Alert: Interested in going for a competitive post-doctoral fellowship with NIH or LANL about ribosome simulation, RNA secondary structure bioinformatics or lncRNA biochemistry? Please email Karissa at firstname.lastname@example.org
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.
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.
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).
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.
Rise of the RNA machines: exploring the structure of long non-coding RNAs.Novikova IV, Hennelly SP, Tung CS, Sanbonmatsu KY Los Alamos National Laboratory, Los Alamos, NM 87545, USA. Journal of Molecular Biology [2013, 425(19):3731-3746].
3S: shotgun secondary structure determination of long non-coding RNAs.Novikova IV, Dharap A, Hennelly SP, Sanbonmatsu KY Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States. Methods (San Diego, Calif.) [2013, 63(2):170-177]
Tackling structures of long noncoding RNAs.Novikova IV, Hennelly SP, Sanbonmatsu KY Los Alamos National Laboratory, Los Alamos, NM 87545, USA. email@example.com. International Journal of Molecular Sciences [2013, 14(12):23672-23684]
Simulating movement of tRNA into the ribosome during decoding.Sanbonmatsu KY, Joseph S, Tung CS Department of Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. firstname.lastname@example.org Proceedings of the National Academy of Sciences of the United States of America [2005, 102(44):15854-15859]
Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. Novikova IV, Hennelly SP, Sanbonmatsu KY, Nucleic acids research (2012). 40: 5034-51
Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch. Hayes RL, Noel JK, Mohanty U, Whitford PC, Hennelly SP, Onuchic JN, Sanbonmatsu KY, Journal of the American Chemical Society (2012). 134: 12043-53
Computational studies of molecular machines: the ribosome. Sanbonmatsu KY, Current opinion in structural biology (2012). 22: 168-74
The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch Hennelly SP, Novikova IV, Sanbonmatsu KY, Nucleic Acids Research, In press