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J Mol Biol. 1995 Oct 6;252(5):672-708.

Acid and thermal denaturation of barnase investigated by molecular dynamics simulations.

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Department of Chemistry Harvard University, Cambridge, MA 02138, USA.


The transition in barnase from the native state to a partially unfolded conformation has been studied by molecular dynamics simulations with explicit water molecules at 360 K and low pH(450 ps), and at 600 K and neutral pH (three simulations of 120, 250 and 200 ps each). The use of several simulations provides evidence that the results are not sensitive to initial conditions. To mimic low pH conditions, the acidic sidechains in barnase were neutralized and the two histidine residues were doubly protonated. Runs at 300 K showed that the solvated structures at low pH (300 ps) and neutral pH (310 ps) are very similar. The main structural differences involved the acidic residues, histidine residues, and the beta-turn connecting strands 4 and 5. When the temperature is raised to 360 K at low pH and to 600 K at neutral pH the barnase molecule begins to unfold. The molecule rapidly expands (Rg changes from 13.9 A to 15.3 A in 450 ps at 360 K and from 13.7 A to between 15.1 and 15.5 A in 120 ps at 600 K). However, the expansion is not uniform. In all the simulations, the chain termini, loops and the N-terminal parts of the main alpha-helix (helix 1) show a continuous and progressive unfolding. An essential step in the denaturation process is that the major alpha-helix (helix 1) separates from the beta-sheet; this is coupled to the exposure of the principal hydrophobic core, many of whose non-polar side chains become solvated by hydrogen-bonded water molecules. The barnase-water interaction energy improves during unfolding at the expense of the barnase self-energy. The deterioration of the intramolecular van der Waals energy suggests that the rupture of the tight packing during the initial unfolding phase contributes to the energy barrier of the denaturation process. The mutationally well-analyzed Asp8-Arg110-Asp12 double salt-bridge on the barnase surface is found to be marginally stable in the folded form in the simulations. A Poisson-Boltzmann calculation indicates that the salt-bridge is unstable; this is probably due to an overestimate of the solvation energy. A detailed analysis of the main hydrophobic core reveals that increase in solvent-accessible surface area and penetration of water molecules are simultaneous in the high-temperature simulation; at lower temperatures there is significant cavity formation and the entrance of the water molecules is somewhat delayed. The cavities occur in the neighborhood of the hydrophobic sidechains; the region formed by the sidechains of Val10, Leu14, Leu20, Tyr24, Ala74, Ile76 and Tyr90 is involved. The loosening of the core packing is coupled to an increase in the number of dihedral transitions.(ABSTRACT TRUNCATED AT 400 WORDS).

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