Docking Peptides on Proteins: How to Open a Lock, in the Dark, with a Flexible Key

In this issue of Structure, Schindler et al. (2015b) present us with pepATTRACT, a protocol embedded in the ATTRACT docking engine for fully blind flexible peptide docking on proteins that yields high quality models of complexes

Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking

Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA. We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success

Toxicity of phenolic compounds extracted from bark residues of different ages

In Quebec, Canada, industrial bark wastelands cover several hundred hectares of land. Bark residue that has piled up for decades tends to remain free of vegetation for years. To assess the revegetation potential of such sites, we sought to determine those factors responsible for poor plant growth. Phenolic compounds from fresh to 20-year-old bark residues were extracted with four solvents and quantified by high-performance liquid chromatography (HPLC). We simulated solutions (mixtures of standard phenolic compounds) to evaluate the potential toxic effects of phenolic compounds on the rhizobial growth, germination index, plant growth, nodule number, and nitrogen fixation activity of two legume species under laboratory conditions. The concentration of individual phenolic compounds varied from none detected to 350 µg/g bark residue. The extracted phenolic compounds differed among solvents and bark residues. The highest concentration of total phenolic compounds was from fresh bark; most of these were soluble in water or 0.1 M NaOH. For older bark residues, the total phenolic content depended on solvent strength, generally in the order of 2.0 M NaOH > 0.1 M NaOH = hot water > cold water. The biological activity of the simulated bark extracts was not established with the rhizobial growth inhibition test but with the germination index and rhizobium–legume symbiosis tests. With these, the toxicity of the simulated phenolic extracts decreased from fresh to the older bark residues. Plant dry weight, nodule number, and nitrogen fixation activity of vetch (Vicia sativa L.) were less negatively affected by high concentrations of phenolics than birdsfoot trefoil (Lotus corniculatus L.), although birdsfoot trefoil grew at lower concentrations. The rhizobium–legume symbiosis has potential for revegetating bark wastelands with less than 1 year old and older bark residues

PTools: an opensource molecular docking library

<p>Abstract</p> <p>Background</p> <p>Macromolecular docking is a challenging field of bioinformatics. Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from scratch for every new software application.</p> <p>Results</p> <p>We present an object-oriented Python/C++ library to help the development of new docking methods. This library contains low-level routines like PDB-format manipulation functions as well as high-level tools for docking and analyzing results. We also illustrate the ease of use of this library with the detailed implementation of a 3-body docking procedure.</p> <p>Conclusion</p> <p>The PTools library can handle molecules at coarse-grained or atomic resolution and allows users to rapidly develop new software. The library is already in use for protein-protein and protein-DNA docking with the ATTRACT program and for simulation analysis. This library is freely available under the GNU GPL license, together with detailed documentation.</p

The poor homology stringency in the heteroduplex allows strand exchange to incorporate desirable mismatches without sacrificing recognition in vivo

RecA family proteins are responsible for homology search and strand exchange. In bacteria, homology search begins after RecA binds an initiating single-stranded DNA (ssDNA) in the primary DNA-binding site, forming the presynaptic filament. Once the filament is formed, it interrogates double-stranded DNA (dsDNA). During the interrogation, bases in the dsDNA attempt to form Watson–Crick bonds with the corresponding bases in the initiating strand. Mismatch dependent instability in the base pairing in the heteroduplex strand exchange product could provide stringent recognition; however, we present experimental and theoretical results suggesting that the heteroduplex stability is insensitive to mismatches. We also present data suggesting that an initial homology test of 8 contiguous bases rejects most interactions containing more than 1/8 mismatches without forming a detectable 20 bp product. We propose that, in vivo, the sparsity of accidental sequence matches allows an initial 8 bp test to rapidly reject almost all non-homologous sequences. We speculate that once the initial test is passed, the mismatch insensitive binding in the heteroduplex allows short mismatched regions to be incorporated in otherwise homologous strand exchange products even though sequences with less homology are eventually rejected

