2024
Alejo JL, Girodat D, Hammerling MJ, Willi JA, Jewett MC, Engelhart AE, Adamala KP. Alternate conformational trajectories in ribosome translocation. PLoS Comput Biol. 2024 Aug 14;20(8):e1012319. doi: 10.1371/journal.pcbi.1012319. PMID: 39141679; PMCID: PMC11346969.
Chowdhury AR, Sapkota D, Girodat D. Conformational changes of ribosomes during translation elongation resolved by molecular dynamics simulations. Curr Opin Struct Biol. 2024 Jun;86:102804. doi: 10.1016/j.sbi.2024.102804. Epub 2024 Apr 3. PMID: 38569462.
2023
Girodat D, Wieden HJ, Blanchard SC, Sanbonmatsu KY. Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding. Nat Commun. 2023 Sep 11;14(1):5582. doi: 10.1038/s41467-023-40404-9. PMID: 37696823; PMCID: PMC10495418.
2022
Nishima W, Girodat D, Holm M, Rundlet EJ, Alejo JL, Fischer K, Blanchard SC, Sanbonmatsu KY. Hyper-swivel head domain motions are required for complete mRNA-tRNA translocation and ribosome resetting. Nucleic Acids Res. 2022 Aug 12;50(14):8302-8320. doi: 10.1093/nar/gkac597. PMID: 35808938; PMCID: PMC9371933.
Smith DD, Girodat D, Abbott DW, Wieden HJ. Construction of a highly selective and sensitive carbohydrate-detecting biosensor utilizing Computational Identification of Non-disruptive Conjugation sites (CINC) for flexible and streamlined biosensor design. Biosens Bioelectron. 2022 Mar 15;200:113899. doi: 10.1016/j.bios.2021.113899. Epub 2021 Dec 20. PMID: 34974264.
2021
2020
Girodat D, Pati AK, Terry DS, Blanchard SC, Sanbonmatsu KY. Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein. PLoS Comput Biol. 2020 Nov 5;16(11):e1008293. doi: 10.1371/journal.pcbi.1008293. PMID: 33151943; PMCID: PMC7643941.
Babaian A, Rothe K, Girodat D, Minia I, Djondovic S, Milek M, Spencer Miko SE, Wieden HJ, Landthaler M, Morin GB, Mager DL. Loss of m1acp3Ψ Ribosomal RNA Modification Is a Major Feature of Cancer. Cell Rep. 2020 May 5;31(5):107611. doi: 10.1016/j.celrep.2020.107611. PMID: 32375039.
Girodat D, Blanchard SC, Wieden HJ, Sanbonmatsu KY. Elongation Factor Tu Switch I Element is a Gate for Aminoacyl-tRNA Selection. J Mol Biol. 2020 Apr 17;432(9):3064-3077. doi: 10.1016/j.jmb.2020.01.038. Epub 2020 Feb 13. PMID: 32061931; PMCID: PMC8259901.
Morse JC, Girodat D, Burnett BJ, Holm M, Altman RB, Sanbonmatsu KY, Wieden HJ, Blanchard SC. Elongation factor-Tu can repetitively engage aminoacyl-tRNA within the ribosome during the proofreading stage of tRNA selection. Proc Natl Acad Sci U S A. 2020 Feb 18;117(7):3610-3620. doi: 10.1073/pnas.1904469117. Epub 2020 Feb 5. PMID: 32024753; PMCID: PMC7035488.
2019
Girodat D, Mercier E, Gzyl KE, Wieden HJ. Elongation Factor Tu's Nucleotide Binding Is Governed by a Thermodynamic Landscape Unique among Bacterial Translation Factors. J Am Chem Soc. 2019 Jul 3;141(26):10236-10246. doi: 10.1021/jacs.9b01522. Epub 2019 May 28. PMID: 31058500.
2018
Tanzawa T, Kato K, Girodat D, Ose T, Kumakura Y, Wieden HJ, Uchiumi T, Tanaka I, Yao M. The C-terminal helix of ribosomal P stalk recognizes a hydrophobic groove of elongation factor 2 in a novel fashion. Nucleic Acids Res. 2018 Apr 6;46(6):3232-3244. doi: 10.1093/nar/gky115. PMID: 29471537; PMCID: PMC5887453.
2017
Smith DD, Girodat D, Wieden HJ, Selinger LB. Streamlined purification of fluorescently labeled Escherichia coli phosphate-binding protein (PhoS) suitable for rapid-kinetics applications. Anal Biochem. 2017 Nov 15;537:106-113. doi: 10.1016/j.ab.2017.09.012. Epub 2017 Sep 21. PMID: 28941789.
Chao Y, Li L, Girodat D, Förstner KU, Said N, Corcoran C, Śmiga M, Papenfort K, Reinhardt R, Wieden HJ, Luisi BF, Vogel J. In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways. Mol Cell. 2017 Jan 5;65(1):39-51. doi: 10.1016/j.molcel.2016.11.002. PMID: 28061332; PMCID: PMC5222698.
2016
2015
Mercier E, Girodat D, Wieden HJ. A conserved P-loop anchor limits the structural dynamics that mediate nucleotide dissociation in EF-Tu. Sci Rep. 2015 Jan 8;5:7677. doi: 10.1038/srep07677. PMID: 25566871; PMCID: PMC4286738.