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School of Pharmacy

team: Lee Lab

http://faculty.washington.edu/kklee/Welcome.html

Se Min Kim

Se Min joins the Lee Lab from the MSC Program in the UW Department of Biology.

Kim SM, Park N, Park HB, Lee J, Chun C, Kim KH, et al. (2024) Exploring novel immunotherapy biomarker candidates induced by cancer deformation. PLoS ONE 19(5): e0303433. https://doi.org/10.1371/journal.pone.0303433

Kim SM, Patel M, Patel R. (2021) PLGA Core-Shell Nano/Microparticle Delivery System for Biomedical Application. Polymers, 13(20):3471. https://doi.org/10.3390/polym13203471

Kim SM, Patel R, Kim JH. (2021) Recent Advance in Microbial Fuel Cell based on Composite Membranes. Membrane Journal, 31(2), 120-132. https://doi.org/10.14579/MEMBRANE_JOURNAL.2021.31.2.120

Nastassia Parker

Stassia joins the Lee Lab from the PhD program at the UW Department of Chemistry.

Jacob Croft, PhD

Publications

Cryo-ET of Env on intact HIV virions reveals structural variation and positioning on the Gag lattice. Mangala Prasad V, Leaman DP, Lovendahl KN, Croft JT, Benhaim MA, Hodge EA, Zwick MB, Lee KK. Cell. 2022 Feb 17;185(4):641-653.e17. doi: 10.1016/j.cell.2022.01.013. Epub 2022 Feb 4.

Nuclear envelope budding is a response to cellular stress. Panagaki D, Croft JT, Keuenhof K, Larsson Berglund L, Andersson S, Kohler V, Büttner S, Tamás MJ, Nyström T, Neutze R, Höög JL. Proc Natl Acad Sci U S A. 2021 Jul 27;118(30):e2020997118. doi: 10.1073/pnas.2020997118.

Instability in a coiled-coil signaling helix is conserved for signal transduction in soluble guanylyl cyclase. Weichsel A, Kievenaar JA, Curry R, Croft JT, Montfort WR. Protein Sci. 2019 Oct;28(10):1830-1839. doi: 10.1002/pro.3707. Epub 2019 Aug 27.

Axonemal doublet microtubules can split into two complete singlets in human sperm flagellum tips. Zabeo D, Croft JT, Höög JL. FEBS Lett. 2019 May;593(9):892-902. doi: 10.1002/1873-3468.13379. Epub 2019 Apr 19.

Composition, structure and function of the eukaryotic flagellum distal tip. Croft JT, Zabeo D, Subramanian R, Höög JL. Essays Biochem. 2018 Dec 7;62(6):815-828. doi: 10.1042/EBC20180032. Print 2018 Dec 7.

Becker, Vada

UW Medicine Lab medicine and Pathology logo graphic

Vada joins the Kelly Lee Lab via the Molecular Medicine and Mechanisms of Disease (M3D) PhD Program in the Department of Laboratory Medicine & Pathology.

Chengbo Chen, PhD

Publications

Potent neutralization of SARS-CoV-2 variants by RBD nanoparticle and prefusion-stabilized spike immunogens. Miranda MC, Kepl E, Navarro MJ, Chen C, Johnson M, Sprouse KR, Stewart C, Palser A, Valdez A, Pettie D, Sydeman C, Ogohara C, Kraft JC, Pham M, Murphy M, Wrenn S, Fiala B, Ravichandran R, Ellis D, Carter L, Corti D, Kellam P, Lee K, Walls AC, Veesler D, King NP.NPJ Vaccines. 2024 Oct 8;9(1):184. doi: 10.1038/s41541-024-00982-1. PMID: 39379400

hACE2-Induced Allosteric Activation in SARS-CoV versus SARS-CoV-2 Spike Assemblies Revealed by Structural Dynamics. Chen C, Zhu R, Hodge EA, Díaz-Salinas MA, Nguyen A, Munro JB, Lee KK. ACS Infect Dis. 2023 Jun 9;9(6):1180-1189. doi: 10.1021/acsinfecdis.3c00010. Epub 2023 May 11. PMID: 37166130

An HIV-1 broadly neutralizing antibody overcomes structural and dynamic variation through highly focused epitope targeting. Hodge, E.A., Chatterjee, A., Chen, C. et al.  npj Viruses 1, 2 (2023). https://doi.org/10.1038/s44298-023-00002-4

 

Three-dimensional ordered DNA network constructed by a biomarker pair for accurate monitoring of colorectal cancer. Chen W, Li T, Chen C, Zhang J, Ma Z, Hou W, Yao Y, Mao W, Liu C, Kong D, Tang S, Shen W. Biosens Bioelectron. 2023 Jul 15;232:115335. doi: 10.1016/j.bios.2023.115335. Epub 2023 Apr 17.

 

Recent Advances in the Application of Covalent Organic Frameworks in Extraction: A Review. Bagheri AR, Aramesh N, Liu Z, Chen C, Shen W, Tang S. Crit Rev Anal Chem. 2022 Jun 26:1-34. doi:10.1080/10408347.2022.2089838. Online ahead of print.

