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Proceedings of the National Academy of... Jul 2024The outer membrane (OM) of gram-negative bacteria serves as a vital organelle that is densely populated with OM proteins (OMPs) and plays pivotal roles in cellular...
The outer membrane (OM) of gram-negative bacteria serves as a vital organelle that is densely populated with OM proteins (OMPs) and plays pivotal roles in cellular functions and virulence. The assembly and insertion of these OMPs into the OM represent a fundamental process requiring specialized molecular chaperones. One example is the translocation and assembly module (TAM), which functions as a transenvelope chaperone promoting the folding of specific autotransporters, adhesins, and secretion systems. The catalytic unit of TAM, TamA, comprises a catalytic β-barrel domain anchored within the OM and three periplasmic polypeptide-transport-associated (POTRA) domains that recruit the TamB subunit. The latter acts as a periplasmic ladder that facilitates the transport of unfolded OMPs across the periplasm. In addition to their role in recruiting the auxiliary protein TamB, our data demonstrate that the POTRA domains mediate interactions with the inner surface of the OM, ultimately modulating the membrane properties. Through the integration of X-ray crystallography, molecular dynamic simulations, and biomolecular interaction methodologies, we located the membrane-binding site on the first and second POTRA domains. Our data highlight a binding preference for phosphatidylglycerol, a minor lipid constituent present in the OM, which has been previously reported to facilitate OMP assembly. In the context of the densely OMP-populated membrane, this association may serve as a mechanism to secure lipid accessibility for nascent OMPs through steric interactions with existing OMPs, in addition to creating favorable conditions for OMP biogenesis.
PubMed: 38959031
DOI: 10.1073/pnas.2402543121 -
Journal of the American Chemical Society Jul 2024The design of small molecules with unique geometric profiles or molecular connectivity represents an intriguing yet neglected challenge in modern organic synthesis. This...
The design of small molecules with unique geometric profiles or molecular connectivity represents an intriguing yet neglected challenge in modern organic synthesis. This challenge is compounded when emphasis is placed on the preparation of new chemotypes that have distinct and practical functions. To expand the structural diversity of boron-containing heterocycles, we report herein the preparation of novel monocyclic hemiboronic acids, diazaborines. These compounds have enabled the study of a pseudoaromatic boranol-containing (B-OH) ring free of influence from an appended aromatic system. Synthetic and spectroscopic studies have provided insight into the aromatic character, Lewis acidic nature, chemical reactivity, and unique ability of the exocyclic B-OH unit to participate in hydroxy exchange, suggesting their use in organocatalysis and as reversible covalent inhibitors. Moreover, density functional theory and nucleus-independent chemical shift calculations reveal that the aromatic character of the boroheterocyclic ring is increased significantly in comparison to known bicyclic benzodiazaborines (naphthoid congeners), consequently leading to attenuated Lewis acidity. Direct structural comparison to a well-established biaryl isostere, 2-phenylphenol, through X-ray crystallographic analysis reveals that -aryl derivatives are strikingly similar in size and conformation, with attenuated log values underscoring the value of the polar BNN unit. Their potential application as low-molecular-weight scaffolds in drug discovery is demonstrated through orthogonal diversification and preliminary antifungal evaluation (), which unveiled analogs with low micromolar inhibitory concentration.
PubMed: 38959009
DOI: 10.1021/jacs.4c06360 -
Journal of Fluorescence Jul 2024This study investigates the interaction between titanium oxide nanoparticles (TiO NPs) and the heterocyclic fluorophore 6-fluoro,4-hydroxy,2-methylquinoline (6-FHMQ),...
Exploring the molecular binding mechanism of 6-fluoro, 4-hydroxy, 2- methyl quinoline with TiO nanoparticles: A spectroscopic, thermodynamic, and insights into the solvatochromic effect.
