Publications

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Publications from UNC-CH

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Prior to UNC-CH

De novo-designed transmembrane proteins bind and regulate a cytokine receptor

Mravic, M.; He, L.; Kratochvil, H. T.; Hu, H.; Nick, S. E.; Bai, W.; Edwards, A.; Jo, H.; Wu, Y.; DiMaio, D.; DeGrado, W. F. Nat. Chem. Biol. 20, 751–760 (2024)

Zfp106 binds to G-quadruplex RNAs and inhibits RAN translation and formation of RNA foci caused by G4C2 repeats

Celona, B., Salomonsson, S. E., Wu, H., Dang, B., Kratochvil, H. T., Clelland, C. D., DeGrado, W. F., and Black, B. L. Proc. Natl. Acad. Sci. USA. 121, 31 (2024).

Transient Water Wires Mediate Selective Proton Conduction in Designed Channel Proteins

Kratochvil, H.T.*; Watkins, L.C.; Mravic, M.; Somberg, N.H.; Thomaston, J.L.; Nicoludis, J.M.; Liu, L.; Hong, M.; Voth, G.A.*; DeGrado, W.F.* Nat. Chem. 15, 1012–1021 (2023)

*denotes co-corresponding authors

Analysis and de novo design of membrane-interactive peptides

Kratochvil, H.T.*; Newberry, R.W.*; Mensa, B.; Mravic, M.; DeGrado, W.F.* Faraday Discuss. 232, 9-48 (2021). 

* denotes co-corresponding authors 


CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes

Gupta, M.; Azumaya, C.M.; Moritz, M.; Pourmal, S.; Diallo, A.; Merz, G.E.; Jang, G.; Bouhaddou, M.; Fossati, A.; Brilot, A.F.; Diwanji, D.; Hernandez, E.; Herrera, N.; Kratochvil, H.T.; Lam, V.L.; Li, F.; Li, Y.; Nguyen, H.C.; Nowotny, C.; Owens, T.W.; Peters, J.K.; Rizo, A.N.; Schulze-Gahmen, U.; Smith, A.M.; Young, I.D.; Yu, Z.; Asarnow, D.; Billesbølle, C.; Campbell, M.G.; Chen, J.; Chen, K-H.; Chio, U.S.; Dickinson, M.S.; Doan, L.; Jin, M.; Kim, K.; Li, J.; Li, Y-L; Linossi, E.; Liu, Y.; Lo, M.; Lopez, J.; Lopez, K.E.; Macino, A.; Moss III, F.R.; Paul, M.D.; Pawar, K.I.; Pelin, A.; Pospiech Jr., T.H.; Puchades, C.; Remesh, S.G.; Safari, M.; Schaefer, K.; Sun, M.; Tabios, M.C.; Thwin, A.C.; Titus, E.W.; Trenker, R.; Tse, E.; Tsui, T.K.M.; Wang, F.; Zhang, K.; Zhang, Y.; Zhao, J.; Zhou, F.; Zhou, Y.; Zulinani-Alvarez, L.; QCRG Structural Biology Consortium; Agard, D.A.; Cheng, Y.; Fraser, J.S.; Jura, N.; Kortemme, T.; Manglik, A.; Southworth, D.R.; Stroud, R.M.; Swaney, D.L.; Krogan, N.J.;Frost, A. Rosenberg; O.S.; Verba, K.A. Available on bioRxiv, 2021. DOI: 10.1101/2021.05.10.443524  

Constructing ion channels from water-soluble α-helical barrels

Scott, A.J.; Niitsu, A.; Kratochvil, H.T.; Lang, E.J.M.; Sengel, J.T.; Dawson, W.M.; Mahendran, K.R.; Mravic, M.; Thomson, A.R.; Brady, R.L.; Liu, L.; Mulholland, A.J.; Bayley, H.; DeGrado, W.F.; Wallace, M.I.; Woolfson, D.N. Nat. Chem. 13 (7), 643-650 (2021).  

Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking

Schuller, M.; Correy, G.J.; Gahbaurer, S.; Feaon, D.; Wu, T.; Díaz, R.E.; Young, I.D.; Martins, L.C.; Smith, D.H.; Schulze-Gahmen, U.; Owens, T.W.; Deshpande, I.; Merz, G.E.; Thwin, A.C.; Biel, J.T.; Peters, J.K.; Moritz, M.; Herrera, N.; Kratochvil, H.T.; QCRG Structural Biology Consortium; Aimon, a.; Bennett, J.M.; Neto, J.B.; Cohen, A.E.; Dias, A.; Douangamath, A.; Dunnett, L.; Fedorov, O.; Ferla, M.P.; Fuchs, M.R.; Gorrie-Stone, T.J.; Holton, J.M.; Johnson, M.G.; Krojer, T.; Meigs, G.; Powell, A.J.; Rack, J.G.M.; Rangel, V.L.; Russi, S.; Skyner, R.E.; Smith, C.A.; Soares, A.S.; Wierman, J.L.; Zhu, K.; O’Brien, P.; Jura, N.; Ashworth, A.; Irwin, J.J.; Thompson, M.C.; Gestwiki, J.E.; Von Delft, F.; Shoichet, B.K.; Fraser, J.S.; Ahel, I. Science Advances 7(16), 1-23 (2021).   