 

Mannose-binding lectin and complement mediate follicular localization and enhanced immunogenicity of diverse protein nanoparticle immunogens. Read BJ, Won L, Kraft JC, Sappington I, Aung A, Wu S, Bals J, Chen C, Lee KK, Lingwood D, King NP, Irvine DJ. Cell Rep. 2022 Jan 11;38(2):110217. doi: 10.1016/j.celrep.2021.110217.

 

Stabilization of the SARS-CoV-2 Spike Receptor-Binding Domain Using Deep Mutational Scanning and Structure-Based Design. Ellis D, Brunette N, Crawford KHD, Walls AC, Pham MN, Chen C, Herpoldt KL, Fiala B, Murphy M, Pettie D, Kraft JC, Malone KD, Navarro MJ, Ogohara C, Kepl E, Ravichandran R, Sydeman C, Ahlrichs M, Johnson M, Blackstone A, Carter L, Starr TN, Greaney AJ, Lee KK, Veesler D, Bloom JD, King NP. Front Immunol. 2021 Jun 29;12:710263. doi: 10.3389/fimmu.2021.710263. eCollection 2021.

 

Elicitation of Potent Neutralizing Antibody Responses by Designed Protein Nanoparticle Vaccines for SARS-CoV-2.   Walls AC, Fiala B, Schäfer A, Wrenn S, Pham MN, Murphy M, Tse LV, Shehata L, O’Connor MA, Chen C, Navarro MJ, Miranda MC, Pettie D, Ravichandran R, Kraft JC, Ogohara C, Palser A, Chalk S, Lee EC, Guerriero K, Kepl E, Chow CM, Sydeman C, Hodge EA, Brown B, Fuller JT, Dinnon KH 3rd, Gralinski LE, Leist SR, Gully KL, Lewis TB, Guttman M, Chu HY, Lee KK, Fuller DH, Baric RS, Kellam P, Carter L, Pepper M, Sheahan TP, Veesler D, King NP. in Cell. 2020 Nov 25;183(5):1367-1382.e17. Epub 2020 Oct 31.

 

Klaus Lovendahl

Publications

Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection.Guenthoer J, Lilly M, Starr TN, Dadonaite B, Lovendahl KN, Croft JT, Stoddard CI, Chohan V, Ding S, Ruiz F, Kopp MS, Finzi A, Bloom JD, Chu HY, Lee KK, Overbaugh J.Proc Natl Acad Sci U S A. 2023 Jun 6;120(23):e2220948120. doi: 10.1073/pnas.2220948120. Epub 2023 May 30.

Cytoplasmic Tail Truncation Stabilizes S1-S2 Association and Enhances S Protein Incorporation into SARS-CoV-2 Pseudovirions. Zhang L, Hom N, Ojha A, Lovendahl KN, Mou H, Lee KK, Choe H. J Virol. 2023 Mar 30;97(3):e0165022. doi: 10.1128/jvi.01650-22. Epub 2023 Feb 15.

Cryo-ET of Env on intact HIV virions reveals structural variation and positioning on the Gag lattice.  Mangala Prasad V, Leaman DP, Lovendahl KN, Croft JT, Benhaim MA, Hodge EA, Zwick MB, Lee KK.Cell. 2022 Feb 17;185(4):641-653.e17. doi: 10.1016/j.cell.2022.01.013. Epub 2022 Feb 4.

Sequence-DirectedCovalentProtein-DNALinkages in a SingleStep Using HUH-Tags. Lovendahl KN, Hayward AN, Gordon WR. J Am Chem Soc. 2017 May 24;139(20):7030-7035. doi: 10.1021/jacs.7b02572. Epub 2017 May 16.

Increasing Cas9-mediated homology-directed repair efficiency through covalent tethering of DNA repair template. Aird EJ, Lovendahl KN, St Martin A, Harris RS, Gordon WR. Commun Biol. 2018 May 31;1:54. doi: 10.1038/s42003-018-0054-2. eCollection 2018.

The Molecular Mechanism of Notch Activation. Lovendahl KN, Blacklow SC, Gordon WR. Adv Exp Med Biol. 2018;1066:47-58. doi: 10.1007/978-3-319-89512-3_3. Review.

Comparisons of Shewanella strains based on genome annotations, modeling, and experiments. Ong WK, Vu TT, Lovendahl KN, Llull JM, Serres MH, Romine MF, Reed JL. BMC Syst Biol. 2014 Mar 12;8:31. doi: 10.1186/1752-0509-8-31.

Kelly Lee

Accepting Students to Lab: Yes

Education

  • AB (Honors), Harvard University
  • PhD, Johns Hopkins University

Research Interests

  • HIV, Influenza A virus
  • Biophysical, structural, and biochemical techniques including X-ray scattering, cryo-electron microscopy, hydrogen/deuterium-exchange mass spectrometry, and fluorescence microscopy to understand the function of viral machinery

Biography

Our lab uses complementary structural and biophysical methods to characterize the conformational changes viruses carry out in order to invade host cells. We focus on the transitions and the critical functional states that often are too transient or dynamic to characterize by classical structural methods. Understanding these events is essential to understanding mechanisms of cell entry, for understanding the activity of neutralizing antibodies, and also for developing novel antivirals that can target the virus prior to infection. Our core expertise is in using Hydrogen/Deuterium-Exchange Mass Spectrometry (HDX-MS), cryo-electron microscopy (cryo-EM) and small-angle X-ray scattering (SAXS) to monitor conformational change of protein complexes and viruses. An NIH K99/R00 Career Award supported my transition to studying influenza virus with techniques such as cryo-electron tomography and SAXS. Current projects apply cryo-ET, SAXS, and HDX-MS to dissect the spring-loaded membrane fusion mechanism of influenza virus hemagglutinin (HA) and HIV Env.

