Publications

Walker, T., Sun, H., Gunnels, T., Wysocki, V., Laganowsky, A., Rye, H., Russell, D. (2023) Dissecting the thermodynamics of ATP binding to GroEL one nucleotide at a time, ACS Central Science, 9: 466-475. PubMed

Kustigian, L., Gong, X., Gai, W., Thongchol, J., Zhang, J., Puchalla, J., Carr, C. M., Rye, H. S. (2023) GTP‐stimulated membrane fission by the N‐BAR protein AMPH‐1, Traffic, 24: 34-47. PubMed

Shoup, D., Roth, A., Puchalla, J. & Rye, H. S. (2022) The impact of hidden structure on aggregate disassembly by molecular chaperones, Frontiers Mol Biosci, 9: 915307. PubMed

Naqvi, M., Avellandeda, M.J., Roth, A., Koers, Roland, A., E., Sunderlikova, V., Kramer, G., Rye, H. S., and Tans, S. J. (2022) Protein chain collapse modulation and folding stimulation by GroEL-ES. Sci Adv, 8: eabl6293. PubMed

Walker, T. E., Mehdi, S., Sun, H.E., McCabe, J. W., Roth, A., Moghadamchargari, Z., Clemmer, D.E., Laganowsky, A., Rye, H.S., Russell, D.H. (2022) Temperature regulates stability, ligand binding (Mg2+ and ATP), and stoichiometry of GroEL–GroES complexes, J Am Chem Soc, 144: 2667-2678. PubMed

Shoup, D., Roth, A., Thapa, R., Puchalla, J. & Rye, H. S. (2021) Development and Application of Multi-Color Burst Analysis Spectroscopy. Biophys J, 120: 2192–2204 . PubMed

Brock, D., Kondow-McConaghy, H., Allen, J., Brkljača, Z., Kustigian, L., Jiang, M., Zhang, J., Rye, H.  Vazdar, M., Pellois, J. (2020). Mechanism of Cell Penetration by Permeabilization of Late Endosomes: Interplay between a Multivalent TAT Peptide and Bis(monoacylglycero)phosphate, Cell Chemical Biology, 27: 1-12. PubMed

D.J. Brock, L. Kustigian, M. Jiang, K. Graham, T.-Y. Wang, A. Erazo-Oliveras, K. Najjar, J. Zhang, H. Rye and J.P. Pellois, (2018) Efficient cell delivery mediated by lipid-specific endosomal escape of supercharged branched peptides, Traffic, 19: 421–435.  PubMed

J. Weaver, M. Jiang, A. Roth, J. Puchalla, J. Zhang, H.S. Rye, (2017) GroEL actively stimulates folding of the endogenous substrate protein PepQ, Nat Commun, 8:  15934. PubMed

Brooks, A., Shoup, D., Kustigian, L., Puchalla, J., Carr, C. M., and Rye, H. S. (2015) Single particle fluorescence burst analysis of Epsin induced membrane fission, PloS One, 10: e0119563. PubMed

Weaver, J., Watts, T., Li, P., and Rye, H.S. (2014) Structural basis of substrate selectivity of E. coli prolidase, PloS One, 9: e111531.   PubMed

Weaver, J. and Rye, H.S. (2014) The C-terminal tails of the bacterial chaperonin GroEL stimulate protein folding by directly altering the conformation of a substrate protein, JBC, 289: 23219-23232.  PubMed

Lin, Z., Puchalla, J., Shoup, D. and Rye, H. S. (2013) Repetitive unfolding by the trans ring of the GroEL-GroES Copmlex stimulates folding, JBC, 288: 30944-30955.  PubMed.

Krantz, K., Puchalla, J., Thapa, R., Kobayashi, C., Bisher, M., Viehweg, J., Carr, C.M. and Rye, H. S. (2013) Single-particle dynamics of yeast clathrin coat disassembly in free solution, JBC, 288: 26721-26730.  PubMed

Chen, D., Madan, D., Weaver, J., Lin, Z., Schröder, G., Chiu, W., and Rye, H. S. (2013) Visualizing GroEL/ES in the act of encapsulating a folding protein, Cell, 153: 1354-1365.  PubMed

Karuri, N., Lin, Z., Kirillova, O., Rye, H. S., and Schwarzbauer, J. E. (2009) Probing the conformation of the fibronectin III1-2 domain with intramolecular fluorescence resonance energy transfer, J. Biol. Chem., 284:3445-34452.  PubMedMadan, D., Lin, Z., and Rye, H. S. (2008) Triggering protein folding within the GroEL-GroES chaperonin complex, J. Biol. Chem, 283: 32003-32013.  PubMed

