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  • 1
    Electronic Resource
    Electronic Resource
    Significant conformational changes in an antigenic carbohydrate epitope upon binding to a monoclonal antibody (1990)
    s.l. : American Chemical Society
    Biochemistry 29 (1990), S. 10906-10911 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00501a007
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  • 2
    Electronic Resource
    Electronic Resource
    Brownian dynamics simulation of a lipid chain in a membrane bilayer (1988)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 89 (1988), S. 1112-1127 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A Brownian dynamics simulation of a lipid chain is used to model the motional properties of a dipalmitoyl phosphatidylcholine bilayer. The effects of the bilayer environment on the chain are represented by a mean field derived from an extension of the Marcelja model. The simulation was run 44 million steps, the equivalent of approximately 0.66 μs for a viscosity of 2.2 cp. The results are compared with those of a 30 million step simulation of the chain in the absence of the mean field. Deuterium order parameters for the methylene groups along the chain and the average chain length calculated from the mean field trajectory are shown to converge to the experimentally determined values for DPPC with an appropriate choice of parameters. An analysis of the torsional dynamics of the chain, including transition rates and kink probabilities, is carried out. It is demonstrated that kink formation is sometimes, though not always, concerted. A comparison of the membrane and free chain simulations implies that the internal dynamics of a hydrocarbon chain in a bilayer is very similar to that of a neat alkane. Thus, the significant limits on the orientational freedom of the chain, as expected by the nonzero order parameters, are induced by a potential that has only a small effect on the local motions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.455218
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  • 3
    Electronic Resource
    Electronic Resource
    A simulation based model of NMR T1 relaxation in lipid bilayer vesicles (1988)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 89 (1988), S. 1128-1140 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The results of the Brownian dynamics simulation of a hydrocarbon chain in a membrane bilayer described in the preceding paper are used to analyze the 13C NMR T1 relaxation in lipid bilayer vesicles. The analysis shows that the frequency dependence of the relaxation does not arise from gauche–trans isomerization or from axial rotation of the entire lipid molecule. However, a model in which fast axial rotation (D(parallel)≈2×1010 s−1) and slow noncollective diffusive director fluctuations (D⊥≈1–2×108 s−1) are superimposed on the internal motions quantitatively accounts for both the magnitude and frequency dependence of the T1 data. An effective viscosity for the interior of the bilayer in the range of 1 cp, and a director order parameter of 0.5–0.7 are required to fit the NMR data. Collective effects do not appear necessary for explaining the NMR T1 data in vesicles, although they may be important for multilamellar dispersions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.455219
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  • 4
    Electronic Resource
    Electronic Resource
    Molecular dynamics simulations of water wires in a lipid bilayer and water/octane model systems (2002)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 116 (2002), S. 2663-2664 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A series of classical molecular dynamics simulations of a water wire in a DPPC bilayer yielded lifetimes τ of up to 90 ps, with τ¯=37±8 ps (not including a significant fraction wires that broke during equilibration). This is sufficiently long to conduct protons across the bilayer through a quantum mechanical hopping mechanism, similar to proton conduction in ice. Lifetimes of wires in the octane region of a water/octane/water "sandwich" were qualitatively similar (τ¯=36±3 ps) though wires were rarely lost during equilibration. Hence, the utility of the water/octane system as a membrane surrogate depends on the application.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1434952
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  • 5
    Electronic Resource
    Electronic Resource
