Docked State Research Articles

Pose detection and docking control for autonomous dynamic docking mechanism with non-cooperative targets

PurposeThis study aims to address the issue of random movement and non coordination between docking mechanisms and locking mechanisms, and proposes a comprehensive dynamic docking control architecture that integrates perception, planning, and motion control.Design/methodology/approachFirstly, the proposed dynamic docking control architecture uses laser sensors and a charge-coupled device camera to perceive the pose of the target. The sensor data are mapped to a high-dimensional potential field space and fused to reduce interference caused by detection noise. Next, a new potential function based on multi-dimensional space is developed for docking path planning, which enables the docking mechanism based on Stewart platform to rapidly converge to the target axis of the locking mechanism, which improves the adaptability and terminal docking accuracy of the docking state. Finally, to achieve precise tracking and flexible docking in the final stage, the system combines a self-impedance controller and an impedance control algorithm based on the planned trajectory.FindingsExtensive simulations and experiments have been conducted to validate the effectiveness of the dynamic docking system and its control architecture. The results indicate that even if the target moves randomly, the system can successfully achieve accurate, stable and flexible dynamic docking.Originality/valueThis research can provide technical guidance and reference for docking task of unmanned vehicles under the ground conditions. It can also provide ideas for space docking missions, such as space simulator docking.

PIP2 Is An Electrostatic Catalyst for Vesicle Fusion by Lowering the Hydration Energy: Arresting Vesicle Fusion by Masking PIP2.

Lipids are key factors in regulating membrane fusion. Lipids are not only structural components to form membranes but also active catalysts for vesicle fusion and neurotransmitter release, which are driven by soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins. SNARE proteins seem to be partially assembled before fusion, but the mechanisms that arrest vesicle fusion before Ca2+ influx are still not clear. Here, we show that phosphatidylinositol 4,5-bisphosphate (PIP2) electrostatically triggers vesicle fusion as an electrostatic catalyst by lowering the hydration energy and that a myristoylated alanine-rich C-kinase substrate (MARCKS), a PIP2-binding protein, arrests vesicle fusion in a vesicle docking state where the SNARE complex is partially assembled. Vesicle-mimicking liposomes fail to reproduce vesicle fusion arrest by masking PIP2, indicating that native vesicles are essential for the reconstitution of physiological vesicle fusion. PIP2 attracts cations to repel water molecules from membranes, thus lowering the hydration energy barrier.

Synthesis, characterization and anti-tubercular activities of copper(II) complexes of substituted 2,3-isatin bisthiosemicarbazones: An experimental and theoretical approach

Copper(II) acetate reacted with 2,3-isatin bisthiosemicarbazone (2,3 H2bitsc), 2,3-isatin bis-N1-methyl thiosemicarbazone (2,3 H2bitsc-N1-Me) and 2,3-isatin N1-phenyl thiosemicarbazone (2,3 H2bitsc-N1-Ph) in 1:1 (M: L) to form complexes of formula, [Cu(L)] (L = 2,3 bitsc 1, 2,3 bitsc-N1-Me 2, 2,3 bitsc-N1-Ph 3). The formation of bisthiosemicarbazone ligands and their complexes are supported by elemental analysis, FTIR, NMR (1H and 13C), ESR, and Mass. For complexes 1–3, two g values obtained are: g‖ = 2.24 (1), 2.17 (2), 2.26 (3) and g⊥ = 2.09 (1), 2.11 (2), 2.08 (3) which confirm axial symmetry. The square planar geometry is confirmed from higher g‖ values than g⊥ and presence g value of free electron in dx2-y2 ground term. Ligand to metal binding ratio of 1:1 is confirmed using UV–visible spectroscopy. The ligands (2,3 H2bitsc, 2,3 H2bitsc-N1-Me and 2,3 H2bitsc-N1-Ph) and complexes (1–3) were assessed for anti-tubercular (M. tuberculosis H37RV strain ATCC27294) and antibacterial (against E. coli and S. aureus) activities. The anti- tuberculosis activity of ligands (50 µg/mL-2,3 H2bitsc, 100 µg/mL-2,3 H2bitsc-N1-Me and H2bitsc-N1-Ph) gets enhanced on complexation with copper (25 µg /mL-1, 50 µg/mL 2 and 3). The minimal binding energies calculated through molecular modeling with mycobacterium tuberculosis enoyl reductase (PDB ID: 2H7M) is −7.6 (2,3 H2bitsc), −7.3 (2,3 H2bitsc-N1-Me), −9.6 (2,3 H2bitsc-N1-Ph), −8.7 (1), −8.9 (2), and −10.7 (3) Kcal/mol. Higher negative binding energy indicates more stabilized structure in the docked state for 1–3 which supports the experimental data. The drug-protein binding study with human serum albumin (HSA) was used to explore effective transport of molecules to their target sites in 2,3 H2bitsc and its complex 1. A high binding constant of complex 1 (6.09 × 105 M−1) with respect to the ligand 2,3 H2bitsc (4.90 × 105 M−1) indicates its strong binding affinities with HSA.

