CYP4CL2 Confers Metabolic Resistance to Pyridaben in the Citrus Pest Mite Panonychus citri

The citrus red mite Panonychus citri has developed strong resistance to acaricides. Cytochrome P450 monooxygenases (P450s) can detoxify pesticides and are involved in pesticide resistance in many insects. Here, a pyridaben-resistant P. citri strain showed cross-resistance to cyenopyrafen, bifenazate, fenpyroximate, and tolfenpyrad. Piperonyl butoxide, a P450 inhibitor, significantly increased the toxicity of pyridaben to resistant (Pyr_Rs) and susceptible (Pyr_Control) P. citri strains. P450 activity was significantly higher in Pyr_Rs than in Pyr_Control. Analyses of RNA-Seq data identified a P450 gene (CYP4CL2) that is potentially involved in pyridaben resistance. Consistently, it was up-regulated in two field-derived resistant populations (CQ_WZ and CQ_TN). RNA interference-mediated knockdown of CYP4CL2 significantly decreased the pyridaben resistance in P. citri. Transgenic Drosophila melanogaster expressing CYP4CL2 showed increased pyridaben resistance. Molecular docking analysis showed that pyridaben could bind to several amino acids at substrate recognition sites in CYP4CL2. These findings shed light on P450-mediated pyridaben resistance in pest mites.

Phaeodactylum tricornutum: An established model species for diatom molecular research and an emerging chassis for algal synthetic biology

Diatoms are prominent and highly diverse microalgae in aquatic environments. Compared with other diatom species, Phaeodactylum tricornutum is an "atypical diatom" displaying three different morphotypes and lacking the usual silica shell. Despite being of limited ecological relevance, its ease of growth in the laboratory and well-known physiology, alongside the steady increase in genome-enabled information coupled with effective tools for manipulating gene expression, have meant it has gained increased recognition as a powerful experimental model for molecular research on diatoms. We here present a brief overview of how over the last 25 years P. tricornutum has contributed to the unveiling of fundamental aspects of diatom biology, while also emerging as a new tool for algal process engineering and synthetic biology.

Linking Redox Characteristics to Dissolved Organic Matter Derived from Different Biowaste Composts: A Theoretical Modeling Approach Based on FT-ICR MS Analysis

Compost dissolved organic matter (DOM) is a complex mixture of redox-active organic molecules that impact various biogeochemical processes in soil environments. However, the impact of chemical complexity (heterogeneity and chemodiversity) on the electron accepting capacity (EAC) and electron donating capacity (EDC) of DOM molecules remains unclear, which hinders our ability to predict their environmental behavior and redox properties. In this study, the applicability of Vienna Soil Organic Matter Modeler 2 (VSOMM2) to the composting system based on the FT-ICR MS data has been validated. A molecular modeling approach using VSOMM2 and Schrödinger software was developed to quantitatively assess the redox sites and molecular interactions of compost DOM. Compost DOM molecules are categorized into three distinct groups based on their heterogeneous origins. In addition, we have developed 18 molecular models of compost DOM based on the links of molecules to EAC/EDC. Finally, Ar-OH, quinone, Ar-SH, and Ar-NH2 were identified as the redox sites; noncovalent contacts, H bonds, salt bridges, and aromatic-H bonds might be significant electronic transmission channels of compost DOM. Our findings contribute to the development of precise regulatory methods for functional molecules within compost DOM, providing the fine standards for composts matching specific ecosystem service requirements.

Interfacial Shear Strength of Single-Walled Carbon Nanotubes-Cement Composites from Molecular Dynamics and Finite Element Studies

Carbon nanotubes (CNTs) are nanometer-sized structures that can be used to reinforce cement matrices. The extent to which the mechanical properties are improved depends on the interfacial characteristics of the resulting materials, that is, on the interactions established between the CNTs and the cement. The experimental characterization of these interfaces is still impeded by technical limitations. The use of simulation methods has a great potential to give information about systems lacking experimental information. In this work, molecular dynamics (MD) and molecular mechanics (MM) were used in conjunction with finite element simulations to study the interfacial shear strength (ISS) of a structure formed by a pristine single-walled CNT (SWCNT) inserted in a tobermorite crystal. The results show that, for a constant SWCNT length, ISS values increase when the SWCNT radius increases, while for a constant SWCNT radius, shorter lengths enhance ISS values.

Unified Modeling Approach for Quantifying the Proton and Metal Binding Ability of Soil Dissolved Organic Matter

Soil dissolved organic matter (DOM) is composed of a mass of complex organic compounds in soil solutions and significantly affects a range of (bio)geochemical processes in soil environment. However, how the chemical complexity (i.e., heterogeneity and chemodiversity) of soil DOM molecules affects their proton and metal binding ability remains unclear, which limits our ability for predicting the environmental behavior of DOM and metals. In this study, we developed a unified modeling approach for quantifying the proton and metal binding ability of soil DOM based on Cu titration experiments, Fourier transform ion cyclotron resonance mass spectrometry data, and molecular modeling method. Although soil DOM samples from different regions have enormously heterogeneous and diverse properties, we found that the molecules of soil DOM can be divided into three representative groups according to their Cu binding capacity. Based on the molecular models for individual molecular groups and the relative contributions of each group in each soil DOM, we were able to further develop molecular models for all soil DOM to predict their molecular properties and proton and metal binding ability. Our results will help to develop mechanistic models for predicting the reactivity of soil DOM from various sources.

