Effect of solution chemistry on the sedimentation, dissolution, and aggregation of the bimetallic Fe/Cu nanoparticles pre- and post-grafted with carboxymethyl cellulose.

The suitability of iron-based nanomaterials or composites for in-situ remediation hinges on their physicochemical stability. Introducing surface modifications like metal doping or polymer grafting can regulate interparticle forces, influencing particle stability. Thus, probing how grafting methods (i.e., pre- or post-grafting) tune material properties controlling interparticle forces, comprehend the synergistic effect of metal doping and polymer grafting, and evaluate stability under varying geochemical conditions are the way forward in designing sustainable remediation strategies. To this end, time-dependent sedimentation, dissolution, and aggregation of four synthesized iron-based nanoparticles (bare iron (Fe), copper doped bimetallic iron/copper (Fe/Cu), pre- and post-grafted Fe/Cu with carboxymethyl cellulose (CMC) - CMCpre-Fe/Cu and CMCpost-Fe/Cu, respectively) were carried out as a function of solution chemistry (i.e., pH - 5 to 10, ionic strength, IS - 0 to 100 mM NaCl, initial particle concentration, C0-20 to 200 mg.L-1) mimicking geoenvironmental conditions. CMCpre-Fe/Cu exhibited markedly higher particle availability (> 91 %) against sedimentation than others (bare Fe/Cu (11.28 %) > bare Fe (7.33 %) > CMCpost-Fe/Cu (6.09 %)) - suggesting the pivotal role of grafting method on particle stability. XDLVO energy profiles revealed pre-grafting altered magnetic properties favoring surface charge-driven electrostatic repulsion over magnetic attraction, thereby limiting aggregation-induced particle settling. In contrast, superior magnetic force overrides the electrostatic behavior for bare and post-grafted particles. Unlike bare and post-grafted nanoparticles, CMCpre-Fe/Cu aggregate size correlated positively with [H+] and IS, consistent with their settling behavior. Rise in C0 showed a visible negative effect on particle aggregation and, thereby, sedimentation except for CMCpre-Fe/Cu by facilitating particle collision through Brownian movement. Both acidic pH and copper doping promoted nanoparticle dissolution, whereas pre-grafting can provide a plausible solution against nanoparticle toxicity and loss of reactivity due to ionic release. To recapitulate, these findings are imperative in building a sustainable framework for environmental remediation application.

Development of covalent chemogenetic K2P channel activators.

K2P potassium channels regulate excitability by affecting cellular resting membrane potential in the brain, cardiovascular system, immune cells, and sensory organs. Despite their important roles in anesthesia, arrhythmia, pain, hypertension, sleep, and migraine, the ability to control K2P function remains limited. Here, we describe a chemogenetic strategy termed CATKLAMP (Covalent Activation of TREK family K+ channels to cLAmp Membrane Potential) that leverages the discovery of a site in the K2P modulator pocket that reacts with electrophile-bearing derivatives of a TREK subfamily small molecule activator, ML335, to activate the channel irreversibly. We show that the CATKLAMP strategy can be used to probe fundamental aspects of K2P function, as a switch to silence neuronal firing, and is applicable to all TREK subfamily members. Together, our findings exemplify a new means to alter K2P channel activity that should facilitate studies both molecular and systems level studies of K2P function and enable the search for new K2P modulators.

EMC chaperone-CaV structure reveals an ion channel assembly intermediate.

Voltage-gated ion channels (VGICs) comprise multiple structural units, the assembly of which is required for function1,2. Structural understanding of how VGIC subunits assemble and whether chaperone proteins are required is lacking. High-voltage-activated calcium channels (CaVs)3,4 are paradigmatic multisubunit VGICs whose function and trafficking are powerfully shaped by interactions between pore-forming CaV1 or CaV2 CaVα1 (ref. 3), and the auxiliary CaVß5 and CaVα2δ subunits6,7. Here we present cryo-electron microscopy structures of human brain and cardiac CaV1.2 bound with CaVß3 to a chaperone-the endoplasmic reticulum membrane protein complex (EMC)8,9-and of the assembled CaV1.2-CaVß3-CaVα2δ-1 channel. These structures provide a view of an EMC-client complex and define EMC sites-the transmembrane (TM) and cytoplasmic (Cyto) docks; interaction between these sites and the client channel causes partial extraction of a pore subunit and splays open the CaVα2δ-interaction site. The structures identify the CaVα2δ-binding site for gabapentinoid anti-pain and anti-anxiety drugs6, show that EMC and CaVα2δ interactions with the channel are mutually exclusive, and indicate that EMC-to-CaVα2δ hand-off involves a divalent ion-dependent step and CaV1.2 element ordering. Disruption of the EMC-CaV complex compromises CaV function, suggesting that the EMC functions as a channel holdase that facilitates channel assembly. Together, the structures reveal a CaV assembly intermediate and EMC client-binding sites that could have wide-ranging implications for the biogenesis of VGICs and other membrane proteins.

