.2 nm • Bilayer undergoes structural rearrangement involving formation of holes between 1.2 – 22 nm • Beyond 22 nm bilayer envelops the particle Ref: Nanoletters, 2008, 8(3), 941-944 Science & Technology 26