Integration of genome and transcriptome reveal molecular regulation mechanism of early flowering trait in Prunus genus (Prunus mume and Prunus persica)

Flowering time is crucial for the survival and reproduction. Prunus genus belongs to the Rosaceae family and includes several hundred species of flowering trees and shrubs with important ornamental and economic values. However, the molecular mechanism underlying early flowering in Prunus genus is unclear. Here, we utilized the genome and transcriptome of P. mume and P. persica to explore the transcriptional regulation mechanism of early flowering. Comparative genomics found that genes accounting for 92.4% of the total P. mume genome and 91.2% of the total P. persica genome belonged to orthogroups. A total of 19,169 orthogroups were found between P. mume and P. persica, including 20,431 corresponding orthologues and 20,080 collinearity gene pairs. A total of 305 differentially expressed genes (DEGs) associated with early flowering were found, among which FT, TLI65, and NAP57 were identified as hub genes in the early flowering regulation pathway. Moreover, we identified twenty-five transcription factors (TFs) from nine protein families, including MADS-box, AP2/ERF, and MYB. Our results provide insights into the underlying molecular model of flowering time regulation in Prunus genus and highlight the utility of multi-omics in deciphering the properties of the inter-genus plants.

Glycyrrhizic Acid Derivatives Bearing Amino Acid Residues in the Carbohydrate Part as Dengue Virus E Protein Inhibitors: Synthesis and Antiviral Activity

Dengue virus (DENV) is one of the most geographically distributed mosquito-borne flaviviruses, like Japanese encephalitis virus (JEV), and Zika virus (ZIKV). In this study, a library of the known and novel Glycyrrhizic acid (GL) derivatives bearing amino acid residues or their methyl/ethyl esters in the carbohydrate part were synthesized and studied as DENV inhibitors in vitro using the cytopathic effect (CPE), viral infectivity and virus yield assays with DENV1 and DENV-2 in Vero E6 and A549 cells. Among the GL conjugates tested, compound hits GL-D-ValOMe 3, GL-TyrOMe 6, GL-PheOEt 11, and GL-LysOMe 21 were discovered to have better antiviral activity than GL, with IC50 values ranging from <0.1 to 5.98 μM on the in vitro infectivity of DENV1 and DENV2 in Vero E6 and A549 cells. Compound hits 3, 6, 11, and 21 had a concentration-dependent inhibition on the virus yield in Vero E6, in which GL-D-ValOMe 3 and GL-PheOEt 11 were the most active inhibitors of DENV2 yield. Meanwhile, the time-of-addition assay indicated that conjugates GL-D-ValOMe 3 and GL-PheOEt 11 exhibited a substantial decrease in the DENV2 attachment stage. Subsequently, chimeric single-round infectious particles (SRIPs) of DENV2 C-prM-E protein/JEV replicon and DENV2 prM-E/ZIKV replicon were utilized for the DENV envelope I protein-mediated attachment assay. GL conjugates 3 and 11 significantly reduced the attachment of chimeric DENV2 C-prM-E/JEV and DENV2 prM-E/ZIKV SRIPs onto Vero E6 cells in a concentration-dependent manner but did not impede the attachment of wild-type JEV CprME/JEV and ZIKV prM-E/ZIKV SRIPs, indicating the inhibition of Compounds 3 and 11 on DENV2 E-mediated attachment. Molecular docking data revealed that Compounds 3 and 11 have hydrophobic interactions within a hydrophobic pocket among the interfaces of Domains I, II, and the stem region of the DENV2 envelope (E) protein. These results displayed that Compounds 3 and 11 were the lead compounds targeting the DENV E protein. Altogether, our findings provide new insights into the structure−activity relationship of GL derivatives conjugated with amino acid residues and can be the new fundamental basis for the search and development of novel flavivirus inhibitors based on natural compounds.

Additions to Alpha-Sheet Based Hypotheses for the Cause of Alzheimer's Disease

Protein amyloid-β (Aβ) oligomers with β-sheet-like backbone (β-structured) form extracellular amyloid plaques associated with Alzheimer's disease (AD). However, the relationship to AD is not known. Some investigations suggest that the toxic Aβ component has α-sheet-like backbone (α-structured) subsequently detoxified by intracellular α-to-β conversion before plaque formation. Our objective is to compare this latter hypothesis with observations made by electron microscopy of thin sections of AD-cerebral cortex. We observe irregular, 200-2,000 nm, intracellular, lipofuscin-like inclusions. Some are light-staining and smooth. Others are dark-staining and made granular by fibers that are usually overlapping and are sometimes individually seen. Aspects unusual for lipofuscin include 1) dark and light inclusions interlocking as though previously one inclusion, 2) dark inclusion-contained 2.6 nm thick sub-fibers that are bent as though α-structured, and 3) presence of inclusions in lysosomes and apparent transfer of dark inclusion material to damaged, nearby lysosomal membranes. These data suggest the following additions to α-structure-based hypotheses: 1) Lipofuscin-associated, α-structured protein toxicity to lysosomal membranes is in the chain of AD causation; 2) α-to-β detoxification of α-structured protein occurs in lipofuscin and causes dark-to-light transition that, when incomplete, is the origin of cell-to-cell transmission essential for development of AD.

