Aggregation of Influenza A Virus Nuclear Export Protein.

Influenza A virus nuclear export protein (NEP) plays an important role in the viral life cycle. Recombinant NEP proteins containing (His)6-tag at either N- or C-terminus were obtained by heterologous expression in Escherichia coli cells and their high propensity for aggregation was demonstrated. Dynamic light scattering technique was used to study the kinetics and properties of NEP aggregation in solutions under different conditions (pH, ionic strength, presence of low-molecular-weight additives and organic solvents). Using atomic force microscopy, the predominance of spherical aggregates in all examined NEP preparations was shown, with some amyloid-like structures being observed in the case of NEP-C protein. A number of structure prediction programs were used to identify aggregation-prone regions in the NEP structure. All-atom molecular dynamics simulations indicate a high rate of NEP molecule aggregation and reveal the regions preferentially involved in the intermolecular contacts that are located at the edges of the rod-like protein molecule. Our results suggest that NEP aggregation is determined by different types of interactions and represents an intrinsic property of the protein that appears to be necessary for its functioning in vivo.

A hypothetical hierarchical mechanism of the self-assembly of the Escherichia coli RNA polymerase σ(70) subunit.

Diverse morphology of aggregates of amyloidogenic proteins has been attracting much attention in the last few years, and there is still no complete understanding of the relationships between various types of aggregates. In this work, we propose the model, which universally explains the formation of morphologically different (wormlike and rodlike) aggregates on the example of a σ(70) subunit of RNA polymerase, which has been recently shown to form amyloid fibrils. Aggregates were studied using AFM in solution and depolarized dynamic light scattering. The obtained results demonstrate comparably low Young's moduli of the wormlike structures (7.8-12.3 MPa) indicating less structured aggregation of monomeric proteins than that typical for ß-sheet formation. To shed light on the molecular interaction of the protein during the aggregation, early stages of fibrillization of the σ(70) subunit were modeled using all-atom molecular dynamics. Simulations have shown that the σ(70) subunit is able to form quasi-symmetric extended dimers, which may further interact with each other and grow linearly. The proposed general model explains different pathways of σ(70) subunit aggregation and may be valid for other amyloid proteins.

[Investigation of the Dependence of Escherichia coli RNA Polymerase σ70-Subunit Structure on Ionic Strength by Molecular Dynamics Simulation Method].

The σ70-subunit of E. coli RNA polymerase (a small protein, being a part of RNA holoenzyme, and responsible for initiation of transcription of constitutive genes) is modeled at different ionic strengths. Two variants of the location of C-end domain 4 are obtained. At low ionic strength domain 4 interacts with the region of high negative charge 190-210 AK within NCR domain. At high ionic strength this region was screened and domain 4 was free and set away from domain NCR. We suppose that this leads to the increase in polymerization rate. Simulation data do not confirm any hypothesis about a self-inhibition mechanism.

[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.