    Molecular dynamics simulations of gel (LβI) phase lipid bilayers in constant pressure and constant surface area ensembles (2000)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 112 (2000), S. 4822-4832 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The results of a series of molecular dynamics simulations of the gel state of a dipalmitoylphosphatidylcholine bilayer at 293 K are described. The simulations, ranging from 40 ps to 2.5 ns, show clearly that: a flexible cell geometry is essential during equilibration; Ewald summation of electrostatics is superior to spherical cutoff methods; water exchange with the carbonyl group of chain 2 takes place on the ns time scale, while there is almost no hydration of chain 1. There is overall good agreement (D-spacing, chain tilt, fraction gauche, and area compressibility modulus) with experiment, though the surface area per lipid is slightly underestimated. The randomization of torsion 1 of chain 2 from exclusively gauche minus (as specified in the initial condition modeled from the crystal structure of a related lipid) to a mixture of g+/g− over the course of approximately 2 ns is a critical feature of the study. The torsional equilibration proceeded steadily when simulating at constant surface tension, but was effectively quenched by simulation at constant area. The associated presence of conformational degeneracy of this torsion, and conformational disorder in the upper region of chain 2, is most likely associated with the seemingly anomalous infrared (IR) results for gauche bonds in the upper region of the chains. It may also be a characteristic of the gel phase, and be related to the long time required for the gel to subgel transition.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.481085
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  • 6
    Electronic Resource
    Electronic Resource
    Harmonic analysis of large systems. III. Comparison with molecular dynamics (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 16 (1995), S. 1554-1566 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Atomic motions in bovine pancreatic trypsin inhibitor (BPTI), derived from molecular dynamics, harmonic analysis, and quasiharmonic analysis, are compared when a single protein model, energy parameters, and environment are employed. Molecular dynamics (MD) was carried out for 2 nanoseconds. An average structure was determined from the last nanosecond of the MD simulation, when no major structural changes were observed. This structure was used for several harmonic analysis calculations as well as for a reference structure for the quasiharmonic analysis, for both full basis and reduced basis sets. In contrast to the harmonic analysis results, the quasiharmonic reduced basis calculation using a spherical harmonics reduced basis provided good agreement with the full basis calculation, suggesting that when anharmonic effects are considered, BPTI can behave as a homogeneous object. An extensive analysis of the normal modes from a diverse set of 201 minimized MD simulation frames was performed. On only the sub-picosecond time scale were energy minima revisited after a transition to another state. This analysis shows that the dynamics average structure is not representative of the simulation frames in terms of energy and vibrational frequencies. For this model of BPTI, 42% of the motion (mean-squared fluctuation) can be attributed to harmonic limit behavior. A spectral analysis of the correlation function of deformation for a particular normal mode or quasiharmonic mode can be used to determine the time scales of motions which correspond to harmonic vibration, large-scale drift, or sharp transitions between local substrates. © 1995 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540161211
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  • 7
    Electronic Resource
    Electronic Resource
    Frictional models for stochastic simulations of proteins (1988)
    New York : Wiley-Blackwell
    Biopolymers 27 (1988), S. 1001-1014 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: As a first step toward a systematic parametrization of friction constants of atoms in proteins, a model in which frictional resistance is placed explicitly on each atom accessible to solvent is used to calculate overall translational and rotational diffusion constants. It is found that these quantities are relatively insensitive to the precise value of the atomic friction constant, as long as the effective hydrodynamic radius of the surface atoms is approximately 1 Å. However, if only protein atoms are included in the calculation, no reasonable range atomic of radii can reproduce the experimental translational diffusion constant to better than 20% for lysozyme and 5% for ribonuclease. When a hydration shell of approximately 70% coverage for lysozyme and 20% for ribonuclease is included, there is quantitative agreement with experimental results. The sensitivity of peptide diffusion to levels of hydration is also investigated; it is found that for glycine, two bound waters are required to provide agreement with experiment. These findings imply that the effects of solvent damping will be underestimated in stochastic simulations of proteins and peptides unless bound waters are taken into account.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360270609
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  • 8
    Electronic Resource
    Electronic Resource
    Conformational states of a TT mismatch from molecular dynamics simulation of duplex d(CGCGATTCGCG) (1992)
    New York : Wiley-Blackwell