Space Station-like Composite Nanoparticles for Co-Delivery of Multiple Natural Compounds from Chinese Medicine and Hydrogen in Combating Sensorineural Hearing Loss.

Ototoxic drugs such as aminoglycoside antibiotics and cisplatin (CDDP) can cause sensorineural hearing loss (SNHL), which is closely related to oxidative stress and the acidification of the inner ear microenvironment. Effective treatment of SNHL often requires multifaceted approach due to the complex pathology, and drug combination therapy is expected to be at the forefront of modern hearing loss treatment. Here, space-station-like composite nanoparticles (CCC@mPP NPs) with pH/oxidation dual responsiveness and multidrug simultaneous delivery capability were constructed and then loaded with various drugs including panax notoginseng saponins (PNS), tanshinone IIA (TSIIA), and ammonia borane (AB) to provide robust protection against SNHL. Molecular dynamics simulation revealed that carboxymethyl chitosan/calcium carbonate-chitosan (CCC) NPs and monomethoxy poly(ethylene glycol)-PLGA (mPP) NPs can rendezvous and dock primarily by hydrogen bonding, and electrostatic forces may be involved. Moreover, CCC@mPP NPs crossed the round window membrane (RWM) and entered the inner ear through endocytosis and paracellular pathway. The docking state was basically maintained during this process, which created favorable conditions for multidrug delivery. This nanosystem was highly sensitive to pH and reactive oxygen species (ROS) changes, as evidenced by the restricted release of payload at alkaline condition (pH 7.4) without ROS, while significantly promoting the release in acidic condition (pH 5.0 and 6.0) with ROS. TSIIA/PNS/AB-loaded CCC@mPP NPs almost completely preserved the hair cells and remained the hearing threshold shift within normal limits in aminoglycoside- or CDDP-treated guinea pigs. Further experiments demonstrated that the protective mechanisms of TSIIA/PNS/AB-loaded CCC@mPP NPs involved direct and indirect scavenging of excessive ROS, and reduced release of pro-inflammatory cytokines. Both in vitro and in vivo experiments showed the high biocompatibility of the composite NPs, even after long-term administration. Collectively, this work suggests that composite NPs is an ideal multi-drug-delivery vehicle and open new avenues for inner ear disease therapies.

In silico studies of the interaction of the minor groove binder Hoechst 33258 with B-DNA

Interaction of the minor groove binder, Hoechst 33258, with the Dickerson-Drew DNA dodecamer sequence has been investigated using docking, MM/QM, MM/GBSA and molecular dynamics computations to study the modes of binding and the interactions responsible for the binding. Besides the original Hoechst 33258 ligand (HT), a total of 12 ionization and stereochemical states for the ligand are obtained at the physiological pH and have been docked into B-DNA. These states have one or the other or both benzimidazole rings in protonated states, apart from the piperazine nitrogen, which has a quaternary nitrogen in all the states. Most of these states are found to exhibit good docking scores and free energy of binding with B-DNA. The best docked state has been taken further for molecular dynamics simulations and compared with the original HT. This state is protonated at both benzimidazole rings besides the piperazine ring and hence has very highly negative coulombic interaction energy. In both cases, there are strong coulombic interactions, but these are offset by the almost equally unfavorable solvation energies. Thus, the nonpolar forces, particularly van der Waals contacts, dominate the interaction, and the polar interactions highlight subtle changes in the binding energies, leading to more highly protonated states having more negative binding energies. Communicated by Ramaswamy H. Sarma

Fast synaptic vesicle docking and cluster rearrangement after short stimuli.

