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Structure and mechanism of SLT70, a bacterial muramidase

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  • Biology
  • Chemistry
  • Medicine


Biophysical Journal Volume 71 August 1996 632-647 Proton Transport across Transient Single-File Water Pores in a Lipid Membrane Studied by Molecular Dynamics Simulations S. J. Marrink,* F. Jahnig,* and H. J. C. Berendsen# *Abteilung Membranbiochemie, Max-Planck-lnstitut fur Biologie, D-72076 Tubingen, Germany, and #Biophysical Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands ABSTRACT To test the hypothesis that water pores in a lipid membrane mediate the proton transport, molecular dynamic simulations of a phospholipid membrane, in which the formation of a water pore is induced, are reported. The probability density of such a pore in the membrane was obtained from the free energy of formation of the pore, which was computed from the average force needed to constrain the pore in the membrane. It was found that the free energy of a single file of water molecules spanning the bilayer is 108(±+10) kJ/mol. From unconstrained molecular dynamic simulations it was further deduced that the nature of the pore is very transient, with a mean lifetime of a few picoseconds. The orientations of water molecules within the pore were also studied, and the spontaneous translocation of a turning defect was observed. The combined data allowed a permeability coefficient for proton permeation across the membrane to be computed, assuming that a suitable orientation of the water molecules in the pore allows protons to permeate the membrane relatively fast by means of a wirelike conductance mechanism. The computed value fits the experimental data only if it is assumed that the entry of the proton into the pore is not rate limiting. INTRODUCTION The presence of ion gradients is of vital importance to the functioning of most living cells. For instance, ion gradients are required as energy sources, for signal transmission, as a way to orient proteins, and as tool to induce phase separa- tions and fusions. Therefore, it is of key importance for the cell to be able accurately to regulate the transport

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