Movement Of Residues Research Articles

Exploring Metalloprotease from Dunaliella sp.: Production, Regulation, and Structural Insight

A green microalgal strain, identified as Dunaliella sp., was isolated from the Tunisian southern region. The enhancement of its protein and protease production was performed through culture condition optimization using the response surface methodology. The optimal conditions for protein and protease production were found to be, respectively, (i) NaCl concentrations of 135 and 45.55 g/L, (ii) NaHCO3 concentrations of 0.5 and 1.5 g/L, (iii) temperature of 28 °C for both, and (iv) light intensities of 400 and 100 µmol photons/m2/s. The optimization led to an increase in microalgae protein content from 11.98% ± 0.26 to 18.39% ± 0.10 and microalgae proteolytic activity from 7.36 ± 0.74 U/mg to 12.54 ± 0.86 U/mg. Specific focus was attributed to ATP-dependent metalloprotease, namely, FtsH2, which is involved in numerous cellular processes including cell division, cell differentiation, signal transduction, and stress response. Differential expression of the FtsH2 gene under various stress conditions showed that this expression was upregulated in response to salt stress, gibberellic acid, and Indole-3-butyric acid. A 3D modeling demonstrated two possible arrangements where the ATPase ring shows either a perfect six-fold symmetry with an open circular entrance covering the crucial pore residues, or a translocated model triggered by substrate binding inward movement of the aromatic pore residues.

Time-series analysis of rhenium(I) organometallic covalent binding to a model protein for drug development.

Metal-based complexes with their unique chemical properties, including multiple oxidation states, radio-nuclear capabilities and various coordination geometries yield value as potential pharmaceuticals. Understanding the interactions between metals and biological systems will prove key for site-specific coordination of new metal-based lead compounds. This study merges the concepts of target coordination with fragment-based drug methodologies, supported by varying the anomalous scattering of rhenium along with infrared spectroscopy, and has identified rhenium metal sites bound covalently with two amino acid types within the model protein. A time-based series of lysozyme-rhenium-imidazole (HEWL-Re-Imi) crystals was analysed systematically over a span of 38 weeks. The main rhenium covalent coordination is observed at His15, Asp101 and Asp119. Weak (i.e. noncovalent) interactions are observed at other aspartic, asparagine, proline, tyrosine and tryptophan side chains. Detailed bond distance comparisons, including precision estimates, are reported, utilizing the diffraction precision index supplemented with small-molecule data from the Cambridge Structural Database. Key findings include changes in the protein structure induced at the rhenium metal binding site, not observed in similar metal-free structures. The binding sites are typically found along the solvent-channel-accessible protein surface. The three primary covalent metal binding sites are consistent throughout the time series, whereas binding to neighbouring amino acid residues changes through the time series. Co-crystallization was used, consistently yielding crystals four days after setup. After crystal formation, soaking of the compound into the crystal over 38 weeks is continued and explains these structural adjustments. It is the covalent bond stability at the three sites, their proximity to the solvent channel and the movement of residues to accommodate the metal that are important, and may prove useful for future radiopharmaceutical development including target modification.

Atributos físico-químicos de um latossolo vermelho distroférrico submetido a sucessões de culturas

ABSTRACT No-till farming is the practice closest to the concept of sustainable agriculture. The minimum soil movement and continuous contribution of crop residues to the farming system reduce erosion, mitigate the greenhouse effect, increase the organic matter content, and improve the physical and chemical quality of the soil. This study aimed to assess the effect of five-year succession cropping on the physical and chemical attributes of oxisol. The crops were sown for five consecutive years in the same plots, using a randomized block design in split plots with four replicates. The plots were crops grown in succession to soybean, namely Congo grass (Urochloa ruziziensis syn. Brachiaria ruziziensis), Congo grass intercropped with maize (Zea mays L.), pearl millet (Pennisetum glaucum), sorghum (Sorghum bicolor L.), maize, and slender leaf rattlebox (Crotalaria ochroleuca). The subplots were the following sampled soil layers: 0-5, 5-10, and 10-20 cm. The physicochemical attributes of these three soil layers were evaluated. Pearl millet cycled K efficiently, providing the soil with K concentrations equivalent to those of the K fertilization treatments. No single crop or intercrop increased the soil P concentration. Congo grass stood out for its ability to increase the Mg concentration. The 0-5 cm soil layer had the best physicochemical attributes based on the accumulated organic matter.

