Predicting protein pKa by environment similarity

A statistical method to predict protein pK_a has been developed by using the 3D structure of a protein and a database of 434 experimental protein pK_a values. Each pK_a in the database is associated with a fingerprint that describes the chemical environment around an ionizable residue. A computational tool, MoKaBio, has been developed to identify automatically ionizable residues in a protein, generate fingerprints that describe the chemical environment around such residues, and predict pK_a from the experimental pK_a values in the database by using a similarity metric. The method, which retrieved the pK_a of 429 of the 434 ionizable sites in the database correctly, was crossvalidated by leave‐one‐out and yielded root mean square error (RMSE) = 0.95, a result that is superior to that obtained by using the Null Model (RMSE 1.07) and other well‐established protein pK_a prediction tools. This novel approach is suitable to rationalize protein pK_a by comparing the region around the ionizable site with similar regions whose ionizable site pK_a is known. The pK_a of residues that have a unique environment not represented in the training set cannot be predicted accurately, however, the method offers the advantage of being trainable to increase its predictive power. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

TGFbeta protects mesoangioblasts from apoptosis via sphingosine kinase-1 regulation

Mesoangioblasts are vessel-derived progenitor cells that can be induced to differentiate into different cell types of the mesoderm such as muscle and bone. Here we examined the role of transforming growth factor-beta (TGFbeta), a pleiotropic cytokine that plays a major role in development and specifically induces smooth muscle differentiation of mesoangioblasts, in the regulation of death and survival of these cells. TGFbeta exerts a marked anti-apoptotic action in mesoangioblasts with a mechanism involving regulation of sphingosine kinase 1 (SphK1), one of the isoforms responsible for S1P formation. Treatment with the cytokine efficaciously protected mesoangioblasts from apoptosis induced by serum starvation or staurosporine treatment assessed by various means such as activation of caspase-3, determination of cytoplasmic histone-associated-DNA-fragments and PE-AnnexinV staining. The protective action of TGFbeta from staurosporine-induced apoptosis was strongly reduced when the SphK activity was inhibited by drugs, when SphK1 but not SphK2 was downregulated by specific siRNA and when a SphK1 dominant negative mutant was overexpressed. Staurosporine treatment induced down-regulation of both SphK isoforms and TGFbeta rescued SphK1 but not SphK2 expression. Interestingly, TGFbeta strongly enhanced SphK activity during staurosporine-induced cell death. Both TGFbeta-induced SphK1 up-regulation and TGFbeta anti-apoptotic action were found to be dependent on p42/44 MAPK activation.     

Differential substrate specificity of group I and group II chaperonins in the archaeon Methanosarcina mazei

Chaperonins are macromolecular machines that assist in protein folding. The archaeon Methanosarcina mazei has acquired numerous bacterial genes by horizontal gene transfer. As a result, both the bacterial group I chaperonin, GroEL, and the archaeal group II chaperonin, thermosome, coexist. A proteome‐wide analysis of chaperonin interactors was performed to determine the differential substrate specificity of GroEL and thermosome. At least 13% of soluble M. mazei proteins interact with chaperonins, with the two systems having partially overlapping substrate sets. Remarkably, chaperonin selectivity is independent of phylogenetic origin and is determined by distinct structural and biochemical features of proteins. GroEL prefers well‐conserved proteins with complex α/β domains. In contrast, thermosome substrates comprise a group of faster‐evolving proteins and contain a much wider range of different domain folds, including small all‐α and all‐β modules, and a greater number of large multidomain proteins. Thus, the group II chaperonins may have facilitated the evolution of the highly complex proteomes characteristic of eukaryotic cells.     

Discovery of the imidazo[1,5-a][1,2,4]-triazolo[1,5-d][1,4]benzodiazepine scaffold as a novel,potent and selective GABAA α5 inverse agonist series

Through iterative design cycles we have discovered a number of novel new classes where the imidazo[1,5-a][1,2,4]-triazolo[1,5-d][1,4]benzodiazepine was deemed the most promising GABA_A α5 inverse agonist class with potential for cognitive enhancement. This class combines a modest subtype binding selectivity with inverse agonism and has the most favourable molecular properties for further lead optimisation towards a central nervous system (CNS) acting medicine.     

Suppressiveness to Fusarium oxysporum f. sp. radicis lycopersici in re-used perlite and perlite–peat substrates in soilless tomatoes

This work reports the occurrence of suppressiveness to Fusarium oxysporum f. sp. radicis lycopersici (FORL) on recycled perlite and perlite–peat mix from closed and open soilless systems. Nine soilless systems were sampled from three different sites in Northern and Southern Italy and different parameters, including sampling site, growing period before sampling, electric conductivity of the nutrient solution, tomato cultivar, and irrigation system were considered. The effects on seed germination and FORL incidence on tomato seedlings were finally assessed with or without additional artificial inoculation of the pathogen and with or without autoclaving the samples prior to inoculation. Suppression of FORL was experimentally evaluated with a technique already adopted for rockwool. Results collected on perlite and perlite–peat confirmed the possibility to reduce FORL severity on recycled substrates. Only the composition of the substrate (perlite, perlite–peat mix) and the disinfestation did affect the incidence of FORL. Suppression of FORL was observed in not disinfected recycled perlite–peat substrates while a reduction of FORL incidence was also been recorded in disinfected and recycled perlite. Disease incidence decreased from an average ranging from 44.4% to 61.9% in new perlite to 2.5–36.3% in recycled one. Similarly disease incidence decreased from an average ranging from 35.9% to 75.2% in new perlite–peat mix to 0.4–26.4% in recycled perlite–peat mix. In conclusion the recorded data suggest the possibility to consider FORL suppression as a predictable phenomenon when recycled substrates (perlite, perlite–peat mix) are adopted.     

