A Structural Basis for 129Xe Hyper-CEST Signal in TEM-1 β-Lactamase

Genetically encoded (GE) contrast agents detectable by magnetic resonance imaging (MRI) enable non-invasive visualization of gene expression and cell proliferation at virtually unlimited penetration depths. Using hyperpolarized ¹²⁹Xe in combination with chemical exchange saturation transfer, an MR contrast approach known as hyper-CEST, enables ultrasensitive protein detection and biomolecular imaging. GE MRI contrast agents developed to date include nanoscale proteinaceous gas vesicles as well as the monomeric bacterial proteins TEM-1 β-lactamase (bla) and maltose binding protein (MBP). To improve understanding of hyper-CEST NMR with proteins, structural and computational studies were performed to further characterize the Xe-bla interaction. X-ray crystallography validated the location of a high-occupancy Xe binding site predicted by MD simulations, and mutagenesis experiments confirmed this Xe site as the origin of the observed CEST contrast. Structural studies and MD simulations with representative bla mutants offered additional insight regarding the relationship between local protein structure and CEST contrast.     

Transport Properties of Fluids in Micropores by Molecular Dynamics Simulation

The transport properties of fluid argon in micropores, i.e. diffusivity and viscosity, were studied by molecular dynamics simulations. The effects of pore width, temperature and density on diffusivity and viscosity were analyzed in micropores with pore widths from 0.8 to 4.0 nm. The results show that the diffusivity in micropores is much lower than the bulk diffusivity, and it decreases as the pore width decreases; but the viscosity in micropores is significantly larger than the bulk one, and it increases sharply in narrow micropores. The diffusivity in channel parallel direction is obviously larger than that in channel perpendicular direction. The temperature and density are important factors that obviously affect diffusivity and viscosity in micropores.     

One-Pot Synthesis of β-Phosphonomalonates Catalyzed by Molecular Iodine

A one-pot procedure has been developed for the synthesis of β-phosphonomalonates via P-C bond formation through tandem Knoevenagel–phospha–Michael reaction catalyzed by iodine as a new, inexpensive, nonmetallic, and commercially available catalyst.

[Supplementary materials are available for this article. Go to the publisher's online edition of Synthetic Communications® for the following free supplemental resource(s): Full experimental and spectral details.]     

Study of catalytic properties of recombinant β-lactamases TEM-1 and TEM-171 of the molecular class A

Homogeneous preparations of recombinant β-lactamases TEM-1 and TEM-171 of molecular class A, differing by an amino acid substitution of valine at position 84 to isoleucine (Val84Ile), was obtained. The kinetic parameters of the β-lactamase TEM-171 were determined using a chromogenic substrate CENTA (K _{M eff} = 23 μM, K _cat = 102 s^–1). The competitive inhibition of recombinant β-lactamases TEM-1 and TEM-171 by tazobactam was ascertained. The values of the inhibition constants in the hydrolysis of the CENTA substrate amount to 0.057 and 0.047 μM for TEM-1 and TEM-171, respectively. It was shown that the Val84Ile mutation leads to a decrease of TEM-171 enzyme thermal stability by 1.5 times.     

L1 β-Lactamase催化反应机理研究

用混合量子力学和分子力学(QM/MM)方法和密度泛函理论讨论了L1 β-Lactamase催化Nitrocefin水解的过程, 研究结果表明, 反应为多步反应: 第一步亲核进攻反应为反应的决速步骤, 并且伴随着酰胺键的断裂, 第二步反应为质子迁移反应. 同时讨论了金属锌在反应中的作用.     