For example, in recent studies using cryo-ET and HDX-MS, for the first time we have been able to visualize the nature of fusion protein-mediated membrane remodeling and to determine the sequence of events in whole viruses and isolated fusion proteins that are needed to produce efficient fusion.

With the support of a Center for AIDS Research Creative and Novel Ideas in HIV Research (CNIHR) award for new investigators and with Gates Foundation support, my lab is working with Shiu-Lok Hu’s group (Pharmaceutics) to investigate the structural basis for antigenicity and immunogenicity of HIV Env glycoproteins. In addition, we have been able to characterize isolate-specific structural differences and their impact on antigenicity of Env; these effects are difficult to study by conventional approaches. Our biophysical approaches have also enabled us to analyze CD4 receptor, entry inhibitors, and neutralizing Abs in complex with the native-like HIV Env trimers. In collaboration with Julie Overbaugh’s group at the Fred Hutchinson Cancer Research Center, we are gaining insight into the nature of Env-dependent HIV transmission and the development of neutralizing antibodies in response to infection.

Dr. Lee also holds an adjunct appointment in the UW Microbiology Department and is a member of a number of cross-departmental graduate programs including the Biological Physics Structure and Design Program, the Pathobiology Graduate Program and the Molecular and Cellular Biology Program.

Recent Publications

Visualizing intermediate stages of viral membrane fusion by cryo-electron tomography. Kephart SM, Hom N, Lee KK.Trends Biochem Sci. 2024 Oct;49(10):916-931. doi: 10.1016/j.tibs.2024.06.012. Epub 2024 Jul 24.

Potent neutralization of SARS-CoV-2 variants by RBD nanoparticle and prefusion-stabilized spike immunogens. Miranda MC, Kepl E, Navarro MJ, Chen C, Johnson M, Sprouse KR, Stewart C, Palser A, Valdez A, Pettie D, Sydeman C, Ogohara C, Kraft JC, Pham M, Murphy M, Wrenn S, Fiala B, Ravichandran R, Ellis D, Carter L, Corti D, Kellam P, Lee K, Walls AC, Veesler D, King NP. NPJ Vaccines. 2024 Oct 8;9(1):184.

mRNA-based VP8* nanoparticle vaccines against rotavirus are highly immunogenic in rodents. Roier S, Mangala Prasad V, McNeal MM, Lee KK, Petsch B, Rauch S. NPJ Vaccines. 2023 Dec 22;8(1):190.

Combinatorial immune refocusing within the influenza hemagglutinin RBD improves cross-neutralizing antibody responses Dosey A, Ellis D, Boyoglu-Barnum S, Syeda H, Saunders M, Watson MJ, Kraft JC, Pham MN, Guttman M, Lee KK, Kanekiyo M, King NP. Cell Rep. 2023 Dec 26;42(12):113553.

De novo design of monomeric helical bundles for pH-controlled membrane lysis. Goldbach N, Benna I, Wicky BIM, Croft JT, Carter L, Bera AK, Nguyen H, Kang A, Sankaran B, Yang EC, Lee KK, Baker D. Protein Sci. 2023 Nov;32(11):e4769.

An HIV-1 broadly neutralizing antibody overcomes structural and dynamic variation through highly focused epitope targeting. Hodge EA, Chatterjee A, Chen C, Naika GJ, Laohajaratsang M, Mangala Prasad V, Lee KK. NPJ Viruses 1, 2 (2023). https://doi.org/10.1038/s44298-023-00002-4

Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection. Guenthoer J, Lilly M, Starr TN, Dadonaite B, Lovendahl KN, Croft JT, Stoddard CI, Chohan V, Ding S, Ruiz F, Kopp MS, Finzi A, Bloom JD, Chu HY, Lee KK, Overbaugh J. Proc Natl Acad Sci U S A. 2023 Jun 6;120(23):e2220948120.

hACE2-Induced Allosteric Activation in SARS-CoV versus SARS-CoV-2 Spike Assemblies Revealed by Structural Dynamics. Chen C, Zhu R, Hodge EA, Díaz-Salinas MA, Nguyen A, Munro JB, Lee KK. ACS Infect Dis. 2023 Jun 9;9(6):1180-1189.

Structural dynamics reveal subtype-specific activation and inhibition of influenza virus hemagglutinin. Garcia NK, Kephart SM, Benhaim MA, Matsui T, Mileant A, Guttman M, Lee KK. J Biol Chem. 2023 Jun;299(6):104765.

Cytoplasmic Tail Truncation Stabilizes S1-S2 Association and Enhances S Protein Incorporation into SARS-CoV-2 Pseudovirions. Zhang L, Hom N, Ojha A, Lovendahl KN, Mou H, Lee KK, Choe H. J Virol. 2023 Mar 30;97(3):e0165022.