Tumor Suppressor Density-enhanced Phosphatase-1 (DEP-1) Inhibits the RAS Pathway by Direct Dephosphorylation of ERK1/2 Kinases

Density-enhanced phosphatase-1 (DEP-1) is a trans-membrane receptor protein-tyrosine phosphatase that plays a recognized prominent role as a tumor suppressor. However, the mechanistic details underlying its function are poorly understood because its primary physiological substrate(s) have not been firmly established. To shed light on the mechanisms underlying the anti-proliferative role of this phosphatase, we set out to identify new DEP-1 substrates by a novel approach based on screening of high density peptide arrays. The results of the array experiment were combined with a bioinformatics filter to identify eight potential DEP-1 targets among the proteins annotated in the MAPK pathway. In this study we show that one of these potential targets, the ERK1/2, is indeed a direct DEP-1 substrate in vivo. Pulldown and in vitro dephosphorylation assays confirmed our prediction and demonstrated an overall specificity of DEP-1 in targeting the phosphorylated tyrosine 204 of ERK1/2. After epidermal growth factor stimulation, the phosphorylation of the activation loop of ERK1/2 can be modulated by changing the concentration of DEP-1, without affecting the activity of the upstream kinase MEK. In addition, we show that DEP-1 contains a KIM-like motif to recruit ERK1/2 proteins by a docking mechanism mediated by the common docking domain in ERK1/2. ERK proteins that are mutated in the conserved docking domain become insensitive to DEP-1 de-phosphorylation. Overall this study provides novel insights into the anti-proliferative role of this phosphatase and proposes a new mechanism that may also be relevant for the regulation of density-dependent growth inhibition.DEP-1⁴ (also known as CD148, HPTPη, and PTPRJ) is a class III receptor protein-tyrosine phosphatase, characterized by eight fibronectin type III repeats within the extracellular domain, a trans-membrane region, and a single cytosolic catalytic domain (1, 2). DEP-1 is expressed in all human hematopoietic cell lineages and was shown to negatively regulate T cell activation. In addition, several epithelial cell types display DEP-1 on their cell membranes (3). Homozygous DEP-1 mutant mice die before embryonic day 11.5, displaying severe defects in vascular organization (4). Interestingly, DEP-1 expression levels were found to augment with increased cell density (2), suggesting a role for this tyrosine phosphatase in sensing cell-cell contacts and in density-dependent growth inhibition (5). Moreover, accumulating evidence supports a prominent role for DEP-1 as a tumor suppressor as it negatively regulates cell proliferation and is poorly expressed in many cancer cell lines (6–10). The observed anti-proliferative effect may be accounted for by the ability of DEP-1 to down-regulate growth factor signaling through the dephosphorylation of various receptor tyrosine kinases, such as PDGFR, VEGFR2, and MET (11–13), resulting in quenching of the downstream RAS-MAPK pathway. However, given the complex pleiotropic functions of DEP-1, it is also possible that additional regulatory circuits mediated by yet unknown DEP-1 substrates may play a functional role in contact inhibition and control of cell proliferation.A variety of in vivo and in vitro approaches has led us to propose a number of DEP-1 substrates as mediators of its function. These include PDGFR, p120 catenin (CTND1), hepatocyte growth factor receptor, SRC kinase, VEGFR2, phosphatidylinositol 3-kinase regulatory subunit α (P85A), and RET receptor kinase (5, 11–16).Here we report a novel, unbiased strategy based on the screening of high density phosphopeptide arrays for their ability to bind phosphatase trapping mutants. A large portion of the phosphoproteome could be explored by this approach, thus unveiling a long list of potential substrates. A selected list of potentially relevant substrates has been obtained by applying a bioinformatics context filter. In this study we report the detailed characterization of one of these substrates, and we propose that DEP-1 modulates the RAS pathway by directly dephosphorylating Tyr-204 of ERK1/2. In addition, we show that the efficient removal of the phosphate group from Tyr-204 requires the integrity of a docking site on the ERK1/2 proteins.     

Performance of olive mill solid waste as a constituent of the substrate in commercial cultivation of Agaricus bisporus

The feasibility of using olive mill waste (OMW) as an ingredient in the substrate used for cultivation of Agaricus bisporus (Lange) Sing. was studied in a large-scale cultivation trial, concerning 2500 m² of mushroom growing area, at a specialized mushroom farm. Standard commercial cultivation technique involving compost preparation, spawning, casing and harvesting was used. The performance indicators such as mushroom yield, biological efficiency, market quality as well as horticultural value of the spent compost showed that the compost prepared with OMW was superior to the control compost in all the categories. The OMW-amended substrate supported higher populations of beneficial microorganisms especially, actinomycetes which enabled the breakdown of the compost ingredients. It is suggested that OMW is a suitable ingredient for the preparation of mushroom substrate. We have demonstrated that conversion of OMW (a liability) into value-added mushroom substrate (an asset) is an effective waste management tool in oleaculture.