My Bibliography

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Mravic M, He L, Kratochvil HT, Hu H, Nick SE, Bai W, Edwards A, Jo H, Wu Y, DiMaio D, DeGrado WF. De novo-designed transmembrane proteins bind and regulate a cytokine receptor. Nat Chem Biol. 2024 Mar 13;. doi: 10.1038/s41589-024-01562-z. [Epub ahead of print] PubMed PMID: 38480980.

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Kratochvil HT, Watkins LC, Mravic M, Thomaston JL, Nicoludis JM, Somberg NH, Liu L, Hong M, Voth GA, DeGrado WF. Transient water wires mediate selective proton transport in designed channel proteins. Nat Chem. 2023 Jul;15(7):1012-1021. doi: 10.1038/s41557-023-01210-4. Epub 2023 Jun 12. PubMed PMID: 37308712; PubMed Central PMCID: PMC10475958.

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Kratochvil H, Watkins L, Mravic M, Thomaston J, Nicoludis J, Somberg N, Liu L, Hong M, Voth G, DeGrado W. Transient water wires mediate selective proton transport in designed channel proteins. Nature Chemistry. 2023 June; 15(7):1012-1021. doi: 10.1038/s41557-023-01210-4.

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Mravic M, He L, Kratochvil H, Hu H, Nick S, Bai W, Edwards A, Jo H, Wu Y, DiMaio D, DeGrado W. Designed Transmembrane Proteins Inhibit the Erythropoietin Receptor in a Custom Binding Topology. [preprint]. 2023 February. doi: 10.1101/2023.02.13.526773.

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Kratochvil H, Watkins L, Mravic M, Somberg N, Thomaston J, Nicoludis J, Liu L, Hong M, Voth G, DeGrado W. Transient Water Wires Mediate Selective Proton Transport in Designed Channel Proteins. [preprint]. 2022 March. doi: 10.1101/2022.03.28.485852.

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Kratochvil HT, Newberry RW, Mensa B, Mravic M, DeGrado WF. Spiers Memorial Lecture: Analysis and de novo design of membrane-interactive peptides. Faraday Discuss. 2021 Dec 24;232(0):9-48. doi: 10.1039/d1fd00061f. PubMed PMID: 34693965; PubMed Central PMCID: PMC8979563.

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Scott AJ, Niitsu A, Kratochvil HT, Lang EJM, Sengel JT, Dawson WM, Mahendran KR, Mravic M, Thomson AR, Brady RL, Liu L, Mulholland AJ, Bayley H, DeGrado WF, Wallace MI, Woolfson DN. Constructing ion channels from water-soluble α-helical barrels. Nat Chem. 2021 Jul;13(7):643-650. doi: 10.1038/s41557-021-00688-0. Epub 2021 May 10. PubMed PMID: 33972753; PubMed Central PMCID: PMC7611114.

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Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Carvalho Martins L, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Moritz M, Herrera N, Kratochvil HT, Aimon A, Bennett JM, Brandao Neto J, Cohen AE, Dias A, Douangamath A, Dunnett L, Fedorov O, Ferla MP, Fuchs MR, Gorrie-Stone TJ, Holton JM, Johnson MG, Krojer T, Meigs G, Powell AJ, Rack JGM, Rangel VL, Russi S, Skyner RE, Smith CA, Soares AS, Wierman JL, Zhu K, O'Brien P, Jura N, Ashworth A, Irwin JJ, Thompson MC, Gestwicki JE, von Delft F, Shoichet BK, Fraser JS, Ahel I. Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking. Sci Adv. 2021 Apr;7(16). doi: 10.1126/sciadv.abf8711. Print 2021 Apr. PubMed PMID: 33853786; PubMed Central PMCID: PMC8046379.

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Bracken CJ, Lim SA, Solomon P, Rettko NJ, Nguyen DP, Zha BS, Schaefer K, Byrnes JR, Zhou J, Lui I, Liu J, Pance K, Zhou XX, Leung KK, Wells JA. Bi-paratopic and multivalent VH domains block ACE2 binding and neutralize SARS-CoV-2. Nat Chem Biol. 2021 Jan;17(1):113-121. doi: 10.1038/s41589-020-00679-1. Epub 2020 Oct 20. PubMed PMID: 33082574; PubMed Central PMCID: PMC8356808.

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Kratochvil H, Newberry R, Mensa B, Mravic M, DeGrado W. Spiers Memorial Lecture: Analysis and de novo design of membrane-interactive peptides. Faraday Discussions. 2021; 232:9-48. doi: 10.1039/D1FD00061F.

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Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbølle CB, Puchades C, Azumaya CM, Kratochvil HT, Zimanyi M, Deshpande I, Liang J, Dickinson S, Nguyen HC, Chio CM, Merz GE, Thompson MC, Diwanji D, Schaefer K, Anand AA, Dobzinski N, Zha BS, Simoneau CR, Leon K, White KM, Chio US, Gupta M, Jin M, Li F, Liu Y, Zhang K, Bulkley D, Sun M, Smith AM, Rizo AN, Moss F, Brilot AF, Pourmal S, Trenker R, Pospiech T, Gupta S, Barsi-Rhyne B, Belyy V, Barile-Hill AW, Nock S, Liu Y, Krogan NJ, Ralston CY, Swaney DL, García-Sastre A, Ott M, Vignuzzi M, Walter P, Manglik A. An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike. Science. 2020 Dec 18;370(6523):1473-1479. doi: 10.1126/science.abe3255. Epub 2020 Nov 5. PubMed PMID: 33154106; PubMed Central PMCID: PMC7857409.

