Estradiol (E2) and E2 oleate associate with high-density lipoproteins (HDLs). Their orientation i... more Estradiol (E2) and E2 oleate associate with high-density lipoproteins (HDLs). Their orientation in HDLs is unknown. We studied the orientation of E2 and E2 oleate in membranes and reconstituted HDLs, finding that E2 and E2 oleate are membrane-associated and highly mobile. Our combination of NMR measurements, molecular dynamics simulation, and analytic theory identifies three major conformations where the long axis of E2 assumes a parallel, perpendicular, or antiparallel orientation relative to the membrane's z-direction. The perpendicular orientation is preferred, and furthermore, in this orientation, E2 strongly favors a particular roll angle, facing the membrane with carbons 6, 7, 15, and 16, whereas carbons 1, 2, 11, and 12 point toward the aqueous phase. In contrast, the long axis of E2 oleate is almost exclusively oriented at an angle of ∼60° to the z-direction. In such an orientation, the oleoyl chain is firmly inserted into the membrane. Thus, both E2 and E2 oleate have a...
Headgroup Conformations of Phospholipids from Molecular Dynamics Simulation: Sampling Challenges and Comparison to Experiment
The importance of accurately accounting for all Coulombic forces in molecular dynamics simulation... more The importance of accurately accounting for all Coulombic forces in molecular dynamics simulations of water at interfaces is demonstrated by comparing the Ewald summation technique with various spherical truncation methods. The increased structure induced by truncation methods at 12 Å leads to water/vapor surface tensions and surface potentials that are respectively 50% and 100% greater than obtained with Ewald. The orientational polarization of water at the lipid/water interface is analyzed within the Marcelja-Radic theory of the hydration force, yielding decay parameters of 2.6 and 1.8 Å for spherical truncation and Ewald, respectively, as compared with 1.7-2.1 Å obtained from experiment. Bulk water transport properties such as the viscosity and diffusion constants differ by as much as 100% between simulations carried out with and without truncation; this may be related to ordering in the neighborhood of the cutoff radius. The diffusion constant calculated from the Ewald simulation is significantly further from experiment than the cutoff result, pointing out the need to reparametrize the TIP3P water model for use with Ewald summation. Appendices describe a method for carrying out the Ewald summation on a distributed memory parallel computer and other computational details relevant when simulating large systems.
Strong scaling of fixed-size classical molecular dynamics to large numbers of nodes is necessary ... more Strong scaling of fixed-size classical molecular dynamics to large numbers of nodes is necessary to extend the simulation time to the scale required to make contact with experimental data and derive biologically relevant insights. This paper describes a novel n-body spatial decomposition and a collective communications technique implemented on both MPI and low level hardware interfaces. Using Blue Matter on Blue Gene/L, we have measured scalability through 16,384 nodes with measured time per time-step of just over 3 milliseconds for a 43,222 atom protein/lipid system. This is equivalent to a simulation rate of 50 nanoseconds per day and represents an unprecedented time-to-solution for biomolecular simulation as well as scaling to fewer than three atoms per node. On a larger 92,224 atom system, we have achieved floating point performance of over 1.5 TeraFlops/second on 16,384 nodes. Scientific results using Blue Matter on prototype BG/L hardware have been published and additional scientific studies are underway which will grow in scale as hardware resources become available.
National center for the design of biomimetic nanoconductors
Nanomedicine-Nanotechnology Biology and Medicine, 2006
Nanomedicine: Nanotechnology, Biology and Medicine , Volume 2, Issue 4, Pages 289-290, December 2... more Nanomedicine: Nanotechnology, Biology and Medicine , Volume 2, Issue 4, Pages 289-290, December 2006, Authors:Eric Jakobsson; Narayan Aluru; Hagan Bayley; Jeff Brinker; Scott Feller; Mark Humayun; David A. LaVan; Gerhard Klimeck; Kevin Leung; Michael McLennan; Steve Plimpton; Umberto Ravaioli; Susan Rempe; Benoit Roux; Marco Saraniti; H. Larry Scott; X Zhu.
Recent NMR experiments and molecular dynamics simulations have indicated that rhodopsin is prefer... more 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.
Proteins: Structure, Function, and Bioinformatics, 2007
The central question in evaluating almost any result from a molecular dynamics simulation is whet... more The central question in evaluating almost any result from a molecular dynamics simulation is whether the calculation has converged. Unfortunately, assessing the ergodicity of a single trajectory is very difficult to do. In this work, we assess the sampling of molecular dynamics simulations of the membrane protein rhodopsin by comparing the results from 26 independent trajectories, each run for 100 ns. By examining principal components and cluster populations, we show that rhodopsin's fluctuations are not well described by 100 ns of dynamics, and that the sampling is not fully converged even for individual loops. The results serve as a reminder of the caution required when interpreting molecular dynamics simulations of macromolecules. Proteins 2007;67:31-40. V V C 2007 Wiley-Liss, Inc.