Vaccination with a structure-based stabilized version of malarial antigen Pfs48/45 elicits ultra-potent transmission-blocking antibody responses. McLeod B, Mabrouk MT, Miura K, Ravichandran R, Kephart S, Hailemariam S, Pham TP, Semesi A, Kucharska I, Kundu P, Huang WC, Johnson M, Blackstone A, Pettie D, Murphy M, Kraft JC, Leaf EM, Jiao Y, van de Vegte-Bolmer M, van Gemert GJ, Ramjith J, King CR, MacGill RS, Wu Y, Lee KK, Jore MM, King NP, Lovell JF, Julien JP. Immunity. 2022 Sep 13;55(9):1680-1692.e8.

Visualization of conformational changes and membrane remodeling leading to genome delivery by viral class-II fusion machinery. Mangala Prasad V, Blijleven JS, Smit JM, Lee KK. Nat Commun. 2022 Aug 15;13(1):4772.

Structural dynamics reveal isolate-specific differences at neutralization epitopes on HIV Env.  Hodge EA, Naika GS, Kephart SM, Nguyen A, Zhu R, Benhaim MA, Guo W, Moore JP, Hu SL, Sanders RW, Lee KK. iScience. 2022 May 23;25(6):104449.

Structure-based design of stabilized recombinant influenza neuraminidase tetramers. Ellis D, Lederhofer J, Acton OJ, Tsybovsky Y, Kephart S, Yap C, Gillespie RA, Creanga A, Olshefsky A, Stephens T, Pettie D, Murphy M, Sydeman C, Ahlrichs M, Chan S, Borst AJ, Park YJ, Lee KK, Graham BS, Veesler D, King NP, Kanekiyo M. Nat Commun. 2022 Apr 5;13(1):1825.

Structure-guided changes at the V2 apex of HIV-1 clade C trimer enhance elicitation of autologous neutralizing and broad V1V2-scaffold antibodies. Sahoo A, Hodge EA, LaBranche CC, Styles TM, Shen X, Cheedarla N, Shiferaw A, Ozorowski G, Lee WH, Ward AB, Tomaras GD, Montefiori DC, Irvine DJ, Lee KK, Amara RR. Cell Rep. 2022 Mar 1;38(9):110436.

Cryo-ET of Env on intact HIV virions reveals structural variation and positioning on the Gag lattice. Mangala Prasad V, Leaman DP, Lovendahl KN, Croft JT, Benhaim MA, Hodge EA, Zwick MB, Lee KK. Cell. 2022 Feb 17;185(4):641-653.e17.

Mannose-binding lectin and complement mediate follicular localization and enhanced immunogenicity of diverse protein nanoparticle immunogens. Read BJ, Won L, Kraft JC, Sappington I, Aung A, Wu S, Bals J, Chen C, Lee KK, Lingwood D, King NP, Irvine DJ. Cell Rep. 2022 Jan 11;38(2):110217.

 


