Ashok Deniz - Publications

Affiliations: 
Scripps Research Institute, La Jolla, La Jolla, CA, United States 
Area:
Single-Molecule Biophysics

50 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Nasir I, Onuchic PL, Labra SR, Deniz AA. Single-molecule fluorescence studies of intrinsically disordered proteins and liquid phase separation. Biochimica Et Biophysica Acta. Proteins and Proteomics. PMID 31054969 DOI: 10.1016/j.bbapap.2019.04.007  0.96
2018 Lee TC, Moran CR, Cistrone PA, Dawson PE, Deniz AA. Site-Specific Three-Color Labeling of α-Synuclein via Conjugation to Uniquely Reactive Cysteines during Assembly by Native Chemical Ligation. Cell Chemical Biology. PMID 29681525 DOI: 10.1016/j.chembiol.2018.03.009  0.92
2018 Milin AN, Deniz AA. Reentrant Phase Transitions and Non-Equilibrium Dynamics in Membraneless Organelles. Biochemistry. PMID 29569441 DOI: 10.1021/acs.biochem.8b00001  0.96
2018 Mitrea DM, Cika JA, Stanley CB, Nourse A, Onuchic PL, Banerjee PR, Phillips AH, Park CG, Deniz AA, Kriwacki RW. Self-interaction of NPM1 modulates multiple mechanisms of liquid-liquid phase separation. Nature Communications. 9: 842. PMID 29483575 DOI: 10.1038/s41467-018-03255-3  1
2017 Moosa MM, Goodman AZ, Ferreon JC, Lee CW, Ferreon ACM, Deniz AA. Denaturant-specific effects on the structural energetics of a protein-denatured ensemble. European Biophysics Journal : Ebj. PMID 29080139 DOI: 10.1007/s00249-017-1260-4  1
2017 Banerjee PR, Milin AN, Moosa MM, Onuchic PL, Deniz A. Reentrant phase transition drives dynamic substructure formation in ribonucleoprotein droplets. Angewandte Chemie (International Ed. in English). PMID 28556382 DOI: 10.1002/anie.201703191  1
2016 Banerjee PR, Moosa MM, Deniz AA. Two-Dimensional Crowding Uncovers a Hidden Conformation of α-Synuclein. Angewandte Chemie (International Ed. in English). PMID 27612332 DOI: 10.1002/anie.201606963  1
2016 Lee TC, Kang M, Kim CH, Schultz PG, Chapman E, Deniz AA. Dual Unnatural Amino Acid Incorporation and Click-Chemistry Labeling to Enable Single-Molecule FRET Studies of p97 Folding. Chembiochem : a European Journal of Chemical Biology. 17: 981-4. PMID 27115850 DOI: 10.1002/cbic.201500695  1
2016 Trelle MB, Ramsey KM, Lee TC, Zheng W, Lamboy J, Wolynes PG, Deniz A, Komives EA. Binding of NFκB Appears to Twist the Ankyrin Repeat Domain of IκBα. Biophysical Journal. 110: 887-95. PMID 26910425 DOI: 10.1016/j.bpj.2016.01.001  0.56
2016 Mitrea DM, Cika JA, Guy CS, Ban D, Banerjee PR, Stanley CB, Nourse A, Deniz AA, Kriwacki RW. Nucleophosmin integrates within the nucleolus via multi-modal interactions with proteins displaying R-rich linear motifs and rRNA. Elife. 5. PMID 26836305 DOI: 10.7554/eLife.13571  0.56
2015 Banerjee PR, Mitrea DM, Kriwacki RW, Deniz AA. Asymmetric Modulation of Protein Order-Disorder Transitions by Phosphorylation and Partner Binding. Angewandte Chemie (International Ed. in English). PMID 26679013 DOI: 10.1002/anie.201507728  1
2015 Moosa MM, Ferreon AC, Deniz AA. Forced folding of a disordered protein accesses an alternative folding landscape. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 16: 90-4. PMID 25345588 DOI: 10.1002/cphc.201402661  1