This study investigates the interaction between titanium oxide nanoparticles (TiO NPs) and the heterocyclic fluorophore 6-fluoro,4-hydroxy,2-methylquinoline (6-FHMQ), aiming to understand fluorescence quenching mechanisms and thermodynamic characteristics. Spectroscopic techniques including spectrofluorometry (FL) and spectrophotometry (UV-Vis) were used, with a lifetime decay (τ) of 0.18 ns for 6-FHMQ measured using time correlated single photon counting (TCSPC). The interaction between 6-FHMQ and TiO NPs revealed a mix of static and dynamic fluorescence quenching mechanisms, with increasing quenching constants (Ksv) and a higher bimolecular quenching rate constant (Kq). The dynamic nature was highlighted by a temperature-dependent increase in binding sites from 1 to ~ 2. Spontaneous complexation was affirmed by negative change in free energy (ΔG), with negative change in enthalpy (ΔH) and a positive change in entropy (ΔS) values indicating favorable electrostatic and ionic interactions. The impact of varying TiO NP concentrations on 6-FHMQ absorption was analyzed using the Benesi-Hildbrand equation, with a quantum yield of 0.61 determined. By forster resonance energy transfer (FRET) theory, the proximity between 6-FHMQ and TiO NPs was found to be less than 70 Å. Ground and excited state dipole moments of 6-FHMQ in different solvents were calculated to demonstrate solvent sensing ability and charge transfer properties. Ultimately, this study serves as a testament to the power of scientific innovation in the realms of drug delivery and tissue engineering.
PubMed: 38958908
DOI: 10.1007/s10895-024-03829-z -
Environmental Geochemistry and Health Jul 2024The present study focused on to determine the concentration and health risk of heavy metals (Cu, Pb, Zn, Cd, Hg, Cr) in e-waste contaminated soils collected from...
The present study focused on to determine the concentration and health risk of heavy metals (Cu, Pb, Zn, Cd, Hg, Cr) in e-waste contaminated soils collected from different provinces of Pakistan. Further, the impact of heavy metals on soil enzyme activities and microbial community was also investigated. The concentration (mg/kg) of Hg, Zn, Fe, Cu, Pb, Cd, and Cr ranged between 0-0.258, 2.284-6.587, 3.005-40.72, 8.67-36.88, 12.05-35.03, 1.03-2.43, and 33.13-60.05, respectively. The results revealed that Lahore site of Punjab province indicated more concentration of heavy metals as compared to other sites. The level of Cr at all sites whereas Hg at only two sites exceeds the World Health Organization standards (WHO) for soil. Soil enzyme activity exhibited dynamic trend among the sites. Maximum enzyme activity was observed for urease followed by phosphatase and catalase. Contamination factor (Cf), Pollution load index (PLI), and geo-accumulation index (I) results showed that all the sites are highly contaminated with Cu, Cd, and Pb. Hazard index (HI) was less than 1 for children and adults suggesting non-carcinogenic health risk. Principle component analysis results depicted relation among Cr, Fr, catalase, and actinomycetes; Cd, OM, urease, and bacteria, and Pb, Cu, Zn, Hg, and phosphatase, suggesting soil enzymes and microbial community profiles were influenced by e-waste pollution. Therefore, there is a dire need to introduce sustainable e-waste recycling techniques as well as to make stringent e-waste management policies to reduce further environmental contamination.
Topics: Metals, Heavy; Pakistan; Soil Pollutants; Risk Assessment; Humans; Electronic Waste; Soil Microbiology; Environmental Monitoring; Waste Disposal Facilities; Soil
PubMed: 38958829
DOI: 10.1007/s10653-024-02052-w -
Journal of Chemical Theory and... Jul 2024Self-splicing ribozymes are small ribonucleic acid (RNA) enzymes that catalyze their own cleavage through a transphosphoesterification reaction. While this process is...
