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A novel method to calculate transition pathways between two known protein conformations is presented. It is based on a molecular dynamics simulation starting from one conformational state as initial structure and using the other for a directing constraint. The method is exemplified with the T ++ R transition of insulin. The most striking difference between these conformational states is that in T the 8 N-terminal residues of the B chain are arranged as an extended strand whereas in R they are forming a helix. Both the transition from T to R and from R to T were simulated. The method proves capable of finding a continuous pathway for each direction which are moderately different. The refolding processes are illustrated by a series of transient structures and pairs of a, t angles selected from the time course of the nimutations. In the T + R direction the helix is formed in the tast third of the transition, while in the R + T direction it is preserved during more than half of the simutation period. The results are discussed in comparison with those of an atternative method recently apptied to the T -. R transition of insulin which is based on targeted energy minimisation.

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Due to the progress of density functional theory (DFT) accurate computations of vibrational spectra of isolated molecules have become a standard task in computational chemistry. This is not yet the case for solution spectra. To contribute to the exploration of corresponding computational procedures, here we suggest a more efficient variant of the so-called instantaneous normal-mode analysis (INMA). This variant applies conventional molecular dynamics (MD) simulations, which are based on nonpolarizable molecular mechanics (MM) force fields, to the rapid generation of a large ensemble of different solvation shells for a solute molecule. Short hybrid simulations, in which the solute is treated by DFT and the aqueous solvent by MM, start from snapshots of the MM solute−solvent MD trajectory and yield a set of statistically independent hydration shells partially adjusted to the DFT/MM force field. Within INMA, these shells are kept fixed at their 300 K structures, line spectra are calculated from the DFT/MM Hessians of the solute, and its inhomogeneously broadened solution spectra are derived by second-order statistics. As our test application we have selected the phosphate ions HPO4 2- and H2PO4 - because sizable solvation effects are expected for the IR spectra of these strongly polarizable ions. The widths, intensities, and spectral positions of the calculated bands are compared with experimental IR spectra recorded by us for the purpose of checking the computational procedures. These comparisons provide insights into the merits and limitations of the available DFT/MM approach to the prediction of IR spectra in the condensed phase.

Protonated networks of internal water molecules appear to be involved in proton transfer in various integral membrane proteins. High-resolution x-ray studies of protein crystals at low temperature deliver mean positions of most internal waters, but only limited information about fluctuations within such H-bonded networks formed by water and residues. The question arises as to how water molecules behave inside and on the surface of a fluctuating membrane protein under more physiological conditions. Therefore, as an example, long-time molecular dynamics simulations of bacteriorhodopsin were performed with explicit membrane/water environment. Based on a recent x-ray model the bacteriorhodopsin trimer was inserted in a fully solvated 16 x 16 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)-bilayer patch, resulting in a system of approximately 84,000 atoms. Unrestrained molecular dynamics calculations of 5 ns were performed using the GROMACS package and force field. Mean water densities were computed to describe the anisotropic distribution of internal water molecules. In the whole protein two larger areas of higher water density are identified. They are located between the central proton binding site, the Schiff base, and the extracellular proton release site. Separated by Arg-82 these water clusters could provide a proton release pathway in a Grotthus-like mechanism as indicated by a continuum absorbance change observed during the photocycle by time-resolved Fourier transform infrared spectroscopy. Residues are identified which are H-bonded to the water clusters and are therefore facilitating proton conduction. Their influence on proton transfer via the H-bonded network as indicated by the continuum absorbance change is predicted. This may explain why several site-directed mutations alter the proton release kinetics without a direct involvement in proton transfer.