2015 Lee T, Moran-Gutierrez CR, Deniz AA. Probing protein disorder and complexity at single-molecule resolution. Seminars in Cell & Developmental Biology. 37: 26-34. PMID 25305580 DOI: 10.1016/j.semcdb.2014.09.027  0.76
2014 Polinkovsky ME, Gambin Y, Banerjee PR, Erickstad MJ, Groisman A, Deniz AA. Ultrafast cooling reveals microsecond-scale biomolecular dynamics. Nature Communications. 5: 5737. PMID 25517430 DOI: 10.1038/ncomms6737  1
2014 Banerjee PR, Deniz AA. Shedding light on protein folding landscapes by single-molecule fluorescence. Chemical Society Reviews. 43: 1172-88. PMID 24336839 DOI: 10.1039/c3cs60311c  1
2013 Ferreon AC, Ferreon JC, Wright PE, Deniz AA. Modulation of allostery by protein intrinsic disorder. Nature. 498: 390-4. PMID 23783631 DOI: 10.1038/nature12294  1
2012 Ferreon AC, Moosa MM, Gambin Y, Deniz AA. Counteracting chemical chaperone effects on the single-molecule α-synuclein structural landscape. Proceedings of the National Academy of Sciences of the United States of America. 109: 17826-31. PMID 22826265 DOI: 10.1073/pnas.1201802109  1
2012 Ferreon AC, Deniz AA. Osmolyte-, binding-, and temperature-induced transitions of intrinsically disordered proteins. Methods in Molecular Biology (Clifton, N.J.). 896: 257-66. PMID 22821530 DOI: 10.1007/978-1-4614-3704-8_17  1
2012 Krishnan R, Goodman JL, Mukhopadhyay S, Pacheco CD, Lemke EA, Deniz AA, Lindquist S. Conserved features of intermediates in amyloid assembly determine their benign or toxic states. Proceedings of the National Academy of Sciences of the United States of America. 109: 11172-7. PMID 22745165 DOI: 10.1073/pnas.1209527109  1
2012 Milles S, Koehler C, Gambin Y, Deniz AA, Lemke EA. Intramolecular three-colour single pair FRET of intrinsically disordered proteins with increased dynamic range. Molecular Biosystems. 8: 2531-4. PMID 22739670 DOI: 10.1039/c2mb25135c  0.96
2012 Luna VM, Fee JA, Deniz AA, Stout CD. Mobility of Xe atoms within the oxygen diffusion channel of cytochrome ba(3) oxidase. Biochemistry. 51: 4669-76. PMID 22607023 DOI: 10.1021/bi3003988  1
2011 Berezhna SY, Supekova L, Sever MJ, Schultz PG, Deniz AA. Dual regulation of hepatitis C viral RNA by cellular RNAi requires partitioning of Ago2 to lipid droplets and P-bodies. Rna (New York, N.Y.). 17: 1831-45. PMID 21868483 DOI: 10.1261/rna.2523911  1
2011 Tyagi NK, Fenton WA, Deniz AA, Horwich AL. Double mutant MBP refolds at same rate in free solution as inside the GroEL/GroES chaperonin chamber when aggregation in free solution is prevented. Febs Letters. 585: 1969-72. PMID 21609718 DOI: 10.1016/j.febslet.2011.05.031  1
2011 Ferreon AC, Deniz AA. Protein folding at single-molecule resolution. Biochimica Et Biophysica Acta. 1814: 1021-9. PMID 21303706 DOI: 10.1016/j.bbapap.2011.01.011  1
2011 Gambin Y, VanDelinder V, Ferreon AC, Lemke EA, Groisman A, Deniz AA. Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing. Nature Methods. 8: 239-41. PMID 21297620 DOI: 10.1038/nmeth.1568  1
2010 Gambin Y, Deniz AA. Multicolor single-molecule FRET to explore protein folding and binding. Molecular Biosystems. 6: 1540-7. PMID 20601974 DOI: 10.1039/c003024d  0.96
