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Pytheas: a software package for the automated analysis of RNA sequences and modifications via tandem mass spectrometry.
D'Ascenzo L, Popova AM, Abernathy S, Sheng K, Limbach PA, Williamson JR. D'Ascenzo L, et al. Among authors: williamson jr. Nat Commun. 2022 May 3;13(1):2424. doi: 10.1038/s41467-022-30057-5. Nat Commun. 2022. PMID: 35505047 Free PMC article.
To provide an analytical tool for sequence characterization of modified RNAs, we developed Pytheas, an open-source software package for automated analysis of tandem MS data for RNA. The main features of Pytheas are flexible handling of isotope labeling and RNA mo …
To provide an analytical tool for sequence characterization of modified RNAs, we developed Pytheas, an open-source software package for auto …
SrmB Rescues Trapped Ribosome Assembly Intermediates.
Rabuck-Gibbons JN, Popova AM, Greene EM, Cervantes CF, Lyumkis D, Williamson JR. Rabuck-Gibbons JN, et al. Among authors: williamson jr. J Mol Biol. 2020 Feb 14;432(4):978-990. doi: 10.1016/j.jmb.2019.12.013. Epub 2019 Dec 23. J Mol Biol. 2020. PMID: 31877323 Free PMC article.
RNA helicases play various roles in ribosome biogenesis depending on the ribosome assembly pathway and stress state of the cell. However, it is unclear how most RNA helicases interact with ribosome assembly intermediates or participate in other cell processes to reg …
RNA helicases play various roles in ribosome biogenesis depending on the ribosome assembly pathway and stress state of the cell. Howe …
Quantitative analysis of rRNA modifications using stable isotope labeling and mass spectrometry.
Popova AM, Williamson JR. Popova AM, et al. Among authors: williamson jr. J Am Chem Soc. 2014 Feb 5;136(5):2058-69. doi: 10.1021/ja412084b. Epub 2014 Jan 27. J Am Chem Soc. 2014. PMID: 24422502 Free PMC article.
Post-transcriptional RNA modifications that are introduced during the multistep ribosome biogenesis process are essential for protein synthesis. ...The RNA modification levels correlate well with previously obtained profiles for the ribosomal proteins, …
Post-transcriptional RNA modifications that are introduced during the multistep ribosome biogenesis process are essential for …
Quantitation of the ribosomal protein autoregulatory network using mass spectrometry.
Sykes MT, Sperling E, Chen SS, Williamson JR. Sykes MT, et al. Among authors: williamson jr. Anal Chem. 2010 Jun 15;82(12):5038-45. doi: 10.1021/ac9028664. Anal Chem. 2010. PMID: 20481440 Free PMC article.
A method for quantifying cellular protein levels using macromolecular standards is presented that does not require complex sample separation, identification of high-responding peptides, affinity purification, or postgrowth modifications. Perturbations in ribosomal protein …
A method for quantifying cellular protein levels using macromolecular standards is presented that does not require complex sample separation …
The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA.
El Yacoubi B, Lyons B, Cruz Y, Reddy R, Nordin B, Agnelli F, Williamson JR, Schimmel P, Swairjo MA, de Crécy-Lagard V. El Yacoubi B, et al. Among authors: williamson jr. Nucleic Acids Res. 2009 May;37(9):2894-909. doi: 10.1093/nar/gkp152. Epub 2009 Mar 13. Nucleic Acids Res. 2009. PMID: 19287007 Free PMC article.
Threonylcarbamoyladenosine (t(6)A) is a universal modification found at position 37 of ANN decoding tRNAs, which imparts a unique structure to the anticodon loop enhancing its binding to ribosomes in vitro. ...Structural and biochemical analyses revealed that the E. coli Y …
Threonylcarbamoyladenosine (t(6)A) is a universal modification found at position 37 of ANN decoding tRNAs, which imparts a unique str …
Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly.
Earnest TM, Lai J, Chen K, Hallock MJ, Williamson JR, Luthey-Schulten Z. Earnest TM, et al. Among authors: williamson jr. Biophys J. 2015 Sep 15;109(6):1117-35. doi: 10.1016/j.bpj.2015.07.030. Epub 2015 Aug 30. Biophys J. 2015. PMID: 26333594 Free PMC article.
Kinetic models of in vitro small-subunit reconstitution at the level of individual protein/ribosomal RNA interactions are developed for two temperature regimes. The model at low temperatures predicts the existence of a novel 5'3'central assembly pathway, which we investiga …
Kinetic models of in vitro small-subunit reconstitution at the level of individual protein/ribosomal RNA interactions are developed f …