Kirmizialtin, S, Loerke, J, Behrmann, E, Spahn, C.M.T, and Sanbonmatsu, K.Y. (2015) Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions. Methods in Enzymology 558, 497-514, published May 9, 2015. doi:10.1016/bs.mie.2015.02.011. View PDF »
Hayes, R.L, Noel, J.K, Mandic, A, Whitford, P.C, Sanbonmatsu, K.Y, Mohanty, U, and Onuchic, J.N. (2015) Generalized Manning Condensation Model Captures the RNA Ion Atmosphere. Physical Review Letters 114 (25), 258105, published June 26, 2015. doi:10.1016/j.molcel.2014.12.016. View PDF »
Muhs, M, Hilal, T, Mielke, T, Skabkin, M.A, Sanbonmatsu, K.Y, Pestova, T.V, and Spahn, C.M.T. (2015) Cryo-EM of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus IRES. Molecular Cell 57 (3), 422-432, published February 5, 2015. doi:10.1016/j.molcel.2014.12.016. View PDF »
Budkevich, T.V, Giesebrecht, J, Behrmann, E, Loerke, J, Ramrath, D.J.F, Mielke, T, Ismer, J, Hildebrand, P.W, Tung, C-S, Nierhaus, K.H, Sanbonmatsu, K.Y, and Spahn, C.M.T. (2014) Regulation of the Mammalian Elongation Cycle by Subunit Rolling: A Eukaryotic-Specific Ribosome Rearrangement. Cell 158 (1), 121-131, published July 3, 2014. doi:10.1016/j.cell.2014.04.044. View PDF »
Sanbonmatsu, K.Y. (2014) Flipping Through the Genetic Code: New Developments in Discrimination between Cognate and Near-Cognate tRNAs and the Effect of Antibiotics. Journal of Molecular Biology 426 (19), 3197-3200, published September 2014. doi:10.1016/j.jmb.2014.07.005. View PDF »
Kaushal, P.S, Sharma, M.R, Booth, T.M, Haque, E.M, Tung, C-S, Sanbonmatsu, K.Y, Spremulli, L.L, and Agrawal, R.K. (2014) Cryo-EM Structure of the Small Subunit of the Mammalian Mitochondrial Ribosome. Proceedings of the National Academy of Sciences 111 (20), 7284-7289, published May 20, 2014. doi:10.1073/pnas.1401657111. View PDF »
Whitford, P.C, and Sanbonmatsu, K.Y. (2013) Simulating Movement of tRNA Through the Ribosome During Hybrid-State Formation. Journal of chemical physics 139, 121919, published September 28, 2013. doi:10.1063/1.4817212. View PDF »
Whitford, P.C, Blanchard, S.C, Cate, J.H.D, and Sanbonmatsu, K.Y. (2013) Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome. PLoS computational biology 9 (3), e1003003, published March 21, 2013. doi:10.1371/journal.pcbi.1003003. View PDF »
Sanbonmatsu, K.Y, Blanchard, S.C, and Whitford, P.C. (2012) Molecular Dynamics Simulations of the Ribosome. Biophysical Approaches to Translational Control of Gene Expression, 51-68, published August 24, 2012. doi:10.1007/978-1-4614-3991-2_3. View article »
Sanbonmatsu, K.Y. (2012) Computational Studies of Molecular Machines: The Ribosome. Current Opinion in Structural Biology 22 (2), 168-174, published February 13, 2012. doi:10.4161/bioa.22592. View PDF »
Whitford, P.C, Ahmed, A, Yu, Y, Hennelly, S.P, Tama, F, Spahn, C.M.T, Onuchic, J.N, and Sanbonmatsu, K.Y. (2011) Excited States of Ribosome Translocation Revealed through Integrative Molecular Modeling. Proceedings of the National Academy of Sciences 108 (47), 18943-18948, published November 11, 2011. doi:10.1073/pnas.1108363108. View PDF »
Zhang, Z, Sanbonmatsu, K.Y, and Voth, G.A. (2011) Key Inter-Molecular Interactions in the E. Coli 70S Ribosome Revealed by Coarse-Grained Analysis. Journal of the American Chemical Society 133 (42), 16828-16838, published October 3, 2011. doi:10.1021/ja2028487. View PDF »
Sanbonmatsu, K.Y, Blanchard, S.C, and Whitford, P.C. (2011) Information Processing by Nanomachines. Molecular Machines 67, published 2011. View PDF »
Whitford, P.C, Altman, R.B, Geggier, P, Terry, D.S, Munro, J.B, Onuchic, J.N, Spahn, C.M.T, Sanbonmatsu, K.Y, and Blanchard, S.C. (2011) Dynamic Views of Ribosome Function: Energy Landscapes and Ensembles. Ribosomes, 303-319, published 2010. doi:10.1007/978-3-7091-0215-2_24. View PDF »
