Results 81 to 90 of about 993,526 (301)

Domain orientation in the RNA helicase YxiN and the role of conformational changes for RNA unwinding [PDF]

, 2010
The RNA helicase YxiN from Bacillus subtilis is a member of the family of DEAD box proteins. YxiN is able to unwind RNA double strands in an ATP-dependent manner. The ability to catalyse RNA rearrangement is in vivo presumably necessary for the bacterial
Karow, Anne R.
core   +1 more source

Cellular conditions of weakly chelated magnesium ions strongly promote RNA stability and catalysis

Nature Communications, 2018
The concentration of divalent cations is well-known to influence molecular processes such as enzymatic activity and RNA folding. Here the authors attempt to reproduce physiological conditions for RNA folding in vitro and establish an important ...
Ryota Yamagami, Jamie L. Bingaman, Erica A. Frankel, Philip C. Bevilacqua   +3 more
doaj   +1 more source

RNA foldings and Stuck Knots

, 2022
We study RNA foldings and investigate their topology using a combination of knot theory and embedded rigid vertex graphs. Knot theory has been helpful in modeling biomolecules, but classical knots place emphasis on a biomolecule's entanglement while ignoring their intrachain interactions.
Ceniceros, Jose, Elhamdadi, Mohamed, Komissar, Josef, Lahrani, Hitakshi   +3 more
openaire   +2 more sources

Partial depletion of plasminogen activator inhibitor‐1 decreases subcutaneous fat cell hypertrophy and liver cholesterol in high‐fat‐fed female mice

FEBS Letters, EarlyView.
Obesity raises blood levels of PAI‐1, a protein linked to metabolic dysfunction‐associated steatotic liver disease in people with obesity. In female mice fed a high‐fat diet, partially lowering PAI‐1 led to smaller subcutaneous fat cells and lower liver cholesterol, without changing body weight or insulin sensitivity.
Claudia E. Ramirez Bustamante, Robert Sharp, Pradip K. Saha, Elizabeth S. Anaya, Elizabeth L. Lieu, Evelyn L. de Groot, Pooja Patel, Mi Jeong Heo, Aaron R. Cox, Kang Ho Kim, Sean M. Hartig   +10 more
wiley   +1 more source

Structural insights into the dynamics and function of the C-terminus of the E. coli RNA chaperone Hfq [PDF]

, 2011
The hexameric Escherichia coli RNA chaperone Hfq (Hfq(Ec)) is involved in riboregulation of target mRNAs by small trans-encoded RNAs. Hfq proteins of different bacteria comprise an evolutionarily conserved core, whereas the C-terminus is variable in ...
Beich-Frandsen, Mads (Department of Structural and Computational Biology, Centre for Molecular Biology, University of Vienna), Kontaxis, Georg (Department of Structural and Computational Biology, Centre for Molecular Biology, University of Vienna), Blasi, U., Rajkowitsch, L., Miles, Andrew (Birkbeck College), Sjöblom, Björn (Department of Structural and Computational Biology, Centre for Molecular Biology, University of Vienna), Miles, Andrew J., Svergun, D.I., Kloiber, K., Kristina Djinović-Carugo, Vecerek, B., Karin Kloiber, Konarev, P.V., Lukas Rajkowitsch, Hämmerle, Hermann Konrad (Department of Biochemistry and Cell Biology, Centre for Molecular Biology, University of Vienna), Georg Kontaxis, Bläsi, Udo (Department of Microbiology, Immunobiology and Genetics, Centre for Molecular Biology, University of Vienna), Djinovic-Carugo, K., Robert Konrat, Branislav Večerek, Konarev, Peter V. (EMBL Hamburg), Andrew J. Miles, Kloiber, Karin (Department of Structural and Computational Biology, Centre for Molecular Biology, University of Vienna), Rajkowitsch, Lukas (Department of Biochemistry and Cell Biology, Centre for Molecular Biology, University of Vienna), Udo Bläsi, Wallace, Bonnie A., Svergun, D. I., Petr V. Konarev, Svergun, Dimitri I. (EMBL Hamburg), Björn Sjöblom, Hammerle, H., Mads Beich-Frandsen, Wallace, B. A., Sjoblom, B., Miles, A. J., Konrat, Robert (Department of Structural and Computational Biology, Centre for Molecular Biology, University of Vienna), Vecerek, Branislav (Department of Microbiology, Immunobiology and Genetics, Centre for Molecular Biology, University of Vienna), Dimitri I. Svergun, B. A. Wallace, Beich Frandsen, M., Djinovic Carugo, K., Konarev, P. V., Beich-Frandsen, M., Konrat, R., Djinovic-Carugo, Kristina (Department of Structural and Computational Biology, Centre for Molecular Biology, University of Vienna), Hermann Hämmerle, Kontaxis, G.   +46 more
core   +1 more source

Multi-objective genetic algorithm for pseudoknotted RNA sequence design

Frontiers in Genetics, 2012
RNA inverse folding is a computational technology for designing RNA sequences which fold into a user-specified secondary structure. Although pseudoknots are functionally important motifs in RNA structures, less reports concerning the inverse folding of ...
Akito eTaneda
doaj   +1 more source

Synergistic perspectives—How single‐molecule biophysics complement biochemical understanding

FEBS Letters, EarlyView.
In this review, we discuss how ensemble biochemistry and single‐molecule approaches are complementary, outline commonly used single‐molecule techniques, and illustrate their relevance through two representative case studies: chromatin organization by SMC complexes and pathway choice during DNA double‐strand break repair.
Sara De Bragança, Eline L. Jansen, Jorine M. Eeftens   +2 more
wiley   +1 more source

Dissecting the influence of Mg2+ on 3D architecture and ligand-binding of the guanine-sensing riboswitch aptamer domain [PDF]

, 2010
Long-range tertiary interactions determine the three-dimensional structure of a number of metabolite-binding riboswitch RNA elements and were found to be important for their regulatory function. For the guanine-sensing riboswitch of the Bacillus subtilis
Wöhnert, Jens, Buck, Janina, Schwalbe, Harald (Prof. Dr.), Noeske, Jonas   +3 more
core   +1 more source

RNA inverse folding using Monte Carlo tree search

BMC Bioinformatics, 2017
Background Artificially synthesized RNA molecules provide important ways for creating a variety of novel functional molecules. State-of-the-art RNA inverse folding algorithms can design simple and short RNA sequences of specific GC content, that fold ...
Xiufeng Yang, Kazuki Yoshizoe, Akito Taneda, Koji Tsuda   +3 more
doaj   +1 more source

From junk to function — How weak selection in eukaryotes builds new parts and drives genomic complexity

FEBS Letters, EarlyView.
How do genomes gain new functional parts? In eukaryotes, which tend to evolve under weak selection, much of the genome is junk. Palazzo and Qiu borrow the logic of Markov chains to show how non‐functional DNA becomes functional through the appearance of intermediate states, which arise due to epistasis, buffering, and biochemical messiness, allowing ...
Alexander F. Palazzo, Yi Qiu
wiley   +1 more source