Isolation of free-living dinitrogen-fixing bacteria and their activity in compost containing de-inking paper sludge

Knowledge of the microbiology of dinitrogen (N2)-fixing bacteria in compost rich in de-inking paper sludge (DPS) is limited. Dinitrogen (N2)-fixing bacteria from DPS composts were isolated and studied for their N2-fixing activity in vitro and in vivo. Two Gram-negative N2-fixing isolates were identified as Pseudomonas. At 20 C, both isolates revealed that N2-fixing activity was higher than that of three arctic Pseudomonas strains. Their N2-fixing activity was found to occur between 18 and 25 C, a pattern that was similar to the reference isolate Azotobacter ATCC 7486. Composts successfully showed N2-fixing activity after carbohydrate amendments both with and without inoculation of a N2-fixing isolate. These results suggest that DPS composts support N2-fixing bacteria and that N2-fixing activity is dependent on a usable carbohydrate source. 2005 Elsevier Ltd. All rights reserved.Keywords: Dinitrogen-fixing bacteria; Compost; Paper sludge; Glucose; Pseudomonas balearica; Pseudomonas putid

Role of AmiA in the Morphological Transition of Helicobacter pylori and in Immune Escape

The human gastric pathogen Helicobacter pylori is responsible for peptic ulcers and neoplasia. Both in vitro and in the human stomach it can be found in two forms, the bacillary and coccoid forms. The molecular mechanisms of the morphological transition between these two forms and the role of coccoids remain largely unknown. The peptidoglycan (PG) layer is a major determinant of bacterial cell shape, and therefore we studied H. pylori PG structure during the morphological transition. The transition correlated with an accumulation of the N-acetyl-D-glucosaminyl-β(1,4)-N-acetylmuramyl-L-Ala–D-Glu (GM-dipeptide) motif. We investigated the molecular mechanisms responsible for the GM-dipeptide motif accumulation, and studied the role of various putative PG hydrolases in this process. Interestingly, a mutant strain with a mutation in the amiA gene, encoding a putative PG hydrolase, was impaired in accumulating the GM-dipeptide motif and transforming into coccoids. We investigated the role of the morphological transition and the PG modification in the biology of H. pylori. PG modification and transformation of H. pylori was accompanied by an escape from detection by human Nod1 and the absence of NF-κB activation in epithelial cells. Accordingly, coccoids were unable to induce IL-8 secretion by AGS gastric epithelial cells. amiA is, to our knowledge, the first genetic determinant discovered to be required for this morphological transition into the coccoid forms, and therefore contributes to modulation of the host response and participates in the chronicity of H. pylori infection

Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments

Homologous recombination is a fundamental process enabling the repair of double-strand breaks with a high degree of fidelity. In prokaryotes, it is carried out by RecA nucleofilaments formed on single-stranded DNA (ssDNA). These filaments incorporate genomic sequences that are homologous to the ssDNA and exchange the homologous strands. Due to the highly dynamic character of this process and its rapid propagation along the filament, the sequence recognition and strand exchange mechanism remains unknown at the structural level. The recently published structure of the RecA/DNA filament active for recombination (Chen et al., Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structure, Nature 2008, 453, 489) provides a starting point for new exploration of the system. Here, we investigate the possible geometries of association of the early encounter complex between RecA/ssDNA filament and double-stranded DNA (dsDNA). Due to the huge size of the system and its dense packing, we use a reduced representation for protein and DNA together with state-of-the-art molecular modeling methods, including systematic docking and virtual reality simulations. The results indicate that it is possible for the double-stranded DNA to access the RecA-bound ssDNA while initially retaining its Watson–Crick pairing. They emphasize the importance of RecA L2 loop mobility for both recognition and strand exchange

What docking studies tell us about the role of disordered protein fragments in macromolecular assembly

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