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  • 1
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 110 (1988), S. 3446-3452 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1520-6882
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Analytical chemistry 58 (1986), S. 1611-1617 
    ISSN: 1520-6882
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Journal of comparative physiology 78 (1972), S. 121-137 
    ISSN: 1432-1351
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary 1. Fossorial rodent burrows exhibit relatively stable environmental conditions with regard to light, y. However, vastly different concentrations of CO2 and O2 are encountered in these burrows. Field observations of shallow pocket gopher burrows (Thomomys bottae) reveal CO2 concentrations to 3.8%, and O2 concentrations from 15.5% to 20.5% (Darden, 1970). Values similar to these have been reported for another genus of gopher,Geomys, by Kennerly (1964) and McNab (1966). 2. The sensitivity of the respiratory control mechanisms of the pocket gopher (T. bottae) O2 was tested and expressed as percent increase in minute volume as a function of the level of inspired CO2 (2% to 8%). The CO3 response curve is markedves for other terrestrial and diving mammals (Figs. 1 and 3). 3. Except for a reduction in slope, the respiratory response to CO2 of gophers can be described as similar to that recorded for humans. Carbon dioxide stimulates both increased ventilatory frequency and tidal volume in a near linear fashion. Individual difference in CO2 sensitivity among gophers was demonstrated (Table 2). 4. The level of alveolar CO2 (P A,CO2) in anesthetized pocket gophers is not significantly altered from values normally observed in man at sea level (Table 4). The reduced ventilatory response is due to a reduction in the slope of the response curve. The possible causes for the decreased sensitivity are discussed. 5. Comparisons of predicted and observed values of tidal volume (V T), rate of ventilation (f), minute volume ( $$\dot V_{\min } $$ ) and respiratory dead space (V D) were made (Table 3). Of these,V D and f and consequently $$\dot V_{\min } $$ were smaller than expected. The reduced value ofV D offsets the low $$\dot V_{\min } $$ and thus alveolar ventilation ( $$\dot V_A $$ ) is only slightly lower than expected. The possible biological significance of the alterations in f andV D are discussed.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 0948-5023
    Keywords: HIV-1 reverse transcriptase ; Minor groove binding track ; Particle-mesh Ewald
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract We have built a molecular dynamics model for human immunodeficiency virus (HIV-1) reverse transcriptase (RT) complexed with a 19/18-mer template/primer by combining the structural information of a low resolution crystal structure of a HIV-1 RT/DNA complex (1hmi) with that of a high resolution crystal structure of unliganded HIV-1 RT (1rtj). The process involved slow forcing of the α-carbons of 1rtj onto those of 1hmi using constrained MD simulations, while immersing the protein in aqueous solution. A similar technique was used to build the bent all-atom DNA duplex, which was then docked into the modeled protein. The resulting model complex was refined using molecular dynamics simulation with the Particle-mesh Ewald method employed to accommodate long-range electrostatic interactions. New parameters of the Amber force field that affect DNA twist are tested and largely validated. The model has been used successfully to explain the results of vertical scanning mutagenesis of residue 266 (Trp266). Recently, the low resolution crystal structure of the HIV-1 RT/DNA complex has been refined to a 2.8 Å resolution (2hmi) and a crystal structure of a HIV-1/RT/dTTP ternary complex has been determined at 3.2 Å resolution (1rtd). A detailed structural comparison of the prior model structure and the two experimental structures becomes possible. Overall, the three structures share many similarities. The root mean square deviations of the α-carbons for the individual subdomains among the three structures are within the same ranges. The secondary structure assignments in the three structures are nearly identical. Key protein-DNA contacts such as those in the region of the primer grip are also similar in the three structures.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 114 (2001), S. 6578-6591 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We present an O(N) multigrid-based method for the efficient calculation of the long-range electrostatic forces needed for biomolecular simulations, that is suitable for implementation on massively parallel architectures. Along general lines, the method consists of: (i) a charge assignment scheme, which both interpolates and smoothly assigns the charges onto a grid; (ii) the solution of Poisson's equation on the grid via multigrid methods; and (iii) the back interpolation of the forces and energy from the grid to the particle space. Careful approaches for the charge assignment and the force interpolation, and a Hermitian approximation of Poisson's equation on the grid allow for the generation of the high-accuracy solutions required for high-quality molecular dynamics simulations. Parallel versions of the method scale linearly with the number of particles for a fixed number of processors, and with the number of processors, for a fixed number of particles. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 3830-3834 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We report two 1 ns molecular dynamic (MD) simulations on Z-DNA for which the long-range Coulomb terms are explicitly evaluated by the Particle–Mesh–Ewald method [J. Chem. Phys. 98, 10089 (1993)]. The starting structures were based on the 1 A(ring) resolution crystallographic structure of Gessner et al. [J. Bio. Chem. 264, 7921 (1989)]. The average simulation structures of the DNA compare well to the crystallographic structure; the root-mean-square position deviations for the DNA double-strand heavy atoms are approximately 0.5 A(ring). Watson–Crick hydrogen bonding patterns are preserved without invoking constraints. These results emphasize the importance of proper treatment of the long-range forces for highly ionic systems. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 155-179 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Current computer simulations of biomolecules typically make use of classical molecular dynamics methods, as a very large number (tens to hundreds of thousands) of atoms are involved over timescales of many nanoseconds. The methodology for treating short-range bonded and van der Waals interactions has matured. However, long-range electrostatic interactions still represent a bottleneck in simulations. In this article, we introduce the basic issues for an accurate representation of the relevant electrostatic interactions. In spite of the huge computational time demanded by most biomolecular systems, it is no longer necessary to resort to uncontrolled approximations such as the use of cutoffs. In particular, we discuss the Ewald summation methods, the fast particle mesh methods, and the fast multipole methods. We also review recent efforts to understand the role of boundary conditions in systems with long-range interactions, and conclude with a short perspective on future trends.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1072-8368
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Proteins that bind with high affinity to specific DNA sequences often do so through hydrogen bonding and electrostatic interactions between the DNA major groove and defined protein structural elements, such as helix-turn-helix motifs, β-ribbon recognition elements and Zn-binding domains1. ...
    Type of Medium: Electronic Resource
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