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Molecular Biophysics Training Grant MBTG
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Graduates of T32GM008326

Graduates are listed by the year they were appointed to the training program

Trainees appointed in 2014

  • Chris Fisher

    Current Position : Founder & Principal at Multivalent Communications

    Linkedin: https://www.linkedin.com/in/christopher-james-fisher/

    Program: Chem/Biochem

    Advisor: Kamil Godula

    Publications:

    Huang ML, Cohen M, Fisher CJ, Schooley RT, Gagneux P, Godula K. (2015) Determination of receptor specificities for whole influenza viruses using multivalent glycan arrays. Chem Commun (Camb). 51(25):5326-9. PMC4359031

    Cohen M, Fisher CJ, Huang ML, Lindsay LL, Plancarte M, Boyce WM, Godula K, Gagneux P. (2016) Capture and characterization of influenza A virus from primary samples using glycan bead arrays. Virology. 493:128-35. PMC4860064

    Huang ML, Fisher CJ, Godula K. (2016) Glycomaterials for probing host-pathogen interactions and the immune response. Exp Biol Med (Maywood). 241(10):1042-53. PMC4950362

    Cohen M, Senaati HP, Fisher CJ, Huang ML, Gagneux P, Godula K. (2016) Synthetic Mucus Nanobarriers for Identification of Glycan-Dependent Primary Influenza A Infection Inhibitors. ACS Cent Sci. 2(10):710-714. PMC5084083

    Huang ML, Michalak AL, Fisher CJ, Christy M, Smith RAA, Godula K. (2018) Small Molecule Antagonist of Cell Surface Glycosaminoglycans Restricts Mouse Embryonic Stem Cells in a Pluripotent State. Stem Cells. 36(1):45-54. PMC6237099

  • Chris Lee

    Current Position: Assistant Professor of Molecular Biology, UCSD Linkedin: https://www.linkedin.com/in/ctleelab/
    Program: Chem/Biochem
    Advisor: J. Andrew McCammon

    Publications:

    Malmstrom RD, Lee CT, Van Wart A, Amaro RE. (2014) On the Application of Molecular-Dynamics Based Markov State Models to Functional Proteins. J Chem Theory Comput.  10(7):2648-2657. PMC4248791

    Lee CT, Comer J, Herndon C, Leung N, Pavlova A, Swift RV, Tung C, Rowley CN, Amaro RE, Chipot C, Wang Y, Gumbart JC. (2016) Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds. J Chem Inf Model. 56(4):721-33. PMC5280572

    Wagner JR, Lee CT, Durrant JD, Malmstrom RD, Feher VA, Amaro RE. (2016) Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chem Rev. 116(11):6370-90. PMC4901368

    Votapka LW, Lee CT, Amaro RE. (2016) Two Relations to Estimate Membrane Permeability Using Milestoning. J Phys Chem B. 120(33):8606-16. PMC5002937

    Jagger BR, Lee CT, Amaro RE. (2018) Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach. J Phys Chem Lett. 9(17):4941-4948. PMC6443090

    Lee CT, Amaro RE. (2018) Exascale Computing: A New Dawn for Computational Biology. Comput Sci Eng. 2018 Sep-Oct;20(5):18-25. PMC6458592

    Taylor BC, Lee CT, Amaro RE. (2019) Structural basis for ligand modulation of the CCR2 conformational landscape. Proc Natl Acad Sci U S A. 116(17):8131-8136. PMC6486717

    Lee CT, Moody JB, Amaro RE, McCammon JA, Holst MJ. (20190 The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation. ACM Trans Math Softw. 45(3). pii: 28. PMC6716611

  • Kristen Ramsey

    Current Position: Assistant Professor, Molecular and Cellular Biology, U. Connecticut Linkedin: https://www.linkedin.com/in/kristen-m-ramsey/
    Program: Chem/Biochem
    Advisor: Elizabeth Komives, Gourisankar Ghosh

    Publications:

    Trelle MB, Ramsey KM, Lee TC, Zheng W, Lamboy J, Wolynes PG, Deniz A, Komives EA. (2016) Binding of NFκB Appears to Twist the Ankyrin Repeat Domain of IκBα. Biophys J.110(4):887-95. PMC4776026

    Ramsey KM, Dembinski HE, Chen W, Ricci CG, Komives EA. (2017) DNA and IκBα Both Induce Long-Range Conformational Changes in NFκB. J Mol Biol. 429(7):999-1008. PMC5389416

    Ramsey KM, Narang D, Komives EA. (2018) Prediction of the presence of a seventh ankyrin repeat in IκBε from homology modeling combined with hydrogen-deuterium exchange mass spectrometry (HDX-MS). Protein Sci.  27(9):1624-1635. PMC6194264

    Ramsey KM, Chen W, Marion JD, Bergqvist S, Komives EA. (2019) Exclusivity and Compensation in NFκB Dimer Distributions and IκB Inhibition. Biochemistry. 58(21):2555-2563. PMC6642826

  • Jeff Wagner

    Current Position: Infrastructure Lead, Open Force Field Initiative Linkedin: https://www.linkedin.com/in/jeffrey-r-wagner/
    Program: Chem/Biochem
    Advisor: Rommie Amaro

    Publications:

    Wagner JR, Lee CT, Durrant JD, Malmstrom RD, Feher VA, Amaro RE. (2016) Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chem Rev. 116(11):6370-90. PMC4901368

    Wagner JR, Sørensen J, Hensley N, Wong C, Zhu C, Perison T, Amaro RE. POVME 3.0: Software for Mapping Binding Pocket Flexibility. J Chem Theory Comput. 13(9):4584-4592. PMC5751414

    Shi K, Demir Ö, Carpenter MA, Wagner J, Kurahashi K, Harris RS, Amaro RE, Aihara H. (2017) Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B. Sci Rep. 7(1):17415. PMC5727031

    Wagner JR, Demir Ö, Carpenter MA, Aihara H, Harki DA, Harris RS, Amaro RE. (2019) Determinants of Oligonucleotide Selectivity of APOBEC3B. J Chem Inf Model. 59(5):2264-2273. PMC6644697

    Wagner JR, Churas CP, Liu S, Swift RV, Chiu M, Shao C, Feher VA, Burley SK, Gilson MK, Amaro RE. (2019) Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking. Structure. 27(8):1326-1335.e4. PMC6685748

Trainees appointed in 2015

  • Rob Alberstein

    Current Position: Principal ML Scientist, Structural & Computational Biology at Prescient Design / Genentech

    Linkedin: https://www.linkedin.com/in/rob-alberstein-31486965/
    Program: Chem/Biochem
    Advisor: Akif Tezcan

    Publications:

    Zhang S*, Alberstein RG*, De Yoreo JJ, Tezcan FA. 2020 Assembly of a patchy protein into variable 2D lattices via tunable multiscale interactions. Nat Commun. 11(1):3770*co-first authors

    Golub E, Subramanian RH, Esselborn J, Alberstein RG, Bailey JB, Chiong JA, Yan X, Booth T, Baker TS, Tezcan FA. 2020 Constructing protein polyhedra via orthogonal chemical interactions. Nature. 578(7793):172-176

    Subramanian RH*, Smith SJ*, Alberstein RG, Bailey JB, Zhang L, Cardone G, Suominen L, Chami M, Stahlberg H, Baker TS, Tezcan FA. 2018. Self-Assembly of a Designed Nucleoprotein Architecture through Multimodal Interactions. ACS Cent Sci. 4(11):1578-1586. *co-first authors

    Churchfield LA, Alberstein RG, Williamson LM, Tezcan FA. 2018. Determining the Structural and Energetic Basis of Allostery in a De Novo Designed Metalloprotein Assembly. J Am Chem Soc. 140(31):10043-10053.

    Alberstein R, Suzuki Y, Paesani F, Tezcan FA. 2018. Engineering the entropy-driven free-energy landscape of a dynamic nanoporous protein assembly. Nat Chem. 10(7):732-739.

     

  • Ben Dick

    Current Position: Scientific Lead at Loxo Oncology at Lilly              Linkedin: https://www.linkedin.com/in/benjamin-dick/

    Program: Chem/Biochem
    Advisor: Seth Cohen (Matching slot)

    Publications:

    Dick BL, Patel A, McCammon JA, Cohen SM. 2017. Effect of donor atom identity on metal-binding pharmacophore coordination. J Biol Inorg Chem. 22(4):605-613.

    Schukraft GEM, Ayala S, Dick BL, Cohen SM. Isoreticular expansion of polyMOFs achieves high surface area materials.2017. Chem Commun (Camb). 53(77):10684-10687.

    Isosteres of hydroxypyridinethione as drug-like pharmacophores for metalloenzyme inhibition. J Biol Inorg Chem. 23(7):1129-1138.

    Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. 2019. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev. 119(2):1323-1455.PMC6405328

    Credille CV, Dick BL, Morrison CN, Stokes RW, Adamek RN, Wu NC, Wilson IA, Cohen SM. 2018. Structure-Activity Relationships in Metal-Binding Pharmacophores for Influenza Endonuclease. J Med Chem. 61(22):10206-10217.

    Perez C, Barkley-Levenson AM, Dick BL, Glatt PF, Martinez Y, Siegel D, Momper JD, Palmer AA, Cohen SM. 2019. Metal-Binding Pharmacophore Library Yields the Discovery of a Glyoxalase 1 Inhibitor. J Med Chem. 2019 Feb 14;62(3):1609-1625.

    Credille CV, Morrison CN, Stokes RW, Dick BL, Feng Y, Sun J, Chen Y, Cohen SM. (2019) SAR Exploration of Tight-Binding Inhibitors of Influenza Virus PA Endonuclease. J Med Chem. 62(21): 9438-9449.

  • Ana Gomez Hirlinger (Matching slot)

    Current Position: 
    Linked-In:

    Program: Chemistry & Biochemistry
    Advisor: Nav Toor

    Publications:

    Gomez A, Toor N. Selecting New RNA Crystal Contacts. Structure. 2018 Sep 4;26(9):1166-1167. doi: 10.1016/j.str.2018.08.009. PMID: 30184479; PMCID: PMC6690054.

    Bassi T*, Hirlinger A*, Grayson L, Vantourout J, Toor N. Fluorescent labeling of RNA and DNA on the Hoogsteen edge using sulfinate chemistry. RNA. 2023 Sep;29(9):1437-1451. doi: 10.1261/rna.079679.123. Epub 2023 Jun 5. PMID: 37277186; PMCID: PMC10573292.

  • Sophie Kantonen

    Current Position: 
    Linkedin:
    Program: Chem/Biochem
    Advisor: Michael Gilson

    Publications:

    Kantonen SA, Henriksen NM, Gilson MK. 2017. Evaluation and Minimization of Uncertainty in ITC Binding Measurements: Heat Error, Concentration Error, Saturation, and Stoichiometry. Biochim Biophys Acta Gen Subj. 1861(2):485-498. PMC5195854

    Kantonen SA, Henriksen NM, Gilson MK. 2018. Accounting for apparent deviations between calorimetric and van't Hoff enthalpies. Biochim Biophys Acta Gen Subj. 1862(3):692-704. PMC5851798

    Kellett K, Kantonen SA, Duggan BM, Gilson MK. Toward expanded diversity of host-guest interactions via synthesis and characterization of cyclodextrin derivatives. J. Sol. Chem. 47: 1597-1608, 2018.

    Kantonen SA, Muddanan HS, Schauperl M, Henriksen NM, Wang L-P,Gilson MK. Data-Driven Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters. J Chem Theory Comput 16:1115–1127, 2020.

  • Charles Lin

    Current Position: Senior Software Engineer at Cold Start Therapeutics
    Linkedin: https://www.linkedin.com/in/charles-l-a9646bb9/
    Program: Chem/Biochem
    Advisor: Ross Walker

    Publications:

    Skjevik ÅA, Madej BD, Dickson CJ, Lin C, Teigen K, Walker RC, Gould IR. (2016) Simulation of lipid bilayer self-assembly using all-atom lipid force fields. Phys Chem Chem Phys. 18(15):10573-84. PMC5091658

    Mermelstein DJ, Lin C, Nelson G, Kretsch R, McCammon JA, Walker RC. (2018) Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package. J Comput Chem. 39(19):1354-1358.

    Lee TS, Cerutti DS, Mermelstein D, Lin C, LeGrand S, Giese TJ, Roitberg A, Case DA, Walker RC, York DM. (2018) GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features. J Chem Inf Model. 58(10):2043-2050. PMC6226240

    Ben-Shalom IY, Lin C, Kurtzman T, Walker RC, Gilson MK. (2019) Simulating Water Exchange to Buried Binding Sites. J Chem Theory Comput. 15(4):2684-2691. PMC6456390

  • Ryan Lumpkin


    Current Position: Senior Scientist - Proteomics

    Linkedin: https://www.linkedin.com/in/ryan-lumpkin-65093841/
    Program: Chem/Biochem
    Advisor: Elizabeth Komives

    Publications:

    Lumpkin, RJ, Gu, H, Zhu, Y, Leonard, M, Ahmad, AS, Clauser, KR, Meyer, JR, Bennett, EJ, Komives, EA (2017) Site-specific identification and quantitation of endogenous SUMO modifications under native conditions Nat Comm 8(1):1171. PMC5660086

    Lumpkin RJ, Komives EA. Mol Cell Proteomics. 2019 DECA, A Comprehensive, Automatic Post-processing Program for HDX-MS Data. 18(12):2516-2523. PMC6885705

    Lumpkin RJ, Baker RW, Leschziner AE, Komives EA. 2020. Structure and dynamics of the ASB9 CUL-RING E3 Ligase. Nat Commun. 2020 11(1):2866. PMC7280518

  • Jeff Mindrebo


    Current Position: Postdoctoral Fellow, Scripps Research Institute Linkedin: https://www.linkedin.com/in/jeffrey-mindrebo-1894897a/
    Program: Chem/Biochem
    Advisor: Joe Noel, Michael Burkart

    Publications:

    Mindrebo JT, Misson LE, Johnson C, Noel JP, Burkart MD. Activity Mapping the Acyl Carrier Protein: Elongating Ketosynthase Interaction in Fatty Acid Biosynthesis. Biochemistry. 2020 Sep 29;59(38):3626-3638. doi: 10.1021/acs.biochem.0c00605. Epub 2020 Sep 11. PMID: 32857494; PMCID: PMC8575500.

    Misson LE, Mindrebo JT, Davis TD, Patel A, McCammon JA, Noel JP, Burkart MD. Interfacial plasticity facilitates high reaction rate of E. coli FAS malonyl-CoA:ACP transacylase, FabD. Proc Natl Acad Sci U S A. 2020 Sep 29;117(39):24224-24233. doi: 10.1073/pnas.2009805117. Epub 2020 Sep 14. PMID: 32929027; PMCID: PMC7533678.

    Mindrebo JT, Chen A, Kim WE, Re RN, Davis TD, Noel JP, Burkart MD. Structure and mechanistic analyses of the gating mechanism of elongating ketosynthases. ACS Catal. 2021 Jun 18;11(12):6787-6799. doi: 10.1021/acscatal.1c00745. Epub 2021 May 26. PMID: 36187225; PMCID: PMC9524369.

    Chen A, Mindrebo JT, Davis TD, Kim WE, Katsuyama Y, Jiang Z, Ohnishi Y, Noel JP, Burkart MD. Mechanism-based cross-linking probes capture the Escherichia coli ketosynthase FabB in conformationally distinct catalytic states. Acta Crystallogr D Struct Biol. 2022 Sep 1;78(Pt 9):1171-1179. doi: 10.1107/S2059798322007434. Epub 2022 Aug 30. PMID: 36048156; PMCID: PMC9435599.

    Mindrebo JT, Nartey CM, Seto Y, Burkart MD, Noel JP. Unveiling the functional diversity of the alpha/beta hydrolase superfamily in the plant kingdom. Curr Opin Struct Biol. 2016 Dec;41:233-246. doi: 10.1016/j.sbi.2016.08.005. Epub 2016 Sep 21. Erratum in: Curr Opin Struct Biol. 2016 Dec;41:256-257. doi: 10.1016/j.sbi.2016.11.008. PMID: 27662376; PMCID: PMC5687975.

    Mindrebo JT, Patel A, Kim WE, Davis TD, Chen A, Bartholow TG, La Clair JJ, McCammon JA, Noel JP, Burkart MD. Gating mechanism of elongating β-ketoacyl-ACP synthases. Nat Commun. 2020 Apr 7;11(1):1727. doi: 10.1038/s41467-020-15455-x. PMID: 32265440; PMCID: PMC7138838.

