The roles of structural dynamics in the cellular functions of RNAs
RNAs fold into 3D structures that range from simple helical elements to complex tertiary
structures and quaternary ribonucleoprotein assemblies. The functions of many regulatory …
structures and quaternary ribonucleoprotein assemblies. The functions of many regulatory …
Naturally occurring tRNAs with non-canonical structures
Transfer RNA (tRNA) is the central molecule in genetically encoded protein synthesis. Most
tRNA species were found to be very similar in structure: the well-known cloverleaf secondary …
tRNA species were found to be very similar in structure: the well-known cloverleaf secondary …
Capturing RNA folding free energy with coarse-grained molecular dynamics simulations
We introduce a coarse-grained RNA model for molecular dynamics simulations, RACER
(RnA CoarsE-gRained). RACER achieves accurate native structure prediction for a number …
(RnA CoarsE-gRained). RACER achieves accurate native structure prediction for a number …
MD simulations of tRNA and aminoacyl-tRNA synthetases: dynamics, folding, binding, and allostery
R Li, LM Macnamara, JD Leuchter… - International Journal of …, 2015 - mdpi.com
While tRNA and aminoacyl-tRNA synthetases are classes of biomolecules that have been
extensively studied for decades, the finer details of how they carry out their fundamental …
extensively studied for decades, the finer details of how they carry out their fundamental …
Pressure pushes tRNALys3 into excited conformational states
J Wang, T Koduru, B Harish… - Proceedings of the …, 2023 - National Acad Sciences
Conformational dynamics play essential roles in RNA function. However, detailed structural
characterization of excited states of RNA remains challenging. Here, we apply high …
characterization of excited states of RNA remains challenging. Here, we apply high …
Interplay between substrate recognition, 5′ end tRNA processing and methylation activity of human mitochondrial RNase P
Human mitochondrial ribonuclease P (mtRNase P) is an essential three-protein complex
that catalyzes the 5′ end maturation of mitochondrial precursor tRNAs (pre-tRNAs) …
that catalyzes the 5′ end maturation of mitochondrial precursor tRNAs (pre-tRNAs) …
Disease-associated mutations in mitochondrial precursor tRNAs affect binding, m1R9 methylation, and tRNA processing by mtRNase P
Mitochondrial diseases linked to mutations in mitochondrial (mt) tRNA sequences are
common. However, the contributions of these tRNA mutations to the development of …
common. However, the contributions of these tRNA mutations to the development of …
Intrinsic properties of tRNA molecules as deciphered via Bayesian network and distribution divergence analysis
S Branciamore, G Gogoshin, M Di Giulio, AS Rodin - Life, 2018 - mdpi.com
The identity/recognition of tRNAs, in the context of aminoacyl tRNA synthetases (and other
molecules), is a complex phenomenon that has major implications ranging from the origins …
molecules), is a complex phenomenon that has major implications ranging from the origins …
Tuning RNA folding and function through rational design of junction topology
M Daher, AM Mustoe, A Morriss-Andrews… - Nucleic Acids …, 2017 - academic.oup.com
Structured RNAs such as ribozymes must fold into specific 3D structures to carry out their
biological functions. While it is well-known that architectural features such as flexible …
biological functions. While it is well-known that architectural features such as flexible …
Synthetic tyrosine tRNA molecules with noncanonical secondary structures
K Sakamoto, A Hayashi - International Journal of Molecular Sciences, 2018 - mdpi.com
The L-shape form of tRNA is maintained by tertiary interactions occurring in the core. Base
changes in this domain can cause structural defects and impair tRNA activity. Here, we …
changes in this domain can cause structural defects and impair tRNA activity. Here, we …