Bacteria and biological systems respond to external perturbations through
several different mechanisms. The origins of external stress are diverse:
chemical, biological and physical.
The sensing mechanisms of external forces by cells have recently been
identified. Membrane proteins forming pores across the membrane are the
basis of these response mechanisms: they can open and close in
correspondence to external stimuli such as touch, sound, gravity,
osmolarity variations etc. Mechanosensitive channels of Large Conductance
(MscL) are the best characterized membrane proteins playing a fundamental
role in cell defense. MscL defines a channel within the cell membrane,
which opens and closes, favoring or disfavoring, respectively, the passage
of effluents inside the cell. Their three dimensional structure, solved by
D. Rees (Science 1998), is reported in Figure 1. The protein is
constituted by repetitive units and is in its closed state. The
fundamental question to understand how cells interact with the environment
is: what is the opening mechanism of MscL? We can answer this question by
computational simulations using the molecular dynamics techniques and the
direct application of force to the protein in a realistic environment.
Molecular dynamics is a technique allowing the observation of the time
evolution of microscopic systems, yielding an atomic detail picture of the
system evolution. Using suitable parameters, the interactions within the
system can be defined and the evolution can be followed using Newton's
laws of motion.
We have thus built a model system consisting in the closed
state protein, a model of the cell membrane and of the water solvent
(Figure 2). The system was subjected to stretching forces acting on the
membrane, with the aim to investigate the initial stages of the channel
opening mechanism. The analysis of various simulations allowed us to
obtain a representation of the opening mechanism, in which, because of the
presence of external forces, two of the external helices open up, creating
room for positioning of one of the internal helices to move in. The final
result is the enlargement of the pore (Figure 3) and the efflux of water
from one side to the other of the membrane (Figure 4).
This work, which required the intensive use of parallel computing
facilities and computing time, clarifies of the channel opening mechanism,
and moreover allows us to define the way biological systems react to
external stimuli. Future developments of this work include the use of
these models to build new nanostructures able to respond selectively to
external mechanical forces, and for the realization of new mutants with a
different activity from the native one. The research has been carried out
in a collaboration between ICRM-CNR and the MD group at the university of
Groningen, and it has been made possible thanks to funding from CNR and
the European Union.
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