In synapses replenishment of the readily releasable pool by physical movement and docking of synaptic vesicles (SVs) to the plasma membrane (PM) is essential for maintaining synaptic transmission. While the kinetics of fusion and re-priming can be measured electrophysiologically, the kinetics of re-docking can be inferred only very indirectly. The inferred repriming rate constants, however, could reflect both priming from an already docked state or docking and subsequent priming. In the Calyx of Held repriming can be as fast as 50 ms, raising the question, whether such fast rates could involve SVs that are not yet docked.

Mechanics of divalent ion sensitivity of the manganese-sensing riboswitch measured by combined high-resolution optical tweezers and single-molecule fluorescence.

Riboswitches are structured non-coding RNA typically found in the 5′ untranslated regions of bacterial mRNAs. They modulate gene expression through the binding of specific ligands that induce changes in the riboswitch structure, most often at the level of transcription and translation. The Mn2+-sensing yybP-ykoY RNA motif is one of the most widespread riboswitches across bacteria, including human and plant pathogens. It contains two divalent metal ion binding sites: one is specific for Mn2+ whereas the other is nonspecific for a divalent metal ion, including Mg2+. Previous crystal structures have shown that Mn2+ binds in between the two distal helical legs of a four-way junction and induces a large “docking” conformational change. It is unclear how competition between Mn2+ and Mg2+ for the two binding sites and the associated RNA conformational changes give rise to Mn2+ detection function and sensitivity. Therefore, we explored the global structural dynamics of the L. lactis Mn2+-sensing riboswitch in the presence of competing divalent cations using high-resolution optical tweezers simultaneous with confocal Förster resonance energy transfer (FRET) spectroscopy. Initial non-equilibrium force ramp measurements revealed force-dependent docking distribution, suggesting a highly selective docked state at suboptimal Mn2+ ion concentration. Follow-up high-resolution equilibrium fixed-force measurements directly measured docking and undocking rate constants versus force to determine docking and undocking mechanics, including transition states and pathways, at varying Mn2+ vs Mg2+ concentrations. Simultaneous FRET measurements confirmed specific conformational transitions. Docking and undocking were symmetric processes with nearly equal force sensitivity and a transition state located nearly midway between the docked and undocked states. Mn2+ sensitivity appears to optimize at a concentration where further increasing Mn2+ competes with Mg2+ ions for the non-specific divalent metal ion binding site.

Optogenetics and electron tomography for structure-function analysis of cochlear ribbon synapses.

Ribbon synapses of cochlear inner hair cells (IHCs) are specialized to indefatigably transmit sound information at high rates. To understand the underlying mechanisms, structure-function analysis of the active zone (AZ) of these synapses is essential. Previous electron microscopy studies of synaptic vesicle (SV) dynamics at the IHC AZ used potassium stimulation, which limited the temporal resolution to minutes. Here, we established optogenetic IHC stimulation followed by quick freezing within milliseconds and electron tomography to study the ultrastructure of functional synapse states with good temporal resolution in mice. We characterized optogenetic IHC stimulation by patch-clamp recordings from IHCs and postsynaptic boutons revealing robust IHC depolarization and neurotransmitter release. Ultrastructurally, the number of docked SVs increased upon short (17-25 ms) and long (48-76 ms) light stimulation paradigms. We did not observe enlarged SVs or other morphological correlates of homotypic fusion events. Our results indicate a rapid recruitment of SVs to the docked state upon stimulation and suggest that univesicular release prevails as the quantal mechanism of exocytosis at IHC ribbon synapses.