2010 Ferreon AC, Moran CR, Gambin Y, Deniz AA. Single-molecule fluorescence studies of intrinsically disordered proteins. Methods in Enzymology. 472: 179-204. PMID 20580965 DOI: 10.1016/S0076-6879(10)72010-3  1
2010 Ferreon AC, Moran CR, Ferreon JC, Deniz AA. Alteration of the alpha-synuclein folding landscape by a mutation related to Parkinson's disease. Angewandte Chemie (International Ed. in English). 49: 3469-72. PMID 20544898 DOI: 10.1002/anie.201000378  1
2010 Gambin Y, Simonnet C, VanDelinder V, Deniz A, Groisman A. Ultrafast microfluidic mixer with three-dimensional flow focusing for studies of biochemical kinetics. Lab On a Chip. 10: 598-609. PMID 20162235 DOI: 10.1039/b914174j  1
2009 Lemke EA, Gambin Y, Vandelinder V, Brustad EM, Liu HW, Schultz PG, Groisman A, Deniz AA. Microfluidic device for single-molecule experiments with enhanced photostability. Journal of the American Chemical Society. 131: 13610-2. PMID 19772358 DOI: 10.1021/ja9027023  1
2009 Vandelinder V, Ferreon AC, Gambin Y, Deniz AA, Groisman A. High-resolution temperature-concentration diagram of alpha-synuclein conformation obtained from a single Förster resonance energy transfer image in a microfluidic device. Analytical Chemistry. 81: 6929-35. PMID 19555081 DOI: 10.1021/ac901008c  1
2009 Gambin Y, Schug A, Lemke EA, Lavinder JJ, Ferreon AC, Magliery TJ, Onuchic JN, Deniz AA. Direct single-molecule observation of a protein living in two opposed native structures. Proceedings of the National Academy of Sciences of the United States of America. 106: 10153-8. PMID 19506258 DOI: 10.1073/pnas.0904461106  1
2009 Ferreon AC, Gambin Y, Lemke EA, Deniz AA. Interplay of alpha-synuclein binding and conformational switching probed by single-molecule fluorescence. Proceedings of the National Academy of Sciences of the United States of America. 106: 5645-50. PMID 19293380 DOI: 10.1073/pnas.0809232106  1
2008 Brustad EM, Lemke EA, Schultz PG, Deniz AA. A general and efficient method for the site-specific dual-labeling of proteins for single molecule fluorescence resonance energy transfer. Journal of the American Chemical Society. 130: 17664-5. PMID 19108697 DOI: 10.1021/ja807430h  1
2008 Wang H, Duennwald ML, Roberts BE, Rozeboom LM, Zhang YL, Steele AD, Krishnan R, Su LJ, Griffin D, Mukhopadhyay S, Hennessy EJ, Weigele P, Blanchard BJ, King J, Deniz AA, et al. Direct and selective elimination of specific prions and amyloids by 4,5-dianilinophthalimide and analogs. Proceedings of the National Academy of Sciences of the United States of America. 105: 7159-64. PMID 18480256 DOI: 10.1073/pnas.0801934105  0.96
2008 Deniz AA, Mukhopadhyay S, Lemke EA. Single-molecule biophysics: at the interface of biology, physics and chemistry. Journal of the Royal Society, Interface / the Royal Society. 5: 15-45. PMID 17519204 DOI: 10.1098/rsif.2007.1021  0.96
2007 Mukhopadhyay S, Deniz AA. Fluorescence from diffusing single molecules illuminates biomolecular structure and dynamics. Journal of Fluorescence. 17: 775-83. PMID 17641956 DOI: 10.1007/s10895-007-0214-0  0.96
2007 Ferreon AC, Deniz AA. Alpha-synuclein multistate folding thermodynamics: implications for protein misfolding and aggregation. Biochemistry. 46: 4499-509. PMID 17378587 DOI: 10.1021/bi602461y  1
