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Protein Engineering vol. 8 no. 1 pp. 5-12, 1995
© 1995 Oxford University Press

RESEARCH-ARTICLE

L3 loop-mediated mechanisms of pore closing in porin: a molecular dynamics perturbation approach

C.M. Soares, J. Björkstén and O. Tapia1

Department of Physical Chemistry, Uppsala University Box 532, S-751 21 Uppsala, Sweden

1To whom correspondence should be addressed

L3 loop-mediated mechanisms for pore closing in porin are investigated with molecular dynamics simulation, using an approach that can be related to the phenomenon of voltage gating. Voltage gating is seen as a perturbation of the electrostatic screening inside the porin pore where, by the influence of the potential gradient, water and counter-ion distribution can be slightly displaced from their equilibrium distribution. This is simulated by perturbing the screening electrostatics of ionizable groups inside the pore. Under these conditions, a localized conformational change takes place, involving 12 (Ile102–Alall3) out of the 44 residues of the loop. The pore is reduced to a sixth of its open state size. The conformational change can be achieved with a small perturbation and it is reversible once the perturbation is switched off (relaxation process). Other types of behaviour predominating at higher simulation temperatures are found for the loop, involving an extra conformational change in the Thr92–Asp96 loop segment. This conformational change completely closes the pore, but is not reversible under the simulation conditions. Both zones involved in the conformational changes contain or overlap the zones which were described previously, using other techniques, to be the most flexible zones of the loop.

Keywords: L3 loop/mechanism of porin closure/molecular dynamics simulation/reversibility/voltage gating

Received April 18, 1994; revised June 23, 1994; accepted September 20, 1994.


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