Numerical study of the effects of pulsed electric field on β-casein

As a non-thermal microbial inactivation technology, pulsed electric field (PEF) treatment can be used in liquid food sterilization. It is necessary to investigate the effects and mechanisms of PEF on the important contents of liquid food. In this study, molecular dynamics (MD) simulation and multiple structural analyses were employed to investigate the effects of PEF on β-casein (BCN) molecule. The investigation focused on examining the impact of PEF on molecular conformation, flexibility, electrostatic properties, and solvent interactions. Results found that high-intensity pulsed electric fields can cause irreversibly complete unfolding of BCN molecule within a picosecond timeframe. The applied PEF changed the dipole moment of BCN molecules, leading to the reorientation of residues towards the direction of the applied electric field. Furthermore, the electric field-induced movement of hydrophobic and hydrophilic residues within the BCN molecules was observed, resulting in concomitant changes in the solvent accessible surface area (SASA) of BCN molecule.Industrial relevance: PEF is an emerging non-thermal processing technology in the food industry. MD simulations were employed to investigate the conformational changes of BCN under different pulse electric fields and exposure times. Our study elucidates the fundamental mechanism of PEF's interaction with protein molecules and may contribute to improving the functional properties of this protein. Analysis at the molecular level can be experimentally validated, providing a theoretical foundation for the widespread application of PEF technology in protein-containing food systems.

Molecular dynamics simulation of interaction between high pressure carbon dioxide (HPCD) and phenylalanine ammonia-lyase (PAL)

High-pressure carbon dioxide (HPCD) could effectively suppress the yellowing phenomenon in Chinese water chestnut (CWC) by significantly inhibiting the activity of the key enzyme—phenylalanine ammonia-lyase (PAL). However, the molecular mechanism underlying this inhibition remains unclear. In this study, we investigated the structural changes and inhibition mechanisms of PAL from CWC subjected to HPCD treatment. Homology modeling was used to construct the 3D structure of CWC PAL. The results showed that CWC PAL was highly conserved and had higher α-helix content. Molecular dynamics simulations and molecular docking were utilized to investigate the non-covalent interaction between CO2 and PAL. Our findings revealed that CO2 induced conformational changes in PAL via hydrogen bonds, polar interactions, and hydrophobic interactions, thereby increasing PAL's α-helix structure and preventing the substrate L-Phe from entering its active site. Additionally, HPCD treatment caused the movement of the Phe-111 residue in the inner lid-loop, resulting in steric hindrance and destruction of the active center of PAL. These results provide a theoretical basis for expanding the application of HPCD in the food processing industry.

Modeling the role of charged residues in thermophilic proteins by rotamer and dynamic cross correlation analysis.

Discerning the determinants of protein thermostability is very important both from the theoretical and applied perspective. Different lines of evidence seem to indicate that a dynamical network of salt bridges/charged residues plays a fundamental role in the thermostability of enzymes. In this work, we applied measures of dynamic variance, like the Gini coefficients, Kullback-Leibler (KL) divergence and dynamic cross correlation (DCC) coefficients to compare the behavior of 3 pairs of homologous proteins from the thermophilic bacterium Thermus thermophilus and mesophilic Escherichia coli. Molecular dynamic (MD) simulations of these proteins were performed at 303K and 363K. In the characterization of their side chain rotamer distributions, the corresponding Gini coefficients and KL-divergence both revealed significant correlations with temperature. Similarly, a DCC analysis revealed a higher trend to de-correlate the movement of charged residues at higher temperatures in the thermophilic proteins, when compared with their mesophilic homologues. These results highlight the importance of dynamic electrostatic network interactions for the thermostability of enzymes.