     

  • Steve Rees


    Current Position: Founder, CEO at Defined Bioscience
    Linkedin: https://www.linkedin.com/in/stevendrees/
    Program: BMS
    Advisor: Geoffrey Chang

    Publications:

    Zaramela LS, Martino C, Alisson-Silva F, Rees SD, Diaz SL, Chuzel L, Ganatra MB, Taron CH, Secrest P, Zuniga C, Huang J, Siegel D, Chang G, Varki A, Zengler K. Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates. Nat Microbiol. 2019. doi: 10.1038/s41564-019-0564-9. PubMed PMID: 31548686. PMC6879853

    Kalogriopoulos NA, Rees SD, Ngo T, Kopcho NJ, Ilatovskiy AV, Sun N, Komives EA, Chang G, Ghosh P, Kufareva I. Structural basis for GPCR-independent activation of heterotrimeric Gi proteins. Proc Natl Acad Sci U S A. 2019;116(33):16394-403. doi: 10.1073/pnas.1906658116. PubMed PMID: 31363053; PMCID: PMC6697900

    Maity K, Heumann JM, McGrath AP, Kopcho NJ, Hsu PK, Lee CW, Mapes JH, Garza D, Krishnan S, Morgan GP, Hendargo KJ, Klose T, Rees SD, Medrano-Soto A, Saier MH, Jr., Pineros M, Komives EA, Schroeder JI, Chang G, Stowell MHB. Cryo-EM structure of OSCA1.2 from Oryza sativa elucidates the mechanical basis of potential membrane hyperosmolality gating. Proc Natl Acad Sci U S A. 2019;116(28):14309-18. doi: 10.1073/pnas.1900774116. PMC6628804

  • Sarah Ur

    Current Position: Vividion Therapeutics
    Linkedin: https://www.linkedin.com/in/sarah-ur-a50773220/
    Program: BMS
    Advisor: Kevin Corbett

    Publications:

    Ye Q, Ur SN, Su TY, Corbett KD. Structure of the Saccharomyces cerevisiae Hrr25:Mam1 monopolin subcomplex reveals a novel kinase regulator. EMBO J. 2016 Oct 4;35(19):2139-2151. doi: 10.15252/embj.201694082. Epub 2016 Aug 4. PMID: 27491543; PMCID: PMC5048352.

    West AM, Rosenberg SC, Ur SN, Lehmer MK, Ye Q, Hagemann G, Caballero I, Usón I, MacQueen AJ, Herzog F, Corbett KD. A conserved filamentous assembly underlies the structure of the meiotic chromosome axis. Elife. 2019 Jan 18;8:e40372. doi: 10.7554/eLife.40372. PMID: 30657449; PMCID: PMC6349405.

    Ur SN, Corbett KD. Architecture and Dynamics of Meiotic Chromosomes. Annu Rev Genet. 2021 Nov 23;55:497-526. doi: 10.1146/annurev-genet-071719-020235. Epub 2021 Sep 16. PMID: 34530636.

    Heldrich J, Milano CR, Markowitz TE, Ur SN, Vale-Silva LA, Corbett KD, Hochwagen A. Two pathways drive meiotic chromosome axis assembly in Saccharomyces cerevisiae. Nucleic Acids Res. 2022 May 6;50(8):4545-4556. doi: 10.1093/nar/gkac227. PMID: 35412621; PMCID: PMC9071447.

    Liang Q, Richey ST, Ur SN, Ye Q, Lau RK, Corbett KD. Structure and activity of a bacterial defense-associated 3'-5' exonuclease. Protein Sci. 2022 Jul;31(7):e4374. doi: 10.1002/pro.4374. PMID: 35762727; PMCID: PMC9214754.

    Milano CR, Ur SN, Gu Y, Zhang J, Allison R, Brown G, Neale MJ, Tromer EC, Corbett KD, Hochwagen A. Chromatin binding by HORMAD proteins regulates meiotic recombination initiation. EMBO J. 2024 Mar;43(5):836-867. doi: 10.1038/s44318-024-00034-3. Epub 2024 Feb 8. PMID: 38332377; PMCID: PMC10907721.

Trainees appointed in 2016

  • Colin Deniston

    Current Position: Scientist, Novartis                                                                                                    Linkedin: https://www.linkedin.com/in/colin-deniston-38773265/
    Program: Chem/Biochem
    Advisor: Andres Leschziner

    Publications:

    Deniston C*, Salogiannis J*, Mathea S*, Snead D, Lahiri I, Matyszewski M, Donosa O, Watanabe R, Bohning J, Shiau AK, Knapp S, Villa E, Reck-Peterson SL and Leschziner AE. (2020) Parkinson’s Disease LRRK2 structure and model for microtubule interaction. Nature (accepted). (* equal contributors) PMCID in progress

  • Benjamin Jagger

    Current Position: Computational chemist and protein engineer, Abiologics                                          Linkedin: https://www.linkedin.com/in/benjaminjagger/

    Program: Chem/Biochem
    Advisor: Rommie Amaro

    Publications:

    Votapka LW, Jagger BR, Heyneman AL, Amaro RE. 2017. SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding. J Phys Chem B. 121(15):3597-3606. PMC5562489

    Jagger BR, Lee CT, Amaro RE. 2018. Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach. J Phys Chem Lett. 9(17):4941-4948. PMC6443090

    Jagger BR, Ojha AA, Amaro RE. Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach. J Chem Theory Comput. 2020 Aug 11;16(8):5348-5357. doi: 10.1021/acs.jctc.0c00495. Epub 2020 Jul 9. PMID: 32579371.

    Ahn SH, Jagger BR, Amaro RE. Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach. J Chem Inf Model. 2020 Nov 23;60(11):5340-5352. doi: 10.1021/acs.jcim.9b00968. Epub 2020 May 7. PMID: 32315175.

    Gan JL, Kumar D, Chen C, Taylor BC, Jagger BR, Amaro RE, Lee CT. Benchmarking ensemble docking methods in D3R Grand Challenge 4. J Comput Aided Mol Des. 2022 Feb;36(2):87-99. doi: 10.1007/s10822-021-00433-2. Epub 2022 Feb 24. PMID: 35199221; PMCID: PMC8907095.

  • Evan Kabori

    Current Position: Postdoctoral fellow UC San Diego                                        Linkedin: https://www.linkedin.com/in/evan-kobori-8989b486/

    Program: Chem/Biochem
    Advisor: Susan Taylor

    Publications:

    Taylor SS, Søberg K, Kobori E, Wu J, Pautz S, Herberg FW, Skålhegg BS. The Tails of Protein Kinase A. Mol Pharmacol. 2022 Apr;101(4):219-225. doi: 10.1124/molpharm.121.000315. Epub 2021 Jul 30. PMID: 34330820; PMCID: PMC9092481.

    Alexa A, Sok P, Gross F, Albert K, Kobori E, Póti ÁL, Gógl G, Bento I, Kuang E, Taylor SS, Zhu F, Ciliberto A, Reményi A. A non-catalytic herpesviral protein reconfigures ERK-RSK signaling by targeting kinase docking systems in the host. Nat Commun. 2022 Jan 25;13(1):472. doi: 10.1038/s41467-022-28109-x. PMID: 35078976; PMCID: PMC8789800.

  • Sarah Kochanek

    Current Position Principal Scientist II at Novartis Institutes for BioMedical Research (NIBR)                        Linkedin: https://www.linkedin.com/in/sarah-kochanek/

    Program: Chem/Biochem
    Advisor: Rommie Amaro

    Publications:

    Jagger BR*, Kochanek SE*, Haldar S, Amaro RE, Mulholland AJ. Multiscale simulation approaches to modeling drug-protein binding. Curr Opin Struct Biol. 2020 Apr;61:213-221. doi: 10.1016/j.sbi.2020.01.014. Epub 2020 Feb 26. PMID: 32113133.

    Durrant JD, Kochanek SE, Casalino L, Ieong PU, Dommer AC, Amaro RE. Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ACS Cent Sci. 2020 Feb 26;6(2):189-196. doi: 10.1021/acscentsci.9b01071. Epub 2020 Feb 19. PMID: 32123736; PMCID: PMC7048371.

  • Noah Kopcho


    Current Position: Field Application ScientistGyros Protein Technologies                                            Linkedin: https://www.linkedin.com/in/noah-kopcho-7a5956193/
    Program: Chem/Biochem
    Advisor: Geoffrey Chang

    Publications:

    Kopcho N, Chang G, Komives EA. Dynamics of ABC Transporter P-glycoprotein in Three Conformational States. Sci Rep. 2019;9(1):15092. doi: 10.1038/s41598-019-50578-2. PubMed PMID: 31641149; PMCID: PMC6805939

    Kalogriopoulos NA, Rees SD, Ngo T, Kopcho NJ, Ilatovskiy AV, Sun N, Komives EA, Chang G, Ghosh P, Kufareva I. Structural basis for GPCR-independent activation of heterotrimeric Gi proteins. Proc Natl Acad Sci U S A. 2019;116(33):16394-403. doi: 10.1073/pnas.1906658116. PubMed PMID: 31363053; PMCID: PMC6697900

    Maity K, Heumann JM, McGrath AP, Kopcho NJ, Hsu PK, Lee CW, Mapes JH, Garza D, Krishnan S, Morgan GP, Hendargo KJ, Klose T, Rees SD, Medrano-Soto A, Saier MH, Jr., Pineros M, Komives EA, Schroeder JI, Chang G, Stowell MHB. Cryo-EM structure of OSCA1.2 from Oryza sativa elucidates the mechanical basis of potential membrane hyperosmolality gating. Proc Natl Acad Sci U S A. 2019;116(28):14309-18. doi: 10.1073/pnas.1900774116. PMC6628804

  • Adam Maloney

    Current Position: Scientist at Emervax
    Linked-In: https://www.linkedin.com/in/adam-maloney-28082a189/                                                      Program: Chemistry & Biochemistry
    Advisor: Simpson Joseph

    Publications:

    Maloney A, Joseph S. Validating the EMCV IRES Secondary Structure with Structure-Function Analysis. Biochemistry. 2024 Jan 2;63(1):107-115. doi: 10.1021/acs.biochem.3c00579. Epub 2023 Dec 11. PMID: 38081770; PMCID: PMC10896073.

