An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids

Improvements in the CHARMM all-atom force field for atomic-level molecular simulations of lipids are reported. Substantial adjustments have been made to the Lennard-Jones (LJ) hydrocarbon and torsional parameters and to the partial atomic charges and torsional parameters of the phosphate moiety. These changes were motivated by a combination of unexpected simulation results and recent high-level ab initio quantum mechanical calculations. The parameter optimization procedure is described, and the resulting energy function validated by an 11 ns molecular dynamics simulation of a hydrated phospholipid bilayer. Of note is the influence of the hydrocarbon LJ parameters on the conformational properties of the aliphatic tails, emphasizing the importance of obtaining the proper balance between the bonded and nonbonded portions of the force field. Compatibility with the CHARMM all-atom parameter sets for proteins and nucleic acids has been maintained such that high quality simulations of biologically interesting membranes are possible. The complete force field is included as Supporting Information and is available from www.pharmacy.umaryland.edu/∼alex

An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids

Improvements in the CHARMM all-atom force field for atomic-level molecular simulations of lipids are reported. Substantial adjustments have been made to the Lennard-Jones (LJ) hydrocarbon and torsional parameters and to the partial atomic charges and torsional parameters of the phosphate moiety. These changes were motivated by a combination of unexpected simulation results and recent high-level ab initio quantum mechanical calculations. The parameter optimization procedure is described, and the resulting energy function validated by an 11 ns molecular dynamics simulation of a hydrated phospholipid bilayer. Of note is the influence of the hydrocarbon LJ parameters on the conformational properties of the aliphatic tails, emphasizing the importance of obtaining the proper balance between the bonded and nonbonded portions of the force field. Compatibility with the CHARMM all-atom parameter sets for proteins and nucleic acids has been maintained such that high quality simulations of biologically interesting membranes are possible. The complete force field is included as Supporting Information and is available from www.pharmacy.umaryland.edu/∼alex

Contribution of Omega-3 Fatty Acids to the Thermodynamics of Membrane Protein Solvation

Recent NMR experiments and molecular dynamics simulations have indicated that rhodopsin is preferentially solvated by omega-3 fatty acids compared to saturated chains. However, to date no physical theory has been advanced to explain this phenomenon. The present work presents a novel thermodynamic explanation for this preferential solvation based on statistical analysis of 26 100 ns all-atom molecular dynamics simulations of rhodopsin in membranes rich in polyunsaturated chains. The results indicate that the preferential solvation by omega-3 chains is entropically driven; all chains experience an entropic penalty when associating with the protein, but the penalty is significantly larger for saturated chains

Polyunsaturated Fatty Acids in Lipid Bilayers: Intrinsic and Environmental Contributions to Their Unique Physical Properties

Polyunsaturated lipids are an essential component of biological membranes, influencing order and dynamics of lipids, protein−lipid interaction, and membrane transport properties. To gain an atomic level picture of the impact of polyunsaturation on membrane properties, quantum mechanical (QM) and empirical force field based calculations have been undertaken. The QM calculations of the torsional energy surface for rotation about vinyl−methylene bonds reveal low barriers to rotation, indicating an intrinsic propensity toward flexibility. Based on QM and experimental data, empirical force field parameters were developed for polyunsaturated lipids and applied in a 16 ns molecular dynamics (MD) simulation of a 1-stearoyl-2-docosahexaenoyl-sn-glyerco-3-phosphocholine (SDPC) lipid bilayer. The simulation results are in good agreement with experimental data, suggesting an unusually high degree of conformational flexibility of polyunsaturated hydrocarbon chains in membranes. The detailed analysis of chain conformation and dynamics by simulations is aiding the interpretation of experimental data and is useful for understanding the unique role of polyunsaturated lipids in biological membranes. The complete force field is included as Supporting Information and is available from http://www.pharmacy.umaryland.edu/faculty/amackere/research.html

Retinal Conformation Governs p<i>K</i>_a of Protonated Schiff Base in Rhodopsin Activation