Molecular Dynamics Study of the Complex Formation of TEM-Type β-Lactamases with Substrates and Inhibitors

The complex formation of TEM-1 β-lactamase and its three mutant forms TEM-32, TEM-37, and TEM-39 with substrates cephalothin and CENTA and serine beta-lactamase inhibitors sulbactam, tazobactam, and clavulanic acid is studied using the methods of molecular dynamics. It is found that the stability of the complexes is caused by the electrostatic attraction between the deprotonated carboxyl group of the β-lactam ring of the substrate (inhibitor) and the positively charged amino groups of the lysine 234 and 73 residues, located in the active site of the enzymes. The formation of a hydrogen bond between this substrate group or its carbonyl oxygen with the hydroxyl group of the catalytic serine 70 residue and also between the negatively charged substituent groups and the positive charge region formed by the arginine 244 guanidine group and the asparagine 276 amino group is observed for some complexes. The binding energy of CENTA with TEM-1 β-lactamase is below the analogous binding energy of cephalothin, which is confirmed by the values of the Michaelis constants, determined experimentally. It is also found that the inhibitors bind to the mutant forms of β-lactamases related to the inhibitor-resistant phenotype, with higher affinity than TEM-1 β-lactamase.     

Molecular Dynamics Simulations of a β-Hairpin Fragment of Protein G by Means of Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics (ABEEMσπ/MM)

There are some controversial opinions about the origin of folding β‐hairpin stability in aqueous solution. In this study, the structural and dynamic behavior of a 16‐residue β‐hairpin from B1 domain of protein G has been investigated at 280, 300, 350 and 450 K using molecular dynamics (MD) simulations by means of Atom‐Bond Electronegativity Equalization Method Fused into Molecular Mechanics i.e., ABEEMδπ/MM and the explicit ABEEM‐7P water solvent model. In addition, a 300 K simulation of one mutant having the aromatic residues substituted with alanines has been performed. The hydrophobic surface area, hydrophilic surface area and some structural properties have been used to measure the role of the hydrophobic interactions. It is found that the aromatic residues substituted with alanines have shown an evident destabilization of the structure and unfolding started after 1.5 ns. It is also found that the number of the main chain hydrogen bonds have different distributions through three different simulations. All above demonstrate that the hydrophobic interactions and the main chain hydrogen bonds play an important role in the stability of the folding structure of β‐hairpin in solution. Furthermore, through the structural analyses of the β‐hairpin structures from four temperature simulations and the comparison with other MD simulations of β‐hairpin peptides, the new ABEEMδπ force field can reproduce the structural data in good agreement with the experimental data.     

The Influence of Temperature on Ethene Diffusion in HZSM-5 Studied by Molecular Dynamics

IntroductionZeolites are microporous aluminosilicates andextensively used as ion- exchangers,molecularsieves and heterogeneous catalysts.In theseapplications,the knowledge of guest- hostinteraction is essential for understanding the uniqueproperty of a zeolite system[1,2 ] .Moleculardynamics( MD) has been widely used to simulatethe difffusion characteristics of hydrocarbons,suchas methane[3— 10 ] ,ethane[3 ] ,ethene[3 ,11— 13 ] ,ethyne[3 ] ,propane[3 ,6] ,butane[14 ] and hexane[14 ] inthe l…     

Molecular Dynamics Simulation of Glass Transition Behavior of Polyimide Ensemble

The prediction of glass transition temperature from chemical structure has a great significance to select and design new high-properties materials. However, for the estimation and correlation methods, the deficiency of parameters for newer groups will lead to invalidity of Tg prediction or greater deviation from experiment. In the present work, we predicted Tg for a polyimide (PI) ensemble with rigid moieties, and analyzed structural factor that regards to the rotation barrier of the bridging…     

Molecular recognition of naphthalenediamine by polyamine modified β-cyclodextrin:yttrium metal complexes

The 6-OH group of β-cyclodextrin was modified by diethylene triamine and triethylene tetramine, respectively, mono[6-diethylenetriamino]-6-deoxy-β-cyclodextrin (DTCD) and mono[6-triethylenetetraamino]-6-deoxy-β-cyclodextrin (TTCD) were synthesized, which included 1,5-naphthalenediamine and 1,8-naphthalenediamine, respectively, in the presence of rare earth metal yttrium chloride. As a result, four ternary inclusion complexes (host–guest-metal) formed, which were characterized via ¹HNMR spectroscopy. The chemical shift variations of host and guest molecules were studied. The stoichiometric proportion of host and guest molecules is 2:1 for all the complexes. Signal degeneration still exists for the guest molecules after the inclusion process, which verifies the symmetrical conformation of guest molecules inside the cavities of two host molecules. All the four complexes exhibit “sandwich”-typed structure.     

