Study On The Assembly Mechanism Of FtsZ Filament By Molecular Modeling Methods

FtsZ(Filamentous temperature sensitive mutant Z)is an ancient tubulin-like guanosine triphosphatase,which can coalesce into a ring-shaped pattern called Z ring.Z ring plays pivotal roles in dividing a cell into two daughter cells.In this thesis,we used a multi-scale computational strategy that combined all-atom molecular dynamics(MD)simulations and coarse-grained models to explore FtsZ's conformational motions and the mechanism of cooperative assembly.The main contents are as follows:1.All-atom molecular dynamics simulations of the assembly dynamics of FtsZ trimers under the regulation of nucleotides.The results demonstrate that the intrinsic structure dynamic of the top end interface in the filament is more considerable than that of the bottom end,and reveal that the top end of FtsZ filament to be the kinetic minus end and the bottom end to be the plus end.Guanosine triphosphate(GTP)hydrolysis can regulate the flexibility of the secondary structure at the subunit-subunit interface and the loop regions,and promote the structural rearrangement of the subunits.Free energy landscape analysis reveals that there are multiple sub-state conformations for both subunits and dimers.Further studies reveal the cooperative movement mechanism within and between subunits under the regulation of nucleotides.The results provide the molecular basis for the cooperative assembly of FtsZ.2.The analysis of the details of subunit-subunit and subunit-nucleotide interactions.We obtained three types of dimer conformations through the analysis of the last 100 ns MD trajectories.Binding free energy calculations show that the three type dimers' subunit-subunit binding free energy are-45.25 kcal/mol,-39.74 kcal/mol and-50.24 kcal/mol.And the three type dimers' subunit-nucleotide binding free energy are-45.34 kcal/mol,-3.68 kcal/mol and-15.82 kcal/mol.The results of the binding free energy reveal one of the possible assembly pathways composed of the three type dimer conformations.Moreover,we identified the key residues involved in nucleotide regulation and monomer-monomer interactions through free energy decomposition at the residue level.The results reveal the energy basis of FtsZ assembly.3.Study of correlated motions in FtsZ based on coarse-grained models.First,the slow modes of four subunit structures were calculated by gaussian network model(GNM).The results reveal that all four structures share common hinge axes and the amplitudes of motion modes are associated with the subunit structures.Then,we performed anisotropic network model(ANM)on a straight single-strand filament containing 31 subunits.We found that motion modes 1,10 and 16 exhibit large-scaled functional motions,and motion modes 172,189 and 259 exhibit highly cooperative motions between the subdomains and between the subunits.Finally,the analysis of cross-correlation maps reveal strong inter-domains and inter-subunits cooperative motions in the dimer and trimer structures,while the correlation within subunit is very limited.These findings are in line with previously experimental results,revealing that polymerization enhances FtsZ's assembly cooperativity.