Identification patterns of Trichoderma strains using morphological characteristics,phylogenetic analyses and lignocellulolytic activities

Molecular Biology Reports - Trichoderma is a genus of soil-borne fungus with an abundance of reports of its economic importance in the agriculture industry. Thus, the correct identification of...     

R248Q mutation—Beyond p53‐DNA binding

R248 in the DNA binding domain (DBD) of p53 interacts directly with the minor groove of DNA. Earlier nuclear magnetic resonance (NMR) studies indicated that the R248Q mutation resulted in conformation changes in parts of DBD far from the mutation site. However, how information propagates from the mutation site to the rest of the DBD is still not well understood. We performed a series of all‐atom molecular dynamics (MD) simulations to dissect sterics and charge effects of R248 on p53‐DBD conformation: (i) wild‐type p53 DBD; (ii) p53 DBD with an electrically neutral arginine side‐chain; (iii) p53 DBD with R248A; (iv) p53 DBD with R248W; and (v) p53 DBD with R248Q. Our results agree well with experimental observations of global conformational changes induced by the R248Q mutation. Our simulations suggest that both charge‐ and sterics are important in the dynamics of the loop (L3) where the mutation resides. We show that helix 2 (H2) dynamics is altered as a result of a change in the hydrogen bonding partner of D281. In turn, neighboring L1 dynamics is altered: in mutants, L1 predominantly adopts the recessed conformation and is unable to interact with the major groove of DNA. We focused our attention the R248Q mutant that is commonly found in a wide range of cancer and observed changes at the zinc‐binding pocket that might account for the dominant negative effects of R248Q. Furthermore, in our simulations, the S6/S7 turn was more frequently solvent exposed in R248Q, suggesting that there is a greater tendency of R248Q to partially unfold and possibly lead to an increased aggregation propensity. Finally, based on the observations made in our simulations, we propose strategies for the rescue of R248Q mutants. Proteins 2015; 83:2240–2250. © 2015 Wiley Periodicals, Inc.     

Discovery of Rab1 binding sites using an ensemble of clustering methods

Targeting non‐native‐ligand binding sites for potential investigative and therapeutic applications is an attractive strategy in proteins that share common native ligands, as in Rab1 protein. Rab1 is a subfamily member of Rab proteins, which are members of Ras GTPase superfamily. All Ras GTPase superfamily members bind to native ligands GTP and GDP, that switch on and off the proteins, respectively. Rab1 is physiologically essential for autophagy and transport between endoplasmic reticulum and Golgi apparatus. Pathologically, Rab1 is implicated in human cancers, a neurodegenerative disease, cardiomyopathy, and bacteria‐caused infectious diseases. We have performed structural analyses on Rab1 protein using a unique ensemble of clustering methods, including multi‐step principal component analysis, non‐negative matrix factorization, and independent component analysis, to better identify representative Rab1 proteins than the application of a single clustering method alone does. We then used the identified representative Rab1 structures, resolved in multiple ligand states, to map their known and novel binding sites. We report here at least a novel binding site on Rab1, involving Rab1‐specific residues that could be further explored for the rational design and development of investigative probes and/or therapeutic small molecules against the Rab1 protein. Proteins 2017; 85:859–871. © 2016 Wiley Periodicals, Inc.     

Sequencing and expression of the gene encoding the Clostridium stercorarium beta-xylosidase Xyl43B in Escherichia coli

The Clostridium stercorarium F-9 xyl43B gene encoding the beta-xylosidase Xyl43B consists of an open reading frame of 1,491 nucleotides that encodes a putative protein, classified in family 43, of 497 amino acids with a predicted molecular weight of 56,355. The deduced amino acid sequence of Xyl43B has sequence similarity with beta-xylosidases from Bacteriodes thetaiotaomicron (57% sequence identity), Prevotella ruminicola (45%), Streptomyces coelicolor (40%), and Clostridium acetobutylicum (36%), all of which have been classified in family 43 of the glycoside hydrolases. Xyl43B was purified from a recombinant Escherichia coli and characterized. The optimum pH of the purified enzyme was 3.5 and it was stable over pH from 3.0 to 8.0. Its optimum temperature was 80 degrees C and it showed thermostability in the temperature range from 50 to 70 degrees C. Xyl43B had a K(m) of 6.2 mM and a V(max) of 15 micromol min(-1) mg(-1) for p-nitrophenyl-beta-D-xylopyranoside.     

