Sanbonmatsu Team

Studying the mechanisms of ribosomes, riboswitches, and LncRNAs.


The Sanbonmatsu team uses computational and experimental approaches to understand the mechanism of a diverse array of non-coding RNA systems, including ribosomes, riboswitches and long non-coding RNAs. Originally focusing on large-scale simulations of the ribosome, we have expanded into joint computational/experimental studies of riboswitches and purely experimental studies of long non-coding RNAs. The ribosome is one of the few large RNA systems that has been studied mechanistically. We are applying our knowledge gained from ribosome studies to long non-coding RNA systems.

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Ribosomes

We are performing large-scale molecular simulations of the ribosome to uncover the energy landscape of tRNA selection and translocation. We are using explicit solvent, reduced-model and enhanced sampling methods.
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Long non-coding RNA and epigenetics

LncRNAs (typically 1-10 kB) play key roles in development and disease and are often involved in epigenetic mechanism. We are using experimental biochemistry appoaches to probe the structure of long non-coding RNAs (lncRNAs).
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Riboswitches

Riboswitches use competing secondary structures to control gene expression. We are using an integrated experiment/computation approach to understand the role of ligand binding, magnesium and the expression platform in controlling riboswitch conformation.

Recent Publications


A G-Rich Motif in the LncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage

Xue, Z, Hennelly, S.P, Doyle, B, Gulati, A.A, Novikova, I.V, Sanbonmatsu, K.Y, and Boyer, L.A. (2016) A G-Rich Motif in the LncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage. Molecular Cell, published September 8, 2016. doi:10.1016/j.molcel.2016.08.010. View article »


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