Transfer and persistence studies of inorganic and organic gunshot residues using synthetic skin membranes

The complex nature of gunshot residue (GSR) transfer and persistence introduces challenges and skepticism in its evidential value. Therefore, this work evaluates the behavior and movement of inorganic and organic gunshot residues to assist in the evidence interpretation. The study encompassed over 650 samples, including 247 collections from human skin after firing a gun and 405 synthetic skin and fabric substrates after depositing a characterized pGSR/OGSR standard. Transfer and persistence experiments were evaluated on different substrates (hands, ears, nostrils, forehead, hair, fabrics, and synthetic skin), at different times after firing (0 to 6 h), and common post-shooting activities (rubbing hands, handshaking, running, washing hands and fabrics). Ground truth knowledge of particle counts and analyte concentrations was used to calculate the recovery for inorganic and organic constituents from clothing and a synthetic skin membrane (StratM®). Authentic shooter skin samples were compared to synthetic skin to establish the validity of skin-substitute models. During controlled experiments, inorganic particles persisted longer than OGSR on inactive samples (9% and < 25% loss at 6 hrs, respectively), but inorganic particles were more prone to secondary transfer than OGSR (up to 35% vs. 0% transfer, respectively). High percentages of particles were lost during vigorous activities like washing hands (99% loss) or rubbing hands (55% loss). In comparison, less loss was observed during the same studies for OGSR (<21%). This study offers a deeper understanding of gunshot residue transfer and persistence mechanisms that can assist analysts and investigators in improving sample collection and interpretation of evidence.

Construction of novel cellulase with high activity, great stability and excellent lignin-resistant for efficient enzymatic hydrolysis by hydrophilic and negatively charged modification

The lignin-derived inhibition on cellulase is the most critical bottleneck that must be addressed when converting lignocellulosic biomass through the sugar-platform process. Herein, a novel modified cellulase with high activity, great stability and excellent lignin-resistant ability was synthesized by chemical modification using hydrophilic and negatively charged polyethylene glycol (PEG) derivatives including HO-PEG-COOH and HOOC-PEG-COOH. Both modifications obviously increased the cellulase activity, with 37% (HO-PEG-COOH modification) and 53% (HOOC-PEG-COOH modification) increase, respectively. In addition, the stabilities of both modified cellulases were significantly enhanced, seeing from their much higher activities at all selected temperatures and pH values. The modification resulted in a movement of tryptophan residues to the exterior of enzyme, allowing the substrate chains to be more easily recruited and thus initiating the hydrolysis. The compactness of secondary structure for enzyme was improved, especially, the α-helix content was increased which requires strong hydrogen bonding to generate it, thus enhancing the stability. High hydrophilicity, negative charge and compactness of enzyme conferred modified cellulase good ability to resist lignin adsorption and destruction, thus improving the enzymatic hydrolysis of corn stover. • Cellulase activity is significantly improved by up to 52% after chemical modification. • The migration of Trp residues allows the hydrolysis to be more easily initiated. • High compactness gives modified cellulase great stability and low level of damage by lignin. • High hydrophilicity and negative charge of modified cellulase prevent lignin adsorption. • The novel modified cellulase exhibits promising potential in converting corn stover.

Determining how almond (Prunus dulcis) harvest and processing contributes to low levels of glyphosate and glufosinate residues in almonds

AbstractCalifornia is the top producer of almonds [Prunus dulcis (Mill.) D.A. Webb] worldwide, generating more than $6 billion in revenue in 2020; the European Union (EU) is the primary importer of California almonds. Weed control in almond orchards is an important part of the preharvest process, because weeds can interfere with harvest equipment and host diseases. Glyphosate and glufosinate are broad-spectrum herbicides commonly used for preharvest weed control. Global differences in maximum residue limits (MRLs) and regulated compounds can pose a challenge for growers who rely on broad-spectrum herbicides such as glyphosate and glufosinate for preharvest weed control. The EU MRL for glyphosate and total glufosinate is currently 0.1 mg kg−1. The U.S. MRL for total glyphosate is 1 mg kg−1, and total glufosinate is 0.5 mg kg−1. An 8-wk field experiment, from spray to harvest, was conducted in an 8-ha commercial orchard to evaluate the potential contribution of the preharvest herbicide treatment to low levels of herbicide residue in almonds. Then, the same batch of almonds was followed through a commercial processing facility to evaluate the potential movement of herbicide residues from soil, debris, and hulls to almond kernels during processing. Glyphosate was not detected in any almond kernel samples at the end of processing. A glufosinate metabolite, 3-(methylphosphinico)propionic acid (MPP), was detected in kernels at the end of processing at about 0.1 mg kg−1, which is above the EU MRL for total glufosinate. Almonds sampled directly from the tree, without any contact with soil, were found to have elevated MPP residues. This indicates glufosinate or MPP translocation may be a factor in low-level glufosinate residues detected in almonds in some EU exports.