Magic-angle-spinning NMR structure of the kinesin-1 motor domain assembled with microtubules reveals the elusive neck linker orientation

Microtubules (MTs) and their associated proteins play essential roles in maintaining cell structure, organelle transport, cell motility, and cell division. Two motors, kinesin and cytoplasmic dynein link the MT network to transported cargos using ATP for force generation. Here, we report an all-atom NMR structure of nucleotide-free kinesin-1 motor domain (apo-KIF5B) in complex with paclitaxel-stabilized microtubules using magic-angle-spinning (MAS) NMR spectroscopy. The structure reveals the position and orientation of the functionally important neck linker and how ADP induces structural and dynamic changes that ensue in the neck linker. These results demonstrate that the neck linker is in the undocked conformation and oriented in the direction opposite to the KIF5B movement. Chemical shift perturbations and intensity changes indicate that a significant portion of ADP-KIF5B is in the neck linker docked state. This study also highlights the unique capability of MAS NMR to provide atomic-level information on dynamic regions of biological assemblies.

Interdomain Interactions Modulate the Active Site Dynamics of Human Inducible Nitric Oxide Synthase.

Nitric oxide synthase (NOS) is a homodimeric flavohemoprotein responsible for catalyzing the oxidation of l-arginine (l-Arg) to citrulline and nitric oxide. Electrons are supplied for the reaction via interdomain electron transfer between an N-terminal heme-containing oxygenase domain and a FMN-containing (sub)domain of a C-terminal reductase domain. Extensive attention has focused on elucidating how conformational dynamics regulate electron transfer between the domains. Here we investigate the impact of the interdomain FMN-heme interaction on the heme active site dynamics of inducible NOS (iNOS). Steady state linear and time-resolved two-dimensional infrared (2D IR) spectroscopy was applied to probe a CO ligand at the heme within the oxygenase domain for full-length and truncated or mutated constructs of human iNOS. Whereas the linear IR spectra of the CO ligand were identical among the constructs, 2D IR spectroscopy revealed variation in the frequency dynamics. The wild-type constructs that can properly form the FMN/oxygenase docked state due to the presence of both the FMN and oxygenase domains showed slower dynamics than the oxygenase domain alone. Introduction of the mutation (E546N) predicted to perturb electrostatic interactions between the domains resulted in measured dynamics intermediate between those for the full-length and individual oxygenase domain, consistent with perturbation to the docked/undocked equilibrium. These results indicate that docking of the FMN domain to the oxygenase domain not only brings the FMN cofactor within electron transfer distance of the heme domain but also modulates the dynamics sensed by the CO ligand within the active site in a way expected to promote efficient electron transfer.

T-cell epitope-based vaccine prediction against Aspergillus fumigatus: a harmful causative agent of aspergillosis

BackgroundAmong the most common causes of invasive aspergillosis and acute bronchopulmonary aspergillosis is Aspergillus fumigatus. Transmission with A. fumigatus produces aggressive aspergillosis in allogeneic haematopoietic stem cell transplant recipients, HIV patients, and cancer patients. Asthmatics and cystic fibrosis patients are allergic to A. fumigatus. MHC class-II binding epitopes can initiate immunogenic responses in patients. In this study, we deployed immunoinformatic study to reveal epitopes from fungal proteins. ResultsIn modern research, we found multiple epitopes ITLKLLHRYSYKLAG, KLVLRAFPNHFRGDS, RYSYKLAGVNQVDVV, GKSFELNQAARAVTQ, and LHRYSYKLAGVNQVD from crucial proteins of A. fumigatus 5,8-linoleate diol synthase (ACO55067.2) and ChainB-chitinase A1 (2XVN_B). RYSYKLAGVNQVDVV, GKSFELNQAARAVTQ, and LHRYSYKLAGVNQVD epitopes interact with HLA-DRB01_0101, while ITLKLLHRYSYKLAG and KLVLRAFPNHFRGDS epitopes interact with HLA-DRB01_1501. Molecular docking analysis reveals atomic contact energy (ACE) value for these five epitopes shown below −5 Kcal/mol in docked state. ConclusionsThe invasive aspergillosis and acute bronchopulmonary aspergillosis are caused by harmful fungal pathogen Aspergillus fumigatus. Our modern immunoinformatic research shows ITLKLLHRYSYKLAG, KLVLRAFPNHFRGDS, RYSYKLAGVNQVDVV, GKSFELNQAARAVTQ, and LHRYSYKLAGVNQVD epitopes could bind to MHC-II HLA allelic determinants and can initiate immunogenic response in patients affected by Aspergillus fumigatus.