Atomic-number (Z)-correlated atomic sizes for deciphering electron microscopic molecular images

Atomic resolution transmission electron microscopy (TEM) has opened up a new era of molecular science by providing atomic video images of dynamic motions of single organic and inorganic molecules. However, the images often look different from the images of molecular models, because these models are designed to visualize the electronic properties of the molecule instead of nuclear electrostatic potentials that are felt by the e-beam in TEM imaging. Here, we propose a molecular model that reproduces TEM images using atomic radii correlated to atomic number (Z). The model serves to provide a priori a useful idea of how a single molecule, molecular assemblies, and thin crystals of organic or inorganic materials look in TEM.

With the advent of atomic resolution transmission electron microscopy (AR-TEM) achieving sub-Ångstrom image resolution and submillisecond time resolution, an era of cinematic molecular science where chemists can visually study the time evolution of molecular motions and reactions at atomistic precision has arrived. However, the appearance of experimental TEM images often differs greatly from that of conventional molecular models, and the images are difficult to decipher unless we know in advance the structure of the specimen molecules. The difference arises from the fundamental design of the molecular models that represent atomic connectivity and/or the electronic properties of molecules rather than the nuclear charge of atoms and electrostatic potentials that are felt by the e-beam in TEM imaging. We found a good correlation between the atomic number (Z) and the atomic size seen in TEM images when we consider shot noise in digital images. We propose Z-correlated (ZC) atomic radii for modeling AR-TEM images of single molecules and ultrathin crystals with which we can develop a good estimate of the molecular structure from the TEM image much more easily than with conventional molecular models. Two parameter sets were developed for TEM images recorded under high-noise (ZC_HN) and low-noise (ZC_LN) conditions. The molecular models will stimulate the imaginations of chemists planning to use AR-TEM for their research.

A Comprehensive Review of Characterization Methods for Metallurgical Coke Structures

The structure of coke affects its reactivity and strength, which directly influences its performance in the blast furnace. This review divides coke structures into chemical structure, physical structure, and optical texture according to their relevant characteristics. The focuses of this review are the current characterization methods and research status of the coke structures. The chemical structures (element composition and functional group) can be characterized by elemental analysis, Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy (Raman), X-ray photoelectron spectroscopy (XPS), and nuclear magnetic resonance imaging technology (13C NMR). The physical structures (pore structure and micro-crystallite structure) can be characterized by image method, X-ray CT imaging technique, mercury intrusion method, nitrogen gas adsorption method, X-ray diffraction method (XRD), and high-resolution transmission electron microscopy (HRTEM). The optical textures are usually divided and counted by a polarizing microscope. In the end, this review provides an idea of the construction of a coke molecular structural model, based on the above characterization. With the coke model, the evolution principles of the coke can be calculated and simulated. Hence, the coke performance can be predicted and optimized.

Application of Edible Montmorillonite Clays for the Adsorption and Detoxification of Microcystin

Exposure to microcystins (MCs) in humans and animals commonly occurs through the consumption of drinking water and food contaminated with cyanobacteria. Although studies have focused on developing water filtration treatments for MCs using activated carbon, dietary sorbents to reduce the bioavailability of MCs from the stomach and intestines have not been reported. To address this need, edible calcium and sodium montmorillonite clays were characterized for their ability to bind MC containing leucine and arginine (MC-LR) under conditions simulating the gastrointestinal tract and compared with a medical-grade activated carbon. Results of in vitro adsorption isotherms and thermodynamics showed that binding plots for MC-LR on montmorillonites fit the Langmuir model with high binding capacity, affinity, Gibbs free energy, and enthalpy. The in silico results from molecular modeling predicted that the major binding mechanisms involved electrostatics and hydrogen bonds, and that interlayers were important binding sites. The safety and detoxification efficacy of the sorbents against MC-LR were validated in a battery of living organisms, including Hydra vulgaris, Lemna minor, and Caenorhabditis elegans. The inclusion of 0.05% and 0.1% montmorillonite clays in hydra media significantly reduced MC-LR toxicity and protected hydra by 60-80%, whereas only slight protection was shown with the heat-collapsed clay. In the Lemna minor assay, montmorillonites significantly enhanced the growth of lemna, as supported by the increase in frond number, surface area, chlorophyll content, and growth rate, as well as the decrease in inhibition rate. Similar results were shown in the C. elegans assay, where montmorillonite clays reduced MC-LR effects on body length and brood size. All 3 bioassays confirmed dose-dependent protection from MC-LR, validated the in vitro and in silico findings, and suggested that edible montmorillonites are safe and efficacious binders for MC-LR. Moreover, their inclusion in diets during algal blooming seasons could protect vulnerable populations of humans and animals.

