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  • 1
    Electronic Resource
    Electronic Resource
    Size-Dependent Separation of Colloidal Particles In Two-Dimensional Convective Self-Assembly (1995)
    s.l. : American Chemical Society
    Langmuir 11 (1995), S. 2975-2978 
    Details
    ISSN: 1520-5827
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/la00008a021
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  • 2
    Electronic Resource
    Electronic Resource
    Model study of two-dimensional protein aggregates in the nucleation stage of crystallization (1993)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 99 (1993), S. 9156-9162 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A two-dimensional (2D) aggregation model was introduced to investigate the nucleation stage of protein crystallization. The constituent protein molecules were positioned at the lattice points of a 2D square. Four specific interaction sites were assigned to the fringe of each molecule, and through these sites the molecules are bound to each other with an effective interaction. Protein molecules were allowed to translate in the vicinity of the lattice points and to rotate within a limited angle. The partition function was calculated for aggregates consisting of 2–16 molecules. Exposed bonds, which connected exposed molecules to the rest part of the aggregates, were the weakest. The peripheral bonds, which connected molecules at the periphery of the aggregates, were weaker than the buried bonds, which were located inside the aggregates. Increasing the size of the aggregate caused both the buried and peripheral bonds to become stronger due to correlation between fluctuating bonds. The more compact an aggregate was, the more stable it was. The free energy was determined by the size, the compactness of the aggregate, and the correlation between bonds. The free-energy gain that results by generating aggregates from individual free molecules was calculated, yielding a critical size, which discriminated growing aggregates from dissociating aggregates.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.465529
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  • 3
    Electronic Resource
    Electronic Resource
    New implementation of and the modeling by the extended simulated annealing process to structures of T4 lysozyme mutants at the 86th residue (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 476-488 
    Details
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The extended simulated annealing process (ESAP) is a useful method for modeling the partial structure of proteins [J. Higo et al., Biopolymers, 32, 33 (1992)]. In ESAP, a protein molecule is divided into two parts: small, flexible fragments constituting the concerned partial structure, and the remaining part, for which the structure is kept rigid during the simulation. We have improved the program of ESAP so that it can be adapted to general macromolecules. Any sidechain on the rigid part can be set to rotate. Soft repulsion between van der Waals spheres is introduced to avoid conformational trapping into local minima. This improved program was tested for modeling structural changes caused by eight kinds of amino acid mutation at the 86th residue in T4 lysozyme. For each mutant we obtained a model structure that was close to the X-ray structure. The root mean square (rms) deviations from the X-ray structure were 0.3 to 0.8 Å for all heavy atoms and about 0.2 Å for the main-chain atoms. We also modeled the structure of an Ile mutant, for which the X-ray structure has not yet been reported. ESAP can be used to model structural changes due to a single residue mutation in proteins. © 1996 by John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Stability of two-dimensional crystalline aggregates of a protein studied by molecular dynamics (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1278-1290 
    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: Two-dimensional protein (ferritin) aggregates with a square lattice symmetry, which were formed within a thin liquid layer on a mercury surface, were studied by molecular dynamics (MD) simulation. For the simulation, the ferritin molecule was modeled by an assembly of 49 spheres, and the intermolecular interactions were given by simple formulae. During the simulation, molecules were confined within a layer, which corresponds to the thin liquid layer. An annealing MD simulation was done starting from a random molecular configuration within the layer, and aggregates with the square lattice symmetry were also obtained. To study the stability of aggregates, dissociation processes of the aggregates were analyzed using MD simulations at room temperature. Interactions between the nearest-neighbor molecules were regarded as bonds. Mean bond energies and correlation coefficients between the bond energies were calculated from the MD trajectories. A decay profile according to the dissociation was obtained, yielding a dissociation rate constant. Buried bonds were stronger than peripheral bonds. The larger the aggregate size, the stronger the bond for each of the buried and peripheral bonds. A simple theoretical account, which is applicable to a general bonded network, was introduced to analyze the dynamics of the aggregates. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151109
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  • 5
    Electronic Resource
    Electronic Resource
    Application of a high-performance, special-purpose computer, GRAPE-2A, to molecular dynamics (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1372-1376 
    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: 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
    URL: http://dx.doi.org/10.1002/jcc.540151207
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  • 6
    Electronic Resource
    Electronic Resource
    Two-component multicanonical Monte Carlo method for effective conformation sampling (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 2086-2092 
    Details
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A multicanonical algorithm, which is one of the most powerful conformation-sampling methods to obtain the density of states described by a component (i.e., the total potential energy), was extended to obtain the density of states described by two components. This method was tested on a simplified model for bacteriorhodopsin, which is a membrane protein consisting of seven helices. Two kinds of simulation were done by adopting different sets of two components: in one set, the components were the site-specific and the non-site-specific energies between helices; and, in the other set, the total potential energy and the end-to-end distance (distance between the first and the seventh helices) were used. In both simulations, a wide and flat probability distribution was obtained, showing the efficiency of the two-component method. A variety of applications may be possible by effectively selecting the two components, such as the van der Waals and electrostatic energies, the intermolecular and intramolecular interactions, the solute-solute and solute-solvent interactions, or an energy and a reaction coordinate.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 2086-2092, 1997
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Development of an extended simulated annealing method: Application to the modeling of complementary determining regions of immunoglobulins (1992)
    New York : Wiley-Blackwell
    Biopolymers 32 (1992), S. 33-43 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An extended simulated annealing process (ESAP) has been developed in order to obtain an ensemble of conformations of a peptide segment from a protein fluctuating at a given temperature. The annealing process was performed with a fast Monte Carlo method using the scaled collective variables developed by Noguti and Gō. The system was divided into two parts: one consists of one or more peptide segments and is flexible around the main-chain and side-chain torsional angles; the other represents the rest of the molecule and was maintained fixed at the atomic positions determined by x-ray experiments. The target function included the nonbonding atomic interactions and a distance function to anchor the N and C terminal ends of each segment to the fixed part. Three systems of complementary determining regions (CDR) of antibodies were tested and compared to x-ray data: L2 loop (7 residues) of the light chain of α-type Bence-Jones protein, H1 and the H2 loops (14 residues) of McPC603, and H1 and H2 loops (12 residues) of HyHEL-5. Each state of CDR conformations was characterized at room temperature by the average of their coordinates (average conformation) and the internal energy. With a limited number of annealing processes (10), starting from the extended conformation, we have obtained states with conformations close to the observed x-ray structures, from 1.1 to 1.7 Å root mean square deviation (rmsd) of main-chain atoms depending on the system. These states were identical or within 0.25 Å rmsd of those of lowest internal energy. For unknown CDR structures the criteria of lowest internal energies from ESAP can be used to predict hypervariable loop structures in antibodies with an accuracy comparable to other methods.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360320106
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