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  • 1
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 0887-3585
    Keywords: phospholipase A2 ; n-dodecylphosphorylcholine ; complex ; inhibitor ; X-ray crystal analysis ; molecular dynamics simulation ; interaction ; calcium-binding ; catalytic network ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of n-dodecylphosphorylcholine (n-C12PC)-bovine pancreas phospholipase A2 (PLA2) complex provided the following structural.characteristics: (1) the dodecyl chain of n-C12PC was located at the PLA2 N -terminal helical region by hydrophobic interactions, which corresponds to the binding pocket of 2-acyl fatty acid chain (β-chain) of the substrate phospholipid, (2) the region from Lys-53 to Lys-56 creates a cholinereceiving pocket of n-C12PC and (3) the N-termillal group of Ala-1 shifts significantly toward the Tyr-52 OH group by the binding of the n-C12PC inhibitor. Since the accuracy of the X-ray analysis (R = 0.275 at 2.3 Å resolution) was insufficient to establish these important X-ray insights, the complex structure was further investigated through the molecular dynamics (M D) simulation, assuming a system in aqueous solution at 310K. The M D simulation covering 176 ps showed that the structural characteristics observed by X-ray analysis are intrinsic and also stable in the dynamic state. Furthermore, the M D simulation made clear that the PLA2 binding pocket is large enough to permit the conformational fluctuation of the n-C12PC hydrocarbon chain. © 1994 Wiley-Liss, Inc. © 1994 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 0887-3585
    Keywords: hardware ; molecular dynamics ; simulation ; special-purpose computer ; supercomputing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulations have been extensively used in research of proteins. Since these simulations are quite computer intensive, their acceleration is of main interest of the research. In molecular dynamics simulations, almost all computing time is consumed in calculating the forces between particles, e.g., Coulomb and van der Waals forces. We have designed and built GRAPE-2A (GRAvity PipE 2A), a special-purpose computer for use in simulations of classical many-body systems. GRAPE-2A calculates forces exerted on a particle from the other particles. GRAPE-2A can calculate force of an arbitrary functional form of a central force. The host computer, which is connected to GRAPE-2A through the VME bus, performs other calculations such as time integration. The peak speed of GRAPE-2A is 180 Mflops. We can also stimulate systems with periodic boundary conditions by the Ewald method, using GRAPE-2A and another special-purpose computer, WINE (Wave space INtegrator for the Ewald method). © 1994 Wiley-Liss, Inc.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1573-5176
    Keywords: algae ; Anti-HSV substance ; Dunaliella ; Lyngbya sp. ; microalgae ; anti-virus ; Herpes simplex virus ; commercial microorganisms
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Among 106 microalgae tested, the cytopathic effect (CPE) upon Vero cells of herpes simplex virus, Type 1 (HSV-1) was inhibited by four methanol extracts of Dunaliella bioculata C-523, D. primolecta C-525, Lyngbya sp. M-9 and Lyngbya aerugineo-coerulea M-12. The green alga, D. primolecta, had the highest anti HSV-1 activity, since 10 μg mL-1 of extract from this alga completely inhibited the CPE. This activity was similar to that of acyclovir at the same concentration. We compared anti-viral activities against adeno virus, herpes simplex virus-2 (HSV-2), Japanese Encephalitis and Polio viruses. Only the CPE of HSV-2 was inhibited. Thus, the factor was specific against HSV. The antiviral activity was apparently excited during HSV adsorption and invasion of the cells. We optimized the conditions for anti HSV-1 activity by prolonging the exposure of HSV-1 to the extract. After 2 h, the CPE of even a high titer of HSV-1 (106 TCID50/0.1 mL) was completely inactivated. By use of various chromatographic techniques, three green substances having anti-HSV activity were purified from the algal mass of D. primolecta, and 5 μg mL-1 of this purified substances completely inhibited the CPE. From the analysis of NMR and MS, the chemical structures of the active substances were identified as pheophorbide-like compounds.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 1573-5176