Conformational dynamics of capping protein and interaction partners: simulation studies

Capping protein (CP) is important for the regulation of actin polymerization. CP binds to the barbed end of the actin filament and prevents actin polymerization. This interaction is modulated through competitive binding by regulatory proteins such as myotrophin (V-1) and the capping protein interacting (CPI) motif from CARMIL. The binding site of myotrophin overlaps with the region of CP that binds to the barbed end of actin filament, whereas CPI binds at a distant site. The binding of CPI to the myotrophin-CP complex dissociates myotrophin from CP. Detailed multicopy molecular dynamics simulations suggest that the binding of CPI shifts the conformational equilibria of CP away from states that favor myotrophin binding. This shift is underpinned by allosteric effects where CPI inhibits CP through suppression of flexibility and disruption of concerted motions that appear to mediate myotrophin binding. Accompanying these effects are changes in electrostatic interactions, notably those involving residue K142β, which appears to play a critical role in regulating flexibility. In addition, accessibility of the site on CP for binding the key hydrophobic residue W8 of myotrophin is modulated by CPI. These results provide insights into the modulation of CP by CPI and myotrophin and indicate the mechanism by which CPI drives the dissociation of the myotrophin-CP complex.     

Increasing CO2 concentration impact upon nutrient absorption and removal efficiency of supra intensive shrimp pond wastewater by marine microalgae Tetraselmis chui

Abstract

The objective of this study was to investigate the effect of increasing CO₂ concentration on the growth and the capability of Tetraselmis chui. in removal of nitrate, ammonium and phosphate from shrimp pond wastewater (SPWW). The factorial experimental design was used with the treatment of SPWW percentage in culture medium, namely: 100% SPWW, 75% SPWW + 25% Sea Water (SW) and 75% SW + 25% SPWW coupled with three CO₂ concentration treatments: 390?ppm, 550?ppm and 1000?ppm using CO₂ system. Growth of T. chui. for lengh of cultivation period tended to be higher at treatments of 390?ppm CO₂ and 100% SPWW, however there was a declining growth over period of cultivation for both treatments. The growth rate of T. chui was higher for all percentage of SPWW treatments in culture medium at 390?ppm CO₂ concentration compared to other percentage of SPWW treatments and CO₂ concentration treatments. There was a decreasing of growth rate with increasing CO₂ concentration at 100% SPWW and 75% SPWW + 25% SW in culture medium. Nitrogen removal efficiency and removal rate by T. chui. were strongly affected by CO₂ concentration. However, there was no significant effect of increasing CO₂ concentration to removal efficiency and rate of PO₄ by T. chui.     

The production of poly(3-hydroxybutyrate) [P(3HB)] by a newly isolated Bacillus sp. ST1C using liquid waste from biodiesel production

A newly isolated poly(3-hydroxybutyrate) [P(3HB)] producing strain, ST1C, was identified as Bacillus aryabhattai based on its morphological, biochemical and molecular characteristics. It synthesized and accumulated relatively high amounts of P(3HB). The aim of this work was to establish if it could convert an inexpensive liquid waste product from the production of biodiesel, biodiesel liquid waste (BLW), to P(3HB). Using a mineral salt medium (MSM) containing 2.0 % (v/v) glycerol present in the BLW and both normal batch and a draw and fill culture method, B. aryabhattai ST1C produced a maximum P(3HB) content and biomass concentration of 72.31 % dry cell weight (DCW) and 7.24 g/L, respectively, over a 24 h cultivation period in the draw and fill cultivation method. From 24 h to the end of cultivation at 72 h both the P(3HB) content and the biomass concentrations continuously reduced. Concentrations of glycerol in the BLW in this MSM above 3.0 % (v/v) or from pure glycerol (PG) or with an added NaCl concentration of greater than 3.0 % significantly reduced both the maximum P(3HB) content and the biomass concentrations.