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Total 36193 results found since Jan 2013.

Reshaping of the conformational search of a protein by the chaperone trigger factor
& Sander J. Tans Protein folding is often described as a search process, in which polypeptides explore different conformations to find their native structure. Molecular chaperones are known to improve folding yields by suppressing aggregation between polypeptides before this conformational search starts, as well as by rescuing misfolds after it ends. Although chaperones have long been speculated to also affect the conformational search itself—by reshaping the underlying folding landscape along the folding trajectory—direct experimental evidence has been scarce so far. In Escherichia coli, the general c...
Source: Nature - July 7, 2013 Category: Research Authors: Alireza MashaghiGünter KramerPhilipp BechtluftBeate Zachmann-BrandArnold J. M. DriessenBernd BukauSander J. Tans Tags: Letter Source Type: research

Dynamics of chromosomal target search by a membrane-integrated one-component receptor
by Linda Martini, Sophie Brameyer, Elisabeth Hoyer, Kirsten Jung, Ulrich Gerland Membrane proteins account for about one third of the cellular proteome, but it is still unclear how dynamic they are and how they establish functional contacts with cytoplasmic interaction partners. Here, we consider a membrane-integrated one-component receptor that also acts as a transcriptional activator, and analyze how it kinetically locates its specific binding site on the genome. We focus on the case of CadC, the pH receptor of the acid stress response Cad system inE. coli. CadC is a prime example of a one-component signaling protein th...
Source: PLoS Computational Biology - February 4, 2021 Category: Biology Authors: Linda Martini Source Type: research

Reshaping of the conformational search of a protein by the chaperone trigger factor
Nature advance online publication 07 July 2013. doi:10.1038/nature12293 Authors: Alireza Mashaghi, Günter Kramer, Philipp Bechtluft, Beate Zachmann-Brand, Arnold J. M. Driessen, Bernd Bukau & Sander J. Tans Protein folding is often described as a search process, in which polypeptides explore different conformations to find their native structure. Molecular chaperones are known to improve folding yields by suppressing aggregation between polypeptides before this conformational search starts, as well as by rescuing misfolds after it ends. Although chaperones have long been speculated to also affect the conformation...
Source: Nature AOP - July 7, 2013 Category: Research Authors: Alireza MashaghiGünter KramerPhilipp BechtluftBeate Zachmann-BrandArnold J. M. DriessenBernd BukauSander J. Tans Tags: Letter Source Type: research

Scoping Review on Search Queries and Social Media for Disease Surveillance: A Chronology of Innovation
Conclusions: The use of search queries and social media for disease surveillance are relatively recent phenomena (first reported in 2006). Both the tools themselves and the methodologies for exploiting them are evolving over time. While their accuracy, speed, and cost compare favorably with existing surveillance systems, the primary challenge is to refine the data signal by reducing surrounding noise. Further developments in digital disease surveillance have the potential to improve sensitivity and specificity, passively through advances in machine learning and actively through engagement of users. Adoption, even as suppor...
Source: Journal of Medical Internet Research - July 18, 2013 Category: Journals (General) Authors: Theresa Marie BernardoAndrijana RajicIan YoungKatie RobiadekMai T PhamJulie A Funk Source Type: research

Large-Scale Recurrent Neural Network Based Modelling of Gene Regulatory Network Using Cuckoo Search-Flower Pollination Algorithm.
Authors: Mandal S, Khan A, Saha G, Pal RK Abstract The accurate prediction of genetic networks using computational tools is one of the greatest challenges in the postgenomic era. Recurrent Neural Network is one of the most popular but simple approaches to model the network dynamics from time-series microarray data. To date, it has been successfully applied to computationally derive small-scale artificial and real-world genetic networks with high accuracy. However, they underperformed for large-scale genetic networks. Here, a new methodology has been proposed where a hybrid Cuckoo Search-Flower Pollination Algorithm...
Source: Advances in Bioinformatics - March 20, 2016 Category: Bioinformatics Tags: Adv Bioinformatics Source Type: research

