Huong Kratochvil • UCSF Profiles

Huong Kratochvil, PhD

Title(s)	Postdoctoral Scholar, Pharmaceutical Chemistry
School	School of Pharmacy
Address	555 Mission Bay Blvd South San Francisco CA 94158
Phone	--
ORCID	0000-0001-8039-6823
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Biography

Education and Training

The University of Texas at Austin, Austin, TX	B.S.	05/2010	Chemistry
University of Wisconsin-Madison, Madison, WI	Ph.D.	10/2016	Chemistry

Research

Research Activities and Funding

Proton Conduction Pathways in Proton Channel Proteins
NIH/NIGMS K99GM138753Sep 1, 2020 - Aug 31, 2022
Description: The flow of protons across membranes is critical for bioenergetics, signaling and other biological processes. The transport of protons across cellular membranes could be potentially toxic to cells had proton channel proteins not fine-tuned their selectivity and rate of transmission (conductivity). This proposal aims to understand the mechanisms by which these proton channels achieve and fine-tune proton selectivity and conductivity through the detailed study of the influenza A virus matrix protein 2 and synthetic designed proton channels.

Proton Conduction Pathways in Proton Channel Proteins
NIH K99GM138753Sep 1, 2020 - Aug 31, 2022
Role: Principal Investigator

A structural and biophysical study of the matrix proteins in influenza A/B viruses: Mechanisms of proton conduction and roles of protein-protein interactions
NIH F32GM125217Sep 1, 2017 - Aug 31, 2020
Role: Principal Investigator

Bibliographic

Publications

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.

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Spiers Memorial Lecture: Analysis and de novo design of membrane-interactive peptides. Faraday Discuss. 2021 12 24; 232(0):9-48. Kratochvil HT, Newberry RW, Mensa B, Mravic M, DeGrado WF. PMID: 34693965; PMCID: PMC8979563.

View in: PubMed Mentions:
CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. Res Sq. 2021 May 19. Verba K, Gupta M, Azumaya C, Moritz M, Pourmal S, Diallo A, Merz G, Jang G, Bouhaddou M, Fossati A, Brilot A, Diwanji D, Hernandez E, Herrera N, Kratochvil H, Lam V, Li F, Li Y, Nguyen H, Nowotny C, Owens T, Peters J, Rizo A, Schulze-Gahmen U, Smith A, Young I, Yu Z, Asarnow D, Billesbølle C, Campbell M, Chen J, Chen KH, Chio US, Dickinson M, Doan L, Jin M, Kim K, Li J, Li YL, Linossi E, Liu Y, Lo M, Lopez J, Lopez K, Mancino A, Iii FM, Paul M, Pawar K, Pelin A, Pospiech T, Puchades C, Remesh S, Safari M, Schaefer K, Sun M, Tabios M, Thwin A, Titus E, Trenker R, Tse E, Tsui TKM, Feng F, Zhang K, Zhang Y, Zhao J, Zhou F, Zhou Y, Zuliani-Alvarez L, Agard D, Cheng Y, Fraser J, Jura N, Kortemme T, Manglik A, Southworth D, Stroud R, Swaney D, Krogan N, Frost A, Rosenberg O. PMID: 34031651; PMCID: PMC8142659.

View in: PubMed Mentions: 1
CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. bioRxiv. 2021 May 11. Gupta M, Azumaya CM, Moritz M, Pourmal S, Diallo A, Merz GE, Jang G, Bouhaddou M, Fossati A, Brilot AF, Diwanji D, Hernandez E, Herrera N, Kratochvil HT, Lam VL, Li F, Li Y, Nguyen HC, Nowotny C, Owens TW, Peters JK, Rizo AN, Schulze-Gahmen U, Smith AM, Young ID, Yu Z, Asarnow D, Billesbølle C, Campbell MG, Chen J, Chen KH, Chio US, Dickinson MS, Doan L, Jin M, Kim K, Li J, Li YL, Linossi E, Liu Y, Lo M, Lopez J, Lopez KE, Mancino A, Moss FR, Paul MD, Pawar KI, Pelin A, Pospiech TH, Puchades C, Remesh SG, Safari M, Schaefer K, Sun M, Tabios MC, Thwin AC, Titus EW, Trenker R, Tse E, Tsui TKM, Wang F, Zhang K, Zhang Y, Zhao J, Zhou F, Zhou Y, Zuliani-Alvarez L, QCRG Structural Biology Consortium, Agard DA, Cheng Y, Fraser JS, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Swaney DL, Krogan NJ, Frost A, Rosenberg OS, Verba KA. PMID: 34013269; PMCID: PMC8132225.

View in: PubMed Mentions:
Constructing ion channels from water-soluble α-helical barrels. Nat Chem. 2021 07; 13(7):643-650. 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. PMID: 33972753; PMCID: PMC7611114.

View in: PubMed Mentions: Fields:
Che Chemistry
Translation:Cells
Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking. Sci Adv. 2021 04; 7(16). 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, QCRG Structural Biology Consortium, 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. PMID: 33853786; PMCID: PMC8046379.

