نتایج جستجو برای: rna inverse folding
تعداد نتایج: 366102 فیلتر نتایج به سال:
Structured RNAs achieve their active states by traversing complex, multidimensional energetic landscapes. Here we probe the folding landscape of the Tetrahymena ribozyme by using a powerful approach: the folding of single ribozyme molecules is followed beginning from distinct regions of the folding landscape. The experiments, combined with small-angle x-ray scattering results, show that the lan...
Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA folding simulations, which follow the stochastic closing and opening of individual RNA helices. The numerical efficacy of these stochastic simulations relies on...
Tertiary folding of the 160-nt P4-P6 domain of the Tetrahymena group I intron RNA involves burying of substantial surface area, providing a model for the folding of other large RNA domains involved in catalysis. Stopped-flow fluorescence was used to monitor the Mg2+-induced tertiary folding of pyrene-labeled P4-P6. At 35 degrees C with [Mg2+] approximately 10 mM, P4-P6 folds on the tens of mill...
We study the stochastic folding kinetics of RNA sequences into secondary structures with a new algorithm based on the formation, dissociation, and the shifting of individual base pairs. We discuss folding mechanisms and the correlation between the barrier structure of the conformational landscape and the folding kinetics for a number of examples based on artificial and natural sequences, includ...
Large RNAs can collapse into compact conformations well before the stable formation of the tertiary contacts that define their final folds. This study identifies likely physical mechanisms driving these early compaction events in RNA folding. We have employed time-resolved small-angle X-ray scattering to monitor the fastest global shape changes of the Tetrahymena ribozyme under different ionic ...
RNA sequences fold into their native conformations by means of an adaptive search of their folding energy landscapes. The energy landscape may contain one or more suboptimal attractor conformations, making it possible for an RNA sequence to become trapped in a suboptimal attractor during the folding process. How the probability that an RNA sequence will find a given attractor before it finds an...
The folding of ribosomal RNAs is central to the biogenesis mitoribosome and a complex, stepwise process. Five recent cryo-EM studies detail late steps maturation human mitoribosomal large subunit RNA that forms catalytic core ribosome: peptidyl transferase center (PTC).
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