Self-splicing ribozymes are small ribonucleic acid (RNA) enzymes that catalyze their own cleavage through a transphosphoesterification reaction. While this process is involved in some specific steps of viral RNA replication and splicing, it is also of importance in the context of the (putative) first autocatalytic RNA-based systems that could have preceded the emergence of modern life. The uncatalyzed phosphoester bond formation is thermodynamically very unfavorable, and many experimental studies have focused on understanding the molecular features of catalysis in these ribozymes. However, chemical reaction paths are short-lived and not easily characterized by experimental approaches, so molecular simulation approaches appear as an ideal tool to unveil the molecular details of the reaction. Here, we focus on the model hairpin ribozyme. We show that identifying a relevant initial conformation for reactivity studies, which is frequently overlooked in mixed quantum-classical studies that predominantly concentrate on the chemical reaction itself, can be highly challenging. These challenges stem from limitations in both available experimental structures (which are chemically altered to prevent self-cleavage) and the accuracy of force fields, together with the necessity for comprehensive sampling. We show that molecular dynamics simulations, combined with extensive conformational phase space exploration with Hamiltonian replica-exchange simulations, enable us to characterize the relevant conformational basins of the minimal hairpin ribozyme in the ligated state prior to self-cleavage. We find that what is usually considered a canonical reactive conformation with active site geometries and hydrogen-bond patterns that are optimal for the addition-elimination reaction with general acid/general base catalysis is metastable and only marginally populated. The thermodynamically stable conformation appears to be consistent with the expectations of a mechanism that does not require the direct participation of ribozyme residues in the reaction. While these observations may suffer from forcefield inaccuracies, all investigated forcefields lead to the same conclusions upon proper sampling, contrasting with previous investigations on shorter timescales suggesting that at least one reparametrization of the Amber99 forcefield allowed to stabilize aligned active site conformations. Our study demonstrates that identifying the most pertinent reactant state conformation holds equal importance alongside the accurate determination of the thermodynamics and kinetics of the chemical steps of the reaction.
PubMed: 38958594
DOI: 10.1021/acs.jctc.4c00294 -
Langmuir : the ACS Journal of Surfaces... Jul 2024Amino acids make up a promising family of molecules capable of direct air capture (DAC) of CO from the atmosphere. Under alkaline conditions, CO reacts with the anionic...
Amino acids make up a promising family of molecules capable of direct air capture (DAC) of CO from the atmosphere. Under alkaline conditions, CO reacts with the anionic form of an amino acid to produce carbamates and deactivated zwitterionic amino acids. The presence of the various species of amino acids and reactive intermediates can have a significant effect on DAC chemistry, the role of which is poorly understood. In this study, all-atom molecular dynamics (MD) based computational simulations and vibrational sum frequency generation (vSFG) spectroscopy studies were conducted to understand the role of competitive interactions at the air-aqueous interface in the context of DAC. We find that the presence of potassium bicarbonate ions, in combination with the anionic and zwitterionic forms of amino acids, induces concentration and charge gradients at the interface, generating a layered molecular arrangement that changes under pre- and post-DAC conditions. In parallel, an enhancement in the surface activity of both anionic and zwitterionic forms of amino acids is observed, which is attributed to enhanced interfacial stability and favorable intermolecular interactions between the adsorbed amino acids in their anionic and zwitterionic forms. The collective influence of these competitive interactions, along with the resulting interfacial heterogeneity, may in turn affect subsequent capture reactions and associated rates. These effects underscore the need to consider dynamic changes in interfacial chemical makeup to enhance DAC efficiency and to develop successful negative emission and storage technologies.
PubMed: 38958522
DOI: 10.1021/acs.langmuir.4c00907 -
Environmental Science & Technology Jul 2024Dissolved organic matter (DOM) in aquatic systems is a highly heterogeneous mixture of water-soluble organic compounds, acting as a major carbon reservoir driving...
Dissolved organic matter (DOM) in aquatic systems is a highly heterogeneous mixture of water-soluble organic compounds, acting as a major carbon reservoir driving biogeochemical cycles. Understanding DOM molecular composition is thus of vital interest for the health assessment of aquatic ecosystems, yet its characterization poses challenges due to its complex and dynamic chemical profile. Here, we performed a comprehensive chemical analysis of DOM from highly urbanized river and seawater sources and compared it to drinking water. Extensive analyses by nontargeted direct infusion (DI) and liquid chromatography (LC) high-resolution mass spectrometry (HRMS) through Orbitrap were integrated with novel computational workflows to allow molecular- and structural-level characterization of DOM. Across all water samples, over 7000 molecular formulas were calculated using both methods (∼4200 in DI and ∼3600 in LC). While the DI approach was limited to molecular formula calculation, the downstream data processing of MS2 spectral information combining library matching and in silico predictions enabled a comprehensive structural-level characterization of 16% of the molecular space detected by LC-HRMS across all water samples. Both analytical methods proved complementary, covering a broad chemical space that includes more highly polar compounds with DI and more less polar ones with LC. The innovative integration of diverse analytical techniques and computational workflow introduces a robust and largely available framework in the field, providing a widely applicable approach that significantly contributes to understanding the complex molecular composition of DOM.
