Multiple Molecular Dynamics For The Binding Mode Of Wild Type And Mutant Transthyretin With Glabridin

In the body's tissues and organs,transthyrein(TTR)due to mutations or environmental factors,tetramer stability decreases,and depolymerize into monomers,causing the formation of large aggregates and deposits,which can cause a variety of amyloid diseases,including familial amyloid polyneuropathy(FAP),familial amyloid cardiomyopathy(FAC),senile systemic amyloidosis(SSA).Therefore,it is of great importance to find small molecule inhibitors that can stabilize TTR tetramers for the prevention and treatment of related amyloid disorders.Our research group has discovered five generations of a family with familial amyloid polyneuropathy with V30 A TTR mutations.In the search for small molecule compound that can stabilize V30 A TTR,it is found that light licorice with isopentenyl may stabilize TTR tetramer by binding TTR protein T4.To further investigate its mechanism,this thesis uses molecular biology experiments with a variety of molecular dynamics simulation to explore the difference between the stability of wild type and mutant V30 A TTR tetramer,and the resulting conformation between subunits variety.In our study,in order to compare the wild type and mutant protein conformation,we proceed on the basis of molecular biology experiments on conventional Molecular Dynamics(MD),Constant p H Molecular Dynamics(Cp HMD),and steered Molecular Dynamics(SMD).The results are listed as follows:Firstly,we investigated the effect of Glabridin(Glabrid)on the protein stability of recombinant wild type TTR,major mutant TTR and serum TTR.It was found that Glab could not only inhibit the formation of amyloid fibrils,but also stabilize the four level structure of r TTR protein in both wild type and mutant.Meanwhile,Glab can selectively bind the TTR protein in human serum to stabilize its tetramer structure.Secondly,in order to further explore the effect of Glab on the structural stability of mutant V30 A and wild type(WT)TTR,we performed several molecular dynamics simulations to verify the above experimental results:1 The conventional dynamics simulations was used to explore the binding mode of WT and V30 A mutant of Glab,and the results showed that the binding Glab to V30 A mutant resulted in a closer contact between AC subunit and BD subunit,and Glab binding in the V30 A TTR make the four dimers stability.2 In order to explore the optimum p H of the wild type and V30 A TTR,we performed PH molecular dynamics simulations,and the results showed that the p Ka of His88 in the C chain of the wild type is 4.92,while in the V30 A TTR is 5.36,causing the spiral motion of EF helix to move close to the EF loop region in the V30 A mutant.The calculation of binding free energy has shown that AC subunit of V30 A TTR was lower,which indicates that the combination of the two subunits of V30 A TTR is more compact,and four dimer structure is more stable.3 The dissociation pathway and the main escape channel of Glab by WT TTR and V30 A TTR were further studied by steered dynamics simulation.The results showed that the channel radius of V30 A is smaller,and the force of Glab is greater when it passes through the channel,which further verifies that the Glab and V30 A TTR are more tightly bound.Our results provide a theoretical clue for the future research of TTR,which is of great significance for the treatment of amyloidosis.