An anionic ligand snap-locks a long-range interaction in a magnesium-folded riboswitch

The archetypical transcriptional crcB fluoride riboswitch from Bacillus cereus is an intricately structured non-coding RNA element enhancing gene expression in response to toxic levels of fluoride. Here, we used single molecule FRET to uncover three dynamically interconverting conformations appearing along the transcription process: two distinct undocked states and one pseudoknotted docked state. We find that the fluoride anion specifically snap-locks the magnesium-induced, dynamically docked state. The long-range, nesting, single base pair A40-U48 acts as the main linchpin, rather than the multiple base pairs comprising the pseudoknot. We observe that the proximally paused RNA polymerase further fine-tunes the free energy to promote riboswitch docking. Finally, we show that fluoride binding at short transcript lengths is an early step toward partitioning folding into the docked conformation. These results reveal how the anionic fluoride ion cooperates with the magnesium-associated RNA to govern regulation of downstream genes needed for fluoride detoxification of the cell.

Guaranteed Safe Spacecraft Docking With Control Barrier Functions

This paper presents a strategy for control of a spacecraft docking with a non-maneuvering target in the presence of safety constraints and bounded disturbances. The presence of disturbances prevents convergence to a unique docking state, so in our formulation, docking is defined as occurring within a set constructed using prescribed tolerances. Safety is ensured via application of Robust Control Barrier Functions to render a designated safe set forward invariant for any allowable disturbance. However, this safety strategy necessarily presumes a worst-case disturbance, and thus restricts trajectories to a subset of the safe set when a worst-case disturbance is not present. The presented controller accounts for this restriction, and guarantees that the spacecraft both remains safe and achieves docking in finite time for any allowable disturbance. The controller is then validated in simulation for a spacecraft landing on an asteroid, and two spacecraft docking in low Earth orbit.

Magnesium Mediated Fluoride Binding Anchors the Docked Conformation of the Fluoride Riboswitch

Riboswitches are structured non-coding RNA elements typically found in the 5' untranslated regions of bacterial mRNAs. They regulate gene expression, most often at the level of transcription and translation, through the binding of specific ligands that induce changes in the riboswitch structure. Fluoride riboswitches are a family of transcriptional riboswitches that are present in many bacteria and archaea; regulate transcription by preventing the formation of an intrinsic terminator in presence of fluoride. Previous studies have shed light on its structure and the importance of the transcriptional machinery for riboswitch folding, a deep conformational analysis at different points during transcription are needed to fully understand the impact of ligand-binding during transcription. Therefore, we explored the conformational dynamics of the Bacillus cereus crcB fluoride riboswitch at the single-molecule level for both isolated RNA and active transcription elongation complexes. We resolved three conformational states: two undocked and one pseudoknot-structured docked state, and determined their fractional population and interconversion rates. The first undocked state was observed at early stage of transcription; while the other two states, a docked and an undocked state, appear when the aptamer is fully transcribed by RNA polymerase. The riboswitch folds into a transient dynamic docked conformation in presence of magnesium, which upon further binding of fluoride folds into a stably docked conformation. This feature is lost upon disrupting a long-range base pair A40-U48. In active transcription elongation complexes, RNA polymerase fine-tunes the activation energy and promotes the riboswitch to fold into the docked conformation. Further, we showed that ligand binding at short transcript lengths is an early step on the pathway to the docked conformation. These results demonstrate a multi-step mechanism of magnesium- and ligand-dependent conformational transitions that enable regulation of downstream gene expression.

Biochemical Characterization and Functional Analysis of Heat Stable High Potential Protease of Bacillus amyloliquefaciens Strain HM48 from Soils of Dachigam National Park in Kashmir Himalaya.

