Publications

2021

• Bailey, E., Gottesman, M. E., Gonzalez, R.L., Jr. (2021) NusG links transcription and translation in Escherichia coli extracts. Submitted. [BioRxiv]
• Fleisher, R.C.*, Michael, N.*, and Gonzalez, R.L., Jr. (2021) Mechanistic studies of non-canonical amino acid mutagenesis. Methods in Enzymology 656 375-428. [Link] [PDF] *These authors contributed equally
• Kinz-Thompson, C.D., Ray, K.K., and Gonzalez, R.L., Jr. (2021) Bayesian inference: The comprehensive approach to analyzing single-molecule experiments. Annual Review of Biophysics 50 (1), 191-208. [Link] [PDF]
• Lerner, E., Barth, A., Hendrix, J., Ambrose, B., Birkedal, V., Blanchard, S. C., ... & Weiss, S. (2021). FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. Elife, 10, e60416. [Link] [PDF]
• Gamper, H.*, Li, H.*, Masuda, I., Szanti-Kis, M., Christian, T., Conn, A.B., Blaha, G., Petersson, E.J., Gonzalez, R.L., Jr., Hou, Y.M. (2021) Insights into Genome Recoding from the Mechanism of a Classic +1-Frameshift-Suppressor tRNA, Nature Communications, 12 (1), 1-18. [Link] [PDF] [Supp Mat] *These authors contributed equally

2020

• Hoffer, E. D., Hong, S., Sunita, S., Maehigashi, T., Gonzalez, R.L., Jr., Whitford, P. C., and Dunham, C. M. (2020). Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon-anticodon pairing. eLife, 9, e51898. [Link] [PDF]
• Hobson, B.D., Kong, L., Hartwick, E.W., Gonzalez, R.L., Jr., and Sims, P.A., (2020) Elongation Inhibitors do not Prevent the Release of Puromycylated Nascent Polypeptide Chains from Ribosomes. eLife, 9, e60048. [Link] [PDF]
• Diez, S., Ryu, J., Caban, K., Gonzalez, R.L., Jr., and Dworkin, J., (2020) The alarmones (p)ppGpp directly regulate translation initiation during entry into quiescence. PNAS. 117 (27), 15565-15572. [Link] [PDF] [Supp Mat]
• Desai, B.J., Gonzalez, R.L., Jr., (2020) Multiplexed genomic encoding of non-canonical amino acids for labeling large complexes. Nat Chem Biol. 1-7. [Link] [PDF] [Supp Mat]
• Haizel, S. A., Bhardwaj, U., Gonzalez, R.L., Jr., Mitra, S., and Goss, D., (2020) 5'-UTR recruitment of the translation initiation factors eIF4GI or DAP5 drives cap-independent translation of a subset of human mRNAs. Journal of Biological Chemistry. 295 (33), 11693-11706. [Link] [PDF] [Supp Mat 1] [Supp Mat 2]

2019

• Kaledhonkar, S., Fu, Z., Caban, K., Li, W., Chen, B., Sun, M., Gonzalez, R.L., Jr., and Frank, J., (2019) Late steps in bacterial translation initiation visualized using time-resolved cryo-EM. Nature. 570, 400-404. [Link (paywall)] [Link (non-paywall)]
• Hon, J., and Gonzalez, R.L., Jr., (2019) Bayesian-estimated hierarchical HMMs enable robust analysis of single-molecule kinetic heterogeneity. Biophysical Journal. 116, 1790-1802. [PDF] [Supp Mat]

2018

• Fleisher, R. C. , Cornish, V. W., and Gonzalez, R.L., Jr., (2018) D-amino acid-mediated translation arrest is modulated by the identity of the incoming aminoacyl-tRNA. Biochemistry. 57, 4241-4246. [PDF] [Supp Mat]
• Subramanyam, S., Kinz-Thompson, C.D., Gonzalez, R.L., Jr., and Spies, M., (2018) Observation and analysis of RAD51 nucleation dynamics at single-monomer resolution. Methods in Enzymology. 600, 201-232. [PDF]
• Kinz-Thompson, C.D. and Gonzalez, R.L., Jr., (2018) Increasing the time resolution of single-molecule experiment with bayesian inference. Biophysical Journal. 114, 289-300. [PDF] [Supp Mat]