Proceedings of the National Academy of Sciences, 2006
Rhodopsin, the G protein-coupled receptor primarily responsible for sensing light, is found in an... more Rhodopsin, the G protein-coupled receptor primarily responsible for sensing light, is found in an environment rich in polyunsaturated lipid chains and cholesterol. Biophysical experiments have shown that lipid unsaturation and cholesterol both have significant effects on rhodopsin's stability and function; -3 polyunsaturated chains, such as docosahexaenoic acid (DHA), destabilize rhodopsin and enhance the kinetics of the photocycle, whereas cholesterol has the opposite effect. Here, we use molecular dynamics simulations to investigate the possibility that polyunsaturated chains modulate rhodopsin stability and kinetics via specific direct interactions. By analyzing the results of 26 independent 100-ns simulations of dark-adapted rhodopsin, we found that DHA routinely forms tight associations with the protein in a small number of specific locations qualitatively different from the nonspecific interactions made by saturated chains and cholesterol. Furthermore, the presence of tightly packed DHA molecules tends to weaken the interhelical packing. These results are consistent with recent NMR work, which proposes that rhodopsin binds DHA, and they suggest a molecular rationale for DHA's effects on rhodopsin stability and kinetics.
Small-angle scattering has been employed to study the structure of lipid bilayers in unilamellar ... more Small-angle scattering has been employed to study the structure of lipid bilayers in unilamellar vesicles. This paper evaluates the use of a model approach for the analysis of such data. A long molecular dynamics simulation of a dipalmitoylphosphatidylcholine bilayer in the L ␣ phase provides detailed structural information from which scattering length density profiles and scattering intensity are obtained. A sequence of increasingly realistic models are defined and then fit to the simulated scattering intensity data for values of q that are experimentally accessible. The models are evaluated by how well they fit the intensity data and the structural parameters of the simulation. Although the conventional approach that extracts only the radius of gyration from a Kratky-Porod plot provides a reasonable fit to much of the data, the available experimental q range supports refined models with two independent parameters. Of the many two-parameter models, we propose that particular choices should be inspired by the functional form of the scattering length density profile of simulations. Constraints that limit realistic models to two independent parameters are described in detail. The analysis supports the proposition that reliable results for area/lipid and hydrocarbon thickness can be obtained from small-angle neutron scattering of unilamellar vesicles.
A series of molecular dynamics computer simulations have been carried out on fully hydrated liqui... more A series of molecular dynamics computer simulations have been carried out on fully hydrated liquid crystalline dipalmitoyl phosphatidylcholine (DPPC) bilayers at constant surface areas corresponding to 59.3, 62.9, 65.5, or 68.1 Å 2 /lipid, the range of values suggested by different experiments in different laboratories. Simulated quantities are compared with those from NMR (deuterium order parameters and contribution of molecular tilt to the order parameter), X-ray scattering (D-spacings and detailed density profiles), and partial molar volumes. The results strongly support the value of 62.9 Å 2 /DPPC recently proposed by Nagle et al. (Biophys. J. 1996, 70, 1419 and demonstrate the feasibility of a combined experimental, and simulation-based approach for determining membrane structure.
G protein-coupled receptors (GPCRs) comprise the largest protein family in the human genome, 1 ye... more G protein-coupled receptors (GPCRs) comprise the largest protein family in the human genome, 1 yet rhodopsin is the only member for which there is a high-resolution crystal structure. 2 Understanding GPCR activation is significant due to its role in drug discovery and development. Of ca. 500 molecular sites for current drug therapy, cellular membrane receptors are the largest subgroup and represent 45% of all targets. 3 Here we show how analysis of the rhodopsin chromophore retinal by molecular dynamics (MD) simulations with experimental 2 H NMR data gives insights into the counterion switch mechanism that stabilizes the protonated Schiff base (PSB). Disruption of the retinal PSB is thermodynamically the most important event that characterizes the activated metarhodopsin II (MII) state. 4 Current advances in supercomputing 5 have made it possible to extend MD simulations to the unprecedented time scales described here. The strength of MD simulations is that they explore the structure and fluctuations of membrane proteins with atomic-level resolution. Such models are the culmination of extensive methods development, where force fields with rigorous inclusion of longrange electrostatics are validated by careful comparison with experimental data. 5,6 We performed two simulations of a system composed of one rhodopsin (Rho) molecule embedded in a lipid bilayer of 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (SDPC), 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphoethanolamine (SDPE), and cholesterol (49:50:24) hydrated by 7400 waters, for 43 222 atoms in total. The simulations were run for 1500 and 2000 ns after flash isomerization 6 and corresponded to metarhodopsin I (MI) formation (cf. Supporting Information, SI). The primary difference between the simulations was the initial protonation state of the Glu181 residue.
