Population density analysis for determining the protonation state of the catalytic dyad in BACE1-tertiary carbinamine-based inhibitor complex

BACE1 is an aspartyl protease with a very relevant role in medicinal chemistry related to Alzheimer Disease since it has demonstrated to be a promising therapeutic target for inhibition and possible control for the progress of the peptide accumulation characteristic of this pathology. The enzymatic activity of this protein is given by the aspartic dyad, Asp93 and Asp289, which can adopt several protonation states depending on the chemical nature of its inhibitors, this is, monoprotonated, diprotonated and di-deprotonated states. In the present study, the analysis of the population density, for a series of protein-inhibitor molecular dynamics simulations, was carried out to identify the most feasible protonation state adopted by the catalytic dyad in the presence of tertiary carbinamine (TC) transition state analog inhibitors. The results revealed that the monoprotonated Asp289i state, in which the Asp93 and Asp289 residue side chains are deprotonated and protonated on the inner oxygen, respectively, is the most preferred in the presence of TC family inhibitors. This result was obtained after evaluating, for all 9 possible protonation state configurations, the individual and combined population densities of a set of parameters sensitive to protonation state of the Aspartic dyad, using an X-ray experimental BACE1/TC crystallographic structure as reference. This case study demonstrates again the usefulness of the concept of population density as a quantitative tool to establish the most stable system settings, among all possible, by measuring the level of occurrence of simultaneous events obtained from a sampling over time. These results will help to clear the phenomena related to the TCs inhibitory pathway, as well as assist in the design of better TC inhibitors against Alzheimer’s protease.     

Molecular characterization influencing metal resistance in the Cupriavidus/Ralstonia genomes

Our environment is stressed with a load of heavy and toxic metals. Microbes, abundant in our environment, are found to adapt well to this metal-stressed condition. A comparative study among five Cupriavidus/Ralstonia genomes can offer a better perception of their evolutionary mechanisms to adapt to these conditions. We have studied codon usage among 1051 genes common to all these organisms and identified 15 optimal codons frequently used in highly expressed genes present within 1051 genes. We found the core genes of Cupriavidus metallidurans CH34 have a different optimal codon choice for arginine, glycine and alanine in comparison with the other four bacteria. We also found that the synonymous codon usage bias within these 1051 core genes is highly correlated with their gene expression. This supports that translational selection drives synonymous codon usage in the core genes of these genomes. Synonymous codon usage is highly conserved in the core genes of these five genomes. The only exception among them is C. metallidurans CH34. This genomewide shift in synonymous codon choice in C. metallidurans CH34 may have taken place due to the insertion of new genes in its genomes facilitating them to survive in heavy metal containing environment and the co-evolution of the other genes in its genome to achieve a balance in gene expression. Structural studies indicated the presence of a longer N-terminal region containing a copper-binding domain in the cupC proteins of C. metallidurans CH3 that helps it to attain higher binding efficacy with copper in comparison with its orthologs.     

Deriving C4 photosynthetic parameters from combined gas exchange and chlorophyll fluorescence using an Excel tool: theory and practice

The higher photosynthetic potential of C₄ plants has led to extensive research over the past 50 years, including C₄‐dominated natural biomes, crops such as maize, or for evaluating the transfer of C₄ traits into C₃ lineages. Photosynthetic gas exchange can be measured in air or in a 2% Oxygen mixture using readily available commercial gas exchange and modulated PSII fluorescence systems. Interpretation of these data, however, requires an understanding (or the development) of various modelling approaches, which limit the use by non‐specialists. In this paper we present an accessible summary of the theory behind the analysis and derivation of C₄ photosynthetic parameters, and provide a freely available Excel Fitting Tool (EFT), making rigorous C₄ data analysis accessible to a broader audience. Outputs include those defining C₄ photochemical and biochemical efficiency, the rate of photorespiration, bundle sheath conductance to CO₂ diffusion and the in vivo biochemical constants for PEP carboxylase. The EFT compares several methodological variants proposed by different investigators, allowing users to choose the level of complexity required to interpret data. We provide a complete analysis of gas exchange data on maize (as a model C₄ organism and key global crop) to illustrate the approaches, their analysis and interpretation. © 2015 John Wiley & Sons Ltd     

