COMPUTER-SIMULATIONS OF THE OMPF PORIN FROM THE OUTER-MEMBRANE OF ESCHERICHIA-COLI

Molecular dynamics simulations were used to study the structure and dy namics of the Escherichia coli OmpF porin, which is composed of three identical 16-stranded beta-barrels. Simulations of the full trimer in the absence of water and the membrane led to significant contraction o f the channel in the interior of each beta-barrel. With very weak harm onic constraints (0.005 kcal/mol Angstrom(2)/atom) applied to the main -chain C-alpha atoms of the beta-barrel, the structure was stabilized without alteration of the average fluctuations. The resulting distribu tion of the fluctuations (small for beta-strands, large for loops and turns) is in good agreement with the x-ray B factors. Dynamic cross-co rrelation functions showed the importance of coupling between the loop motions and barrel flexibility. This was confirmed by the application of constraints corresponding to the observed temperature factors to t he barrel C-alpha atoms. With these constraints, the beta-barrel fluct uations were much smaller than the experimental values because of the intrinsic restrictions on the atomic motions, and the loop motions wer e reduced significantly. This result indicates that considerable care is required in introducing constraints to keep proteins close to the e xperimental structure during simulations, as has been done in several recent studies, Loop 3, which is thought to be important in gating the pore, undergoes a displacement that shifts it away from the x-ray str ucture. Analysis shows that this arises from the breakdown of a hydrog en bond network, which appears to result more from the absence of solv ent than from the use of standard ionization states for the side chain s of certain beta-barrel residues.