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Molecular dynamics simulations

Molecular dynamic simulations and structural alphabet

In order to capture the dynamic nature of enzymes, the static data derived from the X-ray structures will be complemented by the data derived from molecular dynamics (MD) simulations to reveal the signatures of communication pathways. MD simulations will be conducted on several representative structures from PNPs (hexameric and trimeric) and AdSS (dimeric). The MD trajectories will be analysed by GSATools package [22] to find possible allosteric hot-spots and communication pathways. MD simulations will provide dynamic information on the residues that play a key role in transferring information from one part of the enzyme to the other. MD trajectories will be analysed in search of the correlations in residue parameters during the MD trajectories, thus revealing otherwise undetectable communication channels. This information will be compared with the information previously present in the database of related enzymes. It is expected that strong correlations should exist in static (X-ray) and dynamic (MD) data in the database, confirming the importance of certain regions and in the enzymes. Special attention in formulation of residue parameters that are going to be used will be paid to differentiation between intra-monomer vs. inter-monomer interfaces, as they are undoubtedly playing quite different roles in oligomeric enzymes. Oligomeric enzymes in the vast majority of cases possess internal symmetry, yet this symmetry is almost always only approximate in the crystal structures. It is still unclear whether this is a result of crystal packing interactions, or does it have some more fundamental significance. Recent findings on some enzymes suggest that this asymmetry is indeed far from accidental [48,49]. Having the residues in a relational database will make possible the comparison of symmetry between all residue local environments and fast identification of those parts that violate the symmetry. Whether this is due to crystal packing influence, or if this is a genuine feature of certain residues, will be immediately apparent as all the information is contained in the database. Furthermore, the connection between this symmetry violations and MD derived data will also be available at the same time, supporting the importance of certain movements and conformational changes. All this will yield new information on mechanism that underpins the information transfer between the monomers in this particular class of oligomeric enzymes. Along the way new programmatic methods will be established that will possibly be applicable to other oligomeric proteins as well.