  • Kevin Sweeney

    Current Position: Assistant Professor of Physical Sciences, Southwestern College
    Linked-In:                                                                                                                                                        Program: Chemistry & Biochemistry
    Advisor: Ulrich Müller

    Publications:

    Sweeney KJ, Han X, Müller UF. A ribozyme that uses lanthanides as cofactor. Nucleic Acids Res. 2023 Aug 11;51(14):7163-7173. doi: 10.1093/nar/gkad513. PMID: 37326001; PMCID: PMC10415125.

    Sweeney KJ, Le T, Jorge MZ, Schellinger JG, Leman LJ, Müller UF. Peptide conjugates with polyaromatic hydrocarbons can benefit the activity of catalytic RNAs. Chem Sci. 2023 Sep 12;14(37):10318-10328. doi: 10.1039/d3sc03540a. PMID: 37772096; PMCID: PMC10529712.

Trainees appointed in 2017

  • Joshua Arriola

    Current Position: Biochemist, Exact Sciences
    Linked-In: https://www.linkedin.com/in/joshua-t-arriola/                                                                          
    Program: Chemistry & Biochemistry
    Advisor: Ulrich Muller

    Publications:

    Arriola JT, Müller UF. A combinatorial method to isolate short ribozymes from complex ribozyme libraries. Nucleic Acids Res. 2020 Nov 18;48(20):e116. doi: 10.1093/nar/gkaa834. PMID: 33035338; PMCID: PMC7672470.

    Akoopie A, Arriola JT, Magde D, Müller UF. A GTP-synthesizing ribozyme selected by metabolic coupling to an RNA polymerase ribozyme. Sci Adv. 2021 Oct 8;7(41):eabj7487. doi: 10.1126/sciadv.abj7487.PMID: 34613767; PMCID: PMC8494290.

    Lin H, Jiménez EI, Arriola JT, Müller UF, Krishnamurthy R. Concurrent Prebiotic Formation of Nucleoside-Amidophosphates and Nucleoside-Triphosphates Potentiates Transition from Abiotic to Biotic Polymerization. Angew Chem Int Ed Engl. 2022 Jan 3;61(1):e202113625. doi: 10.1002/anie.202113625. PMID: 34738300.

    Arriola JT, Poordian S, Valdivia EM, Le T, Leman LJ, Schellinger JG, Müller UF. Weak effects of prebiotically plausible peptides on self-triphosphorylation ribozyme function. RSC Chem Biol. 2024 Sep 12;5(11):1122–31. doi: 10.1039/d4cb00129j. PMID: 39279875; PMCID: PMC11391260.

  • John Gillies

    Current Position: Research Lab Specialist Senior at University of Michigan

    Linked-In:  www.linkedin.com/in/john-gillies-588342341.                                                                                  Program: Biological Sciences

    Advisor: Samara Reck-Peterson

    Publications:

    Htet ZM, Gillies JP, Baker RW, Leschziner AE, DeSantis ME, Reck-Peterson SL. LIS1 promotes the formation of activated cytoplasmic dynein-1 complexes. Nat Cell Biol. 2020 May;22(5):518-525. doi: 10.1038/s41556-020-0506-z. Epub 2020 Apr 27. PMID: 32341549; PMCID: PMC7271980.

    Gillies JP, Reimer JM, Karasmanis EP, Lahiri I, Htet ZM, Leschziner AE, Reck-Peterson SL. Structural basis for cytoplasmic dynein-1 regulation by Lis1. Elife. 2022 Jan 7;11:e71229. doi: 10.7554/eLife.71229. PMID: 34994688; PMCID: PMC8824474.

    Kusakci E, Htet ZM, Zhao Y, Gillies JP, Reck-Peterson SL, Yildiz A. Lis1 slows force-induced detachment of cytoplasmic dynein from microtubules. Nat Chem Biol. 2024 Apr;20(4):521-529. doi: 10.1038/s41589-023-01464-6. Epub 2023 Nov 2. PMID: 37919547; PMCID: PMC11164236.

  • Riley Peacock

    Current Position: Upper School Chemistry Teacher,The Park School, Maryland                                          Linkedin: https://www.linkedin.com/in/dr-riley-peacock/                                                                            Program: Chem/Biochem
    Advisor: Elizabeth Komives

    Publications:

    Peacock RB, Davis JR, Markwick PRL, Komives EA. Dynamic Consequences of Mutation of Tryptophan 215 in Thrombin. Biochemistry. 2018 May 8;57(18):2694-2703. doi: 10.1021/acs.biochem.8b00262. Epub 2018 Apr 19. PMID: 29634247; PMCID: PMC5940494.

    Markwick PRL, Peacock RB, Komives EA. Accurate Prediction of Amide Exchange in the Fast Limit Reveals Thrombin Allostery. Biophys J. 2019 Jan 8;116(1):49-56. doi: 10.1016/j.bpj.2018.11.023. Epub 2018 Nov 24. PMID: 30558884; PMCID: PMC6342732.
    Peacock RB, McGrann T, Tonelli M, Komives EA. Serine protease dynamics revealed by NMR analysis of the thrombin-thrombomodulin complex. Sci Rep. 2021 Apr 30;11(1):9354. doi: 10.1038/s41598-021-88432-z. PMID: 33931701; PMCID: PMC8087772.
    Peacock RB, Komives EA. Hydrogen/Deuterium Exchange and Nuclear Magnetic Resonance Spectroscopy Reveal Dynamic Allostery on Multiple Time Scales in the Serine Protease Thrombin. Biochemistry. 2021 Nov 23;60(46):3441-3448. doi: 10.1021/acs.biochem.1c00277. Epub 2021 Jun 23. PMID: 34159782; PMCID: PMC9659328.
    Peacock RB, McGrann T, Zaragoza S, Komives EA. How Thrombomodulin Enables W215A/E217A Thrombin to Cleave Protein C but Not Fibrinogen. Biochemistry. 2022 Jan 18;61(2):77-84. doi: 10.1021/acs.biochem.1c00635. Epub 2022 Jan 3. PMID: 34978431; PMCID: PMC9427096.

  • Kira Podolsky

    Current Position: Schmidt Science Fellow at MIT
    Linked-In:  https://www.linkedin.com/in/kira-podolsky-974a35341/                                                                Program: Biomedical Sciences                                                                                                           Advisor: Neal Devaraj

    Publications: 

    Seoane A, Brea RJ, Fuertes A, Podolsky KA, Devaraj NK. Biomimetic Generation and Remodeling of Phospholipid Membranes by Dynamic Imine Chemistry. J Am Chem Soc. 2018 Jul 11;140(27):8388-8391. doi: 10.1021/jacs.8b04557. Epub 2018 Jun 13. PMID: 29886740; PMCID: PMC6251970.

    Johnson M, Bhattacharya A, Brea RJ, Podolsky KA, Devaraj NK. Temperature-Dependent Reversible Morphological Transformations in N-Oleoyl β-d-Galactopyranosylamine. J Phys Chem B. 2020 Jul 2;124(26):5426-5433. doi: 10.1021/acs.jpcb.0c01410. Epub 2020 Jun 19. PMID: 32437154; PMCID: PMC8849015.

    Bhattacharya A, Niederholtmeyer H, Podolsky KA, Bhattacharya R, Song JJ, Brea RJ, Tsai CH, Sinha SK, Devaraj NK. Lipid sponge droplets as programmable synthetic organelles. Proc Natl Acad Sci U S A. 2020 Aug 4;117(31):18206-18215. doi: 10.1073/pnas.2004408117. Epub 2020 Jul 21. Erratum in: Proc Natl Acad Sci U S A. 2020 Sep 1;117(35):21821. doi: 10.1073/pnas.2015703117. PMID: 32694212; PMCID: PMC7414067.