Using SQL Databases for Sequence Similarity Searching and Analysis.
Authors: Pearson WR, Mackey AJ Abstract Relational databases can integrate diverse types of information and manage large sets of similarity search results, greatly simplifying genome-scale analyses. By focusing on taxonomic subsets of sequences, relational databases can reduce the size and redundancy of sequence libraries and improve the statistical significance of homologs. In addition, by loading similarity search results into a relational database, it becomes possible to explore and summarize the relationships between all of the proteins in an organism and those in other biological kingdoms. This unit describes ...
Source: Current Protocols in Bioinformatics - September 14, 2017 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

RecA: Regulation and Mechanism of a Molecular Search Engine.
Abstract Homologous recombination maintains genomic integrity by repairing broken chromosomes. The broken chromosome is partially resected to produce single-stranded DNA (ssDNA) that is used to search for homologous double-stranded DNA (dsDNA). This homology driven 'search and rescue' is catalyzed by a class of DNA strand exchange proteins that are defined in relation to Escherichia coli RecA, which forms a filament on ssDNA. Here, we review the regulation of RecA filament assembly and the mechanism by which RecA quickly and efficiently searches for and identifies a unique homologous sequence among a vast excess o...
Source: Trends in Biochemical Sciences - May 3, 2016 Category: Biochemistry Authors: Bell JC, Kowalczykowski SC Tags: Trends Biochem Sci Source Type: research

Recurrent neural network-based modeling of gene regulatory network using elephant swarm water search algorithm.
Abstract Correct inference of genetic regulations inside a cell from the biological database like time series microarray data is one of the greatest challenges in post genomic era for biologists and researchers. Recurrent Neural Network (RNN) is one of the most popular and simple approach to model the dynamics as well as to infer correct dependencies among genes. Inspired by the behavior of social elephants, we propose a new metaheuristic namely Elephant Swarm Water Search Algorithm (ESWSA) to infer Gene Regulatory Network (GRN). This algorithm is mainly based on the water search strategy of intelligent and social...
Source: Journal of Bioinformatics and Computational Biology - June 13, 2017 Category: Bioinformatics Authors: Mandal S, Saha G, Pal RK Tags: J Bioinform Comput Biol Source Type: research

A search for the in trans role of GraL, an Escherichia coli small RNA.
Abstract Small RNA are very important post-transcriptional regulators in both, bacteria and eukaryotes. One of such sRNA is GraL, encoded in the greA leader region and conserved among enteric bacteria. Here, we conducted a bioinformatics search for GraL's targets in trans and validated our findings in vivo by constructing fusions of probable targets with lacZ and measuring their activity when GraL was overexpressed. Only one target's activity (nudE) decreased under those conditions and was thus selected for further analysis. In the absence of GraL and greA, the nudE::lacZ fusion's β-galactosidase activity was inc...
Source: Acta Biochim Pol - March 12, 2018 Category: Biochemistry Authors: Dylewski M, Ćwiklińska M, Potrykus K Tags: Acta Biochim Pol Source Type: research

DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid.
Abstract Transcription factors must diffuse through densely packed and coiled DNA to find their binding sites. Using a coarse-grained model of DNA and lac repressor (LacI) in the Escherichia coli nucleoid, simulations were performed to examine how LacI diffuses in such a space. Despite the canonical picture of LacI diffusing rather freely, in reality the DNA is densely packed, is not rigid but highly mobile, and the dynamics of DNA dictates to a great extent the LacI motion. A possibly better picture of unbound LacI motion is that of gated diffusion, where DNA confines LacI in a cage, but LacI can move between cag...
Source: Biophysical Journal - June 6, 2017 Category: Physics Authors: Chow E, Skolnick J Tags: Biophys J Source Type: research