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Schoof M, Faust B, Saunders R, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbølle C, Puchades C, Azumaya C, Kratochvil H, Zimanyi M, Deshpande I, Liang J, Dickinson S, Nguyen H, Chio C, Merz G, Thompson M, Diwanji D, Schaefer K, Anand A, Dobzinski N, Zha B, Simoneau C, Leon K, White K, Chio U, Gupta M, Jin M, Li F, Liu Y, Zhang K, Bulkley D, Sun M, Smith A, Rizo A, Moss F, Brilot A, Pourmal S, Trenker R, Pospiech T, Gupta S, Barsi-Rhyne B, Belyy V, Barile-Hill A, Nock S, Liu Y, Krogan N, Ralston C, Swaney D, García-Sastre A, Ott M, Vignuzzi M, Walter P, Manglik A, Azumaya C, Puchades C, Sun M, Braxton J, Brilot A, Gupta M, Li F, Lopez K, Melo A, Merz G, Moss F, Paulino J, Pospiech T, Pourmal S, Rizo A, Smith A, Thomas P, Wang F, Yu Z, Dickinson M, Nguyen H, Asarnow D, Campbell M, Chio C, Chio U, Diwanji D, Faust B, Gupta M, Hoppe N, Jin M, Li J, Liu Y, Merz G, Sangwan S, Tsui T, Trenker R, Trinidad D, Tse E, Zhang K, Zhou F, Herrera N, Kratochvil H, Schulze-Gahmen U, Thompson M, Young I, Biel J, Deshpande I, Liu X, Billesbølle C, Nowotny C, Smith A, Zhao J, Bowen A, Hoppe N, Li Y, Nguyen P, Safari M, Schaefer K, Whitis N, Moritz M, Owens T, Diallo A, Kim K, Peters J, Titus E, Chen J, Doan L, Flores S, Lam V, Li Y, Lo M, Thwin A, Wankowicz S, Zhang Y, Bulkley D, Joves A, Joves A, McKay L, Tabios M, Rosenberg O, Verba K, Agard D, Cheng Y, Fraser J, Frost A, Jura N, Kortemme T, Krogan N, Manglik A, Southworth D, Stroud R. An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike. Science. 2020 December; 370(6523):1473-1479. doi: 10.1126/science.abe3255.

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Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR 3rd, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH Jr, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D, Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL, Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, Ott M, Palmarini M, Shokat KM, García-Sastre A, Rassen JA, Grosse R, Rosenberg OS, Verba KA, Basler CF, Vignuzzi M, Peden AA, Beltrao P, Krogan NJ. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 Dec 4;370(6521). doi: 10.1126/science.abe9403. Epub 2020 Oct 15. PubMed PMID: 33060197; PubMed Central PMCID: PMC7808408.

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Wu H, Saltzberg DJ, Kratochvil HT, Jo H, Sali A, DeGrado WF. Glutamine Side Chain (13)C═(18)O as a Nonperturbative IR Probe of Amyloid Fibril Hydration and Assembly. J Am Chem Soc. 2019 May 8;141(18):7320-7326. doi: 10.1021/jacs.9b00577. Epub 2019 Apr 24. PubMed PMID: 30998340; PubMed Central PMCID: PMC6800148.

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Zhang K, Ahmed IA, Kratochvil HT, DeGrado WF, Gai F, Jo H. Synthesis and application of the blue fluorescent amino acid l-4-cyanotryptophan to assess peptide-membrane interactions. Chem Commun (Camb). 2019 Apr 25;55(35):5095-5098. doi: 10.1039/c9cc01152h. PubMed PMID: 30957824; PubMed Central PMCID: PMC6508085.

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Wu H, Saltzberg D, Kratochvil H, Jo H, Sali A, DeGrado W. Glutamine Side Chain 13 C═ 18 O as a Nonperturbative IR Probe of Amyloid Fibril Hydration and Assembly. Journal of the American Chemical Society. 2019 April; 141(18):7320-7326. doi: 10.1021/jacs.9b00577.

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Zhang K, Ahmed I, Kratochvil H, DeGrado W, Gai F, Jo H. Synthesis and application of the blue fluorescent amino acid <scp>l</scp> -4-cyanotryptophan to assess peptide–membrane interactions. Chemical Communications. 2019; 55(35):5095-5098. doi: 10.1039/C9CC01152H.

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Zhang SQ, Huang H, Yang J, Kratochvil HT, Lolicato M, Liu Y, Shu X, Liu L, DeGrado WF. Designed peptides that assemble into cross-α amyloid-like structures. Nat Chem Biol. 2018 Sep;14(9):870-875. doi: 10.1038/s41589-018-0105-5. Epub 2018 Jul 30. PubMed PMID: 30061717; PubMed Central PMCID: PMC6497057.