Ratje, A.H, Loerke, J, Mikolajka, A, Brünner, M, Hildebrand, P.W, Starosta, A.L, Dönhöfer, A, Connell, S.R, Fucini, P, Mielke, T, Whitford, P.C, Onuchic, J.N, Yu, Y, Sanbonmatsu, K.Y, Hartmann, R.K, Penczek, P.A, Wilson, D.N, and Spahn, C.M.T. (2010) Head Swivel on the Ribosome Facilitates Translocation Via Intra-Subunit tRNA Hybrid Sites. Nature 468 (7324), 713-716, published December 2, 2010. doi:10.1038/nature09547. View PDF »
Whitford, P.C, Onuchic, J.N, and Sanbonmatsu, K.Y. (2010) Connecting Energy Landscapes with Experimental Rates for Aminoacyl-tRNA Accommodation in the Ribosome. Journal of the American Chemical Society 132 (38), 13170-13171, published September 29, 2010. doi:10.1021/ja1061399. View PDF »
Whitford, P.C, Geggier, P, Altman, R.B, Blanchard, S.C, Onuchic, J.N, and Sanbonmatsu, K.Y. (2010) Accommodation of Aminoacyl-tRNA Into the Ribosome Involves Reversible Excursions Along Multiple Pathways. RNA 16 (6), 1196-1204, published June 2010. doi:10.1261/rna.2035410. View PDF »
Munro, J.B, Altman, R.B, Tung, C-S, Cate, J.H.D, Sanbonmatsu, K.Y, and Blanchard, S.C. (2009) Spontaneous Formation of the Unlocked State of the Ribosome is a Multistep Process. Proceedings of the National Academy of Sciences 107 (2), 709-714, published December 17, 2009. doi:10.1073/pnas.0908597107. View PDF »
Munro, J.B, Altman, R.B, Tung, C-S, Sanbonmatsu, K.Y, and Blanchard, S.C. (2009) A Fast Dynamic Mode of the EF-G-Bound Ribosome. The EMBO journal 29 (4), 770-781, published December 24, 2009. doi:10.1038/emboj.2009.384. View PDF »
Munro, J.B, Altman, R.B, Tung, C-S, Sanbonmatsu, K.Y, and Blanchard, S.C. (2009) Navigating the Ribosome's Metastable Energy Landscape. The EMBO journal 29 (4), 770-781, published December 24, 2009. doi:10.1038/emboj.2009.384. View PDF »
Vaiana, A.C. and Sanbonmatsu, K.Y. (2009) Stochastic Gating and Drug–Ribosome Interactions. Journal of Molecular Biology 386 (3), 648-661, published February 27, 2009. doi:10.1016/j.jmb.2008.12.035. View PDF »
Munro, J.B, Vaiana, A, Sanbonmatsu, K.Y, and Blanchard, S.C. (2008) A New View of Protein Synthesis: Mapping the Free Energy Landscape of the Ribosome Using Single-Molecule FRET. Biopolymers 89 (7), 565-577, published July 2008. doi:10.1002/bip.20961. View PDF »
Sanbonmatsu, K.Y. and Tung, C-S. (2006) Large-Scale Simulations of the Ribosome: A New Landmark in Computational Biology. Journal of Physics: Conference Series 46 (1), 334-342, published 2006. View PDF »
Sanbonmatsu, K.Y. (2006) Alignment/Misalignment Hypothesis for tRNA Selection by the Ribosome. Biochimie 88 (8), 1075-1089, published August 2006. doi:10.1016/j.biochi.2006.07.002. View PDF »
Sanbonmatsu, K.Y. (2006) Energy Landscape of the Ribosomal Decoding Center. Biochimie 88 (8), 1053-1059, published August 2006. doi:10.1016/j.biochi.2006.07.002. View PDF »
Sanbonmatsu, K.Y. (2006) Using Computer Simulations to Study Decoding by the Ribosome. Computational Studies of RNA and DNA, 327-342, published 2006. doi:10.1007/978-1-4020-4851-3_13. View article »
Sanbonmatsu, K.Y, Joseph, S, and Tung, C-S. (2005) Simulating Movement of tRNA Into the Ribosome During Decoding. Proceedings of the National Academy of Sciences 102 (44), 15854-15859, published October 25, 2005. doi:10.1073/pnas.0503456102. View PDF »
Tung, C-S. and Sanbonmatsu, K.Y. (2004) Atomic Model of the Thermus thermophilus 70S Ribosome Developed in Silico. Biophysical journal 87 (4), 2714-2722, published October 2004. doi:10.1529/biophysj.104.040162. View PDF »
Sanbonmatsu, K.Y. and Joseph, S. (2003) Understanding Discrimination by the Ribosome: Stability Testing and Groove Measurement of Codon–Anticodon Pairs. Journal of Molecular Biology 328 (1), 33-47, published April 18, 2003. doi:10.1016/S0022-2836(03)00236-5. View PDF »
Tung, C-S, Joseph, S, and Sanbonmatsu, K.Y. (2002) All-Atom Homology Model of the Escherichia coli 30S Ribosomal Subunit. Nature Structural & Molecular Biology 9 (10), 750-755, published September 16, 2002. doi:10.1038/nsb841. View PDF »