2017

• Caban, K., Pavlov, M., Ehrenberg, M., and Gonzalez, R.L., Jr., (2017) A conformational switch in initiation factor 2 controls the fidelity of translation initiation in bacteria. Nature Communications. 8, 1475. [PDF] [Supp Mat]
• Gonzalez, R.L., Jr., (2017) Survivor: ribosome edition. The EMBO Journal. e201797518. [PDF]
• Vernick, S., Trocchia, S. M., Warren, S. B., Young, E. F., Bouilly, D., Gonzalez, R.L. Jr., Nuckolls, C., and Shepard, K. L., (2017) Electrostatic melting in a single-molecule field-effect transistor with applications in genomic identification. Nature Communications. 8, 15450. [PDF] [Supp Mat]

2016

• Kinz-Thompson, C.D., Bailey, N.A., and Gonzalez, R.L., Jr., (2016) Precisely and accurately inferring single-molecule rate constants. Methods in Enzymology. 581. [PDF]
• Bouilly, D., Hon, J., Daly, N.S., Trocchia, S., Vernick, S., Yu, J., Warren, S., Wu, Y., Gonzalez, R.L., Jr.*, Shepard, K.L.*, and Nuckolls, C.* (2016) Single-molecule reaction chemistry in patterned nanowells. Nano Letters. 16, 4679-4685. (*Co-corresponding authors) [PDF] [Supp Mat]

2015

• Ruehle, M.D., Zhang, H., Sheridan, R.M., Mitra, S., Chen, Y., Gonzalez, R.L., Jr., Cooperman, B.S., and Kieft, J.S. (2015) A dynamic RNA loop in an IRES affects multiple steps of elongation factor-mediated translation initiation. eLife. 4. [PDF]
• Pereira, S.F.F., Gonzalez, R.L., Jr., and Dworkin, J. (2015) Protein synthesis during cellular quiescence is inhibited by phosphorylation of a translational elongation factor. Proc. Natl. Acad. Sci. USA. 112, 3274-3282. [PDF] [Supp Mat]
• Chen, B., Kaledhonkar, S., Sun, M., Shen, B., Lu, Z., Barnard, D., Lu, T.-M., Gonzalez, R.L., Jr., and Frank, J. (2015) Structural dynamics of ribosome subunit association studied by mixing-spraying time-solved cryo-EM. Structure. 23, 1097-1105. [PDF] [Supp Mat]
  • Featured as a Preview in Structure, 23, 977-978. [PDF]
• Caban, K. and Gonzalez, R.L., Jr. (2015) The emerging role of rectified thermal fluctuations in initiator aa-tRNA- and start codon selection during translation initiation. Biochimie. 114, 30-38. [PDF]
• Englander, M.T., Avins, J.L., Fleisher, R.C., Liu, B., Effraim, P.R., Wang, J., Schulten, K., Leyh, T.S., Gonzalez, R.L., Jr.* and Cornish, V.W.* (2015) The ribosome can discriminate the chirality of amino acids within its peptidyl-transferase center. Proc. Natl. Acad. Sci. USA. 112, 6038-6043. (*Co-corresponding authors) [PDF] [Supp Mat]
  • Featured as a Microbiology Article Recommendation by Faculty of 1000 [HTML]
• Kinz-Thompson, C.D., Sharma, A.K., Frank, J., Gonzalez, R.L., Jr., and Chowdhury, D. (2015) Quantitative connection between ensemble thermodynamics and single-molecule kinetics: A case study using cryogenic electron microscopy and single-molecule fluorescence resonance energy transfer investigations of the ribosome. J. Phys. Chem. B. 119, 10888-10901. [PDF]
• Wang, J., Caban, K., and Gonzalez, R.L., Jr. (2015) Ribosomal initiation complex-driven changes in the stability and dynamics of initiation factor 2 regulate the fidelity of translation initiation. J. Mol. Biol. 427, 1819-1834. [PDF] [Supp Mat]
• MacDougall D.D. and Gonzalez, R.L., Jr. (2015) Translation initiation factor 3 regulates switching between different modes of ribosomal subunit joining. J. Mol. Biol. 427, 1801-1818. [PDF] [Supp Mat]
• Greenfield, M., van de Meent, J.-W., Pavlichin, D.S., Mabuchi, H., Wiggins, C.H., Gonzalez, R.L., Jr., and Herschlag, D. (2015) Single-molecule dataset (SMD): A generalized storage format for raw and processed single-molecule data. BMC Bioinformatics. 16, 3. [PDF]

