Ferreon Lab Publications

Sun Y, U Coskun, PS Tsoi, JC Ferreon, AC Ferreon, B Barbieri and S-CJ Liao* (2016) Quantitative multi-parameter analysis of single molecule dynamics by PIE FastFLIM microscopy. Proc. of SPIE 10069, 100691X. DOI: 10.1117/12.2255961.

Sun Y, U Coskun, AC Ferreon, B Barbieri and S-CJ Liao* (2016) Tunable PIE and synchronized gating detections by FastFLIM for quantitative microscopy measurements of fast dynamics of single molecules. Proc. of SPIE 9712, 97120S. DOI: 10.1117/12.2217434.

Ren Z, J Lee, MM Moosa, Y Nian, L Hu, Z Xu, JG McCoy, ACM Ferreon*, W Im* and M Zhou* (2018) Structure of an EIIC sugar transporter trapped in an inward-facing conformation. Proc. Natl. Acad. Sci. USA. 115(23):5962-5967. PMID: 29784777. DOI: 10.1073/pnas.1800647115.

Moosa MM, JC Ferreon* and ACM Ferreon* (2018) Ligand interactions and the protein order-disorder energetic continuum. Semin. Cell Dev. Biol. pii: S1084-9521(17)30391-9. PMID: 29753880. DOI: 10.1016/j.semcdb.2018.05.007. (Review)

Ferreon JC*, A Jain, KJ Choi, PS Tsoi, KR MacKenzie, SY Jung and AC Ferreon* (2018) Acetylation disfavors Tau phase separation. Int. J. Mol. Sci. 19(5). PII: E1360. PMID: 29734651. DOI: 10.3390/ijms19051360.

Moosa MM, AZ Goodman, JC Ferreon, CW Lee, ACM Ferreon* and AA Deniz* (2018) Denaturant-specific effects on the structural energetics of a protein-denatured ensemble. Eur. Biophys. J. 47(1):89-94. PMID: 29080139. DOI: 10.1007/s00249-017-1260-4.

Tsoi PS, KJ Choi, PG Leonard, A Sizovs, MM Moosa, KR MacKenzie, JC Ferreon* and ACM Ferreon* (2017) The N-terminal domain of ALS-linked TDP-43 assembles without misfolding. Angew. Chem. Int. Ed. Engl. 56(41):12590-12593. PMID: 28833982. DOI: 10.1002/anie.201706769.

Jiang X, J Chen, A Bajić, C Zhang, X Song, SL Carroll, ZL Cai, M Tang, M Xue, N Cheng, CP Schaaf, F Li, KR MacKenzie, ACM Ferreon, F Xia, MC Wang, M Maletić-Savatić and J Wang* (2017) Quantitative real-time imaging of glutathione. Nat. Commun. 8:16087. PMID: 28703127. DOI: 10.1038/ncomms16087.

Krois A, Ferreon JC, Martinez-Yamout MA, Dyson HJ, Wright PE. Recognition of the disordered p53 transactivation domain by the transcriptional adapter zinc finger domains of CREB-binding protein. Proc Natl Acad Sci USA (2016) 113(13):E1853-62.

Moosa MM, ACM Ferreon* and AA Deniz* (2015) Forced folding of a disordered protein accesses an alternative folding landscape. Chemphyschem. 16(1):90-4. PMID: 25345588. DOI: 10.1002/cphc.201402661.

Ferreon ACM*, JC Ferreon*, PE Wright and AA Deniz (2013) Modulation of allostery by protein intrinsic disorder. Nature. 498(7454):390-4. PMID: 23783631. DOI: 10.1038/nature12294.
• Featured in TSRI News & Views, ScienceDaily, and Chemical & Engineering News (Jun 2013)
• Highlighted in Nature Research News & Views, Jun 2013
• Featured in Cell (Leading Edge Select), Aug 2013
• Faculty of 1000 Recommended Paper, Jul 2013

Ferreon ACM, MM Moosa, Y Gambin and AA Deniz* (2012) Counteracting chemical chaperone effects on the single-molecule α-synuclein structural landscape. Proc. Natl. Acad. Sci. USA 109(44):17826-31. PMID: 22826265. DOI: 10.1073/pnas.1201802109. (Direct Submission)
• PNAS Chemical Physics of Protein Folding Special Feature
• Highlighted in BioTechniques, May 2014

Ferreon ACM* and AA Deniz* (2012) Osmolyte-, binding-, and temperature-induced transitions of intrinsically disordered proteins. Methods Mol. Biol. 896:257-66. PMID: 22821530. DOI: 10.1007/978-1-4614-3704-8_17. (Book Chapter)

Arai M, Ferreon JC, Wright PE. (2012) Quantitative analysis of multisite protein ligand interactions by NMR: binding of intrinsically disordered p53 transactivation subdomains with the TAZ2 domain of CBP. J Am Chem Soc 134(8):3792-803.