Atomic Model Structure of the NIST Monoclonal Antibody (NISTmAb) Reference Material

As monoclonal antibodies have become a vital resource in medicine, knowledge of their complex molecular structures has increased in importance. Thousands of antibody components (Fab and Fc fragments) are described in the Protein Data Bank. Whole antibodies have been imaged by electron microscopy methods and in a few cases, crystallized. The central hinge lacks a unique stable conformation and its dynamic properties are important to antibody function. Monte Carlo and molecular dynamics simulations and small-angle scattering methods have been used to analyze the wide range of configurations that are accessible to antibodies in solution. In order to support the development of antibody-based medicines, the National Institute of Standards and Technology (NIST) has released an extensively characterized IgG1κ monoclonal antibody (mAb), called the NISTmAb Reference Material 8671. To facilitate modeling of whole antibodies we now report the construction of an all-atom 3-D model of the NISTmAb.

Residues in Transmembrane Segments of the P2X4 Receptor Contribute to Channel Function and Ethanol Sensitivity

Mouse models of alcohol use disorder (AUD) revealed purinergic P2X4 receptors (P2X4Rs) as a promising target for AUD drug development. We have previously demonstrated that residues at the transmembrane (TM)–ectodomain interface and within the TM1 segment contribute to the formation of an ethanol action pocket in P2X4Rs. In the present study, we tested the hypothesis that there are more residues in TM1 and TM2 segments that are important for the ethanol sensitivity of P2X4Rs. Using site-directed mutagenesis and two electrode voltage-clamp electrophysiology in Xenopus oocytes, we found that arginine at position 33 (R33) in the TM1 segment plays a role in the ethanol sensitivity of P2X4Rs. Molecular models in both closed and open states provided evidence for interactions between R33 and aspartic acid at position 354 (D354) of the neighboring TM2 segment. The loss of ethanol sensitivity in mixtures of wild-type (WT) and reciprocal single mutants, R33D:WT and D354R:WT, versus the WT-like response in R33D-D354R:WT double mutant provided further support for this interaction. Additional findings indicated that valine at TM1 position 49 plays a role in P2X4R function by providing flexibility/stability during channel opening. Collectively, these findings identified new activity sites and suggest the importance of TM1-TM2 interaction for the function and ethanol sensitivity of P2X4Rs.

Structural analysis reveals a "molecular calipers" mechanism for a LATERAL ORGAN BOUNDARIES DOMAIN transcription factor protein from wheat

LATERAL ORGAN BOUNDARIES DOMAIN (LBD) proteins, a family of plant-specific transcription factors harboring a conserved Lateral Organ Boundaries (LOB) domain, are regulators of plant organ development. Recent studies have unraveled additional pivotal roles of the LBD protein family beyond defining lateral organ boundaries, such as pollen development and nitrogen metabolism. The structural basis for the molecular network of LBD-dependent processes remains to be deciphered. Here, we solved the first structure of the homodimeric LOB domain of Ramosa2 from wheat (TtRa2LD) to 1.9 Å resolution. Our crystal structure reveals structural features shared with other zinc-finger transcriptional factors, as well as some features unique to LBD proteins. Formation of the TtRa2LD homodimer relied on hydrophobic interactions of its coiled-coil motifs. Several specific motifs/domains of the LBD protein were also involved in maintaining its overall conformation. The intricate assembly within and between the monomers determined the precise spatial configuration of the two zinc fingers that recognize palindromic DNA sequences. Biochemical, molecular modeling, and small-angle X-ray scattering experiments indicated that dimerization is important for cooperative DNA binding and discrimination of palindromic DNA through a molecular calipers mechanism. Along with previously published data, this study enables us to establish an atomic-scale mechanistic model for LBD proteins as transcriptional regulators in plants.

The phagophore in four dimensions-a study in wood

One of the key features of macroautophagy/autophagy is the dynamic nature of the membrane rearrangements that take place during expansion of the phagophore, the sequestering compartment that matures into an autophagosome. There are various ways to depict this process, but in most cases the method ultimately relies on a two-dimensional medium. Most people working in the field of autophagy realize that the typical 'C'-shaped drawing of a phagophore is meant to represent a cup- or bowl-like structure that exists in the cell in 3 dimensions. However, explaining this concept to a lay person often leads to confusion and misinterpretation. Accordingly, we decided to generate a four-dimensional version of the expanding phagophore as a wood sculpture, that depicts this transient compartment in 3 dimensions over time.

ABBREVIATIONS

ER: endoplasmic reticulum.

A Novel Molecular Model of Plant Lectin-Induced Programmed Cell Death in Cancer

Plant lectin, a class of highly diverse non-immune origin and carbohydrate-binding proteins, has been reported to specially induce cancer cell through programmed cell death (PCD) pathways (apoptosis and/or autophagy), shedding lights on screening promising anti-cancer candidate agent for further therapeutic trials. However, the complicated molecular mechanisms by which plant lectins induced the programmed death of tumor cells, have not yet been fully clarified. Here, we summarized a novel model, based on vast amount of research, by which plant lectins eliminate various types of cancer cells via three major pathways, including a) direct ribosome inactivating, b) endocytosis-dependent mitochondrial dysfunction and c) sugar-containing receptors binding. A better understanding of the role of plant lectins played and further elucidation of the strategies targeting PCD would provide a new clue for the applications and modifications of plant lectin as a potential anti-cancer agent from bench to clinic.