An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike

Schoof, M.; Faust, B.; Saunders, R. A.; Sangwan, S.; Rezelj, V.; Hoppe, N.; Boone, M.; Billesbølle, C. B.; Puchades, C.; Azumaya, C. M.; Kratochvil, H. T.; Zimanyi, M.; Deshpande, I.; Liang, J.; Dickinson, S.; Nguyen, H. C.; Chio, C. M.; Merz, G. E.; Thompson, M. C.; Diwanji, D.; Schaefer, K.; Anand, A. A.; Dobzinski, N.; Zha, B. S.; Simoneau, C. R.; Leon, K.; White, K. M.; Chio, U. S.; Gupta, M.; Jin, M.; Li, F.; Liu, Y.; Zhang, K.; Bulkley, D.; Sun, M.; Smith, A. M.; Rizo, A. N.; Moss, F.; Brilot, A. F.; Pourmal, S.; Trenker, R.; Pospiech, T.; Gupta, S.; Barsi-Rhyne, B.; Belyy, V.; Barile-Hill, A. W.; Nock, S.; Liu, Y.; Krogan, N. J.; Ralston, C. Y.; Swaney, D. L.; García-Sastre, A.; Ott, M.; Vignuzzi, M.; QCRG Structural Biology Consortium; Walter, P.; Manglik, A. Science 370, 1437-149 (2020).  

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

Gordon, D.E.;Hiatt, J.; Bouhaddou, M.; Rezelj, V.V.; Ulferts, S.; Braberg, H.; Jureka, A.; Obernier, K.; Guo, J.Z.; Batra, J.; Kaake, R.M.; Weckstein, A.R.; Owens, T.W.; Gupta, M.; Pourmal, S.; Titus, E.W.; Cakir, m.; Soucheray, M.; McGregor, M.; Kair, Z.; Jang, G.; O’Meara, M.J.; Tummino, T.A.; Zhang, Z.; Foussard, H.; Rojc, A.; Zhou, Y.; Kuchenov, D.; Hüttenhain, R.; Xu, J.; Eckhardt, M.; Swaney, D.L.; Fabius, J.M.; Ummadi, M.; Tutuncuoglu, B.; Rathore, U.; Modak, M.; Haas, P.; Haas, K.M.; Naing, Z.Z.C.; Pulido, E.H.; Shi, Y.; Barrio-Hernandez, I. Memon, D.; Petsalaki, E.; Dunham, A.; Marrero, M.C.; Burke, D.; Koh, C.; Vallet, T.; Silvas, J.A.; Azumaya, C.M.; Billesbølle C.; Brilot, A.F.; Campbell, M.G.; Diallo, A.; Dickinson, M.S.; Diwanji, D.; Herrera, N.; Hoppe, N.; Kratochvil, H.T.; Liu, Y.; Merz, G.E.; Moritz, M.; Nguyen, H.C.; Nowotny, C.; Puchades, C.; Rizo, A.N.; Schulze-Gahmen, U.; Smith, A.M.; Sun, M.; Young, I.D.; Zhao, J.; Asarnow, D.; Biel, J.; Bowen, A.; Braxton, J.R.; Chen, J.; Chio, C.M.; Chio, U.S.; Deshpande, I.; Doan, L.; Faust, B.; Flores, S.; Jin, M.; Kim, K.; Lam, V.L.; Li, J.; Li, Y-L.; Li, Y.; Liu, X.; Lo, M.; Lopez, K.E.; Melo, A.A.; Moss III, F.R.; Nguyen, P.; Paulino, J.; Pawar, K.I.; Peters, J.K.; Pospiech Jr., T.H.; Safari, M.; Sangwan, S.; Schaefer, K.; Thomas, P.V.; Thwin, A.C.; Trenker, R.; Tse, E.; Tsu, T.K.M.; Wang, F.; Whitis, N.; Yu, Z.; Zhang, K.; Zhang, Y.; Zhou, F.; Saltzberg, D.; QCRG Structural Biology Consortium; Hodder, A.J.; Shun-Shion, A.S.;  Williams, D.M.; White, K.M.; Rosales, R.; Kehrer, T.; Miorin, L.; Moreno, E.; Patel, A.H.; Rihn, S.; Khalid, M.M.; Vellejo-Gracia, A.; Fozouni, P.; Simoneau, C.R.; Roth, T.L.; Wu, D.; Karim, M.A.; Ghoussaini, M.; Duham, I.; Berardi, F.; Weigang, S.; Chazal, M.; Park, J.; Logue, J.; McGrath, M.; Weston, s.; Haupt, R.; Hastie, C.J.; Elliot, M.; Brown, F.; Burness, K.A.; Reid, E.; Dorward, M.; Johnson, C.; Wilkinson, S.G.; Geyer, A.; Giesel, D.M.; Caillie, C.; Raggett, S.; Leech, H.; Toth, R.; Goodman, N.; Keough, K.C.; Lind, A.L.; Zoonomania Consortium; Klesh, R.J.; Hemphill, K.R.; Carlson-Stevermer, J.; Oki, J.; Holden, K.; Maures, T.; Pollard, K.S.; Sali, A.; Agard, D.A.; Cheng, Y.; Fraser, J.S.; Frost, A.; Jura, N.; Kortemme, T.; Manglik, A.; Southworth, D.R.; Stroud, R.M.; Alessi, D.R.; Davies, P.; Frieman, M.B.; Ideker, T.; Abate, C.; Jouvenet, N.; Kocks, G.; Shoichet, B.; Ott, M.; Palmarini, M.; Shokat, K.M.; García-Sastre, A.; Rassen, J.A.; Grosse, R.; Rosenberg, O.S.; Verba, K.A.; Basler, C.F.; Vignuzzi, M.; Peden, A.A.; Beltrao, P.; Krogan, N.J. Science 370 (6521), 1-26 (2020).  