Effects of Acetylcholine, Cytochalasin B and Amiprophosmethyl on Phloem Transport in Radish （Raphanus sativas）

We investigated the role of the ＂sieve tube-companion cell complex＂ lining the tube periphery, particularly the microfilament and microtubule, in assisting the pushing of phloem sap flow. We made a simple phloem transport system with a living radish plant, in which the conducting channel was exposed for local treatment with chemicals that are effective in modulating protoplasmic movement （acetylcholine, （ACh） a neurotransmitter in animals and insects; cytochalasin B, （CB） a specific inhibitor of many cellular responses that are mediated by microfilament systems and amiprophos-methyl, （APM） a specific inhibitor of many cellular responses that are mediated by microtubule systems）. Their effects on phloem transport were estimated by two experimental devices： （i） a comparison of changes in the amount of assimilates in terms of carbohydrates and ^14C-labeled photosynthetic production that is left in the leaf blade of treated plants; and （ii） distribution patterns of ^14C-labeled leaf assimilates in the phloem transport system. The results indicate that CB and APM markedly inhibited the transfer of photosynthetic product from leaf to root via the leaf vein, while ACh enhanced the transfer of photosynthetic product in low concentrations （5.0×10^-4 mol/L） but inhibited it in higher concentrations （2.0×10^-3 mol/L） from leaf to root via the leaf vein. Autoradiograph imaging clearly reveals that ACh treatment is more effective than the control, and both CB and APM treatments effectively inhibit the passage of radioactive assimilates. All of the results support the postulation that the peripheral protoplasm in the sieve tube serves not only as a passive semi-permeable membrane, but is also directly involved in phloem transport.     

Identification of assembly precursors to photosystems emitting fluorescence at 683 nm and 687 nm by cryogenic fluorescence microspectroscopy

Photosystem I (PSI) and photosystem II (PSII) play key roles in photoinduced electron-transfer reaction in oxygenic photosynthesis. Assemblies of these PSs can be initiated by illumination of the etiolated seedlings (greening). The study aimed to identify specific fluorescence spectral components relevant to PSI and PSII assembly intermediates emerging in greening seedlings of Zea mays, a typical C4 plant. The different PSII contents between the bundle sheath (BS) and mesophyll (M) cells were utilized to spectrally isolate the precursors to PSI and PSII. The greening Zea mays leaf thin sections were observed with the cryogenic microscope combined with a spectrometer. With the aid of the singular-value decomposition analysis, we could identify four independent fluorescent species, SAS677, SAS685, SAS683, and SAS687, named after their fluorescence peak wavelengths. SAS677 and SAS685 are the dominant components after the 30-minute greening, and the distributions of these components showed no clear differences between M and BS cells, indicating immature cell differentiation in this developing stage. On the other hand, the 1-hour greening resulted in reduced distributions of SAS683 in BS cells leading us to assign this species to PSII precursors. The 2-hour greening induced the enrichment of SAS687 in BS cells suggesting its PSI relevance. Similarity in the peak wavelengths of SAS683 and the reported reaction center of PSII implied their connection. SAS687 showed an intense sub-band at around 740 nm, which can be assigned to the emission from the red chlorophylls specific to the mature PSI.     

Mechanotransduction-Dependent Control of Stereocilia Dimensions and Row Identity in Inner Hair Cells

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Relationship Between Amino Acid Properties and Protein Stability: Buried Mutations

In order to understand the mechanism of protein stability and to develop a simple method for predicting mutation-induced stability changes, we analyzed the relationship between stability changes caused by buried mutations and changes in 48 amino acid properties. As expected from the importance of hydrophobicity, properties reflecting hydrophobicity are strongly correlated with the stability of proteins. We found that subgroup classification based on secondary structure increased correlations significantly, and mutations within -strand segments correlated better than did those in -helical segments, which may result from stronger hydrophobicity of the -strands. Multiple regression analyses incorporating combinations of three properties from among all possible combinations of the 48 properties increased the correlation coefficient to 0.88 and by an average of 13% for all data sets. Analyzing the stability of tryptophan synthase mutants with Glu49 replaced by all other residues except Arg revealed that combining buriedness, solvent-accessible surface area for denatured protein, and unfolding Gibbs free energy change increased the correlation to 0.95. Consideration of sequence and structural information (neighboring residues in sequence and in space) did not significantly strengthen the correlations in buried mutations, suggesting that nonspecific interactions dominate in the interior of proteins.     