Discovery of an Unexplored Protein Structural Scaffold of Serine Protease from Big Blue Octopus (Octopus cyanea): A New Prospective Lead Molecule

BACKGROUND

Serine proteases are a group of enzymes that hydrolyses the peptide bonds in proteins. In mammals, these enzymes help in the regulation of several major physiological functions such as digestion, blood clotting, responses of immune system, reproductive functions and the complement system.

OBJECTIVE

Serine proteases obtained from the venom of Octopodidae family is a relatively unexplored area of research. In the present work, we tried to effectively utilize comparative composite molecular modeling technique. Our key aim was to propose the first molecular model structure of unexplored serine protease 5 derived from big blue octopus. The other objective of this study was to analyze the distribution of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, hydrophobicity molecular surface analysis and electrostatic potential analysis with the aid of different bioinformatic tools.

METHODS

In the present study, molecular model has been generated with the help of I-TASSER suite. Afterwards the refined structural model was validated with standard methods. For functional annotation of protein molecule we used Protein Information Resource (PIR) database. Serine protease 5 of big blue octopus was analyzed with different bioinformatical algorithms for the distribution of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, hydrophobicity molecular surface analysis and electrostatic potential analysis. The functionally critical amino acids and ligand- binding site (LBS) of the proteins (modeled) were determined using the COACH program.

RESULT

The molecular model data in cooperation to other pertinent post model analysis data put forward molecular insight to proteolytic activity of serine protease 5, which helps in the clear understanding of procoagulant and anticoagulant characteristics of this natural lead molecule.

CONCLUSION

Our approach was to investigate the octopus venom protein as a whole or a part of their structure that may result in the development of new lead molecule.

Specificity of the connexin W3/4 locus for functional gap junction formation

The N-terminal (NT) domain of the connexins forms an essential transjunctional voltage (Vj) sensor and pore-forming domain that when truncated, tagged, or mutated often leads to formation of a nonfunctional channel. The NT domain is relatively conserved among the connexins though the α- and δ-group connexins possess a G2 residue not found in the β- and γ-group connexins. Deletion of the connexin40 G2 residue (Cx40G2Δ) affected the Vj gating, increased the single channel conductance (γj), and decreased the relative K(+)/Cl(-) permeability (PK/PCl) ratio of the Cx40 gap junction channel. The conserved α/β-group connexin D2/3 and W3/4 loci are postulated to anchor the NT domain within the pore via hydrophilic and hydrophobic interactions with adjacent connexin T5 and M34 residues. Cx40D3N and D3R mutations produced limited function with progressive reductions in Vj gating and noisy low γj gap junction channels that reduced the γj of wild-type Cx40 channels from 150 pS to < 50 pS when coexpressed. Surprisingly, hydrophobic Cx40 W4F and W4Y substitution mutations were not compatible with function despite their ability to form gap junction plaques. These data are consistent with minor and major contributions of the G2 and D3 residues to the Cx40 channel pore structure, but not with the postulated hydrophobic W4 intermolecular interactions. Our results indicate an absolute requirement for an amphipathic W3/4 residue that is conserved among all α/β/δ/γ-group connexins. We alternatively hypothesize that the connexin D2/3-W3/4 locus interacts with the highly conserved FIFR M1 motif to stabilize the NT domain within the pore.

Identification and characterization of wheat drought-responsive MYB transcription factors involved in the regulation of cuticle biosynthesis

A plant cuticle forms a hydrophobic layer covering plant organs, and plays an important role in plant development and protection from environmental stresses. We examined epicuticular structure, composition, and a MYB-based regulatory network in two Australian wheat cultivars, RAC875 and Kukri, with contrasting cuticle appearance (glaucousness) and drought tolerance. Metabolomics and microscopic analyses of epicuticular waxes revealed that the content of β-diketones was the major compositional and structural difference between RAC875 and Kukri. The content of β-diketones remained the same while those of alkanes and primary alcohols were increased by drought in both cultivars, suggesting that the interplay of all components rather than a single one defines the difference in drought tolerance between cultivars. Six wheat genes encoding MYB transcription factors (TFs) were cloned; four of them were regulated in flag leaves of both cultivars by rapid dehydration and/or slowly developing cyclic drought. The involvement of selected MYB TFs in the regulation of cuticle biosynthesis was confirmed by a transient expression assay in wheat cell culture, using the promoters of wheat genes encoding cuticle biosynthesis-related enzymes and the SHINE1 (SHN1) TF. Two functional MYB-responsive elements, specifically recognized by TaMYB74 but not by other MYB TFs, were localized in the TdSHN1 promoter. Protein structural determinants underlying the binding specificity of TaMYB74 for functional DNA cis-elements were defined, using 3D protein molecular modelling. A scheme, linking drought-induced expression of the investigated TFs with downstream genes that participate in the synthesis of cuticle components, is proposed.