Kinetics of dCas9 target search in Escherichia coli
How fast can a cell locate a specific chromosomal DNA sequence specified by a single-stranded oligonucleotide? To address this question, we investigate the intracellular search processes of the Cas9 protein, which can be programmed by a guide RNA to bind essentially any DNA sequence. This targeting flexibility requires Cas9 to unwind the DNA double helix to test for correct base pairing to the guide RNA. Here we study the search mechanisms of the catalytically inactive Cas9 (dCas9) in living Escherichia coli by combining single-molecule fluorescence microscopy and bulk restriction-protection assays. We find that it takes a...
Source: ScienceNOW - September 28, 2017 Category: Science Authors: Jones, D. L., Leroy, P., Unoson, C., Fange, D., Curic, V., Lawson, M. J., Elf, J. Tags: Biochemistry reports Source Type: news

Search for shorter portions of the proline-rich antimicrobial peptide fragment Bac5(1-25) that retain antimicrobial activity by blocking protein synthesis.
Abstract The spreading of antibiotic-resistant pathogens boosted the search for new antimicrobial drugs. Proline-rich antimicrobial peptides are promising lead compounds for the development of next-generation antibiotics, due to their very low cytotoxicity and their good antimicrobial activity targeting the bacterial ribosome. Bac5(1-25) is a N-terminal fragment of the bovine proline-rich antimicrobial peptide Bac5 whose mode of action has been recently described. In this work we tested a number of Bac5(1-25) fragments and we characterized their antimicrobial activity against Escherichia coli, Acinetobacter bauman...
Source: ChemMedChem - January 7, 2019 Category: Chemistry Authors: Mardirossian M, Sola R, Degasperi M, Scocchi M Tags: ChemMedChem Source Type: research

The search of potential inhibitors of the AcrAB-TolC system of multidrug-resistant Escherichia coli: an in silico approach.
Abstract The number of infections caused by multidrug antibiotic resistance (MDR) species is increasing globally. The efflux pump system, AcrAB-TolC, confers Escherichia coli resistance to many antibiotics and results in poor treatment outcomes. Different rational drug design techniques were employed to search for a safe and effective AcrAB-TolC system inhibitor. Ligand docking was performed to analyze the binding of different ArcB substrates and/or inhibitors in the different AcrAB crystal structure binding sites. The validated docking site using the established docking preferences was used to perform virtual hig...
Source: Applied Microbiology and Biotechnology - June 16, 2019 Category: Microbiology Authors: Abdel-Halim H, Al Dajani A, Abdelhalim A, Abdelmalek S Tags: Appl Microbiol Biotechnol Source Type: research

Quick and clean: Cracking sentences encoded in E. coli by LC–MS/MS, de novo sequencing, and dictionary search
In this study, we faced the challenge of deciphering a protein that has been designed and expressed by E. coli in such a way that the amino acid sequence encodes two concatenated English sentences. The letters ‘O’ and ‘U’ in the sentence are both replaced by ‘K’ in the protein. The sequence cannot be found online and carried to-be-discovered modifications. With limited information in hand, to solve the challenge, we developed a workflow consisting of bottom-up proteomics, de novo sequencing and a bioinformatics pipeline for data processing and searching for frequently appearing words. We assembled a complete fi...
Source: EuPA Open Proteomics - July 30, 2019 Category: Bioinformatics Source Type: research

Immunohistochemical search for viral and bacterial antigens in Crohn's disease
Conclusions: Of the agents demonstrated in this search, none was located in granulomas or inflamed lymphatics. Finding the common gut microbes, E. coli and clostridia, in the mucus of patients and controls was not unexpected. The minor focal staining of E. coli and clostridia does not suggest a primary role for these pathogens in CD. Positive staining for listeria in patients and controls may very well represent cross reactivity rather than specific identification.
Source: Journal of Critical Care - April 27, 2012 Category: Gastroenterology Authors: William S. Magin, Herbert J. Van Kruiningen, Jean-Frédéric Colombel Tags: Regular papers Source Type: research