We have explored the relationship between conformational energetics and the protonation state of the Schiff base in retinal, the covalently bound ligand responsible for activating the G protein-coupled receptor rhodopsin, using quantum chemical calculations. Guided by experimental structural determinations and large-scale molecular simulations on this system, we examined rotation about each bond in the retinal polyene chain, for both the protonated and deprotonated states that represent the dark and photoactivated states, respectively. Particular attention was paid to the torsional degrees of freedom that determine the shape of the molecule, and hence its interactions with the protein binding pocket. While most torsional degrees of freedom in retinal are characterized by large energetic barriers that minimize structural fluctuations under physiological temperatures, the C6–C7 dihedral defining the relative orientation of the β-ionone ring to the polyene chain has both modest barrier heights and a torsional energy surface that changes dramatically with protonation of the Schiff base. This surprising coupling between conformational degrees of freedom and protonation state is further quantified by calculations of the pKa as a function of the C6–C7 dihedral angle. Notably, pKa shifts of greater than two units arise from torsional fluctuations observed in molecular dynamics simulations of the full ligand-protein-membrane system. It follows that fluctuations in the protonation state of the Schiff base occur prior to forming the activated MII state. These new results shed light on important mechanistic aspects of retinal conformational changes that are involved in the activation of rhodopsin in the visual process

Molecular Organization of a Raft-like Domain in a Polyunsaturated Phospholipid Bilayer: A Supervised Machine Learning Analysis of Molecular Dynamics Simulations

Numerous health benefits are associated with omega-3 polyunsaturated fatty acids (n-3 PUFA) consumed in fish oils. An understanding of the mechanism remains elusive. The plasma membrane as a site of action is the focus in this study. With large-scale all-atom MD simulations run on a model membrane (1050 lipid molecules), we observed the evolution over time (6 μs) of a circular (raft-like) domain composed of N-palmitoylsphingomyelin (PSM) and cholesterol embedded into a surrounding (non-raft) patch composed of polyunsaturated 1-palmitoyl-2-docosahexaenoylphosphatylcholine (PDPC) (1:1:1 mol). A supervised machine learning algorithm was developed to characterize the migration of each lipid based on molecular conformation and the local environment. PDPC molecules were seen to infiltrate the ordered raft-like domain in a small amount, while a small concentration of PSM and cholesterol molecules was seen to migrate into the disordered non-raft region. Enclosing the raft-like domain, a narrow (∼2 nm in width) interfacial zone composed of PDPC, PSM, and cholesterol that buffers the substantial difference in order (ΔSCD ≈ 0.12) between raft-like and non-raft environments was seen to form. Our results suggest that n-3 PUFA regulate the architecture of lipid rafts enriched in sphingolipids and cholesterol with a minimal effect on order within their interior in membranes

Role of Cholesterol and Polyunsaturated Chains in Lipid−Protein Interactions: Molecular Dynamics Simulation of Rhodopsin in a Realistic Membrane Environment

We present a 118-ns molecular dynamics simulation of rhodopsin embedded in a bilayer composed of a 2:2:1 mixture of 1-stearoyl-2-docosahexaenoyl-phosphatidylcholine (SDPC), 1-stearoyl-2-docosahexaenoyl-phosphatidylethanolamine (SDPE), and cholesterol, respectively. The simulation demonstrates that the protein breaks the lateral and transverse symmetry of the bilayer. Lipids near the protein preferentially reorient such that their unsaturated chains interact with the protein, while the distribution of cholesterol in the membrane complements the variations in rhodopsin's transverse profile. The latter phenomenon suggests a molecular-level mechanism for the experimental finding that cholesterol stabilizes the native dark-adapted state of rhodopsin without binding directly to the protein

Molecular-Level Organization of Saturated and Polyunsaturated Fatty Acids in a Phosphatidylcholine Bilayer Containing Cholesterol^†

