Biomedical subjects

Richard W Pastor

Publications and source records attributed to Richard W Pastor.

13 recordsLinked to original sources

PubMed2006

Dynamical motions of lipids and a finite size effect in simulations of bilayers.

Molecular dynamics (MD) simulations of dipalmitoylphosphatidylcholine bilayers composed of 72 and 288 lipids are used to examine system size dependence on dynamical properties associated with the particle mesh Ewald (PME) treatment of electrostatic interactions. The lateral diffusion constant Dl is 2.92 x 10(-7) and 0.95 x 10(-7) cm2/s for 72 and 288 lipids, respectively. This dramatic finite size effect originates from the correlation length of lipid diffusion, which extends to next-nearest neighbors in the 288 lipid system. Consequently, diffusional events in smaller systems can propagate across the boundaries of the periodic box. The internal dynamics of lipids calculated from the PME simulations are independent of the system size. Specifically, reorientational correlation functions for the slowly relaxing phosphorus-glycerol hydrogen, phosphorus-nitrogen vectors, and more rapidly relaxing CH vectors in the aliphatic chains are equivalent for the 72 and 288 lipid simulations. A third MD simulation of a bilayer with 72 lipids using spherical force-shift electrostatic cutoffs resulted in interdigitated chains, thereby rendering this cutoff method inappropriate.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2006

Simulation-based methods for interpreting x-ray data from lipid bilayers.

The fully hydrated liquid crystalline phase of the dimyristoylphosphatidycholine lipid bilayer at 30 degrees C was simulated using molecular dynamics with the CHARMM potential for five surface areas per lipid (A) in the range 55-65 A(2) that brackets the previously determined experimental area 60.6 A(2). The results of these simulations are used to develop a new hybrid zero-baseline structural model, denoted H2, for the electron density profile, rho(z), for the purpose of interpreting x-ray diffraction data. H2 and also the older hybrid baseline model were tested by fitting to partial information from the simulation and various constraints, both of which correspond to those available experimentally. The A, rho(z), and F(q) obtained from the models agree with those calculated directly from simulation at each of the five areas, thereby validating this use of the models. The new H2 was then applied to experimental dimyristoylphosphatidycholine data; it yields A = 60.6 +/- 0.5 A(2), in agreement with the earlier estimate obtained using the hybrid baseline model. The electron density profiles also compare well, despite considerable differences in the functional forms of the two models. Overall, the simulated rho(z) at A = 60.7 A(2) agrees well with experiment, demonstrating the accuracy of the CHARMM lipid force field; small discrepancies indicate targets for improvements. Lastly, a simulation-based model-free approach for obtaining A is proposed. It is based on interpolating the area that minimizes the difference between the experimental F(q) and simulated F(q) evaluated for a range of surface areas. This approach is independent of structural models and could be used to determine structural properties of bilayers with different lipids, cholesterol, and peptides.

Computer Simulation↗

PubMed2005

Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme.

The recently developed CMAP correction to the CHARMM22 force field (C22) is evaluated from 25 ns molecular dynamics simulations on hen lysozyme. Substantial deviations from experimental backbone root mean-square fluctuations and N-H NMR order parameters obtained in the C22 trajectories (especially in the loops) are eliminated by the CMAP correction. Thus, the C22/CMAP force field yields improved dynamical and structural properties of proteins in molecular dynamics simulations.

Animals↗

PubMed2005

Molecular dynamics simulations of the influenza hemagglutinin fusion peptide in micelles and bilayers: conformational analysis of peptide and lipids.

Molecular dynamics simulations of the influenza hemagglutinin fusion peptide in two differently sized dodecylphosphocholine micelles and a palmitoyl oleoyl phosphatidylcholine bilayer were generated to analyze the influence of the environment. Four independent trajectories (5 ns each for the bilayer, and 2 ns each for the micelles) were generated for each system. The peptide lies at the surface of the micelles, while its N-terminal region inserts deeply in the bilayer. This leads to a substantial increase of the solvation and rigidity of the peptide in micelles as compared to the bilayer. The average structures, nevertheless, are similar in all three systems and agree reasonably with micelle-based NMR structures. When in the bilayer, the peptide increases the chain gauche population and area of adjacent lipids in the same binding leaflet, while it has the opposite effect for the nearby lipids of the other leaflet. These changes, which occur spontaneously to fill voids and defects, cause a decrease in the thickness of the membrane in the neighborhood of the peptide. They would be expected to promote positive curvature, as consistent with the formation of the convex bulge, or "nipple", in the initial stage of membrane fusion. An extension of the classical surfactant theory of Israelachvili based on shapes is proposed to introduce the concept of a "dynamically induced shape" of the membrane lipids by the peptide.

