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  • 1995-1999  (2)
  • 1995  (2)
  • Selectivity filters  (1)
  • computer simulation  (1)
  • 1
    ISSN: 1432-1424
    Keywords: Water pore sizes ; Water channels ; Reflection coefficients ; Selectivity filters ; Proximal kidney tubule ; Single file transport
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Proximal straight tubules (PST) were dissected from rabbit kidneys, held by crimping pipettes in a chamber and bathed in a buffered isosmotic (295 mOsm/kg) solution containing 200 mm mannitol (MBS). Changes in tubule diameter were monitored on line with an inverted microscope, TV camera and image processor. The PST were then challenged for 20 sec with MBS made 35 mOsm/kg hyperosmotic by addition of either NaCl, KCl, mannitol (M), glycerol (G), ethylene glycol (E), glycine (g), urea (U), acetamide (A) or formamide (F). With NaCl, KCl, M, G, E, g, U, and A, tubules shrunk osmometrically within 0.5 sec and remained shrunk for as long as 20 sec without recovering their original volume (sometimes A showed some recovery). PST barely shrunk with F and quickly recovered their original volume. The permeability coefficients were 0 μm/sec (NaCl, M, g, E and U), 1 μm/sec (A), 84 μm/sec (F) and 0.02 μm/sec (G). The reflection coefficients σ = 1.0 (NaCl, KCl, M, G, E, g and U), 0.95 (A) and 0.62 (F). Similar σ values were obtained by substituting 200 mOsm/kg M in MBS by either NaCl, KCl, G, E, g, U, a or F. The olive oil/water partition coefficients are 5 (M), 15 (U), 85 (A) and 75 (F) (all x10−5). Thus, part of F permeates the cell membrane through the lipid bilayer. The probing molecules van der Waals diameters are 7.4×8.2×12.0 (M), 3.6×5.2×5.4 (U), 3.8×5.2 ×5.4 (A) and (3.4×4.5×5.4 (F) Å. We conclude that only F clearly permeates the water channel (WCH). Water molecules must single file within the WCH. After subtraction of the bilayer permeability of the probes, we estimate for the WCH selectivity filter cross-section a diameter of 4.2–4.7 Å (if it is circular) and 3.6×4.2 Å (if it is rectangular). But if the oxygens facing the WCH lumen H bond with the molecules crossing the WCH, the WCH selectivity filter would be 3.3–3.8 Å (circular) and 3.6×4.0 Å (rectangular).
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1573-9171
    Keywords: hydration ; computer simulation ; Monte Carlo ; potential functions ; intermolecular interactions ; nucleic acids
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Three systems of potential functions (PF) which are used in simulations of hydration of bioorganic molecules have been compared: Poltev and Malenkov (PM), Weiner and Kollman (WK) (used in the widespread AMBER program), and OPLS (optimized potentials for liquid simulations) of Jorgensen (J). The values of interaction energies of individual water molecules with single molecules of nucleic bases calculatedvia PM potentials are in somewhat better accord with mass spectrometric data than those calculatedvia WK PF. OPLS give much smaller energy values for all compounds considered; therefore they were not used in further computations. Monte Carlo simulation of hydration of 9-methyladenine, 1-methyluracil, and 1-methylthymine in systems with 300 water molecules and periodic boundary conditions have been performed. Simulations with PM potentials give better agreement with the experimental data on hydration energies than those with WK PF that allows to prefer PM PF for simulation of hydration of nucleic acids.
    Type of Medium: Electronic Resource
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