Bi-paratopic and multivalent VH domains block ACE2 binding and neutralize SARS-CoV-2

Bracken, C. J.; Lim, S. A.; Solomon, P.; Rettko, N. J.; Nguyen, D. P.; Zha, B. S.; Schaefer, K.; Byrnes, J. R.; Zhou, J.; Lui, I.; Liu, J.; Pance, K.; Zhou, X. X.; QCRG Structural Biology Consortium; Leung, K. K.; Wells, J. A. Nat. Chem. Biol. 17, 113–121 (2021).

*Work done as part of the QCRG Structural Biology Consortium (see SI for contributions)


Glutamine side chain 13C=18O as a non-perturbative IR probe of amyloid fibril hydration and assembly

Wu, H.; Saltzberg, D.J.; Kratochvil, H.T.; Jo, H.; Sali, A.; DeGrado, W.F.  J. Am. Chem. Soc. 141 (18), 7320-7326 (2019).


Synthesis and application of the blue fluorescent amino acid L-4-cyanotryptophan to assess peptide-membrane interactions

Zhang, K.; Ahmed, I.A.; Kratochvil, H.T.; DeGrado, W.F.; Gai, F.; Jo, H. Chem. Comm. 55 (35), 5095-5098 (2019). 


Designed peptides that assemble into cross-α amyloid-like structures

Zhang, S-Q.; Huang, H.; Yang, J.; Kratochvil, H.T.; Lolicato, M.; Liu, Y.; Shu, X.; Liu, L.; DeGrado, W.F. Nat. Chem. Biol. 14, 870-875 (2018).


Two-dimensional infrared (2D IR) spectroscopy for elucidating ion occupancies in the selectivity filter of ion channels

Kratochvil, H.T.; Zanni, M.T. Biomed. Spectrosc. Imaging 7 (1-2), 3-15 (2018) 

Probing the Effects of Gating on the Ion Occupancy of the K+ Channel Selectivity Filter Using 2D IR Spectroscopy

Kratochvil, H.T.; Maj, M.; Mutalef, K.; Annen, A;. Ostmeyer, J.; Perozo, E; Roux, B.; Valiyaveetil, F.; Zanni, M.T. J. Am. Chem. Soc. 139 (26), 8837-8845 (2017).


Solvent Independent Anharmonicity for Carbonyl Oscillators

Schneider, S.H.; Kratochvil, H.T.; Zanni, M.T.; Boxer, S.G. J. Chem. Phys. B.  121 (10), 2331-2338 (2017).


Instantaneous Ion Configurations in the K+ Ion Channel Selectivity Filter Revealed by 2D IR Spectroscopy

Kratochvil, H.T.; Carr, J.K.; Mutalef, K.;Annen, A.W.;Li,H.; Maj, M.;Ostmeyer,J.; Raghuraman,H.; Moran, S.D.; Skinner, J.L.; Perozo, E.; Roux, B.; Valiyaveetil, F.; Zanni, M.T. Science 353, 1040 (2016).


Counting Tagged Molecules One by One: Quantitative Photoactivation and Bleaching of Photoactivatable Fluorophores

Kratochvil, H.T.*; Ha, D.G.*, Zanni, M.T. J. Chem. Phys. 143, 104201 (2015).

*Authors contributed equally


Mechanism of IAPP Amyloid Fibril Formation Involves an Intermediate with a Transient β-Sheet

Buchanan, L.E.; Dunkelberger, E.B.; Tran, H.Q.; Cheng, P.; Chiu, C.; Cao, P.; Raleigh, D.P.; de Pablo, J.J.; Nowick, J.S.; Zanni, M.T. Proc. Natl. Acad. Sci. U.S.A. 110(48):19285-19290, (2013).