Publications

2020

Partial spontaneous intersubunit rotations in actively translating ribosomes. Huang T, Choi J, Prabhakar A, Puglisi JD, Petrov A. BioRxiv doi:10.1101/2020.12.23.423865.

2019

eIF5B gates the transition from translation initiation to elongation. Wang J, Johnson AG, Lapointe CP, Choi J, Prabhakar A, Chen DH, Petrov AN, Puglisi JD. Nature. 2019 Sep;573(7775):605-608.

2018

Johnson AG, Petrov AN, Fuchs G, Majzoub K, Grosely R, Choi J, Puglisi JD. Fluorescently- tagged human eIF3 for single-molecule spectroscopy. Nucleic Acids Res. 2018 Jan 25;46(2):e8.

Choi J, Indrisiunaite G, DeMirci H, Ieong KW, Wang J, Petrov A, Prabhakar A, Rechavi G, Dominissini D, He C, 
Ehrenberg M & Puglisi JD, 2018. How 2′-O-methylation in mRNA disrupts tRNA decoding during translation elongation. Nat Struct Mol Biol. 2018 Mar;25(3):208-216. 

2017

Balázs Z, Tombácz D, Szűcs A, Csabai Z, Megyeri K, Petrov AN, Snyder M, Boldogkői Z. Long-Read Sequencing of Human Cytomegalovirus Transcriptome Reveals RNA Isoforms Carrying Distinct Coding Potentials. Sci Rep. 2017 Nov 22;7(1):15989.

Prabhakar A, Capece MC, Petrov A, Choi J, Puglisi JD. Post-termination Ribosome Intermediate Acts as the Gateway to Ribosome Recycling. Cell Rep. 2017 Jul 5;20(1):161-172.

 

Prabhakar A, Choi J, Wang J, Petrov A, Puglisi JD. Dynamic basis of fidelity and speed in translation: Coordinated multistep mechanisms of elongation and termination. Protein Sci. 2017 Jul;26(7):1352-1362.

 

Johnson AG, Grosely R, Petrov A, Puglisi JD. Dynamics of IRES-mediated translation. Phil. Trans. R. Soc. 2017 Mar 19;372(1716):20160177.

2016

Chen J, Choi J, O’Leary SE, Prabhakar A, Petrov A, Grosely R, Puglisi EV, Puglisi JD. The molecular choreography of protein synthesis: translational control, regulation, and pathways. Q Rev Biophys. 2016 Jan;49:e11.

Petrov A, Grosely R, Chen J, O’Leary SE, Puglisi JD.  Multiple Parallel Pathways of Translation Initiation on the CrPV IRES. Mol Cell. 2016 Apr 7;62(1):92-103.

 

Choi J, Ieong KW, Demirci H, Chen J, Petrov A, Prabhakar A, O’Leary SE, Dominissini D, Rechavi G, Soltis SM, Ehrenberg M, and Puglisi JD.  N(6)-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics. Nat Struct Mol Biol. 2016 Feb;23(2):110-5.

2015

Chen J, Coakley A, O’Connor M, Petrov A, O’Leary SE, Atkins JF and Puglisi JD. 2015. Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions. Cell 163(5):1267–1280.

 

Capece MC, Kornberg GL, Petrov A, Puglisi JD. 2015. A simple real-time assay for in vitro translation. RNA 21 (2), 296-305

 

Petrov A, Fuchs G, Marceau CD, Popov LM, Chen J, O’Leary SE, Wang R, Carette JE, Sarnow P, Puglisi JD. 2015. Kinetic pathway of 40S subunit recruitment to hepatitis C virus internal ribosome entry site.

Proc Natl Acad Sci USA. Dec 16. 112, 319–325

2014

Chen J, Petrov A, Johansson M, Tsai A, O'Leary SE, Puglisi JD. 2014. Dynamic pathways of -1 translational frameshifting. Nature. Aug 21;512(7514):328-32.

Noriega TR, Tsai A, Elvekrog MM, Petrov A, Neher SB, Chen J, Bradshaw N, Puglisi JD, Walter P. 2014. Signal recognition particle-ribosome binding is sensitive to nascent-chain length. Journal of Biological Chemistry, JBC. M114. 563239

Chen J, Dalal RV, Petrov AN, Tsai A, O'Leary SE, Chapin K, Cheng J, Ewan M, Hsiung PL, Lundquist P, Turner SW, Hsu DR, Puglisi

JD. 2014. High-throughput platform for real-time monitoring of biological processes by multicolor single-molecule fluorescence. Proceedings of the National Academy of Sciences of the United States of America, Jan 14;111(2):664-9.

2013

O'Leary SE, Petrov A, Chen J, Puglisi JD. 2013. Dynamic recognition of the mRNA cap by Saccharomyces cerevisiae eIF4E. Structure, Dec 3;21(12):2197-207.

Chen J, Petrov A, Tsai A, O'Leary S, and Puglisi JD. 2013. Coordinated conformational and compositional dynamics drives ribosome translocation. Nat. Struct. Mol. Biol.

Petrov A, Tsai A, Puglisi JD. 2013. Analysis of RNA by analytical polyacrylamide gel electrophoresis. Methods Enzymol 530, 301-313

Petrov A, Wu T, Puglisi EV, Puglisi JD. 2013. RNA purification by preparative polyacrylamide gel electrophoresis. Methods Enzymol 530, 315-330

2012

Chen J, Tsai A, O'Leary S, Petrov A, and Puglisi JD. 2012. Unraveling the dynamics of ribosome translocation. Current Opinion in Structural Biology, 22, 804-814.

Tsai A, Petrov A, Marshall RA, Korlach J, Uemura S, and Puglisi JD. 2012. Heterogeneous pathways and timing of factor departure during translation initiation. Nature, 487, 390-393.

Petrov A, Chen J, O'Leary S, Tsai A, and Puglisi JD. 2012. Single-Molecule Analysis of Translational Dynamics. Cold Spring Harb Perspect Biol.

Chen J, Tsai A, Petrov A, and Puglisi JD. 2012. Non-fluorescent Quenchers to Correlate Single- Molecule Conformational and Compositional Dynamics. Journal of the American Chemical Society, doi:10.1021/ja2119964.

Masuda T, Petrov AN, Iizuka R, Funatsu T, Puglisi JD, and Uemura S. 2012. Initiation factor 2, tRNA, and 50S subunits cooperatively stabilize mRNAs on the ribosome during initiation. Proceedings of the National Academy of Sciences of the United States of America, doi:10.1073/pnas.1118452109.

2011

Petrov A, Kornberg G, O'Leary S, Tsai A, Uemura S, Puglisi JD. 2011. Dynamics of the translational machinery. Current Opinion in Structural Biology 21(1): 137-145.

2010

Petrov A, and Puglisi JD. 2010. Site-specific labeling of Saccharomyces cerevisiae ribosomes for single-molecule manipulations. Nucleic Acids Res. 38(13): e143.

Aitken CE, Petrov A, and Puglisi JD. 2010. Single ribosome dynamics and the mechanism of translation. Annual Review of Biophysics 39: 491-513.