Molecular simulation investigation on the interaction between barrier-to-autointegration factor dimer or its XXXX mutant and LEM domain of @entity28464 .

@entity36942 @entity7097 @entity28464 @entity71732 @entity74 @entity367 @entity71731 @entity2574
The interaction between barrier-to-autointegration factor dimer ( @entity71731 ) and LEM domain of @entity28464 (Em(LEM)) was studied by molecular simulation methods. Nonspecific fragment of double-strand DNA molecule was docked with each chain of @entity71731 by ZDOCK program. The model of @entity36942 : @entity71731 :Em(LEM) was thus constructed. The mutant @entity71732 of @entity71731 was manually constructed to explore the detailed effect of the mutation on the binding of @entity71731 and Em(LEM). It has been experimentally suggested that point mutation @entity71732 can disturb the binding between @entity71731 and Em(LEM). Then, @entity74 ( @entity74 ) simulations were performed on @entity36942 : @entity71731 ( @entity7097 ):Em(LEM) and @entity36942 : @entity71731 (MT):Em(LEM) complexes. 30ns trajectories revealed that the trajectory fluctuations of MT complex are more violent than that of the @entity7097 complex. Further, the binding free energy analysis showed that the electronegative residues @entity2574 57, @entity367 61 and @entity2574 65 from chain A, glu36 from chain B of @entity71731 mainly contribute to interact with Em(LEM). Besides, a stable   -   stack between trp62 and phe39 from @entity71731 ( @entity7097 ) chain B is destroyed by @entity367 25 in @entity71731 (MT). As a result, trp62 forms an interaction with glu25, and phe39 converts to strengthen affinity to Em(LEM). On the other hand, Trp62 from chain A also forms a strong interaction with MT @entity367 25. Thus, with the docking of DNA, @entity71731 (MT) has higher affinity with Em(LEM) than @entity71731 ( @entity7097 ).