Ferreon ACM and AA Deniz* (2011) Protein folding at single-molecule resolution. Biochim. Biophys. Acta. 1814(8):1021-9. PMID: 21303706. DOI: 10.1016/j.bbapap.2011.01.011. (Review)
• Journal Cover Art

Gambin Y*, V Vandelinder, ACM Ferreon, EA Lemke, A Groisman* and AA Deniz* (2011) Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing. Nat. Methods 8(3):239-41. PMID: 21297620. DOI: 10.1038/nmeth.1568.
• Featured in TSRI News & Views (Feb 2011), Genetic Engineering & Biotechnology News (Mar 2011), Physics Today (Apr 2011), and ACS Chemical Biology Spotlight (Apr 2011)
• Highlighted in Nature Methods News & Views, Mar 2011
• Faculty of 1000 Must Read Paper, Apr 2011

Lee CW, JC Ferreon*, ACM Ferreon*, M Arai and PE Wright* (2010) Graded enhancement of p53 binding to CBP by multisite phosphorylation. Proc. Natl. Acad. Sci. USA 107(45):19290-5. PMID: 20962272. DOI: 10.1073/pnas.1013078107.
• Featured in Nature Signaling Gateway, Nov 2010

Ferreon ACM, CR Moran, Y Gambin and AA Deniz* (2010) Single-molecule fluorescence studies of intrinsically disordered proteins. Methods Enzymol. 472:179-204. PMID: 20580965. DOI: 10.1016/S0076-6879(10)72010-3. (Book Chapter)

Ferreon ACM, CR Moran, JC Ferreon and AA Deniz* (2010) Alteration of the alpha-synuclein folding landscape by a mutation related to Parkinson's disease. Angew. Chem. Int. Ed. Engl. 49:3469-72. PMID: 20544898. DOI: 10.1002/anie.201000378.
• Highlighted by Angewandte as a Very Important Paper

Ferreon JC*, Lee CW, Arai M, Martinez-Yamout MA, Dyson HJ, Wright PE. (2009) Cooperative regulation of p53 by modulation of ternary complex formation with CBP and HDM2. Proc Natl Acad Sci USA 106(16):6591-6.

Ferreon JC, Martinez-Yamout MA, Dyson HJ, Wright PE. (2009) Molecular basis for subversion of cellular control mechanisms by the Adenoviral E1A oncoprotein. Proc Natl Acad Sci USA 106(32):13260-5.
• Highlighted in TSRI Scripps News and Views Aug 10, 2009

Manson A, Whitten ST, Ferreon JC, Fox RO, Hilser VJ. (2009) Characterizing the role of ensemble modulation in mutation-induced changes in binding affinity. J Am Chem Soc 131(19):6785-93.

Vandelinder V, ACM Ferreon, Y Gambin, AA Deniz* and A Groisman* (2009) High-resolution temperature-concentration diagram of alpha-synuclein conformation obtained from a single Förster resonance energy transfer image in a microfluidic device. Anal. Chem. 81(16):6929-35. PMID: 19555081. DOI: 10.1021/ac901008c.

Gambin Y, A Schug, EA Lemke, JJ Lavinder, ACM Ferreon, TJ Magliery*, JN Onuchic* and AA Deniz* (2009) Direct single-molecule observation of a protein living in two opposed native structures. Proc. Natl. Acad. Sci. USA 106(25):10153-8. PMID: 19506258. DOI: 10.1073/pnas.0904461106.
• Featured in TSRI News & Views, Jun 2009
• Faculty of 1000 Must Read Paper, Oct 2009

Ferreon ACM, Y Gambin, EA Lemke and AA Deniz* (2009) Interplay of alpha-synuclein binding and conformational switching probed by single-molecule fluorescence. Proc. Natl. Acad. Sci. USA 106(14):5645-50. PMID: 19293380. DOI: 10.1073/pnas.0809232106. (Direct Submission)
• Featured in TSRI News & Views, Mar 2009
• Highlighted in the Biophysical Society Newsletter, May 2009

Whitten ST, Ferreon JC, Hamburger JB, Hilser VJ. (2008) Calorimetric Determination of the Thermodynamics of Polyproline II (PII) Helix Formation in the Unfolded States of Protein. In Unfolded Proteins: From Denatured to Intrinsically Disordered Ed. Trevor Creamer, Nova Science Publishing.