View in: PubMed Mentions: 8 Fields:
Sci Science
Translation:Humans Cells
Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking. bioRxiv. 2020 Nov 24. Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Martins LC, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Moritz M, Herrera N, Kratochvil HT, QCRG Structural Biology Consortium, Aimon A, Bennett JM, Neto JB, Cohen AE, Dias A, Douangamath A, Dunnett L, Fedorov O, Ferla MP, Fuchs M, Gorrie-Stone TJ, Holton JM, Johnson MG, Krojer T, Meigs G, Powell AJ, Johannes Gregor Matthias Rack, Rangel VL, Russi S, Skyner RE, Smith CA, Soares AS, Wierman JL, Zhu K, Jura N, Ashworth A, Irwin J, Thompson MC, Gestwicki JE, von Delft F, Shoichet BK, Fraser JS, Ahel I. PMID: 33269349; PMCID: PMC7709169.

View in: PubMed Mentions:
An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike. Science. 2020 12 18; 370(6523):1473-1479. 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, QCRG Structural Biology Consortium, Walter P, Manglik A. PMID: 33154106; PMCID: PMC7857409.

View in: PubMed Mentions: 60 Fields:
Sci Science
Translation:Humans Animals Cells
Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 12 04; 370(6521). 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, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH, 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, QCRG Structural Biology Consortium, 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, Zoonomia Consortium, 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, et al. PMID: 33060197; PMCID: PMC7808408.

View in: PubMed Mentions: 105 Fields:
Sci Science
Translation:Humans Cells
An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation. bioRxiv. 2020 Aug 17. 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, QCRG Structural Biology Consortium, Walter P, Manglik A. PMID: 32817938; PMCID: PMC7430568.

View in: PubMed Mentions: 2
Roles of Hydrogen-Bonding Networks in Proton Channel Function as Revealed through de novo Designed Proton Channels. Biophysical Journal. 2020 Feb 1; 118(3):483a. Kratochvil KH, Nicoludis NJ, DeGrado DW. .

View in: Publisher Site Mentions:
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. Zhang K, Ahmed IA, Kratochvil HT, DeGrado WF, Gai F, Jo H. PMID: 30957824; PMCID: PMC6508085.

View in: PubMed Mentions: 6 Fields:
Che Chemistry
Translation:Humans Cells
Glutamine Side Chain 13C═18O as a Nonperturbative IR Probe of Amyloid Fibril Hydration and Assembly. J Am Chem Soc. 2019 05 08; 141(18):7320-7326. Wu H, Saltzberg DJ, Kratochvil HT, Jo H, Sali A, DeGrado WF. PMID: 30998340; PMCID: PMC6800148.

View in: PubMed Mentions: 3 Fields:
Che Chemistry
Designed peptides that assemble into cross-α amyloid-like structures. Nat Chem Biol. 2018 09; 14(9):870-875. Zhang SQ, Huang H, Yang J, Kratochvil HT, Lolicato M, Liu Y, Shu X, Liu L, DeGrado WF. PMID: 30061717; PMCID: PMC6497057.

View in: PubMed Mentions: 12 Fields:
Bio Biology Che Chemistry
Translation:Humans Cells
Two-dimensional infrared (2D IR) spectroscopy for elucidating ion occupancies in the selectivity filter of ion channels1. Biomedical Spectroscopy and Imaging. 2018 May 7; 7(1-2):3-15. Kratochvil KH, Zanni ZM. .

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De Novo Design of Cross-a Amyloid-Like Fibrils with Cellular Activity. Biophysical Journal. 2018 Feb 1; 114(3):410a. Zhang ZS, Liu LL, Yang YJ, Lolicato LM, Kratochvil KH, Shu SX, DeGrado DW. .

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Proton Stabilization and Conduction Pathway in the Matrix Protein M2. Biophysical Journal. 2018 Feb 1; 114(3):240a-241a. Kratochvil KH, Thomaston TJ, Gai GF, DeGrado DW. .

View in: Publisher Site Mentions:
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 07 05; 139(26):8837-8845. Kratochvil HT, Maj M, Matulef K, Annen AW, Ostmeyer J, Perozo E, Roux B, Valiyaveetil FI, Zanni MT. PMID: 28472884; PMCID: PMC5544906.

View in: PubMed Mentions: 13 Fields:
Che Chemistry
Translation:Cells
Solvent-Independent Anharmonicity for Carbonyl Oscillators. J Phys Chem B. 2017 03 16; 121(10):2331-2338. Schneider SH, Kratochvil HT, Zanni MT, Boxer SG. PMID: 28225620; PMCID: PMC5453717.

View in: PubMed Mentions: 5 Fields:
Che Chemistry
Translation:Cells
Instantaneous ion configurations in the K+ ion channel selectivity filter revealed by 2D IR spectroscopy. Science. 2016 09 02; 353(6303):1040-1044. 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. PMID: 27701114; PMCID: PMC5544905.

View in: PubMed Mentions: 45 Fields:
Sci Science
Translation:Cells
Counting tagged molecules one by one: Quantitative photoactivation and bleaching of photoactivatable fluorophores. J Chem Phys. 2015 Sep 14; 143(10):104201. Kratochvil HT, Ha DG, Zanni MT. PMID: 26374025; PMCID: PMC4567578.

View in: PubMed Mentions: 1 Fields:
Bio Biophysics Che Chemistry Phy Physics
Translation:Cells
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. Buchanan LE, Dunkelberger EB, Tran HQ, Cheng PN, Chiu CC, Cao P, Raleigh DP, de Pablo JJ, Nowick JS, Zanni MT. PMID: 24218609; PMCID: PMC3845187.

View in: PubMed Mentions: 75 Fields:
Sci Science
Translation:Humans Cells