A review on the scope of remediating chlorinated paraffin contaminated water bodies and soils/sediments.

Chlorinated paraffins (CPs) involve a wide range of complex mixtures of chlorinated alkanes. The versatility of their physicochemical properties and their wide range of use has turned them into ubiquitous materials. This review covers the scope of remediating CP-contaminated water bodies and soil/sediments via thermal, photolytic, photocatalytic, nanoscale zero-valent iron (NZVI), microbial and plant-based remediation techniques. Thermal treatments above 800 °C can lead to almost 100 % degradation of CPs by forming chlorinated polyaromatic hydrocarbons and thus should be supported with appropriate pollution control measures leading to high operational and maintenance costs. The hydrophobic nature of CPs lowers their water solubility and reduces their subsequent photolytic degradation. However, photocatalysis can have considerably higher degradation efficiency and generates mineralized end products. The NZVI also showed promising CP removal efficiency, especially at lower pH, which is challenging to achieve during field application. CPs can also be bioremediated by introducing both naturally occurring bacteria and also by engineered bacterial strains which are capable of producing specific enzymes (like LinA2 and LinB) to catalyze CP degradation. Depending on the type of CP, bioremediation can even achieve a dechlorination efficiency of >90 %. Moreover, enhanced degradation rates can be achieved through biostimulation. Phytoremediation has also exhibited CP bioaccumulation and transformation tendencies, both at lab-scale and in field-scale studies. The future research scope can include developing more definitive analytical techniques, toxicity and risk assessment studies of CPs and their degradation products, and technoeconomic and environmental assessment of different remediation approaches.

Structural basis for CaVα2δ:gabapentin binding.

Gabapentinoid drugs for pain and anxiety act on the CaVα2δ-1 and CaVα2δ-2 subunits of high-voltage-activated calcium channels (CaV1s and CaV2s). Here we present the cryo-EM structure of the gabapentin-bound brain and cardiac CaV1.2/CaVß3/CaVα2δ-1 channel. The data reveal a binding pocket in the CaVα2δ-1 dCache1 domain that completely encapsulates gabapentin and define CaVα2δ isoform sequence variations that explain the gabapentin binding selectivity of CaVα2δ-1 and CaVα2δ-2.

Porous media transport of iron nanoparticles for site remediation application: A review of lab scale column study, transport modelling and field-scale application.

Injection of surface modified zero valent iron nanoparticles for in situ remediation of soil, contaminated with an array of pollutants has attracted great attention due to the high reactivity of zero valent iron towards a broad range of contaminants, its cost effectiveness, minimal physical disruption and low toxicity. The effectiveness of this technology relies on the stability and mobility of injected iron nanoparticles. Hence the development of a modelling tool capable of predicting nZVI transport is indispensable. This review provides state of the art knowledge on the mobility of iron nanoparticles in porous media, mechanisms involved in subsurface retention of nZVI based on continuum models and field scale application. Special attention is given to the identification of the influential parameters controlling the transport potential of iron nanoparticles and the available numerical models for the simulation of laboratory scale transport data.

Arginine 37 of Glycine Linker Dictates Regulatory Function of HapR.

HapR is designated as a high cell density quorum sensing master regulatory protein of Vibrio cholerae. It is a member of the TetR family protein and functions both as an activator and a repressor by directly communicating with cognate promoters, thus controlling the expression of a plethora of genes in a density-dependent manner. Molecular insights reveal the domain architecture and further unveil the significance of a cross talk between the DNA binding domain and the dimerization domain for the functionality of the wild-type protein. The DNA binding domain is made up of three α-helices, where a helix-turn-helix motif spans between the helices α2 and α3. The essentiality of the glycine-rich linker linking helices α1 and α2 came into prominence while unraveling the molecular basis of a natural non-functional variant of HapR. Subsequently, the importance of linker length was demonstrated. The present study, involving a series of biochemical analyses coupled with molecular dynamics simulation, has illustrated the indispensability of a critical arginine within the linker at position 37 contributing to HapR-DNA binding activity.

Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins.

Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge-based potential. Proteins 2017; 85:1046-1055. © 2017 Wiley Periodicals, Inc.

Transition of phosphopantetheine adenylyltransferase from catalytic to allosteric state is characterized by ternary complex formation in Pseudomonas aeruginosa.

BACKGROUND: Phosphopantetheine adenylyltransferase (PPAT) is a rate limiting enzyme which catalyzes the conversion of ATP and pantetheine to dephosphocoenzyme and pyrophosphate. The enzyme is allosteric in nature and regulated by Coenzyme A (CoA) through feedback inhibition. So far, several structures have been solved to decipher the catalytic mechanism of this enzyme. METHODS: To address catalytic and inhibitory mechanisms of PPAT, structural insights from single crystal X-ray diffraction method were primarily used, followed by biophysical and biochemical analysis. RESULTS: We have solved the structures of PPAT from Pseudomonas aeruginosa with its substrate analogue AMP-PNP and inhibitor CoA. For the first time, a co-crystal structure of PPAT with Acetyl-CoA (AcCoA) was determined. Enzymatic analysis was performed to decipher the catalytic, allosteric and inhibitory mechanisms involved in regulation of PPAT. Binding affinities of PPAT with its substrates and inhibitors were determined by SPR. CONCLUSION: Previous studies from Escherichia coli and Arabidopsis indicated the inhibitory activity of AcCoA. PPAT-AcCoA structure along with some biochemical methods established AcCoA as an inhibitor to PPAT and illustrated its inhibitory mechanism. Transition from catalytic to allosteric state involves formation of ternary complex. We have studied the structural features of the ternary complex of PPAT along with its product pyrophosphate and inhibitor CoA and validated it with other biophysical and biochemical methods. Extensive analysis of all these 3D structures indicates that changes in side chains R90 and D94 are responsible for transition between catalytic and allosteric inhibitory states. GENERAL SIGNIFICANCE: These enzymatic studies provide new insights into the allosteric mechanism of PPAT.

Structural analysis of inter-genus complexes of V-antigen and its regulator and their stabilization by divalent metal ions.

Gram-negative bacteria like Yersinia, Pseudomonas, and Aeromonas need type III secretion system (T3SS) for their pathogenicity. V-antigen and its regulator are essential for functioning of T3SS. There is significant functional conservation amongst V-antigen and its regulator belonging to the Ysc family. In this study, we have structurally characterized the inter-genus complexes of V-antigen and its regulator. ConSurf analysis demonstrates that V-antigens belonging to the Ysc family show high structural identity predominantly confined to the two long helical regions. The regulator of V-antigen shows high conservation in its first intramolecular coiled-coil domain, responsible for interaction with V-antigen. ∆LcrG(1-70) localizes within the groove formed by long helices of LcrV, as observed in PcrV-∆PcrG(13-72) interaction. Inter-genus complexes of LcrV-PcrG and PcrV-LcrG exhibited elongated conformation and 1:1 heterodimeric state like the native complex of PcrV-PcrG and LcrV-LcrG. Both native and inter-genus complexes showed rigid tertiary structure, solvent-exposed hydrophobic patches, and cooperative melting behavior with high melting temperature. LcrV-PcrG and PcrV-LcrG showed nanomolar affinity of interaction, identical to PcrV-PcrG interaction, but stronger than LcrV-LcrG interaction. Calcium (a secretion blocker of T3SS) propels all the complexes towards a highly monodisperse form. Calcium and magnesium increase the helicity of the native and inter-genus complexes, and causes helix-helix stabilization. Stabilization of helices leads to a slight increase in the melting temperature by 1.5-2.0 °C. However, calcium does not alter the affinity of interaction of V-antigen and its regulator, emphasizing the effect of divalent of cations at the structural level without any regulatory implications. Therefore, the structural conservation of these inter-genus complexes could be the basis for their functional complementation.