Molecular evolution of bacterial β-lactam resistance

Background: Two groups of penicillin-destroying enzymes, the class A and class C β-lactamases, may have evolved from bacterial transpeptidases that transfer x-d-Ala-d-Ala peptides to the growing peptidoglycan during cell wall synthesis. Both the transpeptidases and the β-lactamases are acylated by β-lactam antibiotics such as penicillin, which mimic the peptide, but breakdown and removal of the antibiotic is much faster in the β-lactamases, which lack the ability to process d-Ala-d-Ala peptides. Stereochemical factors driving this evolution in specificity are examined.Results: We have compared the crystal structures of two classes of β-lactamases and a β-lactam-sensitive d-alanyl-d-alanine-carboxypeptidase/transpeptidase (DD-peptidase). The class C β-lactamase is more similar to the DD-peptidase than to another β-lactamase of class A.Conclusions: The two classes of β-lactamases appear to have developed from an ancestral protein along separate evolutionary paths. Structural differentiation of the β-lactamases from the DD-peptidases appears to follow differences in substrate shapes. The structure of the class A β-lactamase has been further optimized to exclude d-alanyl peptides and process penicillin substrates with near catalytic perfection. Keywords: drug resistance, enzymology, penicillin antibiotics, protein ancestry Received: 7 October 1996     

Mechanism of Metallo-β-Lactamase Inhibition by Oxacephalosporin Antibiotic

Metallo-β-lactamases is a family of bacterial zinc-dependent enzymes that hydrolyze β-lactam antibiotics and are responsible for the bacterial resistance to them. As a result of the reaction, the slowly hydrolyzed substrate moxalactam undergoes not only chemical transformations in the structure of the β-lactam ring but a negatively charged fragment is also released on the periphery of the molecule, resulting in the formation of an intermediate firmly bound to the active site. In the paper, we present the results of the calculations of the mechanism of this process by a combined quantum mechanics/molecular mechanics approach.     

Transport Coefficients Of Ar—Kr Mixtures by Molecular Dynamics Computer Simulation

Abstract

Equilibrium molecular dynamics computer simulations have been used to determine the transport coefficients of model Ar—Kr mixtures, which are represented by Lennard-Jones pair potentials with Lorentz—Berthelot rules for the cross-species interactions. The component self-diffusion and mutual-diffusion coefficients are calculated from time correlation functions and mean square displacements. Time correlation functions are used to evaluate the shear and bulk viscosity, thermal conductivity and the thermal diffusion coefficient (Soret/Dufour coefficient). In the case of the thermal transport coefficients, the partial enthalpy of the two species is required at each state point to define the heat flux rigorously. We obtain this and the partial volume (and species resolved chemical potential) using particle-exchange (and particle insertion) techniques implemented in separate [NPT] simulations at the same state point.

The viscoelasticity of the fluids is characterised by the relaxation times for bulk and shear stress relaxation. The results are for dense liquids close to the triple point temperature and density. Agreement with experiment and previous simulation is particularly good for the density of the mixtures, the shear modulus, shear viscosity, shear stress relaxation time and thermal conductivity. As for the single component noble gas fluids (simulated and experiment) there is a significant qualitative difference in the temperature and, for mixtures, composition dependence of the bulk viscosity.     

