Scott Blanchard, Ph.D.

Professor of Physiology and Biophysics

646-962-6893

Belfer Research Building
413 E 69th Street, Room BB-1530
New York, NY 10021


Techniques

Research Areas


Research Summary:

Imaging Molecular Machines at the Single-Molecule Scale

Research efforts in the Blanchard lab are bridging the intellectual gap between knowledge of static molecular architecture and the fundamentally dynamic nature of biological processes. A layman’s statement of the question we aim to address is: How do enzymes move when they work?

To answer this question the lab is actively engaged in the development and implementation of single-molecule imaging techniques. Investigations at the single-molecule scale shed light on processes masked by ensemble averaging in bulk investigations and provide the first direct means of measuring stochastic, time-dependent fluctuations in enzyme structure and/or composition. Our investigations probe how these processes relate to their essential functions. We are particularly interested in developing broadly applicable methods for measuring enzyme function from an intuitive perspective of motion using single-molecule Fluorescence Resonance Energy Transfer (smFRET).

Efforts in the lab are presently focused on the function of macromolecular machines, highly organized amalgams of numerous individual gene products. These complex enzymes are central to many biological processes and are proven drug targets. They also typically defy reductionist approaches to structural and functional interrogations. Using smFRET, combined with computational modeling and molecular dynamics simulations, ongoing investigations focus on the generation of experimentally-validated movies of working molecular machines and a deeper understanding of basic enzyme function and regulation.

Recent Publications:

  1. Prakash, V, Carson, BB, Feenstra, JM, Dass, RA, Sekyrova, P, Hoshino, A et al.. Ribosome biogenesis during cell cycle arrest fuels EMT in development and disease. Nat Commun. 2019;10 (1):2110. doi: 10.1038/s41467-019-10100-8. PubMed PMID:31068593 PubMed Central PMC6506521.
  2. Lu, M, Ma, X, Castillo-Menendez, LR, Gorman, J, Alsahafi, N, Ermel, U et al.. Associating HIV-1 envelope glycoprotein structures with states on the virus observed by smFRET. Nature. 2019;568 (7752):415-419. doi: 10.1038/s41586-019-1101-y. PubMed PMID:30971821 .
  3. Pellegrino, S, Meyer, M, Könst, ZA, Holm, M, Voora, VK, Kashinskaya, D et al.. Understanding the role of intermolecular interactions between lissoclimides and the eukaryotic ribosome. Nucleic Acids Res. 2019;47 (6):3223-3232. doi: 10.1093/nar/gkz053. PubMed PMID:30759226 PubMed Central PMC6451132.
  4. Parks, MM, Kurylo, CM, Batchelder, JE, Theresa Vincent, C, Blanchard, SC. Implications of sequence variation on the evolution of rRNA. Chromosome Res. 2019;27 (1-2):89-93. doi: 10.1007/s10577-018-09602-w. PubMed PMID:30719681 .
  5. Flis, J, Holm, M, Rundlet, EJ, Loerke, J, Hilal, T, Dabrowski, M et al.. tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis. Cell Rep. 2018;25 (10):2676-2688.e7. doi: 10.1016/j.celrep.2018.11.040. PubMed PMID:30517857 PubMed Central PMC6314685.
  6. Broadwater, DWB Jr, Altman, RB, Blanchard, SC, Kim, HD. ERASE: a novel surface reconditioning strategy for single-molecule experiments. Nucleic Acids Res. 2018; :. doi: 10.1093/nar/gky1168. PubMed PMID:30462308 PubMed Central PMC6379648.
  7. Farber, G, Parks, MM, Lustgarten Guahmich, N, Zhang, Y, Monette, S, Blanchard, SC et al.. ADAM10 controls the differentiation of the coronary arterial endothelium. Angiogenesis. 2019;22 (2):237-250. doi: 10.1007/s10456-018-9653-2. PubMed PMID:30446855 PubMed Central PMC6475616.
  8. Kurylo, CM, Parks, MM, Juette, MF, Zinshteyn, B, Altman, RB, Thibado, JK et al.. Endogenous rRNA Sequence Variation Can Regulate Stress Response Gene Expression and Phenotype. Cell Rep. 2018;25 (1):236-248.e6. doi: 10.1016/j.celrep.2018.08.093. PubMed PMID:30282032 PubMed Central PMC6312700.
  9. Riederer, EA, Focke, PJ, Georgieva, ER, Akyuz, N, Matulef, K, Borbat, PP et al.. A facile approach for the in vitro assembly of multimeric membrane transport proteins. Elife. 2018;7 :. doi: 10.7554/eLife.36478. PubMed PMID:29889023 PubMed Central PMC6025958.
  10. Blanchard, SC. A Much-Needed Boost for the Dwindling Antibiotic Pipeline. Mol. Cell. 2018;70 (1):3-5. doi: 10.1016/j.molcel.2018.03.023. PubMed PMID:29625037 PubMed Central PMC6296369.
  11. Ma, X, Lu, M, Gorman, J, Terry, DS, Hong, X, Zhou, Z et al.. HIV-1 Env trimer opens through an asymmetric intermediate in which individual protomers adopt distinct conformations. Elife. 2018;7 :. doi: 10.7554/eLife.34271. PubMed PMID:29561264 PubMed Central PMC5896952.
  12. Parks, MM, Kurylo, CM, Dass, RA, Bojmar, L, Lyden, D, Vincent, CT et al.. Variant ribosomal RNA alleles are conserved and exhibit tissue-specific expression. Sci Adv. 2018;4 (2):eaao0665. doi: 10.1126/sciadv.aao0665. PubMed PMID:29503865 PubMed Central PMC5829973.
  13. Terry, DS, Kolster, RA, Quick, M, LeVine, MV, Khelashvili, G, Zhou, Z et al.. A partially-open inward-facing intermediate conformation of LeuT is associated with Na+ release and substrate transport. Nat Commun. 2018;9 (1):230. doi: 10.1038/s41467-017-02202-y. PubMed PMID:29335402 PubMed Central PMC5768729.
  14. Herschhorn, A, Gu, C, Moraca, F, Ma, X, Farrell, M, Smith, AB 3rd et al.. Publisher Correction: The β20-β21 of gp120 is a regulatory switch for HIV-1 Env conformational transitions. Nat Commun. 2018;9 (1):158. doi: 10.1038/s41467-017-02463-7. PubMed PMID:29311557 PubMed Central PMC5758816.
  15. Prokhorova, I, Altman, RB, Djumagulov, M, Shrestha, JP, Urzhumtsev, A, Ferguson, A et al.. Aminoglycoside interactions and impacts on the eukaryotic ribosome. Proc. Natl. Acad. Sci. U.S.A. 2017;114 (51):E10899-E10908. doi: 10.1073/pnas.1715501114. PubMed PMID:29208708 PubMed Central PMC5754804.
  16. Dyla, M, Terry, DS, Kjaergaard, M, Sørensen, TL, Lauwring Andersen, J, Andersen, JP et al.. Dynamics of P-type ATPase transport revealed by single-molecule FRET. Nature. 2017;551 (7680):346-351. doi: 10.1038/nature24296. PubMed PMID:29144454 PubMed Central PMC5872817.
  17. Herschhorn, A, Gu, C, Moraca, F, Ma, X, Farrell, M, Smith, AB 3rd et al.. The β20-β21 of gp120 is a regulatory switch for HIV-1 Env conformational transitions. Nat Commun. 2017;8 (1):1049. doi: 10.1038/s41467-017-01119-w. PubMed PMID:29051495 PubMed Central PMC5648922.
  18. Alejo, JL, Blanchard, SC. Miscoding-induced stalling of substrate translocation on the bacterial ribosome. Proc. Natl. Acad. Sci. U.S.A. 2017;114 (41):E8603-E8610. doi: 10.1073/pnas.1707539114. PubMed PMID:28973849 PubMed Central PMC5642701.
  19. Gregorio, GG, Masureel, M, Hilger, D, Terry, DS, Juette, M, Zhao, H et al.. Single-molecule analysis of ligand efficacy in β2AR-G-protein activation. Nature. 2017;547 (7661):68-73. doi: 10.1038/nature22354. PubMed PMID:28607487 PubMed Central PMC5502743.
  20. Vušurović, N, Altman, RB, Terry, DS, Micura, R, Blanchard, SC. Pseudoknot Formation Seeds the Twister Ribozyme Cleavage Reaction Coordinate. J. Am. Chem. Soc. 2017;139 (24):8186-8193. doi: 10.1021/jacs.7b01549. PubMed PMID:28598157 PubMed Central PMC5697751.
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