Results 111 to 120 of about 12,203 (191)

Correcting pervasive errors in RNA crystallography through enumerative structure prediction

, 2012
Three-dimensional RNA models fitted into crystallographic density maps exhibit pervasive conformational ambiguities, geometric errors and steric clashes. To address these problems, we present enumerative real-space refinement assisted by electron density
AT Brunger, DJ Mandell, F DiMaio, F DiMaio, Fang-Chieh Chou, J Praznikar, JA Cruz, JJ Headd, JS Richardson, KS Keating, M Forconi, MD Winn, N Ban, P Gendron, P Sripakdeevong, Parin Sripakdeevong, PD Adams, PV Afonine, R Das, R Das, Rhiju Das, RJ Read, Sergey M Dibrov, SM Dibrov, Thomas Hermann, VB Chen, VB Chen, X Wang   +27 more
core   +1 more source

Small-Molecule-Binding Riboswitches

Microbiology Spectrum, 2018
ABSTRACT RNA is a versatile biomolecule capable of transferring information, taking on distinct three-dimensional shapes, and reacting to ambient conditions. RNA molecules utilize a wide range of mechanisms to control gene expression. An example of such regulation is riboswitches.
Thea S, Lotz, Beatrix, Suess
openaire   +2 more sources

Riboswitches: Fold and Function

Chemistry & Biology, 2006
Riboswitches in the 5'-untranslated regions of mRNAs cotranscriptionally couple ligand binding and gene regulation. In this issue of Chemistry & Biology, Lemay et al. describe folding of a key tertiary interaction in the adenine riboswitch and its mechanistic consequences.
Gilbert, Sunny D., Batey, Robert T.
openaire   +2 more sources

Insights into the cotranscriptional and translational control mechanisms of the Escherichia coli tbpA thiamin pyrophosphate riboswitch

Communications Biology
Riboswitches regulate gene expression by modulating their structure upon metabolite binding. These RNA orchestrate several layers of regulation to achieve genetic control.
Jonathan P. Grondin, Mélanie Geffroy, Maxime Simoneau-Roy, Adrien Chauvier, Pierre Turcotte, Patrick St-Pierre, Audrey Dubé, Julie Moreau, Eric Massé, J. Carlos Penedo, Daniel A. Lafontaine   +10 more
doaj   +1 more source

Abundance and functional diversity of riboswitches in microbial communities

BMC Genomics, 2007
Background Several recently completed large-scale enviromental sequencing projects produced a large amount of genetic information about microbial communities ('metagenomes') which is not biased towards cultured organisms.
Gelfand Mikhail S, Vitreschak Alexey G, Kazanov Marat D   +2 more
doaj   +1 more source

Evolving methods for rational de novo design of functional RNA molecules

, 2019
Artificial RNA molecules with novel functionality have many applications in synthetic biology, pharmacy and white biotechnology. The de novo design of such devices using computational methods and prediction tools is a resource-efficient alternative to ...
Findeiß, Sven, Günzel, Christian, Hammer, Stefan, Mörl, Mario   +3 more
core   +1 more source

Mammalian RNA switches: Molecular rheostats in gene regulation, disease, and medicine

Computational and Structural Biotechnology Journal, 2019
Alteration of RNA structure by environmental signals is a fundamental mechanism of gene regulation. For example, the riboswitch is a noncoding RNA regulatory element that binds a small molecule and causes a structural change in the RNA, thereby ...
Kadiam C. Venkata Subbaiah, Omar Hedaya, Jiangbin Wu, Feng Jiang, Peng Yao   +4 more
doaj   +1 more source

Identifying RNA contacts from SHAPE-MaP by partial correlation analysis [PDF]

, 2014
In a recent paper Siegfried et al. published a new sequence-based structural RNA assay that utilizes mutational profiling to detect base pairing (MaP).
Doudna, Jennifer, Pachter, Lior, Tambe, Akshay   +2 more
core   +3 more sources

Mechanistic analysis of Riboswitch Ligand interactions provides insights into pharmacological control over gene expression

Nature Communications
Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Understanding the mechanisms by which small molecules impact riboswitch activity is key to developing potent, selective ligands for these and ...
Shaifaly Parmar, Desta Doro Bume, Colleen M. Connelly, Robert E. Boer, Peri R. Prestwood, Zhen Wang, Henning Labuhn, Krishshanthi Sinnadurai, Adeline Feri, Jimmy Ouellet, Philip Homan, Tomoyuki Numata, John S. Schneekloth   +12 more
doaj   +1 more source

Scaffold-enabled high-resolution cryo-EM structure determination of RNA

Nature Communications
Cryo-EM structure determination of protein-free RNAs has remained difficult with most attempts yielding low to moderate resolution and lacking nucleotide-level detail.
Daniel B. Haack, Boris Rudolfs, Shouhong Jin, Alexandra Khitun, Kevin M. Weeks, Navtej Toor   +5 more
doaj   +1 more source