Molecular Dynamics Studies on Thermal Behavior of a FAU-type Zeolite

IntroductionZeolitesaregenerallycrystallinealuminosilicates.TheirframeworksarecomposedofinterconnectedTO.(T=Si.Al)tetrahetralnetworkswhichhavenumerousmoleculardimensionalmicropores.Itisknownthatzeoliteframeworkscanvibratethermallyorbedistortedbychangeoftemperatureorthepresenceofsorbedmolecules.Thecatalyticpropertiesofthezeolitesandthestabilityoftheframeworkaregreatlyaffectedbythetemperatures.Itisthusmeaningfultomodeltheflexibleframeworksinasimulationinordertounderstandthepropertiesofthezeol…     

Catalytic properties of recombinant class a TEM-1 β-lactamase and its inhibition by sulbactam,tazobactam, and clavulanic acid

A homogeneous preparation of recombinant class A TEM-1 β-lactamase was used in various expression constructs as a genetic marker to provide cell resistance to ampicillin; its kinetic parameters (K _M = 22 μM, V = 0.39 μM/s, k _cat = 31.2 s⁻¹, k _cat/K _M =1/4 μM/s⁻¹) were determined using the chromogenic substrate CENTA. Comparative analysis of the obtained K _M value and the literature data demonstrated that the recombinant enzyme is 3 times more specific against the CENTA substrate than the native enzyme (K _M = 70 μM). Competitive inhibition of recombinant β-lactamase by sulbactam, tazobactam, and clavulanic acid was demonstrated. The CENTA inhibition constants for sulbactam, tazobactam, and clavulanic acid (K _{I (sulbactam)} = 0.43 μM, K _{I (tazobactam)} = 0.041 μM, and K _{I (clavulanic acid)} = 0.046 μM) were determined for the first time. It was shown that tazobactam and clavulanic acids are the most efficient inhibitors of recombinant β-lactamase and produced the same inhibitory effect.     

Anisotropy of Thermal-expansion for β-Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine: Quantum Chemistry Calculation and Molecular Dynamics Simulation

Molecular dynamics simulations on octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) at 303-383 K and atmospheric pressure are carried out under NPT ensemble and COMPASS force field, the equilibrium structures at elevated temperatures were obtained and showed that the stacking style of molecules don't change. The coefficient of thermal expansion (CTE) values were calculated by linear fitting method. The results show that the CTE values are close to the experimental results and show anisotropy. The total energies of HMX cells with separately increasing expansion rates (100%-105%) along each crystallographic axis was calculated by periodic density functional theory method, the results of the energy change rates are anisotropic, and the correlation equations of energy change-CTE values are established. Thus the hypostasis of the anisotropy of HMX crystal's thermal expansion, the determinate molecular packing style, is elucidated.     

Molecular dynamics study of the influence of solvents on the chiral discrimination of alanine enantiomers by β-cyclodextrin

The influence of solvents on the separation of alanine enantiomers using β-cyclodextrin as a chiral selector was studied by means of a molecular dynamics simulation at a constant temperature. The potential energy of the interaction is modelled by the AMBER force field, where different polar and non-polar solvents are represented by the dielectric constant ? and two configurations for the amino acid derived from its electric charge distribution: the AMBER data base or its zwitterion state. The l enantiomer has more positions inside the cavity of a β-cyclodextrin where it is more stable than the d-enantiomer in vacuo and solution, except for solvents such as hydrocarbons in which most positions of the d-alanine inside and outside the cavity are more stable. In all cases, the greatest differences are located near the cavity walls. Molecular dynamics simulations show that Ala is able to form inclusion complexes with β-cyclodextrin in vacuo and in solvents such as hydrocarbons, benzene, acetone, ethanol or water. The chiral discrimination of Ala by β-cyclodextrin is mainly due to the adaptation of the guest to the host in the presence of non-polar agents, whereas the nonbonded interaction is the driving force for zwitterions. The elution order depends on the type of organic modifiers while a reversal of the enantiomeric elution order can be observed in solvents with higher dielectric constants.     

Diastereomeric β-cyclodextrin Complexes With Cizolirtine and Its Carbinol. A Molecular Dynamics Study

The enantiodifferentiation observed in the complexation of cizolirtine and its parent carbinol with g -cyclodextrin is due to differences in the average structure of each diastereomeric complex, as deduced from molecular dynamics simulations. Bimodal complexation is possible for all these molecules; both computations and experiments indicate the inclusion of the phenyl group. Two distinct inclusion orientations of this group were considered; although the preferred orientation was determined, the other one may contribute to the final average structure depending on the enantiomeric guest molecule.