PI Association PMID Publication Year First Author Title Citation DOI
Nath 36194135 2022 Kunk C MitoNEET's Reactivity of Lys55 toward Pyridoxal Phosphate Demonstrates its Activity as a Transaminase Enzyme ACS Chem Biol. 2022 Oct 21;17(10):2716-2722. doi: 10.1021/acschembio.2c00572. Epub 2022 Oct 4. 10.1021/acschembio.2c00572 https://doi.org/10.1021/acschembio.2c00572
Nath 38352474 2024 James EI Tryptanthrin Analogs Substoichiometrically Inhibit Seeded and Unseeded Tau4RD Aggregation bioRxiv [Preprint]. 2024 Feb 3:2024.02.02.578649. doi: 10.1101/2024.02.02.578649. 10.1101/2024.02.02.578649 https://doi.org/10.1101/2024.02.02.578649
Nath 37861473 2023 Larsen HA The origins of nonideality exhibited by monoclonal antibodies and Fab fragments in human serum Protein Sci. 2023 Dec;32(12):e4812. doi: 10.1002/pro.4812. 10.1002/pro.4812 https://doi.org/10.1002/pro.4812
Nath 37562955 2023 Alade N The Utility of Mixed Effects Models in the Evaluation of Complex Genomic Traits In Vitro Drug Metab Dispos. 2023 Nov;51(11):1455-1462. doi: 10.1124/dmd.123.001260. Epub 2023 Aug 10. 10.1124/dmd.123.001260 https://doi.org/10.1124/dmd.123.001260
Nath 36948348 2023 Redhair M Low molecular weight ligands bind to CYP3A4 via a branched induced fit mechanism: Implications for O(2) binding Arch Biochem Biophys. 2023 May 1;739:109582. doi: 10.1016/j.abb.2023.109582. Epub 2023 Mar 21. 10.1016/j.abb.2023.109582 https://doi.org/10.1016/j.abb.2023.109582
Nath 34384764 2021 Larsen HA Probing interactions of therapeutic antibodies with serum via second virial coefficient measurements Biophys J. 2021 Sep 21;120(18):4067-4078. doi: 10.1016/j.bpj.2021.08.007. Epub 2021 Aug 10. 10.1016/j.bpj.2021.08.007 https://doi.org/10.1016/j.bpj.2021.08.007
Nath 41279711 2025 James EI Tau4RD fibril polymorphism is imprinted during early aggregation bioRxiv [Preprint]. 2025 Oct 14:2025.10.12.681486. doi: 10.1101/2025.10.12.681486. 10.1101/2025.10.12.681486 https://doi.org/10.1101/2025.10.12.681486
Nath 32814060 2020 Vane EW Rapid Formation of Peptide/Lipid Coaggregates by the Amyloidogenic Seminal Peptide PAP(248-286) Biophys J. 2020 Sep 1;119(5):924-938. doi: 10.1016/j.bpj.2020.07.029. Epub 2020 Aug 6. 10.1016/j.bpj.2020.07.029 https://doi.org/10.1016/j.bpj.2020.07.029
Nath 31974309 2020 Baughman HER Release of a disordered domain enhances HspB1 chaperone activity toward tau Proc Natl Acad Sci U S A. 2020 Feb 11;117(6):2923-2929. doi: 10.1073/pnas.1915099117. Epub 2020 Jan 23. 10.1073/pnas.1915099117 https://doi.org/10.1073/pnas.1915099117
Nath 33057715 2021 Shen T Identification of a novel tedizolid resistance mutation in rpoB of MRSA after in vitro serial passage J Antimicrob Chemother. 2021 Jan 19;76(2):292-296. doi: 10.1093/jac/dkaa422. 10.1093/jac/dkaa422 https://doi.org/10.1093/jac/dkaa422
Nath 38293009 2024 Yabut KCB Drugs Form Ternary Complexes with Human Liver Fatty Acid Binding Protein (FABP1) and FABP1 Binding Alters Drug Metabolism bioRxiv [Preprint]. 2024 Jan 19:2024.01.17.576032. doi: 10.1101/2024.01.17.576032. 10.1101/2024.01.17.576032 https://doi.org/10.1101/2024.01.17.576032
Nath 38580446 2024 Yabut KCB Drugs Form Ternary Complexes with Human Liver Fatty Acid Binding Protein 1 (FABP1) and FABP1 Binding Alters Drug Metabolism Mol Pharmacol. 2024 May 17;105(6):395-410. doi: 10.1124/molpharm.124.000878. 10.1124/molpharm.124.000878 https://doi.org/10.1124/molpharm.124.000878
Nath 33161206 2021 Sager JE Corrigendum to "In vitro to in vivo extrapolation of the complex drug-drug interaction of bupropion and its metabolites with CYP2D6; simultaneous reversible inhibition and CYP2D6 downregulation" [Biochem. Pharmacol. 123(2017)85-96] Biochem Pharmacol. 2021 Jan;183:114306. doi: 10.1016/j.bcp.2020.114306. Epub 2020 Nov 5. 10.1016/j.bcp.2020.114306 https://doi.org/10.1016/j.bcp.2020.114306
Atkins 31961139 2020 Redhair M Dynamics and Location of the Allosteric Midazolam Site in Cytochrome P4503A4 in Lipid Nanodiscs Biochemistry. 2020 Feb 18;59(6):766-779. doi: 10.1021/acs.biochem.9b01001. Epub 2020 Jan 27. 10.1021/acs.biochem.9b01001 https://doi.org/10.1021/acs.biochem.9b01001
Atkins 31982812 2020 Lockart MM Multiple drug binding modes in Mycobacterium tuberculosis CYP51B1 J Inorg Biochem. 2020 Apr;205:110994. doi: 10.1016/j.jinorgbio.2020.110994. Epub 2020 Jan 13. 10.1016/j.jinorgbio.2020.110994 https://doi.org/10.1016/j.jinorgbio.2020.110994
Atkins 32786398 2020 Paço L Dynamics and Mechanism of Binding of Androstenedione to Membrane-Associated Aromatase Biochemistry. 2020 Aug 25;59(33):2999-3009. doi: 10.1021/acs.biochem.0c00460. Epub 2020 Aug 11. 10.1021/acs.biochem.0c00460 https://doi.org/10.1021/acs.biochem.0c00460
Atkins 33350827 2021 Clouser AF Cholesterol Asymmetrically Modulates the Conformational Ensemble of the Nucleotide-Binding Domains of P-Glycoprotein in Lipid Nanodiscs Biochemistry. 2021 Jan 12;60(1):85-94. doi: 10.1021/acs.biochem.0c00824. Epub 2020 Dec 22. 10.1021/acs.biochem.0c00824 https://doi.org/10.1021/acs.biochem.0c00824
Atkins 34715072 2021 Redhair M Analytical and functional aspects of protein-ligand interactions: Beyond induced fit and conformational selection Arch Biochem Biophys. 2021 Dec 15;714:109064. doi: 10.1016/j.abb.2021.109064. Epub 2021 Oct 26. 10.1016/j.abb.2021.109064 https://doi.org/10.1016/j.abb.2021.109064