Molecular mechanism of Zn2+ inhibition of a voltage-gated proton channel

Voltage-gated proton (Hv1) channels are involved in many physiological processes, such as pH homeostasis and the innate immune response. Zn²⁺ is an important physiological inhibitor of Hv1. Sperm cells are quiescent in the male reproductive system due to Zn²⁺ inhibition of Hv1 channels, but become active once introduced into the low-Zn²⁺-concentration environment of the female reproductive tract. How Zn²⁺ inhibits Hv1 is not completely understood. In this study, we use the voltage clamp fluorometry technique to identify the molecular mechanism of Zn²⁺ inhibition of Hv1. We find that Zn²⁺ binds to both the activated closed and resting closed states of the Hv1 channel, thereby inhibiting both voltage sensor motion and gate opening. Mutations of some Hv1 residues affect only Zn²⁺ inhibition of the voltage sensor motion, whereas mutations of other residues also affect Zn²⁺ inhibition of gate opening. These effects are similar in monomeric and dimeric Hv1 channels, suggesting that the Zn²⁺-binding sites are localized within each subunit of the dimeric Hv1. We propose that Zn²⁺ binding has two major effects on Hv1: (i) at low concentrations, Zn²⁺ binds to one site and prevents the opening conformational change of the pore of Hv1, thereby inhibiting proton conduction; and (ii) at high concentrations, Zn²⁺, in addition, binds to a second site and inhibits the outward movement of the voltage sensor of Hv1. Elucidating the molecular mechanism of how Zn²⁺ inhibits Hv1 will further our understanding of Hv1 function and might provide valuable information for future drug development for Hv1 channels.

Structural insights into SAM domain-mediated tankyrase oligomerization

Tankyrase 1 (TNKS1; a.k.a. ARTD5) and tankyrase 2 (TNKS2; a.k.a ARTD6) are highly homologous poly(ADP-ribose) polymerases (PARPs) that function in a wide variety of cellular processes including Wnt signaling, Src signaling, Akt signaling, Glut4 vesicle translocation, telomere length regulation, and centriole and spindle pole maturation. Tankyrase proteins include a sterile alpha motif (SAM) domain that undergoes oligomerization in vitro and in vivo. However, the SAM domains of TNKS1 and TNKS2 have not been structurally characterized and the mode of oligomerization is not yet defined. Here we model the SAM domain-mediated oligomerization of tankyrase. The structural model, supported by mutagenesis and NMR analysis, demonstrates a helical, homotypic head-to-tail polymer that facilitates TNKS self-association. Furthermore, we show that TNKS1 and TNKS2 can form (TNKS1 SAM-TNKS2 SAM) hetero-oligomeric structures mediated by their SAM domains. Though wild-type tankyrase proteins have very low solubility, model-based mutations of the SAM oligomerization interface residues allowed us to obtain soluble TNKS proteins. These structural insights will be invaluable for the functional and biophysical characterization of TNKS1/2, including the role of TNKS oligomerization in protein poly(ADP-ribosyl)ation (PARylation) and PARylation-dependent ubiquitylation.

The peptide agonist-binding site of the glucagon-like peptide-1 (GLP-1) receptor based on site-directed mutagenesis and knowledge-based modelling

Mutagenesis and molecular pharmacological analysis of the glucagon-like peptide-1 (GLP-1) receptor highlighted several residues involved in peptide agonist recognition. Coupled with a new molecular model of the full-length agonist-docked receptor, the binding site and a pharmacophore for agonist peptides are described.

Glucagon-like peptide-1 (7–36)amide (GLP-1) plays a central role in regulating blood sugar levels and its receptor, GLP-1R, is a target for anti-diabetic agents such as the peptide agonist drugs exenatide and liraglutide. In order to understand the molecular nature of the peptide–receptor interaction, we used site-directed mutagenesis and pharmacological profiling to highlight nine sites as being important for peptide agonist binding and/or activation. Using a knowledge-based approach, we constructed a 3D model of agonist-bound GLP-1R, basing the conformation of the N-terminal region on that of the receptor-bound NMR structure of the related peptide pituitary adenylate cyclase-activating protein (PACAP21). The relative position of the extracellular to the transmembrane (TM) domain, as well as the molecular details of the agonist-binding site itself, were found to be different from the model that was published alongside the crystal structure of the TM domain of the glucagon receptor, but were nevertheless more compatible with published mutagenesis data. Furthermore, the NMR-determined structure of a high-potency cyclic conformationally-constrained 11-residue analogue of GLP-1 was also docked into the receptor-binding site. Despite having a different main chain conformation to that seen in the PACAP21 structure, four conserved residues (equivalent to His-7, Glu-9, Ser-14 and Asp-15 in GLP-1) could be structurally aligned and made similar interactions with the receptor as their equivalents in the GLP-1-docked model, suggesting the basis of a pharmacophore for GLP-1R peptide agonists. In this way, the model not only explains current mutagenesis and molecular pharmacological data but also provides a basis for further experimental design.