Understanding the anchoring interaction of coagulation factor Va light chain on zeolites: A molecular dynamics study

HypothesisFactor Va (FXa) and Xa (FVa) can assemble on the phosphatidylserine (PS) membrane (of platelet) to form prothrombinase complex and contribute to blood clotting. Very recently, we discovered that Ca-zeoliteacts as a type of reinforced activated inorganic platelet to enable assembly of prothrombinase complex and display an unusual zymogen (prothrombin) activation pattern. Inspired but not constrained by nature, it is of great interest to understand how FVa and FXa assembly on the inorganic surface (e.g., zeolites) and perform their biocatalytic function. ExperimentsGiven the important role of FVa C1-C2 domains in the assembly and activity of the prothrombinase complex, in this work, molecular dynamics simulations were performed to investigate the binding details of FVa A3-C1-C2 domains on the PS membranes and Ca2+-LTA-type (CaA) zeolite surface. FindingsWe found that different from the natural PS membrane, FVa light chain repeatedly exhibits a strong C2 domain anchoring interaction on the CaA zeolite. It mainly arises from the porous surface structure of CaA zeolite and local highly dense solvation water clusters on the CaA zeolite surface restrict the movement of some lysine residues on the C2 domain. The anchoring interaction can be suppressed by reducing the surface negative charge density, so that FVa light chain can change from single-foot (only C2 domain) to double-foot (both C1-C2 domain) adsorption states on the zeolite surface. This double-foot adsorption state is similar to natural PS membrane systems, which may make FVa have higher cofactor activity.

New biochemical insights into the dynamics of water molecules at the GMP or IMP binding site of human GMPR enzyme: A molecular dynamics study.

Human GMP reductase (hGMPR) enzyme is involved in a cellular metabolic pathway, converting GMP into IMP, and also it is an important target for anti-leukemic agents. Present computational investigations explain dynamical behavior of water molecules during the conformational transition process from GMP to IMP using molecular dynamics simulations. Residues at substrate-binding site of cancerous protein (PDB Id. 2C6Q) are mostly more dynamic in nature than the normal protein (PDB Id. 2BLE). Nineteen conserved water molecules are identified at the GMP/IMP binding site and are classified as (i) conserved stable dynamic and (ii) infrequent dynamic. Water molecules W11, W14, and W16 are classified as conserved stable dynamic due to their immobile character, whereas remaining water molecules (W1, W2, W3, W4, W5, W7, W8, W9, W10, W12, W13, W15, W17, W18, and W19) are infrequent with dynamic nature. Entrance or displacement of these infrequent water molecules at GMP/IMP sites may occur due to forward and backward movement of reference residues involving ligands. Four water molecules of hGMPR-I and nine water molecules of hGMPR-II are observed in repetitive transitions from GMP to IMP pathway, which indicates discrimination between two isoforms of hGMPRs. Water molecules in cancerous protein are more dynamic and unstable compared to normal protein. These water molecules execute rare dynamical events at GMP binding site and could assist in detailed understanding of conformational transitions that influence the hGMPR's biological functionality. The present study should be of interest to the experimental community engaged in leukemia research and drug discovery for CML cancer.

Modelling of an autonomous Nav1.5 channel system as a part of in silico pharmacology study.