Atkins 35384651 2022 Clouser AF Long Range Communication between the Drug-Binding Sites and Nucleotide Binding Domains of the Efflux Transporter ABCB1 Biochemistry. 2022 Apr 19;61(8):730-740. doi: 10.1021/acs.biochem.2c00056. Epub 2022 Apr 6. 10.1021/acs.biochem.2c00056 https://doi.org/10.1021/acs.biochem.2c00056
Atkins 37080138 2023 Paço L Nanodisc-embedded cytochrome P450 P3A4 binds diverse ligands by distributing conformational dynamics to its flexible elements J Inorg Biochem. 2023 Jul;244:112211. doi: 10.1016/j.jinorgbio.2023.112211. Epub 2023 Apr 5. 10.1016/j.jinorgbio.2023.112211 https://doi.org/10.1016/j.jinorgbio.2023.112211
Atkins 36948348 2023 Redhair M Low molecular weight ligands bind to CYP3A4 via a branched induced fit mechanism: Implications for O(2) binding Arch Biochem Biophys. 2023 May 1;739:109582. doi: 10.1016/j.abb.2023.109582. Epub 2023 Mar 21. 10.1016/j.abb.2023.109582 https://doi.org/10.1016/j.abb.2023.109582
Atkins 31173761 2020 Goulet DR Considerations for the Design of Antibody-Based Therapeutics J Pharm Sci. 2020 Jan;109(1):74-103. doi: 10.1016/j.xphs.2019.05.031. Epub 2019 Jun 4. 10.1016/j.xphs.2019.05.031 https://doi.org/10.1016/j.xphs.2019.05.031
Atkins 31702857 2020 Goulet DR Design and characterization of novel dual Fc antibody with enhanced avidity for Fc receptors Proteins. 2020 May;88(5):689-697. doi: 10.1002/prot.25853. Epub 2019 Nov 20. 10.1002/prot.25853 https://doi.org/10.1002/prot.25853
Atkins 34383776 2021 Kachapila M Preliminary model assessing the cost-effectiveness of preoperative chlorhexidine mouthwash at reducing postoperative pneumonia among abdominal surgery patients in South Africa PLoS One. 2021 Aug 12;16(8):e0254698. doi: 10.1371/journal.pone.0254698. eCollection 2021. 10.1371/journal.pone.0254698 https://doi.org/10.1371/journal.pone.0254698
Atkins 34384764 2021 Larsen HA Probing interactions of therapeutic antibodies with serum via second virial coefficient measurements Biophys J. 2021 Sep 21;120(18):4067-4078. doi: 10.1016/j.bpj.2021.08.007. Epub 2021 Aug 10. 10.1016/j.bpj.2021.08.007 https://doi.org/10.1016/j.bpj.2021.08.007
Atkins 34871379 2021 STARSurg Collaborative and COVIDSurg Collaborative Death following pulmonary complications of surgery before and during the SARS-CoV-2 pandemic Br J Surg. 2021 Dec 1;108(12):1448-1464. doi: 10.1093/bjs/znab336. 10.1093/bjs/znab336 https://doi.org/10.1093/bjs/znab336
Atkins 35750401 2022 STARSurg Collaborative and TASMAN Collaborative Evaluation of prognostic risk models for postoperative pulmonary complications in adult patients undergoing major abdominal surgery: a systematic review and international external validation cohort study Lancet Digit Health. 2022 Jul;4(7):e520-e531. doi: 10.1016/S2589-7500(22)00069-3. 10.1016/S2589-7500(22)00069-3 https://doi.org/10.1016/s2589-7500(22)00069-3
Atkins 31663687 2020 Atkins WM Mechanisms of promiscuity among drug metabolizing enzymes and drug transporters FEBS J. 2020 Apr;287(7):1306-1322. doi: 10.1111/febs.15116. Epub 2019 Nov 12. 10.1111/febs.15116 https://doi.org/10.1111/febs.15116
Atkins 36830698 2023 Scian M Reversibility and Low Commitment to Forward Catalysis in the Conjugation of Lipid Alkenals by Glutathione Transferase A4-4 Biomolecules. 2023 Feb 9;13(2):329. doi: 10.3390/biom13020329. 10.3390/biom13020329 https://doi.org/10.3390/biom13020329
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Xu 41388019 2025 Chac D Gut bacteria-derived sphingolipids alter innate immune responses to oral cholera vaccine antigens Nat Commun. 2025 Dec 12. doi: 10.1038/s41467-025-67388-y. Online ahead of print. 10.1038/s41467-025-67388-y https://doi.org/10.1038/s41467-025-67388-y
Xu 38014966 2023 Pruitt EL Elucidating the impact of bacterial lipases, human serum albumin, and FASII inhibition on the utilization of exogenous fatty acids by Staphylococcus aureus mSphere. 2023 Dec 20;8(6):e0036823. doi: 10.1128/msphere.00368-23. Epub 2023 Nov 28. 10.1128/msphere.00368-23 https://doi.org/10.1128/msphere.00368-23
Xu 41366203 2025 Zhao HN A resource to empirically establish drug exposure records directly from untargeted metabolomics data Nat Commun. 2025 Dec 9;16(1):10600. doi: 10.1038/s41467-025-65993-5. 10.1038/s41467-025-65993-5 https://doi.org/10.1038/s41467-025-65993-5
Xu 39416075 2024 Zhao HN Empirically establishing drug exposure records directly from untargeted metabolomics data bioRxiv [Preprint]. 2024 Oct 26:2024.10.07.617109. doi: 10.1101/2024.10.07.617109. 10.1101/2024.10.07.617109 https://doi.org/10.1101/2024.10.07.617109
Xu 35175195 2022 Ting SY Discovery of coordinately regulated pathways that provide innate protection against interbacterial antagonism Elife. 2022 Feb 17;11:e74658. doi: 10.7554/eLife.74658. 10.7554/eLife.74658 https://doi.org/10.7554/elife.74658
Xu 39192580 2024 Weakly HMJ Several common methods of making vesicles (except an emulsion method) capture intended lipid ratios Biophys J. 2024 Oct 1;123(19):3452-3462. doi: 10.1016/j.bpj.2024.08.019. Epub 2024 Aug 26. 10.1016/j.bpj.2024.08.019 https://doi.org/10.1016/j.bpj.2024.08.019
Xu 33652836 2021 Pfeffer BA Transcriptomic Changes Associated with Loss of Cell Viability Induced by Oxysterol Treatment of a Retinal Photoreceptor-Derived Cell Line: An In Vitro Model of Smith-Lemli-Opitz Syndrome Int J Mol Sci. 2021 Feb 26;22(5):2339. doi: 10.3390/ijms22052339. 10.3390/ijms22052339 https://doi.org/10.3390/ijms22052339
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Xu 33868951 2021 Hrubec TC Altered toxicological endpoints in humans from common quaternary ammonium compound disinfectant exposure Toxicol Rep. 2021 Mar 9;8:646-656. doi: 10.1016/j.toxrep.2021.03.006. eCollection 2021. 10.1016/j.toxrep.2021.03.006 https://doi.org/10.1016/j.toxrep.2021.03.006