Ferreon ACM and AA Deniz* (2007) Alpha-synuclein multistate folding thermodynamics: implications for protein misfolding and aggregation. Biochemistry 46(15):4499-509. PMID: 17378587.
• 11th Most-Accessed Biochemistry Article for Apr-Jun 2007

Ferreon ACM, JC Ferreon, DW Bolen and J Rösgen* (2007) Protein phase diagrams II: Nonideal behavior of biochemical reactions in the presence of osmolytes. Biophys. J. 92(1):245-56. PMID: 17028144.

Auton M, ACM Ferreon and DW Bolen* (2006) Metrics that differentiate the origins of osmolyte effects on protein stability: A test of the surface tension proposal. J. Mol. Biol. 361(5): 983-92. PMID: 16889793.

Ferreon JC, ACM Ferreon, K Li and SM Lemon* (2005) Molecular determinants of TRIF proteolysis mediated by the hepatitis C virus NS3/4A protease. J. Biol. Chem. 280(21): 20483-92. PMID: 15767257.

Li K, E Foy, JC Ferreon, M Nakamura, ACM Ferreon, M Ikeda, SC Ray, M Gale, Jr. and SM Lemon* (2005) Immune evasion by hepatitis C virus NS3/4A protease-mediated cleavage of the Toll-like receptor 3 adaptor protein TRIF. Proc. Natl. Acad. Sci. USA 102(8): 2992–7. PMID: 15710891. (Direct Submission)
• Featured in Nat’l AIDS and Treatment Advocacy Project News
• Faculty of 1000 Recommended Paper, Feb 2005

Ferreon ACM and DW Bolen* (2004) Thermodynamics of denaturant-induced unfolding of a protein that exhibits variable two-state denaturation. Biochemistry 43(42):13357-69. PMID: 15491142.

Ferreon JC, Hamburger JB, Whitten ST, Hilser VJ. (2004) An experimental strategy to evaluate the thermodynamic stability of highly dynamic binding sites in proteins using hydrogen exchange. J Am Chem Soc 126(40):12774-5.

Ferreon JC and Hilser VJ. (2004) Thermodynamics of binding to SH3 domains: the energetic impact of polyproline II (PII) helix formation. Biochemistry 43(24):7787-97.

Ferguson MR, Fan X, Mukherjee M, Luo J, Khan R, Ferreon JC, Hilser VJ, Shope RE, and Fox RO. (2004) Directed discovery of bivalent peptide ligands to an SH3 domain. Protein Sci 13(3):626-32.

Hamburger JB, Ferreon JC, Whitten ST, Hilser VJ. (2004) Thermodynamic mechanism and consequences of the polyproline II (PII) structural bias in the denatured states of proteins. Biochemistry 43(30):9790-9.

Ferreon JC and Hilser VJ. (2003) The effect of the polyproline II (PPII) conformation on the denatured state entropy. Protein Sci 12(3):447-57.

Ferreon JC and Hilser VJ. (2003) Ligand-induced changes in dynamics in the RT loop of the C-terminal SH3 domain of SEM-5 indicate cooperative conformational coupling. Protein Sci 12(5):982-96.

Ferreon JC, Volk DE, Luxon BA, Gorenstein DG, and Hilser VJ. (2003) Solution structure, dynamics and thermodynamics of the native state ensemble of the SEM-5 C-terminal SH3 domain. Biochemistry 42(19):5582-91.

Tabbada KA, Magno MM, Delfin FC, Calacal GC, Tan M, C-Ferreon J, Halos SC, De Ungria MCA. (2002) Allele Frequencies of Eight Short Tandem Repeat Loci in Three Visayas Regional Populations of the Philippines. J Forensic Sci 47(6):1397-8.

Soman KV, Midoro-Horiuti T, Ferreon JC, Goldblum RM, Brooks EG, Kurosky A, Braun W, Schein C. (2000) Homology modeling and characterization of IgE binding epitopes of mountain cedar allergen Jun a 3. Biophys J 79(3):1601-9.

Yang M, ACM Ferreon and DW Bolen* (2000) Structural thermodynamics of a random coil protein in guanidine hydrochloride. Proteins Suppl 4:44-9. PMID: 11013399.

Halos SC*, JY Chu, ACM Ferreon and MMF Magno (1999) Philippine population database at nine microsatellite loci for forensic and paternity applications. Forensic Sci. Int. 101(1):27-32. PMID: 10376334

Halos SC*, ES Fortuno III, ACM Ferreon, JY Chu, J Miranda, S Harada and M Benecke (1998) Allele frequency distributions of the polymorphic STR loci HUMVWA, HUMFES, HUMF13A01 and the VNTR D1S80 in a Filipino population from Metro Manila. Int. J. Legal Med. 111(4):224-6. PMID: 9646171.