2007 Mukhopadhyay S, Krishnan R, Lemke EA, Lindquist S, Deniz AA. A natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating structures. Proceedings of the National Academy of Sciences of the United States of America. 104: 2649-54. PMID 17299036 DOI: 10.1073/pnas.0611503104  0.96
2006 Tian F, Debler EW, Millar DP, Deniz AA, Wilson IA, Schultz PG. The effects of antibodies on stilbene excited-state energetics. Angewandte Chemie (International Ed. in English). 45: 7763-5. PMID 17089439 DOI: 10.1002/anie.200602720  1
2006 Berezhna SY, Supekova L, Supek F, Schultz PG, Deniz AA. siRNA in human cells selectively localizes to target RNA sites. Proceedings of the National Academy of Sciences of the United States of America. 103: 7682-7. PMID 16684885 DOI: 10.1073/pnas.0600148103  1
2005 Zhu P, Clamme JP, Deniz AA. Fluorescence quenching by TEMPO: a sub-30 A single-molecule ruler. Biophysical Journal. 89: L37-9. PMID 16199509 DOI: 10.1529/biophysj.105.071027  0.92
2005 Clamme JP, Deniz AA. Three-color single-molecule fluorescence resonance energy transfer. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 6: 74-7. PMID 15688649 DOI: 10.1002/cphc.200400261  0.92
2004 Pljevaljcić G, Millar DP, Deniz AA. Freely diffusing single hairpin ribozymes provide insights into the role of secondary structure and partially folded states in RNA folding. Biophysical Journal. 87: 457-67. PMID 15240479 DOI: 10.1529/biophysj.103.036087  0.52
2003 Wang L, Xie J, Deniz AA, Schultz PG. Unnatural amino acid mutagenesis of green fluorescent protein. The Journal of Organic Chemistry. 68: 174-6. PMID 12515477 DOI: 10.1021/jo026570u  1
2001 Grunwell JR, Glass JL, Lacoste TD, Deniz AA, Chemla DS, Schultz PG. Monitoring the conformational fluctuations of DNA hairpins using single-pair fluorescence resonance energy transfer. Journal of the American Chemical Society. 123: 4295-303. PMID 11457196 DOI: 10.1021/ja0027620  1
2001 Deniz AA, Laurence TA, Dahan M, Chemla DS, Schultz PG, Weiss S. Ratiometric single-molecule studies of freely diffusing biomolecules. Annual Review of Physical Chemistry. 52: 233-53. PMID 11326065 DOI: 10.1146/annurev.physchem.52.1.233  1
2000 Deniz AA, Laurence TA, Beligere GS, Dahan M, Martin AB, Chemla DS, Dawson PE, Schultz PG, Weiss S. Single-molecule protein folding: diffusion fluorescence resonance energy transfer studies of the denaturation of chymotrypsin inhibitor 2. Proceedings of the National Academy of Sciences of the United States of America. 97: 5179-84. PMID 10792044 DOI: 10.1073/pnas.090104997  1
1999 Deniz AA, Dahan M, Grunwell JR, Ha T, Faulhaber AE, Chemla DS, Weiss S, Schultz PG. Single-pair fluorescence resonance energy transfer on freely diffusing molecules: observation of Förster distance dependence and subpopulations. Proceedings of the National Academy of Sciences of the United States of America. 96: 3670-5. PMID 10097095 DOI: 10.1073/pnas.96.7.3670  1
1999 Ha T, Ting AY, Liang J, Caldwell WB, Deniz AA, Chemla DS, Schultz PG, Weiss S. Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism. Proceedings of the National Academy of Sciences of the United States of America. 96: 893-8. PMID 9927664 DOI: 10.1073/pnas.96.3.893  1
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