A homology model of Nav1.5, based mainly on the crystal structures of Nav1.2/1.5 was built, optimized and successfully inserted into the membrane bilayer. We applied steered and free MD simulation protocols for the visualization of the mechanism of Nav1.5 activation. We constrained dihedrals of S4 trigger to introduce a structural tension with further rearrangement and movement of secondary structure elements. From these, we observed an intracellular gate opening and movement of the Lys1419 residue caused by a gradual displacement of the distal S6 α-helix with the extended S4 3-10 helix of voltage-sensing domains (VSD). A construction containing the Lys1419 residue in P-loop also changed its position due to the extension of this helix and subsequent induction of the pore-forming helixes motion. From this point, a double membrane system was generated, implying a free of ligand Nav1.5 protein and on the opposite side its copy containing a docked bupivacaine molecule inside the pore channel. The system can be used for the design of selective inhibitors against the Nav1.7 channel, instead of mixed effect on both channels.

Off-site movement of quinclorac from rice fields

The off-site movement of quinclorac from rice paddies was studied in a district and field study during the 2014 and 2015 growing seasons. Quinclorac residues were monitored on in-field surface waters, and out-field water entering and leaving an irrigation district. The behaviour of quinclorac residues in paddy water pointed out that the movement of herbicides from interconnected paddies is not negligible. This phenomenon was particularly evident in the days following the re-flooding of paddies after spraying. The water entering the uphill paddy fields have partially flushed quinclorac residues in the downhill paddy fields. Both the district and the field studies, showed the continuous presence of quinclorac residues in inlet waters. Even because of the continuous uploading of residues from inlet waters, traces of quinclorac in paddy water were detected up to 70 DAT. The presence of quinclorac in inlet water could be related to phenomena of drainage and drift during herbicide application in the paddies located upstream. The analysis carried out on waters leaving the district showed the presence of quinclorac residues in all the outlet floodgates, particularly from the end of May and late August. The results of this study suggest that appropriate management practices adopted at field scale may be required to lower the water contamination at irrigation district level. Considering that the highest losses of quinclorac occurred during the first 10-15 days after its application, to prevent these losses could be helpful avoiding water discharge from the treated fields for at least this period of time. In addition, a deep effort must be laid upon education and training of farmers on these environmental thematic throughout specific initiatives organized by public and private stakeholders. Highlights - Quinclorac persistence in paddy water is affected by its residues in entering waters. - Entering waters often contain quinclorac residues. - A water holding period of at least 10 days may limit the offsite movement of quinclorac residues from paddy fields.

Dynamic cross correlation analysis of Thermus thermophilus alkaline phosphatase and determinants of thermostability

BackgroundUnderstanding the determinants of protein thermostability is very important both from the theoretical and applied perspective. One emerging view in thermostable enzymes seems to indicate that a salt bridge/charged residue network plays a fundamental role in their thermostability. MethodsThe structure of alkaline phosphatase (AP) from Thermus thermophilus HB8 was solved by X-ray crystallography at 2.1 Å resolution. The obtained structure was further analyzed by molecular dynamics studies at different temperatures (303 K, 333 K and 363 K) and compared to homologous proteins from the cold-adapted organisms Shewanella sp. and Vibrio strain G15–21. To analyze differences in measures of dynamic variation, several data reduction techniques like principal component analysis (PCA), residue interaction network (RIN) analysis and rotamer analysis were used. Using hierarchical clustering, the obtained results were combined to determine residues showing high degree dynamical variations due to temperature jumps. Furthermore, dynamic cross correlation (DCC) analysis was carried out to characterize networks of charged residues. ResultsTop clustered residues showed a higher propensity for thermostabilizing mutations, indicating evolutionary pressure acting on thermophilic organisms. The description of rotamer distributions by Gini coefficients and Kullback–Leibler (KL) divergence both revealed significant correlations with temperature. DCC analysis revealed a significant trend to de-correlation of the movement of charged residues at higher temperatures. SignificanceThe de-correlation of charged residues detected in Thermus thermophilus AP, highlights the importance of dynamic electrostatic network interactions for the thermostability of this enzyme.