Xu 33476305 2021 Daggubati V Smoothened-activating lipids drive resistance to CDK4/6 inhibition in Hedgehog-associated medulloblastoma cells and preclinical models J Clin Invest. 2021 Mar 15;131(6):e141171. doi: 10.1172/JCI141171. 10.1172/JCI141171 https://doi.org/10.1172/jci141171
Xu 33057715 2021 Shen T Identification of a novel tedizolid resistance mutation in rpoB of MRSA after in vitro serial passage J Antimicrob Chemother. 2021 Jan 19;76(2):292-296. doi: 10.1093/jac/dkaa422. 10.1093/jac/dkaa422 https://doi.org/10.1093/jac/dkaa422
Xu 34646861 2021 Zhang R Synergy Between Beta-Lactams and Lipo-, Glyco-, and Lipoglycopeptides, Is Independent of the Seesaw Effect in Methicillin-Resistant Staphylococcus aureus Front Mol Biosci. 2021 Sep 9;8:688357. doi: 10.3389/fmolb.2021.688357. eCollection 2021. 10.3389/fmolb.2021.688357 https://doi.org/10.3389/fmolb.2021.688357
Xu 33269585 2021 Do Q Development and Application of a Peroxyl Radical Clock Approach for Measuring Both Hydrogen-Atom Transfer and Peroxyl Radical Addition Rate Constants J Org Chem. 2021 Jan 1;86(1):153-168. doi: 10.1021/acs.joc.0c01920. Epub 2020 Dec 3. 10.1021/acs.joc.0c01920 https://doi.org/10.1021/acs.joc.0c01920
Xu 37873113 2025 Li A MALDI-IM-MS Imaging of Brain Sterols and Lipids in a Mouse Model of Smith-Lemli-Opitz Syndrome bioRxiv [Preprint]. 2025 Aug 12:2023.10.02.560415. doi: 10.1101/2023.10.02.560415. 10.1101/2023.10.02.560415 https://doi.org/10.1101/2023.10.02.560415
Xu 37904970 2023 Miller WR Membrane Lipids Augment Cell Envelope Stress Signaling and Resistance to Antibiotics and Antimicrobial Peptides in Enterococcus faecalis bioRxiv [Preprint]. 2023 Oct 19:2023.10.17.562839. doi: 10.1101/2023.10.17.562839. 10.1101/2023.10.17.562839 https://doi.org/10.1101/2023.10.17.562839
Xu 32866650 2021 Werth BJ Dalbavancin exposure in vitro selects for dalbavancin-non-susceptible and vancomycin-intermediate strains of methicillin-resistant Staphylococcus aureus Clin Microbiol Infect. 2021 Jun;27(6):910.e1-910.e8. doi: 10.1016/j.cmi.2020.08.025. Epub 2020 Aug 28. 10.1016/j.cmi.2020.08.025 https://doi.org/10.1016/j.cmi.2020.08.025
Xu 34179085 2021 Shen T Varied Contribution of Phospholipid Shedding From Membrane to Daptomycin Tolerance in Staphylococcus aureus Front Mol Biosci. 2021 Jun 11;8:679949. doi: 10.3389/fmolb.2021.679949. eCollection 2021. 10.3389/fmolb.2021.679949 https://doi.org/10.3389/fmolb.2021.679949
Xu 35510938 2022 Zhang R Emergence of Dalbavancin, Vancomycin, and Daptomycin Nonsusceptible Staphylococcus aureus in a Patient Treated With Dalbavancin: Case Report and Isolate Characterization Clin Infect Dis. 2022 Oct 29;75(9):1641-1644. doi: 10.1093/cid/ciac341. 10.1093/cid/ciac341 https://doi.org/10.1093/cid/ciac341
Xu 39936452 2025 Werth BJ Simulated exposures of oritavancin in in vitro pharmacodynamic models select for methicillin-resistant Staphylococcus aureus with reduced susceptibility to oritavancin but minimal cross-resistance or seesaw effect with other antimicrobials J Antimicrob Chemother. 2025 Apr 2;80(4):1108-1115. doi: 10.1093/jac/dkaf042. 10.1093/jac/dkaf042 https://doi.org/10.1093/jac/dkaf042
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Xu 39500386 2025 Raskovic D Growth of Staphylococcus aureus in the presence of oleic acid shifts the glycolipid fatty acid profile and increases resistance to antimicrobial peptides Biochim Biophys Acta Biomembr. 2025 Jan;1867(1):184395. doi: 10.1016/j.bbamem.2024.184395. Epub 2024 Nov 3. 10.1016/j.bbamem.2024.184395 https://doi.org/10.1016/j.bbamem.2024.184395
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Xu 39957787 2025 Elapavalore A PubChemLite Plus Collision Cross Section (CCS) Values for Enhanced Interpretation of Nontarget Environmental Data Environ Sci Technol Lett. 2025 Jan 24;12(2):166-174. doi: 10.1021/acs.estlett.4c01003. eCollection 2025 Feb 11. 10.1021/acs.estlett.4c01003 https://doi.org/10.1021/acs.estlett.4c01003
Xu 41190598 2025 Kula J Maternal and Placental Inflammation Influence Formation of Neural Tube Defects in Quaternary Ammonium Compound Exposed Mice Birth Defects Res. 2025 Nov;117(11):e2539. doi: 10.1002/bdr2.2539. 10.1002/bdr2.2539 https://doi.org/10.1002/bdr2.2539
Xu 41506459 2026 Li A Temporal transcriptomic changes during neurodevelopment in a mouse model of Smith-Lemli-Opitz syndrome Li A, Tomita H, Xu L. Temporal transcriptomic changes during neurodevelopment in a mouse model of Smith-Lemli-Opitz syndrome. J Steroid Biochem Mol Biol. 2026 Mar;257:106935. doi: 10.1016/j.jsbmb.2026.106935. Epub 2026 Jan 6. 10.1016/j.jsbmb.2026.106935 https://doi.org/10.1016/j.jsbmb.2026.106935 4/28/26
Xu 38578967 2025 Miller WR Membrane Lipids Augment Cell Envelope Stress Signaling via the MadRS System to Defend Against Antimicrobial Peptides and Antibiotics in Enterococcus faecalis J Infect Dis. 2025 Feb 20;231(2):307-317. doi: 10.1093/infdis/jiae173. 10.1093/infdis/jiae173 https://doi.org/10.1093/infdis/jiae173
Xu 40912167 2025 Colonna MB Expansion of genotype/phenotype correlation in an individual with compound heterozygous variants in CYP51A1 and congenital cataract Mol Genet Metab. 2025 Sep-Oct;146(1-2):109230. doi: 10.1016/j.ymgme.2025.109230. Epub 2025 Sep 2. 10.1016/j.ymgme.2025.109230 https://doi.org/10.1016/j.ymgme.2025.109230