2014

• Kinz-Thompson, C.D. and Gonzalez, R.L., Jr. (2014) smFRET studies of the 'encounter' complexes and subsequent intermediate states that regulate the selectivity of ligand binding. FEBS Lett. 588, 3526-3538. [PDF]
• Ning, W., Fei, J., and Gonzalez, R.L., Jr. (2014) The ribosome uses cooperative conformational changes to maximize and regulate the efficiency of protein synthesis Proc. Natl. Acad. Sci. USA. 111, 12073-12078. [PDF] [Supp Mat]
• Cheng, L., Mahendran, A., Gonzalez, R.L., Jr.*, and Breslow, R.* (2014) Deoxypolypeptides (DOPPs) Bind and Cleave RN. Proc. Natl. Acad. Sci. USA. 111, 7920-7924. (*Co-corresponding authors) [PDF] [Supp Mat]
• Kim, H.K-., Liu, F., Fei, J., Bustamante, C., Gonzalez, R.L., Jr., and Tinoco, I. (2014) A frameshifting stimulatory stem loop destabilizes the hybrid state and impedes ribosomal translocation. Proc. Natl. Acad. Sci. USA. 111, 5538-5543. [PDF] [Supp Mat]
• van de Meent, J.-W., Bronson, J.E., Wiggins, C. and Gonzalez, R.L., Jr. (2014) Empirical Bayes methods enable advanced population-level analyses of single-molecule FRET experiments. Biophys. J. 106, 1327-1337. [PDF] [Supp Mat]
• Chen, B., Boel, G., Hashem, Y., Ning, W., Fei, J., Wang, C., Gonzalez, R.L., Jr., Hunt, J.F. and Frank, J. (2014) EttA binds to the tRNA-exit site of the ribosome and regulates translation by restricting ribosome and tRNA dynamics. Nat. Struct. Mol. Biol. 21, 152-159. [PDF] [Supp Mat]
  • Featured as a News and Views Highlight in Nat. Struc. Mol. Biol., 21, 115-116. [PDF]
• Boel, G., Smith, P.C., Ning, W., Englander, M.T., Chen, B., Hashem, Y., Testa, A.J., Fischer, J.J., Wieden, H.-J., Frank, J., Gonzalez, R.L., Jr. and Hunt, J.F. (2014) The ABC-F protein EttA gates ribosome entry into the translation elongation cycle. Nat. Struct. Mol. Biol. 21, 143-151. [PDF] [Supp Mat]
  • Featured as a News and Views Highlight in Nat. Struc. Mol. Biol., 21, 115-116. [PDF]

2013

• Kinz-Thompson, C.D., Palma, M., Pulukkunat, D.K., Chenet, D., Hone, J., Wind, S.J. and Gonzalez, R.L., Jr. (2013) Robustly passivated, gold nanoaperture arrays for single-molecule fluorescence microscopy. ACS Nano. 7, 8158-8166. [PDF] [Supp Mat]
• van de Meent, J.-W., Bronson, J.E., Wood, F., Gonzalez, R.L., Jr. and Wiggins, C. (2013) Hierarchically-coupled hidden Markov models for learning kinetic rates from single-molecule data. JMLR W&CP. 28, 361-369. [PDF]
• Elvekrog, M.M. and Gonzalez, R.L., Jr. (2013) Conformational selection of a translation initiation factor 3 conformer signals proper substrate selection. Nat. Struct. Mol. Biol. 20, 628-33. [PDF] [Supp Mat]

