Abstract：
:Metallo-β-lactamases (MβLs) can hydrolyze and deactivate lactam-containing antibiotics, which are the major mechanism to cause drug resistance in the treatment of bacterial infections. This has become a global concern due to the lack of clinically approved inhibitors so far. SMB-1 from Serratia marcescents is a novel B3 subclass MβL, which could inactivate nearly all β-lactam-containing antibiotics, e.g., cephalosporins and carbapenems. It represents a new round of worrisome bacterial resistance. In this work, the Michaelis model of SMB-1 in complex with ampicillin was simulated using combined quantum mechanical and molecular mechanical method. Similar with other dizinc MβLs, a Zn-bridged hydroxide ion was simulated as the nucleophile for the hydrolysis reaction assisted by D120. The protonation of D120 could lead to the loss of Oδ2-Zn2 coordination bond, whereas the C3 carboxylate group moves down to become a new ligand to Zn2. The initial β-lactam ring-opening reaction leads to a conserved nitrogen anionic intermediate, which forms a new ligation between the resulted nitrogen anion and Zn2. The corresponding reaction free energy barrier for the first step of lactam ring-opening reaction was calculated to be 19.2 kcal/mol. During the reaction, Q157 serves as the putative "oxyanion hole" rather than Zn1 in L1 enzyme, which was confirmed via the site-directed mutagenesis simulation of Q157A. Our theoretical studies showed some insights into the substrate binding and catalytic mechanism of the SMB-1 metallo-β-lactamase.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Mu X,Xu Ddoi
10.1007/s00894-020-4330-ysubject
Has Abstractpub_date
2020-03-07 00:00:00pages
71issue
4eissn
1610-2940issn
0948-5023pii
10.1007/s00894-020-4330-yjournal_volume
26pub_type
杂志文章abstract：:The energetic and electronic structure of various water dimer isomers has been explored through DFT methodology. Six different possible water dimers come in two broad categories, planar and non-planar. In each of the categories, three distinct topologies (i) linear, (ii) ring and (iii) bifurcated, have been obtained. ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-4274-2
更新日期：2020-01-06 00:00:00
abstract：:B-C binary monolayers and fullerenes (borafullerenes) have received considerable attention in recent years. Inspired by the newly reported B4C3 semiconducting boron carbide monolayer isovalent to graphene (Tian et al., Nanoscale, 2019, 11, 11099), we predict herein at density functional theory level a new class of bor...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-020-04425-1
更新日期：2020-07-07 00:00:00
abstract：:Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the l...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-004-0216-7
更新日期：2004-12-01 00:00:00
abstract：:We present a theoretical investigation of the electric properties of two kinds of one-dimensional lithium bonded chains: (NC-Li)n and (NC-CC-Li)n (n = 1-8). The resulting (NC-Li)n and (NC-CC-Li)n were found to exhibit enhanced first hyperpolarizabilities (β 0) with increasing n, and a slight change in the absorption m...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2532-x
更新日期：2014-12-01 00:00:00
abstract：:The dopamine (DAT), serotontin (SERT) and noradrenalin (NET) transporters are molecular targets for different classes of psychotropic drugs. The crystal structure of Aquifex aeolicus LeuT(Aa) was used as a template for molecular modeling of DAT, SERT and NET, and two putative drug binding sites (pocket 1 and 2) in eac...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-009-0478-1
更新日期：2009-10-01 00:00:00
abstract：:The original version of this article unfortunately contained a mistake. Schemes I and II were missing. These important components are given below. ...