From molecular signatures to predictive biomarkers: modeling disease pathophysiology and drug mechanism of action

Omics profiling significantly expanded the molecular landscape describing clinical phenotypes. Association analysis resulted in first diagnostic and prognostic biomarker signatures entering clinical utility. However, utilizing Omics for deepening our understanding of disease pathophysiology, and further including specific interference with drug mechanism of action on a molecular process level still sees limited added value in the clinical setting. We exemplify a computational workflow for expanding from statistics-based association analysis toward deriving molecular pathway and process models for characterizing phenotypes and drug mechanism of action. Interference analysis on the molecular model level allows identification of predictive biomarker candidates for testing drug response. We discuss this strategy on diabetic nephropathy (DN), a complex clinical phenotype triggered by diabetes and presenting with renal as well as cardiovascular endpoints. A molecular pathway map indicates involvement of multiple molecular mechanisms, and selected biomarker candidates reported as associated with disease progression are identified for specific molecular processes. Selective interference of drug mechanism of action and disease-associated processes is identified for drug classes in clinical use, in turn providing precision medicine hypotheses utilizing predictive biomarkers.

Biophysical aspects of cyclodextrin interaction with paraoxon

Cyclodextrins are torus-shaped polymers of glucose that can bind organophosphorous compounds such as nerve agents and pesticides. We demonstrate here that cyclodextrin can bind up to two paraoxon molecules with a K(av) of 6775 M(-1). Molecular modeling shows that the paraoxon appears to bind in polar opposite orientation and have an average binding energy of -89 Kcals/mol. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.

Stereo-selective binding of monoclonal antibodies to the poly-γ-D-glutamic acid capsular antigen of Bacillus anthracis

Bacillus anthracis is surrounded by an anti-phagocytic capsule that is entirely composed of γ-linked D-glutamic acid (γDPGA). γDPGA is required for virulence and is produced in large quantities following spore germination. We have previously described the isolation of several γDPGA-reactive mAbs. The reagents are effective in both immunoprotection and diagnostic applications. The current work was done to further investigate the specificity of γDPGA-reactive mAbs. The specificity of each mAb was characterized using surface plasmon resonance. Our results indicate that each mAb is stereoselective for binding to D-glutamic acid oligomers, but to varying degrees. In particular, mAb F26G3 is highly selective for γDPGA; alterations in stereochemistry disrupted recognition. These differences in mAb reactivity suggest that binding of γDPGA by mAb F26G3 is more specific than non-directional ionic interactions between a negatively charged antigen and a positively charged antibody.

Milk lipid secretion: recent biomolecular aspects

Neonates of most species depend on milk lipids for calories, fat-soluble vitamins, and bioactive lipid components for growth and development during the postnatal period. To meet neonatal nutrition and development needs, the mammary gland has evolved efficient mechanisms for synthesizing and secreting large quantities of lipid during lactation. Although the biochemical steps involved in milk lipid synthesis are understood, the identities of the genes mediating these steps and the molecular physiology of milk lipid production and secretion have only recently begun to be understood in detail through advances in mouse genetics, gene expression analysis, protein structural properties, and the cell biology of lipid metabolism. This review discusses emerging data about the molecular, cellular, and structural determinants of milk lipid synthesis and secretion within the context of physiological functions.

An all-atom model of the structure of human copper transporter 1

Human copper transporter 1 (hCTR1) is the major high affinity copper influx transporter in mammalian cells that also mediates uptake of the cancer chemotherapeutic agent cisplatin. A low resolution structure of hCTR1 determined by cryoelectron microscopy was recently published. Several protein structure simulation techniques were used to create an all-atom model of this important transporter using the low resolution structure as a starting point. The all-atom model provides new insights into the roles of specific residues of the N-terminal extracellular domain, the intracellular loop, and C-terminal region in metal ion transport. In particular, the model demonstrates that the central region of the pore contains four sets of methionine triads in the intramembranous region. The structure confirms that two triads of methionine residues delineate the intramembranous region of the transporter, and further identifies two additional methionine triads that are located in the extracellular N-terminal part of the transporter. Together, the four triads create a structure that promotes stepwise transport of metal ions into and then through the intramembranous channel of the transporter via transient thioether bonds to methionine residues. Putative copper-binding sites in the hCTR1 trimer were identified by a program developed by us for prediction of metal-binding sites. These sites correspond well with the known effects of mutations on the ability of the protein to transport copper and cisplatin.

Dissection of the components for PIP2 activation and thermosensation in TRP channels

Phosphatidylinositol 4,5-bisphosphate (PIP2) plays a central role in the activation of several transient receptor potential (TRP) channels. The role of PIP2 on temperature gating of thermoTRP channels has not been explored in detail, and the process of temperature activation is largely unexplained. In this work, we have exchanged different segments of the C-terminal region between cold-sensitive (TRPM8) and heat-sensitive (TRPV1) channels, trying to understand the role of the segment in PIP2 and temperature activation. A chimera in which the proximal part of the C-terminal of TRPV1 replaces an equivalent section of TRPM8 C-terminal is activated by PIP2 and confers the phenotype of heat activation. PIP2, but not temperature sensitivity, disappears when positively charged residues contained in the exchanged region are neutralized. Shortening the exchanged segment to a length of 11 aa produces voltage-dependent and temperature-insensitive channels. Our findings suggest the existence of different activation domains for temperature, PIP2, and voltage. We provide an interpretation for channel-PIP2 interaction using a full-atom molecular model of TRPV1 and PIP2 docking analysis.

