[Application of molecular dynamics simulation to the interpretation of atomic force microscopy data].

A new approach to the interpretation and refining of experimental atomic force microscopy (AFM) data has been developed, which is based on the comparison with the simulated static imaging mode operations output. We have applied the approach to atomic force microscopy studies of lisozyme. During this test, we have obtained distinct precise AFM images of lysozyme monomers adsorbed from a clear aqueous solution onto a mica wafer. The images were compared with the corresponding images obtained by molecular dynamics simulations. We performed two steps of simulations to reproduce the environment and processes of the AFM study of lysozyme. The first step was intended to obtain the adsorbed structure of lysozyme; it was performed using the NAMD molecular dynamics software. At this step, the simulated environment of lysozyme was a water box, and the mica wafer was manually modeled according to its crystal structure. At the second step, we applied molecular mechanics calculations to reproduce tip interactions with the lysozyme on the surface. As a result, we have obtained the height as a function of horizontal coordinates. The function was compared with the AFM real experimental surface height function for adsorbed lysozyme. The results of this comparison showed the excellent equivalence in the shape of experimental and modeled lysozyme structures and a significant difference in their sizes. The investigation of this difference led us to the conclusion that more detailed simulations of AFM imaging are needed to reach a better correspondence between the experiment and the model. We consider our approach to be applicable to refine the AFM images of proteins by a visual comparison with the results of simulation based on precise X-ray structures of these proteins. The first results of the application of this approach provide sufficient information on how to improve the accuracy in further applications.

[Can the local energy minimization refine the PDB structures of different resolution universally?].

The local energy minimization was statistically validated as the refinement strategy for PDB structure pairs of different resolution. Thirteen pairs of structures with the only difference in resolution were extracted from PDB, and the structures of 11 identical proteins obtained by different X-ray diffraction techniques were represented. The distribution of RMSD value was calculated for these pairs before and after the local energy minimization of each structure. The MMFF94 field was used for energy calculations, and the quasi-Newton method was used for local energy minimization. By comparison of these two RMSD distributions, the local energy minimization was proved to statistically increase the structural differences in pairs so that it cannot be used for refinement purposes. To explore the prospects of complex refinement strategies based on energy minimization, randomized structures were obtained by moving the initial PDB structures as far as the minimized structures had been moved in a multidimensional space of atomic coordinates. For these randomized structures, the RMSD distribution was calculated and compared with that for minimized structures. The significant differences in their mean values proved the energy surface of the protein to have only few minima near the conformations of different resolution obtained by X-ray diffraction for PDB. Some other results obtained by exploring the energy surface near these conformations are also presented. These results are expected to be very useful for the development of new protein refinement strategies based on energy minimization.