Glycoside hydrolase family 5: structural snapshots highlighting the involvement of two conserved residues in catalysis

The ability of retaining glycoside hydrolases (GHs) to transglycosylate is inherent to the double-displacement mechanism. Studying reaction intermediates, such as the glycosyl-enzyme intermediate (GEI) and the Michaelis complex, could provide valuable information to better understand the molecular factors governing the catalytic mechanism. Here, the GEI structure of RBcel1, an endo-1,4-β-glucanase of the GH5 family endowed with transglycosylase activity, is reported. It is the first structure of a GH5 enzyme covalently bound to a natural oligosaccharide with the two catalytic glutamate residues present. The structure of the variant RBcel1_E135A in complex with cellotriose is also reported, allowing a description of the entire binding cleft of RBcel1. Taken together, the structures deliver different snapshots of the double-displacement mechanism. The structural analysis revealed a significant movement of the nucleophilic glutamate residue during the reaction. Enzymatic assays indicated that, as expected, the acid/base glutamate residue is crucial for the glycosylation step and partly contributes to deglycosylation. Moreover, a conserved tyrosine residue in the -1 subsite, Tyr201, plays a determinant role in both the glycosylation and deglycosylation steps, since the GEI was trapped in the RBcel1_Y201F variant. The approach used to obtain the GEI presented here could easily be transposed to other retaining GHs in clan GH-A.

Efficient activity of soil depending on of precursors and major treatment of soil when cultivating winter wheat

The article presents data on the change in the enzymatic activity of the soil in winter wheat crops under the influence of the methods and techniques of tillage and the previous crop in the Central Ciscaucasus zone. The studies were carried out in the zone of the Central Ciscaucasia on the basis of the experimental station of Stavropol State Agrarian University. The determination of the activity of invertase shows that its maximum values are in the variants of the combined treatment, which is associated with more favorable hydrothermal conditions of the arable layer of the soil. Thus, according to its predecessor, pea + oats for green fodder, invertase activity is 27.9 mg of glucose per 1 g of soil for 40 hours, which is almost twice as high in comparison with surface treatment and three times with plowing. The decrease in the activity of invertase during dump processing indicates a rapid rate of mineralization of organic matter. Catalase activity on the studied precursors: on peas with oats for green fodder 1.6 and 1.3; 1.5 and 1.8 peas; for corn silage 1.5 and 1.4 ml 0.1 n. KMnO4 per 1 g of soil for 20 minutes. Revealed a decrease in activity under the influence of plowing, as urease enters the soil with plant debris. When dumping treatment due to movement of plant residues in the underlying layers, the activity of this enzyme decreases to 0.8–0.9 mg of N-NH4 per 10 g of soil for 4 hours, whereas with surface treatment, depending on its predecessor, it is 0.8–– 1.3 mg of N-NH4 / 10 g of soil for 4 hours, with a combination of 1.0–1.1, and for shallow soil, 1.1–1.2 mg of N-NH4 / 10 g of soil in 4 hours.

Crystal structures of glutathione- and inhibitor-bound human GGT1: critical interactions within the cysteinylglycine binding site

Overexpression of γ-glutamyl transpeptidase (GGT1) has been implicated in an array of human diseases including asthma, reperfusion injury, and cancer. Inhibitors are needed for therapy, but development of potent, specific inhibitors of GGT1 has been hampered by a lack of structural information regarding substrate binding and cleavage. To enhance our understanding of the molecular mechanism of substrate cleavage, we have solved the crystal structures of human GGT1 (hGGT1) with glutathione (a substrate) and a phosphate-glutathione analog (an irreversible inhibitor) bound in the active site. These are the first structures of any eukaryotic GGT with the cysteinylglycine region of the substrate-binding site occupied. These structures and the structure of apo-hGGT reveal movement of amino acid residues within the active site as the substrate binds. Asn-401 and Thr-381 each form hydrogen bonds with two atoms of GSH spanning the γ-glutamyl bond. Three different atoms of hGGT1 interact with the carboxyl oxygen of the cysteine of GSH. Interactions between the enzyme and substrate change as the substrate moves deeper into the active site cleft. The substrate reorients and a new hydrogen bond is formed between the substrate and the oxyanion hole. Thr-381 is locked into a single conformation as an acyl bond forms between the substrate and the enzyme. These data provide insight on a molecular level into the substrate specificity of hGGT1 and provide an explanation for seemingly disparate observations regarding the enzymatic activity of hGGT1 mutants. This knowledge will aid in the design of clinically useful hGGT1 inhibitors.