Nancy Hom

Publications

Visualizing intermediate stages of viral membrane fusion by cryo-electron tomography. Kephart SM, Hom N, Lee KK. Trends Biochem Sci. 2024 Oct;49(10):916-931. doi: 10.1016/j.tibs.2024.06.012. Epub 2024 Jul 24.

Cytoplasmic Tail Truncation Stabilizes S1-S2 Association and Enhances S Protein Incorporation into SARS-CoV-2 Pseudovirions. Zhang L, Hom N, Ojha A, Lovendahl KN, Mou H, Lee KK, Choe H. J Virol. 2023 Mar 30;97(3):e0165022. doi: 10.1128/jvi.01650-22. Epub 2023 Feb 15.

Deep Mutational Scan of the Highly Conserved Influenza A Virus M1 Matrix Protein Reveals Substantial Intrinsic Mutational Tolerance. Hom N, Gentles L, Bloom JD, Lee KK. J Virol. 2019 Jun 14;93(13):e00161-19. doi: 10.1128/JVI.00161-19. Print 2019 Jul 1.

Dissection of Epitope-Specific Mechanisms of Neutralization of Influenza Virus by Intact IgG and Fab Fragments. Williams JA, Gui L, Hom N, Mileant A, Lee KK. J Virol. 2018 Feb 26;92(6). pii: e02006-17. doi: 10.1128/JVI.02006-17. Print 2018 Mar 15.

Structure of the magnetosome-associated actin-like MamK filament at subnanometer resolution. Bergeron JR, Hutto R, Ozyamak E, Hom N, Hansen J, Draper O, Byrne ME, Keyhani S, Komeili A, Kollman JM. Protein Sci. 2017 Jan;26(1):93-102. Epub 2016 Aug 19.

In-depth quantitative proteomic analysis of de novo protein synthesis induced by brain-derived neurotrophic factor. Zhang G, Bowling H, Hom N, Kirshenbaum K, Klann E, Chao MV, Neubert TA. J Proteome Res. 2014 Dec 5;13(12):5707-14. Epub 2014 Oct 13.

Anisotropic nanocrystal arrays organized on protein lattices formed by recombinant clathrin fragments. Hom N, Mehta KR, Chou T, Foraker AB, Brodsky FM, Kirshenbaum K, Montclare JK. J Mater Chem. 2012 Dec 28;22(44):23335-23339.

Therapeutic anti-Prion Monoclonal Antibody 6D11 Facilitates PrPsc Degradation in Prion Cell culture model. Pankiewicz J, Asuni A, Kascsak RB, Kascsak RJ, Prelli F, Kirshenbaum K, Hom N, Sadowski M Alzheimer’s and Dementia 2011 July 2011;7(4):S661