Puchalla, J., Krantz, K., Austin, R., and Rye, H. S. (2008) Burst analysis spectroscopy: a versatile, single-particle approach for studying the distributions of protein aggregates and fluorescent assemblies, PNAS, 105: 14400-14405.  PubMed

Lin, Z., Madan, D. and Rye, H. S. (2008) GroEL stimulates protein folding through forced unfolding, Nat Stuct Mol Bio, 15: 303-311.  PubMed

Lin, Z. and Rye, H.S. (2006) GroEL-mediated protein folding: making the impossible, possible. Crit Rev Biochem Mol Biol, 41: 211-239.  PubMed

Rye, H. S. (2004) Fluorescence Resonance Energy Transfer, Ergito.com in Techniques.

Lin, Z and Rye, H. S. (2004) Expansion and compression of a protein folding intermediate by GroEL. Mol. Cell, 16: 23-24.  PubMed

Chaudhry C., Farr G.W., Todd M.J., Rye H.S., Brunger A.T., Adams P.D., Horwich A.L., Sigler P.B.  (2003) Role of the gamma-phosphate of ATP in triggering protein folding by GroEL-GroES: function, structure and energetics.  EMBO J, 22: 4877-87.  PubMed

Rye, H.S.  (2001) Application of fluorescence resonance energy transfer to the GroEL-GroES chaperonin reaction.  Methods, 24: 278-288.  PubMed

Rye, H.S., Roseman, A. M., Saibil, H. R., Furtak, K. and Horwich, A. L. (1999) Cycling of the GroEL-GroES machine: nucleotide and non-native polypeptide direct alternation of folding-active rings.  Cell  97:325-338.  PubMed

Sigler, P. B., Xu, Z., Rye, H. S., Burston, S. G., Fenton, W. A., and Horwich, A. L. (1998) Structure and function in GroEL-mediated protein folding.  Annu. Rev. Biochem. 67:581-608.  PubMed

Horwich, A. L., Burston, S. G., Rye, H. S., Weissman, J. S. and Fenton, W. A.  (1998) Construction of single-ring and two-ring versions of bacterial chaperonin GroEL.  Methods Enzymol. 290: 141-146.  PubMed

Rye, H. S., Burston, S. G., Fenton, W. A., Beechem, J. M., Xu, Z., Sigler, P. B., Horwich, A. L. (1997)  Distinct actions of cis and trans ATP within the double ring of the chaperonin GroEL.  Nature  388:792-798.  PubMed

Drees, B. L., Rye, H. S., Glazer, A. N. and Nelson, C. M. (1996) Environment-sensitive labels in multiplex fluorescence analysis of protein-DNA complexes.  J. Biol. Chem. 271:32168-32173.  PubMed

Weissman, J. S., Rye, H. S., Fenton W. A., Beechem, J. M., and Horwich, A. L. (1996) Characterization of the active intermediate of a GroEL–GroES-mediated protein folding reaction.  Cell  84:481-490.  PubMed

Rye, H. S. and Glazer, A. N. (1995) Interaction of dimeric intercalating dyes with single stranded DNA.  Nucleic Acids Res. 23:1215-1222.  PubMed

Zhu, H., Clark, S. M., Benson, S. C., Rye, H. S., Glazer, A. N. and Mathies, R. A. (1994) High-sensitivity capillary electrophoresis of double-stranded DNA fragments using monomeric and dimeric fluorescent intercalating dyes.  Anal. Chem. 66:1941-1948.  PubMed

Mathies, R. M., Scherer, J. R., Quesada, M. A., Rye, H. S. and Glazer, A. N. (1994) Laser-excited confocal-fluorescence gel scanner.  Rev. Sci. Instrum. 65:807-812.

Rye, H. S., Yue, S., Quesada, M. A., Haugland, R. P., Mathies, R. A. and Glazer, A. N. (1993) Picogram detection of stable dye-DNA intercalation complexes with a two-color laser-excited confocal fluorescence gel scanner.  Methods Enzymol. 217:414-431.  PubMed

Rye, H. S., Drees, B. L., Nelson, H. C. M. and Glazer, A. N. (1993) Stable fluorescent dye-DNA complexes in high sensitivity detection of protein-DNA interactions.  J. Biol. Chem. 268:25229-25238.  PubMed

Rye, H. S., Dabora, J. M., Quesada, M. A., Mathies, R. A. and Glazer, A. N. (1993) Fluorometric assay using dimeric dyes for double and single stranded DNA and RNA with picogram sensitivity.  Anal. Biochem. 208:144-150.  PubMed