Rhodopsin Exhibits a Preference for Solvation by Polyunsaturated Docosohexaenoic Acid
Journal of the American Chemical Society, 2003
An all-atom molecular dynamics simulation of rhodopsin in a membrane environment has been carried... more An all-atom molecular dynamics simulation of rhodopsin in a membrane environment has been carried out with lipid composition similar to that of the retinal membrane. The initial conformation of the protein was taken from the X-ray crystallographic structure (1F88), while those of the lipids came from a previous molecular dynamics simulation. During the course of the 12.5 ns simulation, the initially randomly placed lipids adopt an anisotropic solvation structure around the protein. The lipids, having one saturated stearic acid chain and one polyunsaturated docosohexaenoic acid chain with a zwitterionic phosphatidylcholine headgroup, arrange themselves to maximize contact between the polyunsaturated chain and the protein surface. This organization is driven by energetically favorable interactions between the transmembrance helices and the docosohexaenoyl chains that are largely of the van der Waals type. These observations are consistent with various experimental studies on rhodopsin and other G-protein coupled receptors and with the picture of extreme flexibility in polyunsaturated fatty acid chains that has arisen from recent NMR and computational work.
Interpretation of NOESY Cross-Relaxation Rates from Molecular Dynamics Simulation of a Lipid Bilayer
Journal of the American Chemical Society, 1999
Rotational diffusion anisotropy of human ubiquitin from 15N NMR relaxation
Journal of the American Chemical Society, 1995
Rotational Diffusion Anisotropy of Human Ubiquitin from 15N ... Nico Tjandra? Scott E. Feller,&am... more Rotational Diffusion Anisotropy of Human Ubiquitin from 15N ... Nico Tjandra? Scott E. Feller,' Richard W. Pastor,' and Ad Bax*7+ ... Contribution from the Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National ...
Polyunsaturated Fatty Acids in Lipid Bilayers: Intrinsic and Environmental Contributions to Their Unique Physical Properties
Journal of the American Chemical Society, 2002
Polyunsaturated lipids are an essential component of biological membranes, influencing order and ... more 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.
Insufficient supply to the developing brain of docosahexaenoic acid (22:6n3, DHA), or its ω-3 fat... more 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-docosapentaenoylsn-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 C 2 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 mixedchain lipids has lower order, in particular in the middle of the chain near carbons C 10-12, 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.
Rhodopsin is currently the only available atomic-resolution template for understanding biological... more Rhodopsin is currently the only available atomic-resolution template for understanding biological functions of the G protein-coupled receptor (GPCR) family. The structural basis for the phenomenal dark state stability of 11-cis-retinal bound to rhodopsin and its ultrafast photoreaction are active topics of research. In particular, the β-ionone ring of the retinylidene inverse agonist is crucial for the activation mechanism. We analyzed a total of 23 independent, 100 ns all-atom molecular dynamics simulations of rhodopsin embedded in a lipid bilayer in the microcanonical (N,V,E) ensemble. Analysis of intramolecular fluctuations predicts hydrogen-out-of-plane (HOOP) wagging modes of retinal consistent with those found in Raman vibrational spectroscopy. We show that sampling and ergodicity of the ensemble of simulations are crucial for determining the distribution of conformers of retinal bound to rhodopsin. The polyene chain is rigidly locked into a single, twisted conformation, consistent with the function of retinal as an inverse agonist in the dark state. Most surprisingly, the β-ionone ring is mobile within its binding pocket; interactions are non-specific and the cavity is sufficiently large to enable structural heterogeneity. We find that retinal occupies two distinct conformations in the dark state, contrary to most previous assumptions. The β-ionone ring can rotate relative to the polyene chain, thereby populating both positively and negatively twisted 6-s-cis enantiomers. This result, while unexpected, strongly agrees with experimental solid-state 2 H NMR spectra. Correlation analysis identifies the residues most critical to controlling mobility of retinal; we find that Trp265 moves away from the ionone ring prior to any conformational transition. Our findings reinforce how molecular dynamics simulations can challenge conventional assumptions for interpreting experimental data, especially where existing models neglect conformational fluctuations.
Rhodopsin, the membrane protein responsible for dim-light vision, until recently was the only G-p... more Rhodopsin, the membrane protein responsible for dim-light vision, until recently was the only G-protein-coupled receptor (GPCR) with a known crystal structure. As a result, there is enormous interest in studying its structure, dynamics, and function. Here we report the results of three allatom molecular dynamics simulations, each at least 1.5 μs, which predict that substantial changes in internal hydration play a functional role in rhodopsin activation. We confirm with 1 H magic angle spinning NMR that the increased hydration is specific to the metarhodopsin-I intermediate. The internal water molecules interact with several conserved residues, suggesting that changes in internal hydration may be important during the activation of other GPCRs. The results serve to illustrate the synergism of long-time-scale molecular dynamics simulations and NMR in enhancing our understanding of GPCR function.
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Papers by Scott Feller