A novel temperature stable alkaline protease yielding bacteria was isolated from the soils of Dachigam National Park, which is known to be inhabited by a wide variety of endemic plant and animal species of Western Himalaya. This high-potential protease producing isolate was characterized and identified as Bacillus amyloliquefaciens strain HM48 by morphological, Gram’s staining and biochemical techniques followed by molecular characterization using 16S rRNA approach. The extracellular protease of B. amyloliquefaciens HM48 was purified by precipitating with ammonium sulfate (80%), followed by dialysis and Gel filtration chromatography increasing its purity by 5.8-fold. The SDS–PAGE analysis of the purified enzyme confirmed a molecular weight of about ≈25 kDa. The enzyme displayed exceptional activity in a broad temperature range (10–90 °C) at pH 8.0, retaining its maximum at 70 °C, being the highest reported for this proteolytic Bacillus sp., with KM and Vmax of 11.71 mg/mL and 357.14 µmol/mL/min, respectively. The enzyme exhibited remarkable activity and stability against various metal ions, surfactants, oxidizing agent (H2O2), organic solvents and displayed outstanding compatibility with widely used detergents. This protease showed effective wash performance by exemplifying complete blood and egg-yolk stains removal at 70 °C and efficiently disintegrated chicken feathers making it of vital importance for laundry purpose and waste management. For functional analysis, protease gene amplification of strain HM48 yielded a nucleotide sequence of about 700 bp, which, when checked against the available sequences in NCBI, displayed similarity with subtilisin-like serine protease of B. amyloliquefaciens. The structure of this protease and its highest-priority substrate β-casein was generated through protein modeling. These protein models were validated through futuristic algorithms following which protein–protein (protease from HM48 and β-casein) docking was performed. The interaction profile of these proteins in the docked state with each other was also generated, shedding light on their finer details. Such attributes make this thermally stable protease novel and suitable for high-temperature industrial and environmental applications.

Docking Safety Assessment and Optimization for Autonomous Aerial Refueling: A Data-Driven Method

Docking safety is a key issue in the autonomous aerial refueling (AAR), but it has not been sufficiently studied. Because the docking system is complicated with multiple disturbances and uncertainties, docking safety is difficult to analyze theoretically. Therefore, a data-driven docking safety assessment and optimization method is proposed in this article to improve the AAR docking safety and success rate. First, a comprehensive AAR docking system is established to generate abundant realistic simulation data for the data-driven framework. Then, a deep learning method is used to extract useful information from the docking data. A safety assessment network (SAN) is proposed to predict the final docking success rate according to the current docking state. A motion prediction network (MPN) is proposed to establish the mapping relationship between the expected probe position and the docking state. Furthermore, a novel probe trajectory optimization method is proposed based on the gradient of the MPN and SAN to improve the docking success rate and improve docking safety. Finally, based on the SAN, a novel safety-oriented docking strategy that can predict failed docking attempts and retreat in advance is proposed to further improve docking safety. The effectiveness of the proposed method is demonstrated by simulations.

AP180 promotes release site clearance and clathrin-dependent vesicle reformation in mouse cochlear inner hair cells.

High-throughput neurotransmission at ribbon synapses of cochlear inner hair cells (IHCs) requires tight coupling of neurotransmitter release and balanced recycling of synaptic vesicles (SVs) as well as rapid restoration of release sites. Here, we examined the role of the adaptor protein AP180 (also known as SNAP91) for IHC synaptic transmission by comparing AP180-knockout (KO) and wild-type mice using high-pressure freezing and electron tomography, confocal microscopy, patch-clamp membrane capacitance measurements and systems physiology. AP180 was found predominantly at the synaptic pole of IHCs. AP180-deficient IHCs had severely reduced SV numbers, slowed endocytic membrane retrieval and accumulated endocytic intermediates near ribbon synapses, indicating that AP180 is required for clathrin-dependent endocytosis and SV reformation in IHCs. Moreover, AP180 deletion led to a high prevalence of SVs in a multi-tethered or docked state after stimulation, a reduced rate of SV replenishment and a hearing impairment. We conclude that, in addition to its role in clathrin recruitment, AP180 contributes to release site clearance in IHCs.This article has an associated First Person interview with the first author of the paper.