PubMed: 38958378
DOI: 10.1021/acs.est.4c00876 -
IUCrJ Jul 2024The manuscript `Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platform Amber' presents a novel protein structure...
The manuscript `Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platform Amber' presents a novel protein structure refinement method claimed to offer improvements over traditional techniques like Refmac5 and Phenix. Our re-evaluation suggests that while the new method provides improvements, traditional methods achieve comparable results with less computational effort.
Topics: Proteins; Molecular Dynamics Simulation; Crystallography, X-Ray; Protein Conformation; Macromolecular Substances; Software; Models, Molecular
PubMed: 38958017
DOI: 10.1107/S2052252524005803 -
Journal of Chemical Theory and... Jul 2024Experimental NMR spectroscopy and theoretical molecular dynamics (MD) simulations provide complementary insights into protein conformational dynamics and hence into...
Experimental NMR spectroscopy and theoretical molecular dynamics (MD) simulations provide complementary insights into protein conformational dynamics and hence into biological function. The present work describes an extensive set of backbone NH and side-chain methyl group generalized order parameters for the ribonuclease HI (RNH) enzyme derived from 2-μs microsecond MD simulations using the OPLS4 and AMBER-FF19SB force fields. The simulated generalized order parameters are compared with values derived from NMR N and CHD spin relaxation measurements. The squares of the generalized order parameters, for the N-H bond vector and for the methyl group symmetry axis, characterize the equilibrium distribution of vector orientations in a molecular frame of reference. Optimal agreement between simulated and experimental results was obtained by averaging or calculated by dividing the simulated trajectories into 50 ns blocks (∼five times the rotational diffusion correlation time for RNH). With this procedure, the median absolute deviations (MAD) between experimental and simulated values of and are 0.030 (NH) and 0.061 (CH) for OPLS4 and 0.041 (NH) and 0.078 (CH) for AMBER-FF19SB. The MAD between OPLS4 and AMBER-FF19SB are 0.021 (NH) and 0.072 (CH). The generalized order parameters for the methyl group symmetry axis can be decomposed into contributions from backbone fluctuations, between-rotamer dihedral angle transitions, and within-rotamer dihedral angle fluctuations. Analysis of the simulation trajectories shows that () backbone and side chain conformational fluctuations exhibit little correlation and that () fluctuations within rotamers are limited and highly uniform with values that depend on the number of dihedral angles considered. Low values of , indicative of enhanced side-chain flexibility, result from between-rotamer transitions that can be enhanced by increased local backbone flexibility.
PubMed: 38957960
DOI: 10.1021/acs.jctc.4c00378 -
Frontiers in Immunology 2024Enteric glial cells (EGCs) are an essential component of the enteric nervous system (ENS) and play key roles in gastrointestinal development, homeostasis, and disease.... (Review)
Review
Enteric glial cells (EGCs) are an essential component of the enteric nervous system (ENS) and play key roles in gastrointestinal development, homeostasis, and disease. Derived from neural crest cells, EGCs undergo complex differentiation processes regulated by various signalling pathways. Being among the most dynamic cells of the digestive system, EGCs react to cues in their surrounding microenvironment and communicate with various cell types and systems within the gut. Morphological studies and recent single cell RNA sequencing studies have unveiled heterogeneity among EGC populations with implications for regional functions and roles in diseases. In gastrointestinal disorders, including inflammatory bowel disease (IBD), infections and cancer, EGCs modulate neuroplasticity, immune responses and tumorigenesis. Recent evidence suggests that EGCs respond plastically to the microenvironmental cues, adapting their phenotype and functions in disease states and taking on a crucial role. They exhibit molecular abnormalities and alter communication with other intestinal cell types, underscoring their therapeutic potential as targets. This review delves into the multifaceted roles of EGCs, particularly emphasizing their interactions with various cell types in the gut and their significant contributions to gastrointestinal disorders. Understanding the complex roles of EGCs in gastrointestinal physiology and pathology will be crucial for the development of novel therapeutic strategies for gastrointestinal disorders.
Topics: Humans; Neuroglia; Enteric Nervous System; Animals; Gastrointestinal Diseases
PubMed: 38957473
DOI: 10.3389/fimmu.2024.1408744