Gonzalez Jr.

Dr. Ruben Gonzalez is pictured.
Associate Professor
614 Havemeyer Hall, 3000 Broadway M.C. 3126
New York
Office Phone: 
(212) 854-1096
Lab Phone: 
(212) 854-0162
(212) 932-1289
Short Research Description: 

Mechanistic studies of protein synthesis by the ribosome using single-molecule fluorescence microscopy and other biophysical and biochemical approaches

Full Research Description: 

Our group uses single-molecule biophysical approaches to investigate the molecular mechanism of one of Nature's most fundamental and conserved cellular processes: protein synthesis by the ribosome. The ribosome is the RNA-based molecular machine that is universally responsible for translating the nucleotide sequence provided by messenger RNAs into the amino acid sequence of the encoded protein products. As such, the ribosome plays a critical role in the mechanism and regulation of gene expression and is the target of numerous cellular protein factors that regulate protein synthesis, small-molecule antibiotic drugs that block protein synthesis, and human viral pathogens that commandeer the process of protein synthesis for their own purposes. Using single-molecule fluorescence microscopy and spectroscopy, we study the conformational dynamics of the ribosome, its aminoacyl-transfer RNA substrates, and its essential protein factors in real time, as they carry out the process of protein synthesis. By integrating the dynamic information that is uniquely available from the single-molecule resolution of our experiments into contemporary structural and biochemical models for protein synthesis, we gain insights into the molecular mechanism of protein synthesis and its regulation that are simply not accessible using traditional ensemble biophysical and biochemical approaches.

An important aspect of research in our group is the ongoing development of new experimental tools that empower single-molecule biophysical studies of complex biological processes such as protein synthesis. For example, we are applying microfluidic technologies to expand the experimental conditions under which we can perform single-molecule fluorescence experiments; optical imaging technologies to increase the information content of our experiments; nanotechnologies to establish entirely new, non-fluorescence based single-molecule detection schemes; and statistical inference approaches to develop algorithms for the statistically rigorous analysis of single-molecule dynamics data. As a result, research in our group is highly interdisciplinary, drawing from the fields of biophysical chemistry, biochemistry, computational biology, physics, and engineering to address complex biological problems that are not easily addressed through any one individual discipline.

Representative Publications: 
  • 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. (In Press)
  • 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. 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., 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. (In Press) [PDF]
  • Wang J, Caban K, Gonzalez RL 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]
  • 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]
  • 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]
  • 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]

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