journal_title：Journal of molecular modeling
pub_type： 已发布勘误
doi：10.1007/s00894-017-3466-x
更新日期：2017-11-01 00:00:00
abstract：:We have systematically explored and investigated the geometrical structures, stability, growth pattern, bonding character, and potential energy surface (PES) of the possible isomers of each cluster for planar B(n)P (n = 1 ∼ 7) at the CCSD(T)/6-311+;G(d)//B3LYP/6-311+G(d) level. A large number of planar structures for ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-010-0801-x
更新日期：2011-05-01 00:00:00
abstract：:Geometries and energies of formation of bilirubin formed by reduction of biliverdin via three meso carbon sites, the beta, gamma and delta positions, have been calculated using semiempirical methods. It has been shown that gamma-bilirubin with a ridge-tile conformation forms six intramolecular hydrogen bonds and is th...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-002-0078-9
更新日期：2002-04-01 00:00:00
abstract：:Insulin-like growth factor-binding proteins (IGFBPs) control bioactivity and distribution of insulin-like growth factors (IGFs) through high-affinity complex of IGFBP and IGF. To get more insight into the binding interaction of IGF system, the site-directed mutagenesis and force-driving desorption methods were employe...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-013-2020-8
更新日期：2013-12-01 00:00:00
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journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1106-4
更新日期：2012-02-01 00:00:00
abstract：:The internal rotation in ammonia borane (AB) was studied on the basis of natural orbitals for chemical valence (NOCV) and eigenvectors for Pauli repulsion (NOPR). We found that the total hyperconjugation stabilization (ca. 5 kcal mol(-1)), based on the charge transfer from the occupied σ (B-H) orbitals into the empty ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2272-y
更新日期：2014-06-01 00:00:00
abstract：:Isothiocyanates (ITC) are well-known chemopreventive agents extracted from vegetables. This activity results from the activation of human oxidoreductase. In this letter, the uncompetitive activatory mechanism of ITC was investigated using docking and molecular dynamics simulations. This indicates that NAD(P)H:quinone ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-009-0628-5
更新日期：2010-07-01 00:00:00
abstract：:A mechanical molecular rotation model for liquid crystal (LC) systems is employed to evaluate phase transition temperature of fluorinated phenylbicyclohexane isomeric LC compounds. Results show that when a fluorine atom is substituted along the molecular long axis, an LC molecule acquires high rotational speed and its...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-008-0341-9
更新日期：2008-11-01 00:00:00
abstract：:Molecular-dynamics (MD) simulations of urea crystals of different shapes (cubic, rectangular prismatic, and sheet) have been performed using our previously published force field for urea. This force field has been validated by calculating values for the cohesive energy, sublimation temperature, and melting point from ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1336-5
更新日期：2012-08-01 00:00:00
abstract：:Density functional calculations have been used to investigate the interactions of 1-(2-hydroxyethyl)-3-methylimidazolium ([C2OHmim](+))-based ionic liquids (hydroxyl ILs) with water (H2O), methanol (CH3OH), and dimethyl sulfoxide (DMSO). It was found that the cosolvent molecules interact with the anion and cation of e...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-3063-4
更新日期：2016-08-01 00:00:00
abstract：:Three potential anticancer agents {trans-[PtCl(2)(NH(3))(thiazole)], cis-[PtCl(2)(NH(3))(piperidine)], and PtCl(2)(NH(3))(cyclohexylamine) (JM118)} were explored and compared with cisplatin and the inactive [PtCl(dien)](+) complex. Basic electronic properties, bonding and stabilization energies were determined, and th...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-008-0285-0
更新日期：2008-08-01 00:00:00
abstract：:We investigate the conformational properties of a potent inhibitor of neuropilin-1, a protein involved in cancer processes and macular degeneration. This inhibitor consists of four aromatic/conjugated fragments: a benzimidazole, a methylbenzene, a carboxythiourea, and a benzene-linker dioxane, and these fragments are ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2472-5
更新日期：2014-11-01 00:00:00
abstract：:The chain tacticity of a polymer is a key influence on its structure and dynamics, which ultimately determine its properties. While they have great potential to elucidate the influence of chain tacticity, all-atom molecular simulations are often restricted to short chains and small systems. In this work, two typical s...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2377-3
更新日期：2014-08-01 00:00:00
