Ribosomes

Over the past decade, we have performed large-scale molecular dynamics simulations of the ribosome to better understand its mechanism. Our goal is to produce an integrated picture of tRNA selection and translocation that ties together the large amount of existing crystallographic, cryo-EM and single molecule FRET data. By quantifying the energy landscapes of these processes, we are elucidating the underlying physics of protein synthesis.

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Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions

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 »

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Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

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 »

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Cryo-EM of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus IRES

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 »

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Regulation of the Mammalian Elongation Cycle by Subunit Rolling

A Eukaryotic-Specific Ribosome Rearrangement

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 »

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Flipping Through the Genetic Code

New Developments in Discrimination between Cognate and Near-Cognate tRNAs and the Effect of Antibiotics

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 »

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Cryo-EM Structure of the Small Subunit of the Mammalian Mitochondrial Ribosome

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 »

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Simulating Movement of tRNA Through the Ribosome During Hybrid-State Formation

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 »

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Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome

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 »

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Molecular Dynamics Simulations of the Ribosome

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 »

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Computational Studies of Molecular Machines: The Ribosome

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 »

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Excited States of Ribosome Translocation Revealed through Integrative Molecular Modeling

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 »

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Key Inter-Molecular Interactions in the E. Coli 70S Ribosome Revealed by Coarse-Grained Analysis

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 »

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Information Processing by Nanomachines

Decoding by the Ribosome

Sanbonmatsu, K.Y, Blanchard, S.C, and Whitford, P.C. (2011) Information Processing by Nanomachines. Molecular Machines 67, published 2011. View PDF »

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Dynamic Views of Ribosome Function

Energy Landscapes and Ensembles

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 »

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Head Swivel on the Ribosome Facilitates Translocation Via Intra-Subunit tRNA Hybrid Sites

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 »

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Connecting Energy Landscapes with Experimental Rates for Aminoacyl-tRNA Accommodation in the Ribosome

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 »

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Accommodation of Aminoacyl-tRNA Into the Ribosome Involves Reversible Excursions Along Multiple Pathways

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 »

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Spontaneous Formation of the Unlocked State of the Ribosome is a Multistep Process

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 »

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A Fast Dynamic Mode of the EF-G-Bound Ribosome

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 »

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Navigating the Ribosome's Metastable Energy Landscape

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 »

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Stochastic Gating and Drug–Ribosome Interactions

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 »

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A New View of Protein Synthesis

Mapping the Free Energy Landscape of the Ribosome Using Single-Molecule FRET

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 »

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Large-Scale Simulations of the Ribosome

A New Landmark in Computational Biology

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 »

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Alignment/Misalignment Hypothesis for tRNA Selection by the Ribosome

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 »

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Energy Landscape of the Ribosomal Decoding Center

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 »

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Using Computer Simulations to Study Decoding by the Ribosome

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 »

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Simulating Movement of tRNA Into the Ribosome During Decoding

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 »

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Atomic Model of the Thermus thermophilus 70S Ribosome Developed in Silico

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 »

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Understanding Discrimination by the Ribosome

Stability Testing and Groove Measurement of Codon–Anticodon Pairs

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 »

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All-Atom Homology Model of the Escherichia coli 30S Ribosomal Subunit

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 »

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Sanbonmatsu Team
Los Alamos National Laboratory
Theoretical Biology and Biophysics Group
P.O. Box 1663, Los Alamos, NM 87545
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kys@lanl.gov

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