Cholesterol's preference for specific fatty acid chains is investigated at the atomic level in a 20 ns molecular dynamics computer simulation of a lipid bilayer membrane consisting of cholesterol and 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (SDPC) in a 1:3 ratio. These simulations reproduce experimental measurements suggesting that cholesterol prefers to be solvated by saturated acyl chains and has a low affinity for polyunsaturated fatty acids. Analyses of the simulation trajectory provide a detailed picture of both the transverse and lateral structures of the lipid bilayer membrane, along with a description of lipid and cholesterol dynamics at high temporal resolution. Comparison with a previous simulation of a pure phospholipid bilayer allows an atomic-level description of the changes in membrane structure and dynamics resulting from incorporation of cholesterol. The observed differential cholesterol interactions with saturated and polyunsaturated lipids provide a mechanism for the formation of laterally inhomogeneous membranes; thus, the simulation provides molecular-level insight into the formation of lipid rafts

Polyunsaturated Docosahexaenoic vs Docosapentaenoic AcidDifferences in Lipid Matrix Properties from the Loss of One Double Bond

Insufficient supply to the developing brain of docosahexaenoic acid (22:6n3, DHA), or its ω-3 fatty acid precursors, results in replacement of DHA with docosapentaenoic acid (22:5n6, DPA), an ω-6 fatty acid that is lacking a double bond near the chain's methyl end. We investigated membranes of 1-stearoyl(d35)-2-docosahexaenoyl-sn-glycero-3-phosphocholine and 1-stearoyl(d35)-2-docosapentaenoyl-sn-glycero-3-phosphocholine by solid-state NMR, X-ray diffraction, and molecular dynamics simulations to determine if the loss of this double bond alters membrane physical properties. The low order parameters of polyunsaturated chains and the NMR relaxation data indicate that both DHA and DPA undergo rapid conformational transitions with correlation times of the order of nanoseconds at carbon atom C2 and of picoseconds near the terminal methyl group. However, there are important differences between DHA- and DPA-containing lipids:  the DHA chain with one additional double bond is more flexible at the methyl end and isomerizes with shorter correlation times. Furthermore, the stearic acid paired with the DHA in mixed-chain lipids has lower order, in particular in the middle of the chain near carbons C10-12, indicating differences in the packing of hydrocarbon chains. Such differences are also reflected in the electron density profiles of the bilayers and in the simulation results. The DHA chain has a higher density near the lipid−water interface, whereas the density of the stearic acid chain is higher in the bilayer center. The loss of a single double bond from DHA to DPA results in a more even distribution of chain densities along the bilayer normal. We propose that the function of integral membrane proteins such as rhodopsin is sensitive to such a redistribution

Polyunsaturated Docosahexaenoic vs Docosapentaenoic AcidDifferences in Lipid Matrix Properties from the Loss of One Double Bond

Insufficient supply to the developing brain of docosahexaenoic acid (22:6n3, DHA), or its ω-3 fatty acid precursors, results in replacement of DHA with docosapentaenoic acid (22:5n6, DPA), an ω-6 fatty acid that is lacking a double bond near the chain's methyl end. We investigated membranes of 1-stearoyl(d35)-2-docosahexaenoyl-sn-glycero-3-phosphocholine and 1-stearoyl(d35)-2-docosapentaenoyl-sn-glycero-3-phosphocholine by solid-state NMR, X-ray diffraction, and molecular dynamics simulations to determine if the loss of this double bond alters membrane physical properties. The low order parameters of polyunsaturated chains and the NMR relaxation data indicate that both DHA and DPA undergo rapid conformational transitions with correlation times of the order of nanoseconds at carbon atom C2 and of picoseconds near the terminal methyl group. However, there are important differences between DHA- and DPA-containing lipids:  the DHA chain with one additional double bond is more flexible at the methyl end and isomerizes with shorter correlation times. Furthermore, the stearic acid paired with the DHA in mixed-chain lipids has lower order, in particular in the middle of the chain near carbons C10-12, indicating differences in the packing of hydrocarbon chains. Such differences are also reflected in the electron density profiles of the bilayers and in the simulation results. The DHA chain has a higher density near the lipid−water interface, whereas the density of the stearic acid chain is higher in the bilayer center. The loss of a single double bond from DHA to DPA results in a more even distribution of chain densities along the bilayer normal. We propose that the function of integral membrane proteins such as rhodopsin is sensitive to such a redistribution