Glazer, A. N. and Rye, H. S. (1992) Stable dye-DNA intercalation complexes as reagents for high-sensitivity fluorescence detection.  Nature 359:859-861.  PubMed

Rye, H. S., Yue, S., Wemmer, D. E., Quesada, M. A., Haugland, R. P., Mathies, R. A. and Glazer, A. N. (1992) Stable fluorescent complexes of double-stranded DNA with bis-intercalating asymmetric cyanine dyes: properties and applications.  Nucleic Acids Res. 20:2803-2812.  PubMed

Rye, H. S., Quesada, M. A., Peck, K., Mathies, R. A. and Glazer, A. N. (1991) High-sensitivity two-color detection of double-stranded DNA with a confocal fluorescence gel scanner using ethidium homodimer and thiazole orange.  Nucleic Acids Res. 19:327-333.  PubMed

C. Carr Publications

Brooks, A., Shoup, D., Kustigian, L., Puchalla, J., Carr, C. M., and Rye, H. S. (2015) Single particle fluorescence burst analysis of Epsin induced membrane fission, PloS One, 10: e0119563. PubMed

Krantz, K., Puchalla, J., Thapa, R., Kobayashi, C., Bisher, M., Viehweg, J., Carr, C.M. and Rye, H. S. (2013) Single-particle dynamics of yeast clathrin coat disassembly in free solution, JBC, JBC, 288: 26721-26730  PubMed

Morgera, F., Sallah, M., Dubuke, M., Gandhi, P., Brewer, D.N., Carr, C., and Munson, M. (2012) Regulation of exocytosis by the exocyst subunit Sec6 and the SM protein Sec1, Mol Biol Cell23, 337-46.  PubMed

Carr CM, Rizo J. (2010) At the junction of SNARE and SM protein function. Curr Opin Cell Biol, 22, 488-495.  PubMed

Pant, S., Sharma, M., Patel, K., Caplan, S., Carr, C.M. and Grant, B.D. (2009) AMPH-1 Amphiphysin/Bin1 functions with RME-1 Ehd1 in endocytic recycling.  Nature Cell Biology 11, 1399-1410.  PubMed

Hashizume, K., Cheng, Y.-S., Hutton, J., Chiu, C. and Carr, C.M. (2009) Yeast Sec1p functions before and after SNARE complex assembly. Mol. Biol. Cell 20, 4673-4685.  PubMed

Carr, C.M. and Munson, M. (2007) Tag team action at the synapse. EMBO Rep. 8, 834-838.  PubMed

Togneri, J., Cheng, Y.-S., Munson, M., Hughson, F.M. and Carr, C.M. (2006) Specific SNARE complex binding mode of the Sec1/Munc-18 protein, Sec1p. Proc. Natl. Acad. Sci. USA 103, 17730-17735.  PubMed

Carr, C.M. (2001) The taming of the SNARE. Nature Struct. Biol. 8, 186-188.  PubMed

Carr, C.M. and Novick, P.J. (2000) Membrane fusion: Changing partners. Nature 404, 347-349.  PubMed

Grote, E., Carr, C.M. and Novick, P.J. (2000) Ordering the Final Events in Yeast Exocytosis. J. Cell Biol. 151, 439-451.  PubMed

Carr, C.M., Grote, E., Munson, M., Hughson, F.M. and Novick, P.J. (1999) Sec1p binds to SNARE complexes and concentrates at sites of secretion. J. Cell Biol. 146, 333-344.  PubMed

Stone, S., Sacher, M., Mao, Y., Carr, C., Lyons, P., Quinn, A.M. and Ferro-Novick, S. (1997) Bet1p activates the v-SNARE Bos1p. Mol. Biol. Cell 8, 1175-1181.  PubMed

Carr, C.M., Chaudhry, C. and Kim, P.S. (1997) Influenza hemagglutinin is spring-loaded by a metastable native conformation. Proc. Natl. Acad. Sci. USA 94, 14306-14313.  PubMed

Carr, C.M. and Kim, P.S. (1994) Flu virus invasion: halfway there. Science 266, 234-236.  PubMed

Lumb, K.J., Carr, C.M. and Kim, P.S. (1994) Subdomain folding of the coiled coil leucine zipper from the bZIP transcriptional activator GCN4. Biochemistry 33, 7361-7367.  PubMed

Carr, C.M. and Kim, P.S. (1993) A spring-loaded mechanism for the conformational change of influenza hemagglutinin. Cell 73, 823-832.  PubMed

Krasney, P.A., Carr, C.M. and Cavener, D.R. (1990) Evolution of the glucose dehydrogenase gene in Drosophila. Mol. Biol. Evol. 7, 155-177.