Molecular Interface of Neuronal Innate Immunity, Synaptic Vesicle Stabilization, and Presynaptic Homeostatic Plasticity

We define a homeostatic function for innate immune signaling within neurons. A genetic analysis of the innate immune signaling genes IMD, IKKβ, Tak1, and Relish demonstrates that each is essential for presynaptic homeostatic plasticity (PHP). Subsequent analyses define how the rapid induction of PHP (occurring in seconds) can be coordinated with the life-long maintenance of PHP, a time course that is conserved from invertebrates to mammals. We define a novel bifurcation of presynaptic innate immune signaling. Tak1 (Map3K) acts locally and is selective for rapid PHP induction. IMD, IKKβ, and Relish are essential for long-term PHP maintenance. We then define how Tak1 controls vesicle release. Tak1 stabilizes the docked vesicle state, which is essential for the homeostatic expansion of the readily releasable vesicle pool. This represents a mechanism for the control of vesicle release, and an interface of innate immune signaling with the vesicle fusion apparatus and homeostatic plasticity.

Molecular characterization, antimicrobial resistance and clinico-bioinformatics approaches to address the problem of extended-spectrum \u03b2-lactamase-producing Escherichia coli in western Saudi Arabia

The goal of this study was to genotypically characterize extended-spectrum β-lactamase-producing Escherichia coli isolates from the western region of Saudi Arabia and to identify active antibiotics against these isolates using phenotypic and molecular modeling. In total, 211 ESBL-producing E. coli isolates recovered from heterogeneous clinical specimens were identified by MALDI-TOF. Thirty-two sequence types (STs) were identified from a multilocus sequence typing (MLST) analysis of ESBL-producing E. coli, including a novel ST (ST8162). The most common ST in the Saudi and expatriate population was ST131, followed by ST38. All the isolates were multidrug resistant (MDR), and >95% of the isolates were resistant to third-generation (ceftriaxone and ceftazidime) and fourth-generation (cefepime) cephalosporins. The ESBL-positive E. coli isolates primarily harbored the blaCTX-M and blaTEM genes. No resistance was observed against the carbapenem antibiotic group. All the ESBL-producing E. coli isolates were observed to be susceptible to a ceftazidime/avibactam combination. Molecular interaction analyses of the docked complexes revealed the amino acid residues crucial for the binding of antibiotics and inhibitors to the modeled CTX-M-15 enzyme. Importantly, avibactam displayed the most robust interaction with CTX-M-15 among the tested inhibitors in the docked state (∆G = −6.6 kcal/mol). The binding free energy values for clavulanate, tazobactam and sulbactam were determined to be −5.7, −5.9 and −5.2 kcal/mol, respectively. Overall, the study concludes that ‘ceftazidime along with avibactam’ should be carefully used as a treatment option against only carbapenem-resistant MDR ESBL-producing E. coli in this region.

Vesicle Adhesion and Fusion Studied by Small-Angle X-Ray Scattering

We have studied the adhesion state (also denoted by docking state) of lipid vesicles as induced by the divalent ions Ca2+ or Mg2+ at well-controlled ion concentration, lipid composition, and charge density. The bilayer structure and the interbilayer distance in the docking state were analyzed by small-angle x-ray scattering. A strong adhesion state was observed for DOPC:DOPS vesicles, indicating like-charge attraction resulting from ion correlations. The observed interbilayer separations of ∼1.6 nm agree quantitatively with the predictions of electrostatics in the strong coupling regime. Although this phenomenon was observed when mixing anionic and zwitterionic (or neutral) lipids, pure anionic membranes (DOPS) with highest charge density σ resulted in a direct phase transition to a multilamellar state, which must be accompanied by rupture and fusion of vesicles. To extend the structural assay toward protein-controlled docking and fusion, we have characterized reconstituted N-ethylmaleimide-sensitive factor attachment protein receptors in controlled proteoliposome suspensions by small-angle x-ray scattering.