    Martin HS, Podolsky KA, Devaraj NK. Probing the Role of Chirality in Phospholipid Membranes. Chembiochem. 2021 Nov 16;22(22):3148-3157. doi: 10.1002/cbic.202100232. Epub 2021 Aug 6. PMID: 34227722.

    Podolsky KA, Devaraj NK. Synthesis of lipid membranes for artificial cells. Nat Rev Chem. 2021 Oct;5(10):676-694. doi: 10.1038/s41570-021-00303-3. Epub 2021 Jul 19. PMID: 37118179.

    Podolsky KA, Masubuchi T, Debelouchina GT, Hui E, Devaraj NK. In Situ Assembly of Transmembrane Proteins from Expressed and Synthetic Components in Giant Unilamellar Vesicles. ACS Chem Biol. 2022 May 20;17(5):1015-1021. doi: 10.1021/acschembio.2c00013. Epub 2022 Apr 28. PMID: 35482050; PMCID: PMC9255206.

    Fracassi A, Podolsky KA, Pandey S, Xu C, Hutchings J, Seifert S, Baiz CR, Sinha SK, Devaraj NK. Characterizing the Self-Assembly Properties of Monoolein Lipid Isosteres. J Phys Chem B. 2023 Mar 2;127(8):1771-1779. doi: 10.1021/acs.jpcb.2c07215. Epub 2023 Feb 16. PMID: 36795462; PMCID: PMC9986874.

  • Hannah Rutledge

    Current Position: Postdoc at the Max Planck Institute for Biochemistry
    Linked-In: https://www.linkedin.com/in/hannahleahrutledge/                                                                Program: Chemistry & Biochemistry
    Advisor: Akif Tezcan

    Publications:

    Rutledge HL, Rittle J, Williamson LM, Xu WA, Gagnon DM, Tezcan FA. Redox-Dependent Metastability of the Nitrogenase P-Cluster. J Am Chem Soc. 2019 Jun 26;141(25):10091-10098. doi: 10.1021/jacs.9b04555. Epub 2019 Jun 13. PMID: 31146522; PMCID: PMC7445746.

    Rutledge HL, Tezcan FA. Electron Transfer in Nitrogenase. Chem Rev. 2020 Jun 24;120(12):5158-5193. doi: 10.1021/acs.chemrev.9b00663. Epub 2020 Jan 30. PMID: 31999100; PMCID: PMC7466952.

    Rutledge HL, Cook BD, Nguyen HPM, Herzik MA Jr, Tezcan FA. Structures of the nitrogenase complex prepared under catalytic turnover conditions. Science. 2022 Aug 19;377(6608):865-869. doi: 10.1126/science.abq7641. Epub 2022 Jul 28. PMID: 35901182; PMCID: PMC9949965.

    Rutledge HL, Field MJ, Rittle J, Green MT, Tezcan FA. Role of Serine Coordination in the Structural and Functional Protection of the Nitrogenase P-Cluster. J Am Chem Soc. 2022 Dec 7;144(48):22101-22112. doi: 10.1021/jacs.2c09480. Epub 2022 Nov 29. PMID: 36445204; PMCID: PMC9957664.

  • Bryce Timm

    Current Position: Staff Scientist at Trace Biosciences                                                                         

    Linked-In: https://www.linkedin.com/in/brycetimm/

    Program: Chemistry & Biochemistry
    Advisor: Kamil Godula       

    Publications: 

    Weiss RJ, Spahn PN, Chiang AWT, Liu Q, Li J, Hamill KM, Rother S, Clausen TM, Hoeksema MA, Timm BM, Godula K, Glass CK, Tor Y, Gordts PLSM, Lewis NE, Esko JD. Genome-wide screens uncover KDM2B as a modifier of protein binding to heparan sulfate. Nat Chem Biol. 2021 Jun;17(6):684-692. doi: 10.1038/s41589-021-00776-9. Epub 2021 Apr 12. Erratum in: Nat Chem Biol. 2022 May;18(5):575. doi: 10.1038/s41589-022-01022-6. PMID: 33846619; PMCID: PMC8159865.

    Porell RN, Follmar JL, Purcell SC, Timm B, Laubach LK, Kozirovskiy D, Thacker BE, Glass CA, Gordts PLSM, Godula K. Biologically Derived Neoproteoglycans for Profiling Protein-Glycosaminoglycan Interactions. ACS Chem Biol. 2022 Jun 17;17(6):1534-1542. doi: 10.1021/acschembio.2c00205. Epub 2022 May 15. PMID: 35574759.

    Timm BM, Follmar JL, Porell RN, Glass K, Thacker BE, Glass CA, Godula K. Human extracellular sulfatases use a dual mechanism for regulation of growth factor interactions with heparan sulfate proteoglycans. bioRxiv [Preprint]. 2023 Nov 22:2023.11.22.568358. doi: 10.1101/2023.11.22.568358. PMID: 38045270; PMCID: PMC10690288.

  • Hetika Vora

    Current Position: Scientist II, Translational Research Kura Oncology, Inc.
    Linked-In: https://www.linkedin.com/in/hetikavora/                                                                     Program: Biomedical Sciences
    Advisor: Neal Devaraj

    Publications: 

    Vora HD, Johnson M, Brea RJ, Rudd AK, Devaraj NK. Inhibition of NRAS Signaling in Melanoma through Direct Depalmitoylation Using Amphiphilic Nucleophiles. ACS Chem Biol. 2020 Aug 21;15(8):2079-2086. doi: 10.1021/acschembio.0c00222. Epub 2020 Jul 13. PMID: 32568509; PMCID: PMC7556697.

Trainees Appointed in 2018

  • Bryce Ackermann


    Linked-In: https://www.linkedin.com/in/bryce-ackermann-798946168/                                                          Current Position: Postdoctoral fellow in the Guseman Lab, UC San Diego
    Program: Chemistry & Biochemistry
    Advisor: Galia Debelouchina

    Publications:

    Lim BJ, Ackermann BE, Debelouchina GT. Targetable Tetrazine-Based Dynamic Nuclear Polarization Agents for Biological Systems. Chembiochem. 2020 May 4;21(9):1315-1319. doi: 10.1002/cbic.201900609. Epub 2020 Jan 21. PMID: 31746101; PMCID: PMC7445144.

    Ackermann BE, Debelouchina GT. Emerging Contributions of Solid-State NMR Spectroscopy to Chromatin Structural Biology. Front Mol Biosci. 2021 Oct 11;8:741581. doi: 10.3389/fmolb.2021.741581. PMID: 34708075; PMCID: PMC8544521.

    Elathram N, Ackermann BE, Debelouchina GT. DNP-enhanced solid-state NMR spectroscopy of chromatin polymers. J Magn Reson Open. 2022 Jun;10-11:100057. doi: 10.1016/j.jmro.2022.100057. Epub 2022 Mar 26. PMID: 35707629; PMCID: PMC9191766.

    Ackermann BE, Lim BJ, Elathram N, Narayanan S, Debelouchina GT. A Comparative Study of Nitroxide-Based Biradicals for Dynamic Nuclear Polarization in Cellular Environments. Chembiochem. 2022 Dec 16;23(24):e202200577. doi: 10.1002/cbic.202200577. Epub 2022 Nov 14. PMID: 36250276; PMCID: PMC9856215.

    Her C, Phan TM, Jovic N, Kapoor U, Ackermann BE, Rizuan A, Kim YC, Mittal J, Debelouchina GT. Molecular interactions underlying the phase separation of HP1α: role of phosphorylation, ligand and nucleic acid binding. Nucleic Acids Res. 2022 Dec 9;50(22):12702-12722. doi: 10.1093/nar/gkac1194. PMID: 36537242; PMCID: PMC9825191.

    Kent JE, Ackermann BE, Debelouchina GT, Marassi FM. Dynamic Nuclear Polarization Illuminates Key Protein-Lipid Interactions in the Native Bacterial Cell Envelope. Biochemistry. 2023 Aug 1;62(15):2252-2256. doi: 10.1021/acs.biochem.3c00262. Epub 2023 Jul 17. PMID: 37459255; PMCID: PMC11019665.

    Elathram N, Ackermann BE, Clark ET, Dunn SR, Debelouchina GT. Phosphorylated HP1α-Nucleosome Interactions in Phase Separated Environments. J Am Chem Soc. 2023 Nov 8;145(44):23994-24004. doi: 10.1021/jacs.3c06481. Epub 2023 Oct 23. PMID: 37870432; PMCID: PMC10636758.

    Yoon J, Zhang YM, Her C, Grant RA, Ponomarenko AI, Ackermann BE, Hui T, Lin YS, Debelouchina GT, Shoulders MD. The immune-evasive proline-283 substitution in influenza nucleoprotein increases aggregation propensity without altering the native structure. Sci Adv. 2024 Apr 19;10(16):eadl6144. doi: 10.1126/sciadv.adl6144. Epub 2024 Apr 19. PMID: 38640233; PMCID: PMC11029814.