    Biopolymers 32 (1992), S. 783-794 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The TT mismatch region in duplex d(CGCGATTCGCG) was studied using a 500-ps molecular dynamics (MD) simulation in water, and a series of 1-ps MD simulations and energy minimizations in vacuum. The DNA maintained its duplex structure, although the mismatch region showed significantly higher flexibility than the GC regions. The predominant conformation in the 500-ps MD simulation involved an average -42° propeller twist between T6 and T′6, and a -22° buckle between A5 and T′7, One hydrogen bond was formed between T6 and T′6, and another between T6 and the O2 of T′7 with both Watson-Crick hydrogen bonds between A5 and T′7 remaining intact. The minimizations resulted in conformations with the equivalent hydrogen-bonding pattern, as well as ones with “wobble pair” hydrogen bonds between T6 and T′6. However, the wobble pair conformation was found to be unstable in the water simulation.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360320707
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  • 9
    Electronic Resource
    Electronic Resource
    Molecular dynamics simulation and nmr study of a blood group H trisaccharide (1994)
    New York : Wiley-Blackwell
    Biopolymers 34 (1994), S. 1079-1088 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular dynamics simulations in vacuum and solution have been carried out on 2′-α-L-fucosyllactitol, a model for blood group H in conjunction with two-dimensional nmr measurements on the same compound. Three independent starting conformations for the dynamics were chosen from low energy conformations obtained by a φ/ψ grid search. Nine 5 ns vacuum simulations of the trisaccharide were performed, employing three different ways to treat electrostatic interactions for each starting conformation: distance-dependent dielectric with ε = r, constant dielectric with ε = 1, or constant dielectric with ε = 80. In vacuum, transitions of φ and ψ for the α-L-Fuc-(1 → 2)-β-D-Gal element occur in a cooperative manner. The virtual distance obtained for H1 in fucose to H2 in galactose from nuclear Overhauser effect spectroscopy experiments agree with one of the conformations of the trisaccharide in one of the three 100 ps aqueous simulations (φ/ψ ca. -100°/150°), indicating this may be a dominant solution conformation. The rms fluctuations of the φ- and ψ-dihedral angles were ∼ 10° for a conformational state, both in the vacuum and the aqueous simulations. For the simulations in vacuum, the agreement with experimental NOE data is reasonable when a constant dielectric of 1 is used (major conformers having φ/ψ ca. -100°/150° and -140°/100°), whereas the agreement was poor with a constant dielectric of 80. Translational diffusion coefficients calculated from the simulation of the oligosaccharides were 0.12-0.18 × 10-5 cm2/s and from nmr measurements 0.27 × 10-5 cm2/s. © 1994 John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360340811
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  • 10
    Electronic Resource
    Electronic Resource
    A method for characterizing transition concertedness from polymer dynamics computer simulations (1995)
    New York : Wiley-Blackwell
    Biopolymers 35 (1995), S. 31-46 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A statistical method based on classifying the transitions among a set of dihedral angles within an “energy transfer window” is developed, and used to analyze Brownian (BD) and molecular dynamics (MD) simulations of the acyl chains in a lipid bilayer, and MD of neat hexadecane. It is shown for the BD simulation that when a transition of the dihedral angle in the center of the chain occurs, a transition of a particular next nearest neighbor (or angle 2-apart) will follow concertedly with a probability of approximately 0.10 within a lime window of approximately 3 ps. The MD bilayer simulations, which are based on a more flexible model of the hydrocarbon chains, yield corresponding concerted transition probabilities of approximately 0.083 and window sizes of 1-2 ps. An analysis of angles 4-apart yields concerted transition probabilities of 0.03 and 0.04 for the BD and MD bilayer simulations, respectively, and window sizes close to those of the corresponding 2-apart cases. Statistical hypothesis testing very strongly rejects the assertion that these follower transitions are occurring at random. Similar analysis reveals marginal or no evidence of concertedness between 1-apart (nearest neighbor) and between 3-apart dihedral angle transitions. The pattern of concertedness for hexadecane is qualitatively similar to that of the lipid chains, although concertedness is somewhat stronger for the 3-apart transitions and somewhat weaker for those 4-apart. Finally, it is suggested that the diffusion of small solute molecules in membranes is better facilitated by non concerted transitions, which are associated with relatively large displacements of the chains, than by concerted transitions, which do little to change the chain shape. © 1995 John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360350105
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