Computer Simulation↗

PubMed2005

A molecular dynamics study of the response of lipid bilayers and monolayers to trehalose.

Surface tensions evaluated from molecular dynamics simulations of fully hydrated dipalmitoylphosphatidylcholine bilayers and monolayers at surface areas/lipid of 54, 64, and 80 A2 are uniformly lowered 4-8 dyn/cm upon addition of trehalose in a 1:2 trehalose/lipid ratio. Constant surface tension simulations of bilayers yield the complementary result: an increase in surface area consistent with the surface pressure-surface area (pi-A) isotherms. Hydrogen bonding by trehalose, replacement of waters in the headgroup region, and modulation of the dipole potential are all similar in bilayers and monolayers at the same surface area. These results strongly support the assumption that experimental measurements on the interactions of surface active components such as trehalose with monolayers can yield quantitative insight to their effects on bilayers. The simulations also indicate that the 20-30 dyn/cm difference in surface tension of the bilayer leaflet and monolayer arises from differences in the chain regions, not the headgroup/water interfaces.

Computer Simulation↗

PubMed2005

Adjacent gauche stabilization in linear alkanes: implications for polymer models and conformational analysis.

High-level ab initio quantum mechanical calculations are used to study various gauche conformational energies of n-pentane to n-decane. The destabilizing "pentane effect" (adjacent gauche states of opposite sign) for alkanes is confirmed, but the energies were found to depend slightly on chain length. In contrast, introducing an adjacent gauche of the same sign requires only 0.22-0.37 kcal/mol, approximately half of the single gauche state energy. This adjacent gauche stabilization should be taken into account when formulating or analyzing rotational isomeric models, carrying out conformational analysis, and developing force fields for alkanes, lipids, and related polymers.

Alkanes↗

PubMed2005

An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer.

Energies of 119 conformations of normal alkanes from butane to heptane were calculated at approximately the CCSD(T)/cc-pVQZ level. Energies of gauche (g) conformers relative to trans (t) decrease as chain length increases. In what is termed the "positive pentane effect", adjacent gauche conformers of the same sign are stabilized compared to nonadjacent conformers; e.g., for hexane the energies of tgt, tgg, and gtg are 0.600, 0.930, and 1.18 kcal/mol, respectively. Torsional terms in the CHARMM27 (C27) force field were fit to the calculated QM energies to yield a revised potential, C27r. Molecular dynamics simulations of normal alkanes (heptane, decane, tridecane, and pentadecane) with C27r yield higher populations of gauche states, increased transition rates, and improved agreement with experiment as compared to C27. In addition, C27r simulations of a hydrated DPPC lipid bilayer yield improved agreement with the experimental NMR deuterium order parameters for the aliphatic chain ends.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2004

Discriminating the helical forms of peptides by NMR and molecular dynamics simulation.

The HNCO NMR pulse sequence was applied to three selectively labeled (15)N and (13)C isotopic homologues of the peptide Ac-WAAAH(AAARA)(3)A-NH(2) to probe directly for hydrogen bonds between residues 8 and 11 (characteristic of a 3(10)-helix), 8 and 12 (alpha-helix), and 8 and 13 (pi-helix). The experiments demonstrate conclusively, and in agreement with circular dichroism studies, that the center of the peptide is alpha-helical; there is no discernible 3(10)- or pi-helix at these specific positions. Molecular dynamics simulations of the preceding peptide and Ac-(AAAAK)(3)A-NH(2) in water using the potential energy parameter set CHARMM22/CMAP correctly yield an alpha-helix, in contrast to simulations with the set CHARMM22, which result in a pi-helix.

Alanine↗

PubMed2003

Application of NMR, molecular simulation, and hydrodynamics to conformational analysis of trisaccharides.

The preferred conformations and conformational flexibilities of the trisaccharides alpha-D-Glcp-(1-->2)-beta-D-Glcp-(1-->3)-alpha-D-Glcp-OMe (I) and alpha-D-Glcp-(1-->3)[beta-D-Glcp-(1-->4)]-alpha-D-Glcp-OMe (II) in aqueous solution were determined using nuclear magnetic resonance (NMR) spectroscopy, molecular dynamics (MD) and Langevin dynamics (LD) simulations, and hydrodynamics calculations. Both trisaccharides have a vicinal substitution pattern in which long range (nonsequential) interactions may play an important role. LD simulation at 600 K indicated that the all-syn conformation predominated, though other conformations were apparent. NOE data and MD and LD simulations at 298 K all indicated that trisaccharide I is a single all-syn conformer in solution. Given that previous studies showed evidence of anti-conformers in beta-D-Glcp-(1-->2)-beta-D-Glcp-(1-->3)-alpha-D-Glcp-OMe, this result provides an example of how changing the anomeric configuration of one residue from beta to alpha can make an oligosaccharide more rigid. Discrepancies in inter-ring distances obtained by experiment and by simulation of the all-syn conformer suggest the presence of an anti-psi conformation at the beta-(1-->4)-linkage for II. A combined analysis of measured and calculated translational diffusion constants and (13)C T(1) relaxation times yield order parameters of 0.9 for each trisaccharide. This implies that any interconversion among conformations is significantly slower than tumbling. Anisotropies of approximately 1.6 and 1.3 calculated for I and II, respectively, are consistent with the observed relatively flat T(1) profiles because the tumbling is not in the motional narrowing regime.