abstract：:The character of the bridged hydrogen atom (Hb) of B2H6 has become a hot issue in recent years. In this work, the complexes B2H6 · · · NH3, B2H2X4 · · · nNH3 (n = 1, 2) and 2HF · · · B2H2X4 · · · 2NH3 (X = Cl, Br, I) were constructed and studied based on the M06-2X calculations to investigate how to enhance the Hb · ·...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-015-2776-0
更新日期：2015-09-01 00:00:00
abstract：:The heme-AB binding energies (AB = CO, O2) in a wild-type myoglobin (Mb) and two mutants (H64L, V68N) of Mb have been investigated in detail with both DFT and dispersion-corrected DFT methods, where H64L and V68N represent two different, opposite situations. Several dispersion correction approaches were tested in the ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-013-1864-2
更新日期：2013-08-01 00:00:00
abstract：:Antihistamines are frequently used pharmaceuticals that treat the symptoms of allergic reactions. Loratadine (LOR) is an active component of the second generation of selective antihistaminic pharmaceutical usually known as Claritin. Frequent usage of this type of pharmaceuticals imposes the need for understanding thei...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-3101-2
更新日期：2016-10-01 00:00:00
abstract：:Periodic DFT method has been firstly used to calculate the bulk structure, electronic structure, electrical transferring and thermodynamic properties of crystalline 5-azido-1H-tetrazole (HCN₇) and its four different salts. The anion CN₇(-) was included in all of the salts such as ammonium 5-azidotetrazolate ([NH₄](+)[...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-013-1788-x
更新日期：2013-06-01 00:00:00
abstract：:Tetrachlorodibenzodioxin (TCDD) is one of the most famous dioxin families that is hazardous to humans and the environment. Designing cheap and novel catalysts for its detecting and removing is an essential need for the environment. In this work, DFT + VdW is used to investigate the potentiality of proposed catalysts i...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-020-04387-4
更新日期：2020-06-03 00:00:00
abstract：:Computational methods are rapidly gaining importance in the field of structural biology, mostly due to the explosive progress in genome sequencing projects and the large disparity between the number of sequences and the number of structures. There has been an exponential growth in the number of available protein seque...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1410-7
更新日期：2012-09-01 00:00:00
abstract：:Tautomerism in monomers/dimers and association of 2,5-dihydroxy-1,8-naphthyridine was studied at the DFT level recently recommended for studies of non-covalent interactions. Studied dimers are stabilized by double and triple hydrogen-bonding. In some associates the intermolecular proton transfer may take place. Transi...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1178-1
更新日期：2012-04-01 00:00:00
abstract：:Carbon monoxide (CO) and oxygen (O2) catalyzed by small neutral iron oxide clusters (FeO(1-3)) was investigated at the density functional level of theory using the Becke-Perdew-Wang functional (BPW91). Three reaction pathways along with singlet, triplet and quintet states were calculated for ascertaining the presence ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2301-x
更新日期：2014-06-01 00:00:00
abstract：:Defects in the nanoscale are common in the 2D materials irrespective of the fabricated method. Material performance gets significantly affected due to the presence of defects in 2D materials. In the present study, electronic and mechanical properties of 2D-hexagonal boron nitride (hBN) are investigated. At the electro...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-020-04452-y
更新日期：2020-07-03 00:00:00
abstract：:The present study analyzed binding of Cu(2+) to tetrapeptides in water solution at several levels of theoretical approximation. The methods used to study the energetic and structural properties of the complexes in question include semiempirical hamiltonians, density functional theory as well as ab initio approaches in...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1162-9
更新日期：2012-04-01 00:00:00
abstract：:The effect of a strong electric field generated by molecular dipoles on the ground state electronic structure and the Q and B states as well as the lowest charge transfer (CT) excited state of porphine-2,5-dimethyl-1,4-benzoquinone (PQ) complex has been investigated theoretically. Density functional theory DFT and tim...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1595-9
更新日期：2013-02-01 00:00:00
abstract：:Following our recent study on triazane, we present a follow-up study on the thermodynamic properties of triazane's unsaturated analog, triazene. We predict optimized structural parameters, vibrational frequencies, enthalpies of formation, enthalpies of combustion, specific enthalpies of combustion, and proton affiniti...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-007-0248-x
更新日期：2008-01-01 00:00:00