Interaction of Serotonin1A Receptors from Bovine Hippocampus with Tertiary Amine Local Anesthetics

1. We have examined the interaction of tertiary amine local anesthetics with the bovine hippocampal serotonin1A (5-HT1A) receptor, an important member of the G-protein-coupled receptor superfamily. 2. The local anesthetics inhibit specific agonist and antagonist binding to the 5-HT1A receptor at a clinically relevant concentration range of the anesthetics. This is accompanied by a concomitant reduction in the binding affinity of the 5-HT1A receptor to the agonist. Interestingly, the extent of G-protein coupling of the receptor is reduced in the presence of the local anesthetics. 3. Fluorescence polarization measurements using depth-dependent fluorescent probes show that procaine and lidocaine do not show any significant change in membrane fluidity. On the other hand, tetracaine and dibucaine were found to alter fluidity of the membrane as indicated by a fluorescent probe which monitors the headgroup region of the membrane. 4. The local anesthetics showed inhibition of agonist binding to the 5-HT1A receptor in membranes depleted of cholesterol more or less to the same extent as that of control membranes in all cases. This suggests that the inhibition in ligand binding to the 5-HT1A receptor brought about by local anesthetics is independent of the membrane cholesterol content. 5. Our results on the effects of the local anesthetics on the ligand binding and G-protein coupling of the 5-HT1A receptor support the possibility that G-protein-coupled receptors could be involved in the action of local anesthetics.     

Ficus rubiginosa 'variegata', a chlorophyll-deficient chimera with mosaic patterns created by cell divisions from the outer meristematic layer

BACKGROUND AND AIMS: Sections leaves of Ficus rubiginosa 'Variegata' show that it is a chimera with a chlorophyll deficiency in the second layer of the leaf meristem (GWG structure). Like other Ficus species, it has a multiseriate epidermis on the adaxial and abaxial sides of the leaf, formed by periclinal cell divisions as well as anticlinal divisions. The upper and lower laminae of the leaf often exhibit small dark and light green patches of tissue overlying internal leaf tissue. METHODS: The distribution of chlorophyll in transverse sections of typical leaves was determined by fluorescence microscopy. KEY RESULTS: Patches of dark and light green tissue which arise in the otherwise colourless palisade and spongy mesophyll tissue in the entire leaf are due to further cell divisions arising from the bundle sheath which is associated with major vascular bundles or from the green multiseriate epidermis. Leaves produced in winter exhibit more patches of green tissue than leaves which expand in mid-summer. Many leaves produced in summer have no spotting and appear like a typical GWG chimera. There is a strong relationship between the number of patches on the adaxial side of leaves and the number on the abaxial side, showing that the cell division in upper and lower layers of leaves is strongly coordinated. In both winter and summer, there are fewer patches on the abaxial side of leaves compared with the adaxial side, indicating that periclinal and anticlinal cell divisions from the outer meristematic layer are less frequent in the lower layers of leaf tissue. Most of the patches are small (<1 mm in longest dimension) and thus the cell divisions which form them occur late in leaf development. Leaves which exhibit large patches generally have them on both sides of the leaves. CONCLUSION: In this cultivar, the outer meristematic layer appears to form vascular bundle sheaths and associated internal leaf tissue in the entire leaf lamina.     

Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing

A novel method for ab initio prediction of protein tertiary structures, PROFESY (PROFile Enumerating SYstem), is proposed. This method utilizes the secondary structure prediction information of a query sequence and the fragment assembly procedure based on global optimization. Fifteen-residue-long fragment libraries are constructed using the secondary structure prediction method PREDICT, and fragments in these libraries are assembled to generate full-length chains of a query protein. Tertiary structures of 50 to 100 conformations are obtained by minimizing an energy function for proteins, using the conformational space annealing method that enables one to sample diverse low-lying local minima of the energy. We apply PROFESY for benchmark tests to proteins with known structures to demonstrate its feasibility. In addition, we participated in CASP5 and applied PROFESY to four new-fold targets for blind prediction. The results are quite promising, despite the fact that PROFESY was in its early stages of development. In particular, PROFESY successfully provided us the best model-one structure for the target T0161.