Papers by Keyword: Molecular Dynamics (MD)

Abstract: Levan is a branched polysaccharide made from fructose monomers linked by β (2-6) and β (2-1) glycosidic bonds. Levan biosynthesis is catalyzed with levansucrase (EC 2.4.1.10) using sucrose as its substrate. In the present study, we are interested in investigating the elongation capability of the polymerase domain of the enzyme. The other study on Bacillus subtilis levansucrase found that the mutation of His243 into Leu has successfully prolonged the elongation of the polymer. The study, however, has not clearly accounted for the effect of the mutation. The current study aimed to employ in silico method to reveal the effect of the mutation. The initial model of substrate binding on the wild-type and H243L mutant levansucrase was prepared by molecular docking. The stability of the substrate-binding was evaluated by molecular dynamics simulation, while the binding affinity was calculated by the MM-PBSA method. The result showed that the H243L mutant was more stable in binding the substrate than the wild type. This was supported by the calculated binding affinity for H243L mutant and wild-type, which were −2.9 and +4,8 kcal/mol, respectively. Further molecular analysis suggested that mutation of His243 into Leu made the nearby Glu340 and Arg246 form additional hydrogen bonds with the substrate.

Abstract: Intermolecular interaction of mononitrotoluenes (MNs) plasticizer with 2,4,6-trinitrotoluene (TNT) and 1,3,5-trinitrohexahydro-1,3,5-triazine (RDX) was experimentally and theoretically investigated. The basis set superposition error (BSSE) and interaction energy of TNT, RDX and plasticizers were computed at MP2/6-311++G** levels. Compared with the weak E_inter between RDX and TNT (−1.586 kJ/mol), E_inter between the o-nitrotoluene and TNT and RDX can increase to −131.557 kJ/mol and −48.487 kJ/mol, indicating there is strong intermolecular-interaction. SEM imagines also show that mononitrotoluene could form layered deposits in TNT and closely surround RDX crystalline. MD simulation results indicate that tensile modulus of (100) TNT and (100) RDX increases when introducing mononitrotoluene plasticizers separately, which agree with the experimental phenomenon of Brazilian disk test.