The Theoretical And Computational Study Of Proteins Related To Drug Resistance

Multidrug resistance(MDR)transporters are the most important drug resistance pumps.Nor M,one member of MDR family,is believed to play critical role in multidrug resistance in bacteria and mammals.The whole structure of Nor M_NG is composed of 12 trans-membrane helices,quite similar to that of Nor M_VC.The N-domain(TM1-6)and C-domain(TM7-12)are connected by the intervening loops and form a hydrophobic central cavity.In substrates-bound Nor M_NG structures determined recently,the substrate-binding site is occupied by three different substrates(P4P,RHQ,ETT),which form complicate close-range interactions between the residues of Nor M_NG and the substrates.In addition,compared with van der Waals interactions,more ionic and H-bonding contacts are made by Nor M_NG.This unusual observation implies that the transport mechanism of Nor M_NG may be quite different from other known multidrug transporters and make it more meaningful to be the focus of research.Here,molecular dynamics simulations are performed to study the dynamics of ions binding and the behaviors of two long loops in substrate-releasing process.In this work,nine-independent all-atoms MD simulations have been performed in a lipid bilayer with or without sodium binding and in different solvation Na Cl or KCl and in apo-/bound state of Nor M_NG(simulation details found in Table1).Further,a MD simulation is also employed to study the enhanced conformational changes of Nor M in solvation KCl.Our results shed lights on the ions binding dynamics in different solvation and help elucidate the dynamics and molecular mechanism underlying the drug extrusion process of Nor M_NG.Our results show key residues(D41,E261 D377)and TMs rearrangements are verified to be essential along the ions binding pathway.A ion-binding mechanism is proposed that D41 is the first station of the entering of ions to the channel,then ions are to be transferred to the second station E261,and finally reach the cation-binding site around E261 and D377.The rearrangements of TM1,TM7 and TM2 help the task of ions transporting and the conformational changes of Nor M to a closed state.Further,substrate-bound simulations show two long Loop3-4 and Loop9-10 may control the releasing process.Without the opening of the two loops,substrates can't be able to be pumped into extracellular space.bla NDM-1 is a newly discovered gene that can transfer among different bacterial populations and causes severe drug resistance through the encoded NDM-1(an MBL that extensively hydrolyzes antibiotics).Therefore,NDM-1 is considered as an effective target for the treatment of these drug-resistant infections.The crystal structure of NDM-1 shows its characteristic MBLs structure,and its active center has two catalytic zinc ions.Although NDM-1 has structural and functional similarities with other reported MBLs,its special primary sequence,unusually large cavities and more flexible loop features distinguish NDM-1 from other reported MBLs.It may also contribute to NDM-1's extensive antibiotic substrate selectivity.We have screened nearly 2,000 approved drug molecules and the screening results have yet to be further validated by biological experiments.By studying the different MD models of metal proteins,it was found that the Ca DA model simulates zinc ion and its coordination atoms to be tetrahedrally bound with the best comprehensive performance.It is recommended to use the Ca DA model to improve the existing virtual screening model.