  • Joshua Corpuz (Matching slot)

    Current Position: Scientist 2, Protein Engineering at Singular Genomics
    Linked-In: https://www.linkedin.com/in/joshuacorpuz/                                                                          Program: Chemistry & Biochemistry
    Advisor: Michael Burkart

    Publications:

    Jaremko MJ, Davis TD, Corpuz JC, Burkart MD. Type II non-ribosomal peptide synthetase proteins: structure, mechanism, and protein-protein interactions. Nat Prod Rep. 2020 Mar 25;37(3):355-379. doi: 10.1039/c9np00047j. PMID: 31593192; PMCID: PMC7101270.

    Corpuz JC, Podust LM, Davis TD, Jaremko MJ, Burkart MD. Dynamic visualization of type II peptidyl carrier protein recognition in pyoluteorin biosynthesis. RSC Chem Biol. 2020 Apr 1;1(1):8-12. doi: 10.1039/c9cb00015a. Epub 2020 Mar 24. PMID: 33305272; PMCID: PMC7723355.

    Corpuz JC, Sanlley JO, Burkart MD. Protein-protein interface analysis of the non-ribosomal peptide synthetase peptidyl carrier protein and enzymatic domains. Synth Syst Biotechnol. 2022 Feb 16;7(2):677-688. doi: 10.1016/j.synbio.2022.02.006. PMID: 35224236; PMCID: PMC8857579.

    Corpuz JC, Patel A, Davis TD, Podust LM, McCammon JA, Burkart MD. Essential Role of Loop Dynamics in Type II NRPS Biomolecular Recognition. ACS Chem Biol. 2022 Oct 21;17(10):2890-2898. doi: 10.1021/acschembio.2c00523. Epub 2022 Sep 29. PMID: 36173802; PMCID: PMC9808923.

    Sztain T, Corpuz JC, Bartholow TG, Sanlley Hernandez JO, Jiang Z, Mellor DA, Heberlig GW, La Clair JJ, McCammon JA, Burkart MD. Interface Engineering of Carrier-Protein-Dependent Metabolic Pathways. ACS Chem Biol. 2023 Sep 15;18(9):2014-2022. doi: 10.1021/acschembio.3c00238. Epub 2023 Sep 6. PMID: 37671411; PMCID: PMC10807135.

  • Cyrus de Rozieres (Matching slot)

    Current Position: 
    Linked-In: https://www.linkedin.com/in/cyrus-de-rozi%C3%A8res-ph-d/                                                    Program: Chemistry & Biochemistry
    Advisor: Simpson Joseph

    Publications:

    Arias-Mireles BH, de Rozieres CM, Ly K, Joseph S. RNA Modulates the Interaction between Influenza A Virus NS1 and Human PABP1. Biochemistry. 2018 Jul 3;57(26):3590-3598. doi: 10.1021/acs.biochem.8b00218. Epub 2018 May 25. PMID: 29782795; PMCID: PMC6205234.

    de Rozières CM, Joseph S. Influenza A Virus NS1 Protein Binds as a Dimer to RNA-Free PABP1 but Not to the PABP1·Poly(A) RNA Complex. Biochemistry. 2020 Nov 24;59(46):4439-4448. doi: 10.1021/acs.biochem.0c00666. Epub 2020 Nov 10. PMID: 33172261; PMCID: PMC8034803.

    de Rozières CM, Pequeno A, Shahabi S, Lucas TM, Godula K, Ghosh G, Joseph S. PABP1 Drives the Selective Translation of Influenza A Virus mRNA. J Mol Biol. 2022 Mar 15;434(5):167460. doi: 10.1016/j.jmb.2022.167460. Epub 2022 Jan 21. PMID: 35074482; PMCID: PMC8897273.

  • Mounir Fizari

    Current Position: Data Scientist, CACI International
    Linked-In: https://www.linkedin.com/in/mounir-fizari/                                                                                      Program: Physics
    Advisor: Doug Smith

    Publications:

    Mo Y, Fizari M, Koharchik K, Smith DE. Determining Trap Compliances, Microsphere Size Variations, and Response Linearities in Single DNA Molecule Elasticity Measurements with Optical Tweezers. Front Mol Biosci. 2021 Mar 22;8:605102. doi: 10.3389/fmolb.2021.605102. PMID: 33829038; PMCID: PMC8019724.

    Fizari M, Keller N, Jardine PJ, Smith DE. Role of DNA-DNA sliding friction and nonequilibrium dynamics in viral genome ejection and packaging. Nucleic Acids Res. 2023 Aug 25;51(15):8060-8069. doi: 10.1093/nar/gkad582. PMID: 37449417; PMCID: PMC10450192.

  • Sonjiala Hotchkiss

    Current Position: 
    Linked-In: https://www.linkedin.com/in/sonjialahotchkiss/                                                                                  Program: Chemistry and Biochemistry
    Advisor: Gourisankar Ghosh

    Publications: 

    none

  • Dominic McGrosso

    Current Position: Postdoctoral fellow with Sam Myers at La Jolla Institute of Immunology
    Linked-In: https://www.linkedin.com/in/dominic-mcgrosso-phd-72a41651/                                                    Program: Biomedical Sciences
    Advisor: Geoffrey Chang then David Gonzalez

    Publications: 

    O'Neill AM, Worthing KA, Kulkarni N, Li F, Nakatsuji T, McGrosso D, Mills RH, Kalla G, Cheng JY, Norris JM, Pogliano K, Pogliano J, Gonzalez DJ, Gallo RL. Antimicrobials from a feline commensal bacterium inhibit skin infection by drug-resistant S. pseudintermedius. Elife. 2021 Oct 19;10:e66793. doi: 10.7554/eLife.66793. PMID: 34664551; PMCID: PMC8592530.

    Geriak M, McGrosso D, Gonzalez DJ, Dehner M, Sakoulas G. Case Series of Successful Intravenous Immunoglobulin (IVIG) Treatment in 4 Pregnant Patients with Severe COVID-19-Induced Hypoxia. Am J Case Rep. 2022 May 14;23:e936734. doi: 10.12659/AJCR.936734. PMID: 35567293; PMCID: PMC9115731.

    Hayat O, Ullah N, Sirajuddin M, Giardini MA, Nguyen JV, Francisco KR, Liu LJ, Sun YU, Maurya S, McGrosso D, Gonzalez DJ, Caffrey CR, Debnath A, Siqueira-Neto JL. A Broad Spectrum Antiparasitic Activity of Organotin (IV) Derivatives and Its Untargeted Proteomic Profiling Using Leishmania donovani. Pathogens. 2022 Nov 26;11(12):1424. doi: 10.3390/pathogens11121424. PMID: 36558759; PMCID: PMC9785441.

    Buzun E, Hsu CY, Sejane K, Oles RE, Vasquez Ayala A, Loomis LR, Zhao J, Rossitto LA, McGrosso DM, Gonzalez DJ, Bode L, Chu H. A bacterial sialidase mediates early-life colonization by a pioneering gut commensal. Cell Host Microbe. 2024 Feb 14;32(2):181-190.e9. doi: 10.1016/j.chom.2023.12.014. Epub 2024 Jan 15. PMID: 38228143; PMCID: PMC10922750.

    Yao Y, Muench M, Alle T, Zhang B, Lucero B, Perez-Tremble R, McGrosso D, Newman M, Gonzalez DJ, Lee VM, Ballatore C, Brunden KR. A small-molecule microtubule-stabilizing agent safely reduces Aβ plaque and tau pathology in transgenic mouse models of Alzheimer's disease. Alzheimers Dement. 2024 Jul;20(7):4540-4558. doi: 10.1002/alz.13875. Epub 2024 Jun 17. PMID: 38884283; PMCID: PMC11247666.

    Patel A, McGrosso D, Hefner Y, Campeau A, Sastry AV, Maurya S, Rychel K, Gonzalez DJ, Palsson BO. Proteome allocation is linked to transcriptional regulation through a modularized transcriptome. Nat Commun. 2024 Jun 19;15(1):5234. doi: 10.1038/s41467-024-49231-y. PMID: 38898010; PMCID: PMC11187210.

  • Elizabeth Porto (Matching slot)

    Current Position: Senior Associate at Lumanity 
    Linked-In: https://www.linkedin.com/in/elizabethmporto/                                                                      Program: Chemistry & Biochemistry
    Advisor: Alexis Komor

    Publications:

    Porto EM, Komor AC, Slaymaker IM, Yeo GW. Base editing: advances and therapeutic opportunities. Nat Rev Drug Discov. 2020 Dec;19(12):839-859. doi: 10.1038/s41573-020-0084-6. Epub 2020 Oct 19. PMID: 33077937; PMCID: PMC7721651.