A novel processive mechanism for DNA synthesis revealed by structure, modeling and mutagenesis of the accessory subunit of human mitochondrial DNA polymerase

Mitochondrial DNA polymerase (pol gamma) is the sole DNA polymerase responsible for replication and repair of animal mitochondrial DNA. Here, we address the molecular mechanism by which the human holoenzyme achieves high processivity in nucleotide polymerization. We have determined the crystal structure of human pol gamma-beta, the accessory subunit that binds with high affinity to the catalytic core, pol gamma-alpha, to stimulate its activity and enhance holoenzyme processivity. We find that human pol gamma-beta shares a high level of structural similarity to class IIa aminoacyl tRNA synthetases, and forms a dimer in the crystal. A human pol gamma/DNA complex model was developed using the structures of the pol gamma-beta dimer and the bacteriophage T7 DNA polymerase ternary complex, which suggests multiple regions of subunit interaction between pol gamma-beta and the human catalytic core that allow it to encircle the newly synthesized double-stranded DNA, and thereby enhance DNA binding affinity and holoenzyme processivity. Biochemical properties of a novel set of human pol gamma-beta mutants are explained by and test the model, and elucidate the role of the accessory subunit as a novel type of processivity factor in stimulating pol gamma activity and in enhancing processivity.

Ligand binding sites of inducible costimulator and high avidity mutants with improved function

Interaction between inducible costimulator (ICOS) and its ligand is implicated in the induction of cell-mediated and humoral immune responses. However, the molecular details of this interaction are unknown. We report here a mutagenesis analysis of residues in ICOS that are critical for ligand binding. A three-dimensional model of the extracellular immunoglobulin-like domain of ICOS was used to map the residues conserved within the CD28 family. This analysis identified a surface patch containing the characteristic "PPP" sequence and is conserved in human and mouse ICOS. Mutations in this region of human ICOS reduce or abolish ligand binding. Our results suggest that the ligand binding site in ICOS maps to a region overlapping yet distinct from the CD80/CD86 binding sites in CD28 and cytotoxic T lymphocyte antigen (CTLA)-4. Thus, the analysis suggests that differences in ligand binding specificity between these related costimulatory molecules have evolved by utilization of overlapping regions with different patterns of conserved and nonconserved residues. Two site-specific mutants generated in the course of our studies bound ICOS ligand with higher avidity than wild-type ICOS. An S76E mutant protein of ICOS blocked T cell costimulatory function of ICOS ligand and inhibited T cell response to allogeneic antigens superior to wild-type ICOS. Our studies thus identified critical residues involving in ICOS receptor-ligand interaction and provide new modulators for immune responses.

Mapping the agonist binding site of the GABAA receptor: evidence for a beta-strand

GABAA receptors, along with the receptors for acetylcholine, glycine, and serotonin, are members of a ligand-gated ion channel superfamily (Ortells and Lunt, 1995). Because of the paucity of crystallographic information for these ligand-gated channels, little is known about the structure of their binding sites or how agonist binding is transduced into channel gating. We used the substituted cysteine accessibility method to obtain secondary structural information about the GABA binding site and to systematically identify residues that line its surface. Each residue from alpha1 Y59 to K70 was mutated to cysteine and expressed with wild-type beta2 subunits in Xenopus oocytes or HEK 293 cells. The sulfhydryl-specific reagent N-biotinylaminoethyl methanethiosulfonate (MTSEA-Biotin) was used to covalently modify the cysteine-substituted residues. Receptors with cysteines substituted at positions alpha1 T60, D62, F64, R66, and S68 reacted with MTSEA-Biotin, and alpha1 F64C, R66C, and S68C were protected from reaction by agonist. We conclude that alpha1 F64, R66, and S68 line part of the GABA binding site. The alternating pattern of accessibility of consecutive engineered cysteines to reaction with MTSEA-Biotin indicates that the region from alpha1 Y59 to S68 is a beta-strand.

Mechanism of action of bacitracin: complexation with metal ion and C 55 -isoprenyl pyrophosphate

The inhibition by bacitracin of the enzymatic dephosphorylation of C(55)-isoprenyl pyrophosphate is abolished by the addition of chelating agents. If, however, the chelating agent is added after a preincubation of bacitracin with a divalent cation and the lipid substrate, then its addition has little effect, indicating that bacitracin, metal ion, and C(55)-isoprenyl pyrophosphate form a complex. Various divalent cations can participate in complex formation, but monovalent cations are ineffective. A direct demonstration of the formation of a complex between the C(55)-isoprenyl pyrophosphate and bacitracin in the presence of metal ions was obtained. Molecular models that show one possible conformation for a complex between bacitracin and the C(55)-isoprenyl pyrophosphate, in which the metal ion acts as a bridge between the two compounds, are presented.