Carbohydrate Conformation↗

PubMed2003

Sample size considerations for establishing clinical bioequivalence of allergen formulations.

Bioequivalence of formulations must be established by proving that the differences between the formulations are within a specified interval according to Equation 1, the Interval Hypothesis. Explicit estimates of sample size determined from Equation 8 and listed in Table 1 are qualitatively larger than those that would be determined from Equation 2, the Hypothesis of No Difference. Equation 8 was derived from the TOST procedure; other valid methods should yield comparable results. In any context, this discussion has illustrated that the failure to demonstrate a difference is not sufficient to demonstrate equivalence, and that a properly powered equivalence study of allergen formulations will generally demand many more than four study subjects.

Allergens↗

PubMed2002

Micelle-bound conformation of a hairpin-forming peptide: combined NMR and molecular dynamics study.

A peptide fragment from a protein hairpin turn region was modified by addition of isoleucine residues to both ends to enhance binding to lipid micelles; the resulting peptide (I(1)-I(2)-C(3)-N(4)-N(5)-P(6)-H(7)-I(8)-I(9)) contains the core sequence I-C-N-N-P-H from an antibody-binding region of hemagglutinin A. Nuclear magnetic resonance (NMR) diffusion measurements indicated partial binding (43-65%) of the peptide to micelles of n-octylglucoside and significantly stronger binding (85%) to dodecylphosphocholine (DPC) micelles. Simulated annealing and conformational analysis using nuclear Overhauser enhancement restraints revealed a type I or III hairpin turn between residues N(5) and I(8) of the DPC-bound peptide. Amide exchange experiments support the possibility that a hydrogen bond forms between N(5) and I(8), stabilizing the turn. In contrast, no discernable structure was observed for the peptide in aqueous solution by either NMR or circular dichroism. Molecular dynamics simulations of DPC micelles and peptide-micelle complexes suggested that the peptide lies flat on the micelle surface and showed rapid rearrangement of the lipids to accommodate the bound peptide. According to a search performed using the basic local alignment search tool (BLAST), the sequences N-P-H-I and N-P-H-V are present as hairpin turns in eight of the nine proteins whose crystal structures were available. The addition of isoleucine residues and the use of lipid micelles to stabilize hairpin conformations equivalent to those found in proteins generates new possibilities for reproducing biologically important hairpin turns from short, linear peptides.

Amino Acid Motifs↗

PubMed2002

Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions.

We demonstrate the ease and utility of simulating heterogeneous interfacial systems with P2(1) and Pc periodic boundary conditions which allow, for example, lipids in a membrane to switch leaflets. In preliminary tests, P2(1) was shown to yield equivalent results to P1 in simulations of bulk water, a water/vacuum interface, and pure DPPC bilayers with an equal number of lipids per leaflet; equivalence of Pc and P1 was also demonstrated for the former two systems. P2(1) was further tested in simulations involving the spreading of an octane film on water, and equilibration of a DPPC bilayer from an initial condition containing different numbers of lipids in the two leaflets. Lastly, a simulation in P2(1) of a DOPC/melittin membrane showed significant passage of lipids to the melittin-containing leaflet from the initial distribution, and lends insight into the condensation of lipids by melittin.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2002

Lipid bilayers, NMR relaxation, and computer simulations.

Brownian and molecular dynamics simulations of a lipid bilayer are described, and the calculated frequency-dependent (13)C NMR T(1) relaxation times are compared with experiment. A consistent model emerges. Through fast internal motions, individual lipids average themselves into relatively cylindrical shapes on the 100 ps time scale and "wobble" in a cone-like potential on the nanosecond time scale. These motions take place in a highly fluid environment, much like a liquid alkane. Lateral diffusion of the lipids is on a significantly longer time scale because of restrictions at the bilayer/water interface, not because the interior of the bilayer is highly viscous.

Computer Simulation↗