    Porto EM, Komor AC. In the business of base editors: Evolution from bench to bedside. PLoS Biol. 2023 Apr 12;21(4):e3002071. doi: 10.1371/journal.pbio.3002071. PMID: 37043430; PMCID: PMC10096463.

  • Clara Posner

    Current Position: Postdoctoral fellow UMC Utrecht, Netherlands
    Linked-In: https://www.linkedin.com/in/clara-posner/                                                                          Program: Bioengineering
    Advisor: Jin Zhang

    Publications: 

    Mo GCH, Posner C, Rodriguez EA, Sun T, Zhang J. A rationally enhanced red fluorescent protein expands the utility of FRET biosensors. Nat Commun. 2020 Apr 15;11(1):1848. doi: 10.1038/s41467-020-15687-x. Erratum in: Nat Commun. 2024 Jan 26;15(1):771. doi: 10.1038/s41467-024-45330-y. PMID: 32296061; PMCID: PMC7160135.

    Lee YU, Li S, Bopp SE, Zhao J, Nie Z, Posner C, Yang S, Zhang X, Zhang J, Liu Z. Unprecedented Fluorophore Photostability Enabled by Low-Loss Organic Hyperbolic Materials. Adv Mater. 2021 Mar;33(9):e2006496. doi: 10.1002/adma.202006496. Epub 2021 Jan 27. PMID: 33506542; PMCID: PMC8783542.

    Lee YU, Posner C, Zhao J, Zhang J, Liu Z. Imaging of Cell Morphology Changes via Metamaterial-Assisted Photobleaching Microscopy. Nano Lett. 2021 Feb 24;21(4):1716-1721. doi: 10.1021/acs.nanolett.0c04529. Epub 2021 Feb 12. PMID: 33576637; PMCID: PMC8858031.

    Lee YU, Zhao J, Ma Q, Khorashad LK, Posner C, Li G, Wisna GBM, Burns Z, Zhang J, Liu Z. Metamaterial assisted illumination nanoscopy via random super-resolution speckles. Nat Commun. 2021 Mar 10;12(1):1559. doi: 10.1038/s41467-021-21835-8. PMID: 33692354; PMCID: PMC7946936.

    Lee YU, Posner C, Nie Z, Zhao J, Li S, Bopp SE, Wisna GBM, Ha J, Song C, Zhang J, Yang S, Zhang X, Liu Z. Organic Hyperbolic Material Assisted Illumination Nanoscopy. Adv Sci (Weinh). 2021 Nov;8(22):e2102230. doi: 10.1002/advs.202102230. Epub 2021 Aug 26. PMID: 34436815; PMCID: PMC8596137.

    Zhou J, Wu Q, Zhao J, Posner C, Lei M, Chen G, Zhang J, Liu Z. Fourier Optical Spin Splitting Microscopy. Phys Rev Lett. 2022 Jul 8;129(2):020801. doi: 10.1103/PhysRevLett.129.020801. PMID: 35867452; PMCID: PMC10035159.

    Greenwald E, Posner C, Bharath A, Lyons A, Salmerón C, Sriram K, Wiley SZ, Insel PA, Zhang J. GPCR Signaling Measurement and Drug Profiling with an Automated Live-Cell Microscopy System. ACS Sens. 2023 Jan 27;8(1):19-27. doi: 10.1021/acssensors.2c01341. Epub 2023 Jan 5. PMID: 36602887; PMCID: PMC9994309.

    Posner C, Mehta S, Zhang J. Fluorescent biosensor imaging meets deterministic mathematical modelling: quantitative investigation of signalling compartmentalization. J Physiol. 2023 Oct;601(19):4227-4241. doi: 10.1113/JP282696. Epub 2023 Sep 25. PMID: 37747358; PMCID: PMC10764149.

    Lee YU, Li S, Zhao J, Posner C, Zhang J, Liu Z. Metamaterial-Assisted Illumination Nanoscopy with Exceptional Axial Resolution. Adv Sci (Weinh). 2024 Oct;11(39):e2404883. doi: 10.1002/advs.202404883. Epub 2024 Aug 20. PMID: 39162105; PMCID: PMC11497044.

  • Douglas Zhang

    Current Position: Graduate student, UCSD                                                                                                      Linked-In: https://www.linkedin.com/in/douglas-zhang-a80a4293/                                                                  Publications:

    Monferrer A, Zhang D, Lushnikov AJ, Hermann T. Versatile kit of robust nanoshapes self-assembling from RNA and DNA modules. Nat Commun. 2019 Feb 5;10(1):608. doi: 10.1038/s41467-019-08521-6. PMID: 30723214; PMCID: PMC6363791.

    Chen S, Xing L, Zhang D, Monferrer A, Hermann T. Nano-sandwich composite by kinetic trapping assembly from protein and nucleic acid. Nucleic Acids Res. 2021 Sep 27;49(17):10098-10105. doi: 10.1093/nar/gkab797. PMID: 34500473; PMCID: PMC8464029.

    Zhang D, Hermann T. Metalated Nucleic Acid Nanostructures. Methods Mol Biol. 2023;2709:97-103. doi: 10.1007/978-1-0716-3417-2_5. PMID: 37572274.   

Trainees appointed in 2019

  • Aileen Button

    Current position:  Postdoctoral fellow, University of Colorado

    Linked-In:

    Program: Chemistry & Biochemistry
    Advisor: Colleen McHugh

    Publications:

    Button AC, Hall SD, Ashley EL, McHugh CA. Dissection of protein and RNA regions required for SPEN binding to XIST A-repeat RNA. RNA. 2024 Feb 16;30(3):240-255. doi: 10.1261/rna.079713.123. PMID: 38164599; PMCID: PMC10870365.

  • Quinn Cowan

    Current position:  Postdoctoral fellow in the Conklin lab, UC San Francisco                                                Linked-In: https://www.linkedin.com/in/quinn-cowan/                                                                                     Program: Chemistry & Biochemistry
    Advisor: Alexis Komor

    Publications:

    Vasquez CA, Cowan QT, Komor AC. Base Editing in Human Cells to Produce Single-Nucleotide-Variant Clonal Cell Lines. Curr Protoc Mol Biol. 2020 Dec;133(1):e129. doi: 10.1002/cpmb.129. PMID: 33151638; PMCID: PMC7654285.

    Gu S, Bodai Z, Cowan QT, Komor AC. Base Editors: Expanding the Types of DNA Damage Products Harnessed for Genome Editing. Gene Genome Ed. 2021 Jun;1:100005. doi: 10.1016/j.ggedit.2021.100005. Epub 2021 Apr 24. PMID: 34368792; PMCID: PMC8341163.

    Lawrence ES, Gu W, Bohlender RJ, Anza-Ramirez C, Cole AM, Yu JJ, Hu H, Heinrich EC, O'Brien KA, Vasquez CA, Cowan QT, Bruck PT, Mercader K, Alotaibi M, Long T, Hall JE, Moya EA, Bauk MA, Reeves JJ, Kong MC, Salem RM, Vizcardo-Galindo G, Macarlupu JL, Figueroa-Mujíca R, Bermudez D, Corante N, Gaio E, Fox KP, Salomaa V, Havulinna AS, Murray AJ, Malhotra A, Powel FL, Jain M, Komor AC, Cavalleri GL, Huff CD, Villafuerte FC, Simonson TS. Functional EPAS1/HIF2A missense variant is associated with hematocrit in Andean highlanders. Sci Adv. 2024 Feb 9;10(6):eadj5661. doi: 10.1126/sciadv.adj5661. Epub 2024 Feb 9. PMID: 38335297; PMCID: PMC10857371.

    Cowan QT, Gu S, Gu W, Ranzau BL, Simonson TS, Komor AC. Development of multiplexed orthogonal base editor (MOBE) systems. Nat Biotechnol. 2024 May 21:10.1038/s41587-024-02240-0. doi: 10.1038/s41587-024-02240-0. Epub ahead of print. PMID: 38773305; PMCID: PMC11579250.

    Cowan QT, Komor AC. Genome editing with DNA-dependent polymerases. Nat Biotechnol. 2024 Aug 23. doi: 10.1038/s41587-024-02372-3. Epub ahead of print. PMID: 39179922.

  • Alexander Hoffnagle

    Current position:  Scientist, Profluent, Inc.                                                                                                  Linked-In: https://www.linkedin.com/in/alex-hoffnagle/                                                                                    Program: Chemistry & Biochemistry
    Advisor: Akif Tezcan

    Publications:

    Zhu J, Avakyan N, Kakkis A, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev. 2021 Nov 24;121(22):13701-13796. doi: 10.1021/acs.chemrev.1c00308. Epub 2021 Aug 18. PMID: 34405992; PMCID: PMC9148388.