    Keywords: algae ; antibiotics ; methicillin resistance ; fatty acids ; linolenic acid ; phytoplankton ; Chlorococcum ; Dunaliella primolecta ; Staphylococcus aureus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Methanol extracts fromChlorococcum strain HS-101 andDunaliella primolecta strongly inhibited the growth of a strain of methicillin-resistantStaphylococcus aureus (MRSA), which is causing serious problems in Japanese hospitals. So that the anti-MRSA substance(s) could be purified and identified, the growth medium was improved for antibiotic production. When the two strains were cultured in their improved media, antibiotic production byChlorococcum strain HS-101 was 1.8-fold that in the standard BG-11 medium, and production byD. primolecta was 2.3-fold. The activity pattern of fractions eluted by silica-gel or gel-permeation chromatography suggested that both strains produced two antibiotic substances. Identification of the purified substances by NMR and GC-MS showed that one of the active substances in both strains wasα-linolenic acid. Ten fatty acids from other sources were tested, and it was found that unsaturated fatty acids had antibiotic activity against MRSA, with the highest activity that of γ-linolenic acid.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A linear relationship in each of the torsion angle pairs, α-β, β-∊, ∊-ζ, and α-γ, has been found by applying a statistical method based on the concept of circular variates to backbone torsion angle data of helical in yeast tTNAPhe. A series of helical dimer models generated with these relationships have been found to be stereochemically acceptable, and the models also indicate that the backbone unit in the RNA helix is geometrically capable of an oscillatory motion with the distance of about 3.4 Å between adjacent bases. The motion of the backbone unit is analogous to that of a helical spring. The adjacent bases, because of being attached to the backbone, oscillate in a manner similar to the oscillatory dimer model proposed by Davis and Tinoco [Davis, R. C. & Tinoco, I., Jr. (1968) Biopolymers 6, 223-242]. Here, the oscillation of the backbone unit in the RNA helix is discussed in terms of two geometrical quantities: the torsion (τ) and curvature (κ) of the helix. On these lines, a stereochemical model of RNA strand separation is proposed.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Special-purpose parallel machines that are plugged into a workstation to accelerate molecular dynamics (MD) simulations are attracting a considerable amount of interest. These machines comprise scalable homogeneous multiprocessors for calculating nonbonded forces (Coulombic and van der Waals forces), which consume more than 99% of the central processing unit (CPU) time in standard MD simulations. Each processor element in the machine has a pipeline architecture to calculate the total nonbonded force exerted on a particle by all of the other particles using information regarding the coordinates, the electric charge, and the species of each particle broadcast by the host computer. The processor then sends the calculated force back to the host computer. This article addresses the precision of the calculated nonbonded forces in the design of a processor LSI with minimal complexity. The precision of the arithmetic inside the processor that is required to calculate forces for MD simulations using Verlet's procedure was critically evaluated. Forward and backward error analysis, coupled with numerical MD experiments on one-dimensional systems, was performed, and the following results were obtained: (1) Each element of the position vector which the processor receives from the host computer should have a precision of at least 25 bits; and (2) the pairwise forces should be calculated using floating point numbers with at least 29 bits of mantissa in the processor. Calculation of a pairwise force, which involves second-order polynomial interpolation using a table-driven algorithm, requires a key which contains a duplicate of at least 11 most significant bits of mantissa of the squared pairwise distance. The final result was that (3) the total force that acts on a particle, which is obtained by summing the forces exerted by all of the other particles, should be calculated using an accumulator that has a mantissa of at least 48 bits. © 1995 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The special-purpose computer GRAPE-2A accelerates the calculation of pairwise interactions in many-body systems. This computer is a back-end processor connected to a host computer through a Versa Module Europe (VME) bus. GRAPE-2A receives coordinates and other physical data for particles from the host and then calculates the pairwise interactions. The host then integrates an equation of motion by using these interactions. We did molecular dynamics simulations for two systems of liquid water: System 1 (1000 molecules), and System 2 (1728 molecules). The time spent for one step of molecular dynamics was 3.9 s (System l), and 10.2 s (System 2). The larger the molecular system, the higher the performance. The speed of GRAPE-2A did not depend on the formula describing the pairwise interaction. The cost performance was about 20 times better than that of the fastest workstations available today, and GRAPE-2A cost only $22,000. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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