2011

• Perez, C.E. and Gonzalez, R.L., Jr. (2011) In vivo and in vitro single-molecule fluorescence imaging of ribosome-catalyzed protein synthesis. Curr. Opin. Chem. Biol. 15, 853-863. [PDF]
• Schepartz, A. and Gonzalez, R.L., Jr. (2011) Molecular imaging: sine labore nihil. Curr. Opin. Chem. Biol. 15, 749-751. [PDF]
• Fei, J., Richard, A.C., Bronson, J.E. and Gonzalez, R.L., Jr. (2011) Transfer RNA-mediated regulation of ribosome dynamics during protein synthesis. Nat Struct Mol Biol. 18, 1043-1052. [PDF] [Supp Mat]
• MacDougall, D.D. Fei, J. and Gonzalez, R.L., Jr. (2011) Single-molecule fluorescence resonance energy transfer investigations of ribosome-catalyzed protein synthesis. Molecular Machines in Biology: Workshop of the Cell, ed. J. Frank, New York, Cambridge University Press. 93-116. [PDF]
• MacDougall, D.D. and Gonzalez, R.L., Jr. (2011) Exploring the structural dynamics of the translational machinery using single-molecule fluorescence resonance energy transfer. Ribosomes: Structure, Function, and Dynamics, eds. M. Rodnina, R. Green, W. Wintermeyer, New York, Springer-Verlag. 267-287 [PDF]
• Tinoco, I., Jr. and Gonzalez, R.L., Jr. (2011) Biological mechanisms, one molecule at a time. Gene Dev, 25, 1205-1231. [PDF]
• Palma, M.M., Abramson, J.J., Gorodetsky, A.A., Penzo, E., Gonzalez, R.L., Jr., Sheetz, M.P., Nuckolls, C., Hone, J. and Wind, S.J. (2011) Selective biomolecular nanoarrays for parallel single-molecule investigations. J Am Chem Soc, 133, 7656-7659. [PDF] [Supp Mat]
• Sorgenfrei, S., Chiu, C.Y., Gonzalez, R.L., Jr., Yu, Y.J., Kim, P., Nuckolls, C. and Shepard, K.L. (2011) Label-free single-molecule detection of DNA hybridization kinetics with a carbon nanotube field effect transistor. Nat Nanotechnol, 6, 126-132. [PDF] [Supp Mat]
• Wang, B., Ho, J., Fei, J., Gonzalez, R.L., Jr. and Lin, Q. (2011) A microfluidic approach for investigating the temperature dependence of biomolecular activity with single-molecule resolution.. Lab Chip, 11, 274-281. [PDF] [Supp Mat]

2010

• Bronson, J.E., Hofman, J.M., Fei, J., Gonzalez, R.L., Jr. and Wiggins, C. (2010) Graphical models for inferring single molecule dynamics. BMC Bioinformatics, 11, Supp 8, S2. [PDF]
• Frank, J. and Gonzalez, R.L, Jr. (2010). Structure and dynamics of a processive Brownian motor: the translating ribosome. Ann Rev Biochem, 79, 381-412. [PDF]
• Fei, J., Wang, J., Sternberg, S.H., MacDougall, D.D., Elvekrog, M.M., Pulukkunat, D., Englander, M.T. and Gonzalez, R.L., Jr. (2010). A highly-purified, fluorescently-labeled in vitro translation system for single molecule studies of protein synthesis. Methods Enzymol, 472, 221-259. [PDF]

