Riboswitches

We are using a joint experiment/computation approach to understand the mechanism of riboswitch operation. Experimentally, we are performing biochemical probing experiments to understand the process of switching and the effect of ligand and magnesium on this process. Computationally, we are using molecular simulation to to understand the interplay between ligand binding, folding and magnesium interactions on riboswitch conformation.

...

Integrating Molecular Dynamics Simulations with Chemical Probing Experiments Using SHAPE-FIT

Kirmizialtin, S, Hennelly, S.P, Schug, A, Onuchic, J.N, and Sanbonmatsu, K.Y. (2015) Integrating Molecular Dynamics Simulations with Chemical Probing Experiments Using SHAPE-FIT. Methods in Enzymology 553, 215-234, published February 7, 2015. doi:10.1016/bs.mie.2014.10.061. View PDF »

...

Dynamics of Riboswitches: Molecular Simulations

Sanbonmatsu, K.Y. (2014) Dynamics of Riboswitches: Molecular Simulations. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1839 (10), 1046-1050. published October 2014. doi:10.1016/j.bbagrm.2014.06.010. View article »

...

Reduced Model Captures Mg(2+)-RNA Interaction Free Energy of Riboswitches

Hayes, R.L, Noel, J.K, Whitford, P.C, Mohanty, U, Sanbonmatsu, K.Y, and Onuchic, J.N. (2014) Reduced Model Captures Mg(2+)-RNA Interaction Free Energy of Riboswitches. Biophysical journal 106 (7), 1508-1519, published April 1, 2014. doi:10.1016/j.bpj.2014.01.042.View PDF »

...

The Expression Platform and the Aptamer

Cooperativity Between Mg2+ and Ligand in the SAM-I Riboswitch

Hennelly, S.P, Novikova, I.V, and Sanbonmatsu, K.Y. (2012) The Expression Platform and the Aptamer: Cooperativity Between Mg2+ and Ligand in the SAM-I Riboswitch. Nucleic acids research 41 (3), 1922-1935, published December 20, 2012. doi:10.1093/nar/gks978. View PDF »

...

Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch

Hayes, R.L, Noel, J.K, Mohanty, U, Whitford, P.C, Hennelly, S.P, Onuchic, J.N, and Sanbonmatsu, K.Y. (2012) Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch. Journal of the American Chemical Society 134 (29), 12043-12053, published July 16, 2012. doi:10.1021/ja301454u. View PDF »

...

Tertiary Contacts Control Switching of the SAM-I Riboswitch

Hennelly, S.P, and Sanbonmatsu, K.Y. (2010) Tertiary Contacts Control Switching of the SAM-I Riboswitch. Nucleic Acids Research 39 (6), 2416-2431, published November 19, 2010. doi:10.1093/nar/gkq1096. View PDF »

...

Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain

Stoddard, C.D, Montange, R.K, Hennelly, S.P, Rambo, R.P, Sanbonmatsu, K.Y, and Batey, R.T. (2010) Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain. Structure 18 (7), 787-797, published July 14, 2010. doi:10.1016/j.str.2010.04.006. View PDF »

...

Nonlocal Helix Formation is Key to Understanding S-Adenosylmethionine-1 Riboswitch Function

Whitford, P.C, Schug, A, Saunders, J, Hennelly, S.P, Onuchic, J.N, and Sanbonmatsu, K.Y. (2009) Nonlocal Helix Formation is Key to Understanding S-Adenosylmethionine-1 Riboswitch Function. Biophysical journal 96 (2), L7-L9, published January 21, 2009. doi:10.1016/j.bpj.2008.10.033. View PDF »

GET IN TOUCH

Sanbonmatsu Team
Los Alamos National Laboratory
Theoretical Biology and Biophysics Group
P.O. Box 1663, Los Alamos, NM 87545
Public Affairs Office: (505) 667-7000
kys@lanl.gov

Operated by Los Alamos National Security, LLC for the U.S. Department of Energy's NNSA
© Copyright 2014 LANS, LLC All rights reserved | Terms of Use | Privacy Policy