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Zhang S, Huang H, Yang J, Kratochvil H, Lolicato M, Liu Y, Shu X, Liu L, DeGrado W. Designed peptides that assemble into cross-α amyloid-like structures. Nature Chemical Biology. 2018-7-; 14(9):870-875. doi: 10.1038/s41589-018-0105-5.

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Kratochvil H, Zanni M. Two-dimensional infrared (2D IR) spectroscopy for elucidating ion occupancies in the selectivity filter of ion channels1. Biomedical Spectroscopy and Imaging. 2018 May; 7(1-2):3-15. doi: 10.3233/BSI-180175.

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Kratochvil HT, Zanni MT. Two-dimensional infrared (2D IR) spectroscopy for elucidating ion occupancies in the selectivity filter of ion channels. Biomedical Spectroscopy and Imaging. 2018 January; 7(1-2):3-15.

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Kratochvil HT, Maj M, Matulef K, Annen AW, Ostmeyer J, Perozo E, Roux B, Valiyaveetil FI, Zanni MT. Probing the Effects of Gating on the Ion Occupancy of the K(+) Channel Selectivity Filter Using Two-Dimensional Infrared Spectroscopy. J Am Chem Soc. 2017 Jul 5;139(26):8837-8845. doi: 10.1021/jacs.7b01594. Epub 2017 May 12. PubMed PMID: 28472884; PubMed Central PMCID: PMC5544906.

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Kratochvil H, Maj M, Matulef K, Annen A, Ostmeyer J, Perozo E, Roux B, Valiyaveetil F, Zanni M. Probing the Effects of Gating on the Ion Occupancy of the K + Channel Selectivity Filter Using Two-Dimensional Infrared Spectroscopy. Journal of the American Chemical Society. 2017 May; 139(26):8837-8845. doi: 10.1021/jacs.7b01594.

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Schneider SH, Kratochvil HT, Zanni MT, Boxer SG. Solvent-Independent Anharmonicity for Carbonyl Oscillators. J Phys Chem B. 2017 Mar 16;121(10):2331-2338. doi: 10.1021/acs.jpcb.7b00537. Epub 2017 Mar 8. PubMed PMID: 28225620; PubMed Central PMCID: PMC5453717.

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Schneider S, Kratochvil H, Zanni M, Boxer S. Solvent-Independent Anharmonicity for Carbonyl Oscillators. The Journal of Physical Chemistry B. 2017 March; 121(10):2331-2338. doi: 10.1021/acs.jpcb.7b00537.

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Kratochvil HT, Carr JK, Matulef K, Annen AW, Li H, Maj M, Ostmeyer J, Serrano AL, Raghuraman H, Moran SD, Skinner JL, Perozo E, Roux B, Valiyaveetil FI, Zanni MT. Instantaneous ion configurations in the K+ ion channel selectivity filter revealed by 2D IR spectroscopy. Science. 2016 Sep 2;353(6303):1040-1044. doi: 10.1126/science.aag1447. PubMed PMID: 27701114; PubMed Central PMCID: PMC5544905.

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Kratochvil H, Carr J, Matulef K, Annen A, Li H, Maj M, Ostmeyer J, Serrano A, Raghuraman H, Moran S, Skinner J, Perozo E, Roux B, Valiyaveetil F, Zanni M. Instantaneous ion configurations in the K + ion channel selectivity filter revealed by 2D IR spectroscopy. Science. 2016 September; 353(6303):1040-1044. doi: 10.1126/science.aag1447.

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Kratochvil HT, Ha DG, Zanni MT. Counting tagged molecules one by one: Quantitative photoactivation and bleaching of photoactivatable fluorophores. J Chem Phys. 2015 Sep 14;143(10):104201. doi: 10.1063/1.4929991. PubMed PMID: 26374025; PubMed Central PMCID: PMC4567578.

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Kratochvil H, Ha D, Zanni M. Counting tagged molecules one by one: Quantitative photoactivation and bleaching of photoactivatable fluorophores. The Journal of Chemical Physics. 2015 September; 143(10):104201-. doi: 10.1063/1.4929991.

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Buchanan LE, Dunkelberger EB, Tran HQ, Cheng PN, Chiu CC, Cao P, Raleigh DP, de Pablo JJ, Nowick JS, Zanni MT. Mechanism of IAPP amyloid fibril formation involves an intermediate with a transient β-sheet. Proc Natl Acad Sci U S A. 2013 Nov 26;110(48):19285-90. doi: 10.1073/pnas.1314481110. Epub 2013 Nov 11. PubMed PMID: 24218609; PubMed Central PMCID: PMC3845187.

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Buchanan L, Dunkelberger E, Tran H, Cheng P, Chiu C, Cao P, Raleigh D, de Pablo J, Nowick J, Zanni M. Mechanism of IAPP amyloid fibril formation involves an intermediate with a transient β-sheet. Proceedings of the National Academy of Sciences. 2013 November; 110(48):19285-19290. doi: 10.1073/pnas.1314481110.