    Hoffnagle AM, Eng VH, Markel U, Tezcan FA. Computationally Guided Redesign of a Heme-free Cytochrome with Native-like Structure and Stability. Biochemistry. 2022 Oct 4;61(19):2063-2072. doi: 10.1021/acs.biochem.2c00369. Epub 2022 Sep 15. PMID: 36106943; PMCID: PMC9949987.

    Hoffnagle AM, Tezcan FA. Atomically Accurate Design of Metalloproteins with Predefined Coordination Geometries. J Am Chem Soc. 2023 Jul 5;145(26):14208-14214. doi: 10.1021/jacs.3c04047. Epub 2023 Jun 23. PMID: 37352018; PMCID: PMC10439731.

  • Calvin Lin

    Current position:  Postdoctoral fellow UC San Diego                                                                                        Linked-In: https://www.linkedin.com/in/calvin-lin-597ba2127/                                                                          Program: Chemistry & Biochemistry
    Advisor: Elizabeth Komives

    Publications:

    Brogan DJ, Chaverra-Rodriguez D, Lin CP, Smidler AL, Yang T, Alcantara LM, Antoshechkin I, Liu J, Raban RR, Belda-Ferre P, Knight R, Komives EA, Akbari OS. Development of a Rapid and Sensitive CasRx-Based Diagnostic Assay for SARS-CoV-2. ACS Sens. 2021 Nov 26;6(11):3957-3966. doi: 10.1021/acssensors.1c01088. Epub 2021 Oct 29. PMID: 34714054.

    Lin CP, Komives EA. Diversity of structure and function in Cullin E3 ligases. Curr Opin Struct Biol. 2024 Oct;88:102879. doi: 10.1016/j.sbi.2024.102879. Epub 2024 Jul 15. PMID: 39013361.

    Lin CP, Li H, Brogan DJ, Wang T, Akbari OS, Komives EA. CRISPR RNA binding drives structural ordering that primes Cas7-11 for target cleavage. bioRxiv [Preprint]. 2024 Sep 14:2024.08.01.606276. doi: 10.1101/2024.08.01.606276. PMID: 39211128; PMCID: PMC11360901.

  • Ryan Weeks

     Current position:  postdoctoral fellow UC San Diego                                                                                         Linked-In: https://www.linkedin.com/in/ryan-weeks-b68629303/                                                             Program: Chemistry & Biochemistry
    Advisor: Jin Zhang

    Publications:

    Weeks R, Zhou X, Yuan TL, Zhang J. Fluorescent Biosensor for Measuring Ras Activity in Living Cells. J Am Chem Soc. 2022 Sep 28;144(38):17432-17440. doi: 10.1021/jacs.2c05203. Epub 2022 Sep 19. PMID: 36122391; PMCID: PMC10031818.

    Weeks R, Mehta S, Zhang J. Genetically encodable biosensors for Ras activity. RSC Chem Biol. 2024 Feb 7;5(4):312-320. doi: 10.1039/d3cb00185g. PMID: 38576721; PMCID: PMC10989514.

  • Christine Stephen

    Current position:  Graduate student UC San Diego                                                                                         Linked-In: https://www.linkedin.com/in/christine-stephen-00781b175/                                                               Program: Chemistry & Biochemistry
    Advisor: Tatiana Mishanina

    Publications:

    Stephen C, Mishanina TV. Alkaline pH has an unexpected effect on transcriptional pausing during synthesis of the Escherichia coli pH-responsive riboswitch. J Biol Chem. 2022 Sep;298(9):102302. doi: 10.1016/j.jbc.2022.102302. Epub 2022 Aug 4. PMID: 35934054; PMCID: PMC9472077.

    Stephen C, Palmer D, Mishanina TV. Opportunities for Riboswitch Inhibition by Targeting Co-Transcriptional RNA Folding Events. Int J Mol Sci. 2024 Sep 29;25(19):10495. doi: 10.3390/ijms251910495. PMID: 39408823; PMCID: PMC11476745.

Trainees appointed in 2020

  • Lannah Abasi

    Current position:  graduate student UC San Diego                                                                                        Linked-In: https://www.linkedin.com/in/lannahabasi/

    Program: Chemistry & Biochemistry
    Advisor: Galia Debelouchina

    Publications:

    Abasi LS, Elathram N, Movva M, Deep A, Corbett KD, Debelouchina GT. Phosphorylation regulates tau's phase separation behavior and interactions with chromatin. Commun Biol. 2024 Mar 1;7(1):251. doi: 10.1038/s42003-024-05920-4. PMID: 38429335; PMCID: PMC10907630.

  • Andrea Dickey

    Current position:  MD/PhD Resident at UC San Francisco                                                                              Linked-In: https://www.linkedin.com/in/andrea-dickey-bb19417b/                                                                    Program: Biological Sciences
    Advisor: Sam Reck-Peterson

    Publications:

    Kendrick AA*, Dickey AM*, Redwine WB, Tran PT, Vaites LP, Dzieciatkowska M, Harper JW, Reck-Peterson SL. Hook3 is a scaffold for the opposite-polarity microtubule-based motors cytoplasmic dynein-1 and KIF1C. J Cell Biol. 2019 Sep 2;218(9):2982-3001. doi: 10.1083/jcb.201812170. Epub 2019 Jul 18. PMID: 31320392; PMCID: PMC6719453.

    Snead DM, Matyszewski M, Dickey AM, Lin YX, Leschziner AE, Reck-Peterson SL. Structural basis for Parkinson's disease-linked LRRK2's binding to microtubules. Nat Struct Mol Biol. 2022 Dec;29(12):1196-1207. doi: 10.1038/s41594-022-00863-y. Epub 2022 Dec 12. PMID: 36510024; PMCID: PMC9758056.

    Reimer JM, Dickey AM, Lin YX, Abrisch RG, Mathea S, Chatterjee D, Fay EJ, Knapp S, Daugherty MD, Reck-Peterson SL, Leschziner AE. Structure of LRRK1 and mechanisms of autoinhibition and activation. Nat Struct Mol Biol. 2023 Nov;30(11):1735-1745. doi: 10.1038/s41594-023-01109-1. Epub 2023 Oct 19. PMID: 37857821; PMCID: PMC10643122.

  • Ximena Garcia Arceo

    Current position:  Biophysicist at UC San Francisco                                                                              Linked-In: https://www.linkedin.com/in/ximena-garcia-arceo-a31996262/                                                      Program: Chemistry and Biochemistry
    Advisor: Brian Zid

    Publications:

    Tsuboi T, Viana MP, Xu F, Yu J, Chanchani R, Arceo XG, Tutucci E, Choi J, Chen YS, Singer RH, Rafelski SM, Zid BM. Mitochondrial volume fraction and translation duration impact mitochondrial mRNA localization and protein synthesis. Elife. 2020 Aug 7;9:e57814. doi: 10.7554/eLife.57814. PMID: 32762840; PMCID: PMC7413667.

    Arceo XG, Koslover EF, Zid BM, Brown AI. Mitochondrial mRNA localization is governed by translation kinetics and spatial transport. PLoS Comput Biol. 2022 Aug 19;18(8):e1010413. doi: 10.1371/journal.pcbi.1010413. PMID: 35984860; PMCID: PMC9432724.

  • Emily Pool

    Current position:  Graduate student at UC San Diego                                                                              Linked-In: https://www.linkedin.com/in/emily-pool-019b8511a/                                                            Program: Chemistry and Biochemistry  
    Advisor: Jin Zhang and Susan Taylor

    Publications:

    Hardy JC, Pool EH, Bruystens JGH, Zhou X, Li Q, Zhou DR, Palay M, Tan G, Chen L, Choi JLC, Lee HN, Strack S, Wang D, Taylor SS, Mehta S, Zhang J. Molecular determinants and signaling effects of PKA RIα phase separation. Mol Cell. 2024 Apr 18;84(8):1570-1584.e7. doi: 10.1016/j.molcel.2024.03.002. Epub 2024 Mar 26. PMID: 38537638; PMCID: PMC11031308.

  • Brandon Rawson

    Current position:  graduate student at UC San Diego                                                                              Linked-In: https://www.linkedin.com/in/brandon-rawson-6538411b6/                                                           Program: Physics  
    Advisor: Doug Smith

    Publications:

    Rawson B, Ordyan M, Yang Q, Sippy J, Feiss M, Catalano CE, Smith DE (2023) Regulation of phage lambda packaging motor-DNA interactions: Nucleotide independent and dependent gripping and friction eLife12:RP91647 https://doi.org/10.7554/eLife.91647.1

  • Full Name