Absorption, distribution, metabolism, and excretion of three [14C]PBDE congeners in laying hens and transfer to eggs.

Polybrominated diphenyl ethers (PBDEs) levels in environmental matrices have generally declined following their phaseout as flame retardants. The objective of this study was to determine the absorption, distribution, metabolism, and excretion of three persistent PBDEs in laying hens and their transfer into eggs. Laying hens (n = 4 per congener) received a single oral dose of BDE-99, -153, or -209 and eggs and excreta were collected daily for 7 days, then tissues were collected and analysed. Cumulative BDE-209 excretion was 93% of dose, and bioavailability was approximately 17%. Lesser amounts of BDE-99 (41%) and -153 (26%) were excreted with bioavailabilities of 87% and 79%, respectively. Phenolic metabolites were observed in excreta extracts from BDE-99 dosed birds. Cumulative transfers based on bioavailability of BDE-99, -153, and -209 to eggs were 17%, 34%, and 15%, respectively. Egg residues were primarily present in yolk (12.3%, 23.5%, and 2.1% of the total dose for BDE-99, -153, and -209, respectively). Adipose, skin, ova, intestine, and thigh muscle contained the highest levels of radioactive tissue residues. These studies demonstrate movement of PBDE residues into edible tissues and eggs of laying hens.

A computational structural biology study to understand the impact of mutation on structure–function relationship of inward-rectifier potassium ion channel Kir6.2 in human

Type 2 diabetes (T2D) is clinically characterized via hyperglycemia. Polymorphism rs5219 in the KCNJ11 gene is a risk factor for developing T2D in humans. KCNJ11 encodes the ‘inward-rectifier potassium ion channel (Kir6.2)’. However, because of the absence of the complete crystal/NMR structures of Kir6.2 proteins, insight into its structure and function and its interaction with diverse ligands remain elusive to date. Therefore, a computational approach was employed for predicting the best plausible ‘three-dimensional’ structure of Kir6.2 as well as for studying the influence of mutation (p. GLU23LYS) on both architectures as well as the function of Kir6.2 employing simulation studies. Results obtained revealed that though, with increased time, ‘Gibbs free energy’ becomes positive, residues in wild type Kir6.2 experiences less random movement as compared to mutant Kir6.2. The less random movement of residues in wild type Kir6.2 represents the standard coupling between open and closing of ‘KATP channel’ and thus the normal secretion of insulin. The more dispersed motion of mutant Kir6.2 residues represents ‘overactivity’ of the ‘KATP channel’ and thus insulin ‘under-secretion’. Further, molecular docking and simulation studies identified two phytochemicals/drugs, namely, A-348441 and chushizisin I, which retains the wild type property of Kir6.2 after binding with mutant protein. Unlike A-348441, this is for the first time, the present study is reporting about the plausible anti-diabetic property of chushizisin I. As these two phytochemicals/drugs, namely, A-348441 and chushizisin I, have passed ADMET test, in the near future, they may be utilized as anti-diabetic drugs after further investigation. Communicated by Ramaswamy H. Sarma

Conformational changes in Apolipoprotein N-acyltransferase (Lnt)

Lipoproteins are important components of the cell envelope and are responsible for many essential cellular functions. They are produced by the post-translational covalent attachment of lipids that occurs via a sequential 3-step process controlled by three integral membrane enzymes. The last step of this process, unique to Gram-negative bacteria, is the N-acylation of the terminal cysteine by Apolipoprotein N-acyltransferase (Lnt) to form the final mature lipoprotein. Here we report 2 crystal forms of Lnt from Escherichia coli. In one form we observe a highly dynamic arm that is able to restrict access to the active site as well as a covalent modification to the active site cysteine consistent with the thioester acyl-intermediate. In the second form, the enzyme crystallized in an open conformation exposing the active site to the environment. In total we observe 3 unique Lnt molecules that when taken together suggest the movement of essential loops and residues are triggered by substrate binding that could control the interaction between Lnt and the incoming substrate apolipoprotein. The results provide a dynamic context for residues shown to be central for Lnt function and provide further insights into its mechanism.