2009

• Bronson, J.E., Fei, J., Hofman, J.M. Gonzalez, R.L, Jr.* and Wiggins, C.H.* (2009). Learning rates and states from biophysical time series: A Bayesian approach to model selection and single-molecule FRET data. Biophys J, 97, 3196-3205. (*Co-corresponding authors) [PDF] [Supp Mat]
  • Featured as one of the Top 5 Most Accessed Articles in Biophys J for December 2009
• Effraim, P.R., Wang, J., Englander, M.T., Avins, J., Leyh, T.S.*, Gonzalez, R.L., Jr.* and Cornish, V.W.* (2009). Natural amino acids do not require their native tRNAs for efficient selection by the ribosome. Nat Chem Biol, 5, 947-953. (*Co-corresponding authors) [PDF] [Supp Mat]
• Fei, J., Bronson, J.E., Hofman, J.M., Srinivas, R.L., Wiggins, C.H. and Gonzalez, R.L., Jr. (2009). Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation. Proc Natl Acad Sci, USA,106, 15702-15707. [PDF] [Supp Mat]
  • Featured as a Science and Technology News Item in Chem. Engn. News, 87, 29 [PDF]
• Sternberg, S., Fei, J., Prywes, N., McGrath, K. and Gonzalez, R.L., Jr. (2009). Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling. Nat Struct Mol Biol, 16, 861-868. [PDF] [Supp Mat]
  • Featured as a Research Highlight in Nat Chem Biol, 5, 540 [PDF]
  • Featured as a Science and Technology News Item in Chem. Engn. News, 87, 29 [PDF]
    

2007-2008

• Gonzalez, R.L., Jr. (2008). Navigating the RNA folding landscape. Nat Chem Biol, 4, 451-452. [PDF]
• Fei, J., Kosuri, P., MacDougall, D. and Gonzalez, R.L., Jr. (2008). Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Mol Cell, 30, 348-359. [PDF] [Supp Mat]
• Wang, B., Fei, J., Nguyen,T., Gonzalez, R.L., Jr. and Lin, Q. (2007) Translocation of the ribosome in temperature-controlled microfluidic channels," Int. Conf. on Miniaturized Chemical and Biochemical Analysis Systems (MicroTAS '07), pp. 796-798, Paris, France. [PDF]
• Wang, B., Fei, J., Nguyen, T., Gonzalez, R.L., Jr. and Lin, Q. (2007) Single-molecule detection in temperature-controlled microchannels," IEEE Int. Conf. Nano/Micro Engineered and Molecular Systems (NEMS '07), pp. 972-976, Bangkok, Thailand. [PDF]
• Gonzalez, R.L., Jr., Chu, S. and Puglisi, J.D. (2007). Thiostrepton inhibition of tRNA delivery to the ribosome. RNA, 13, 348-359. [PDF]

1999-2004

• Dorywalska, M., Blanchard, S.C., Gonzalez, R.L., Jr., Chu, S. and Puglisi, J.D. (2004). Site-specific labeling of 16S rRNA for single-molecule spectroscopy. Nucleic Acids Res. 31, 182-189. [PDF]
• Blanchard, S.C., Gonzalez, R.L., Jr., Kim, H.D., Chu, S. and Puglisi, J.D. (2004). tRNA selection and proofreading in translation. Nat Struct Mol Biol, 11, 1008-1014. [PDF] [Supp Mat]
• Blanchard, S.C.*, Kim, H.D.*, Gonzalez, R.L., Jr.*, Puglisi, J.D. and Chu, S. (2004). tRNA dynamics on the ribosome during translation. Proc Natl Acad Sci USA, 101, 12893-12898. (*Equal Authorship). [PDF] [Supp Mat]
• Lynch, S.R., Gonzalez, R.L., Jr. and Puglisi, J.D. (2003). Comparison of X-Ray crystal structure of the 30S subunit-antibioticc omplex with NMR structure of decoding site oligonucleotide paromomycin complex. Structure, 11, 43-53. [PDF]
• Gonzalez, R.L., Jr. and Tinoco, I. Jr. (2000). NMR spectroscopic techniques for the identification and characterization of metal ion binding sites in RNA. Methods Enzymol, 338, 421-443. [PDF]
• Yuen, H-W., Tinoco, I. Jr. and Gonzalez, R.L., Jr. (2000). The effect of magnesium (II) ion and cobalt (III) hexammine ion on an RNA pseudoknot. Berkeley Scientific, 4, 139-143.
• Gonzalez, R.L., Jr. and Tinoco, I. Jr. (1999). Solution structure and thermodynamics of a divalent metal ion binding site in an RNA pseudoknot. J Mol Biol, 289, 1267-1282. [PDF]