Publications from the Barad Lab

Publications


Mapping Protein Dynamics at High-Resolution with Temperature-Jump X-ray Crystallography
Wolff AM, Nango E, Young ID, Brewster AS, Kubo M, Nomura T, Sugahara M, Owada S, Barad BA, Ito K, Bhowmick A, Carbajo S, Hino T, Holton JM, Im D, O’Riordan LJ, Tanaka T, Tanaka R, Sierra RG, Yumoto F, Tono K, Iwata S, Sauter NK, Fraser JS, Thompson MC
Nature Chemistry, 2023


Nanoscale details of mitochondrial constriction revealed by cryo-electron tomography
Mageswaran SK, Grotjahn DA†✉, Zeng X, Barad BA, Medina M, Hoang MH, Dobro MJ, Chang YW, Xu M, Yang WY, Jensen, GJ
Biophysical Journal, 2023
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Quantifying organellar ultrastructure in cryo-electron tomography using a surface morphometrics pipeline
Barad BA, Medina M, Fuentes D, Wiseman, RL, Grotjahn DA
Journal of Cell Biology, 2023


CellPAINT: Turnkey illustration of molecular cell biology
Gardner A, Ludovic A, Fuentes D, Maritan M, Barad BA, Medina, M, Olson AJ, Grotjahn DA, Goodsell DS
Frontiers in Bioinformatics, 2021
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Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge
Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, Fraser JS, Jr. Herzik MA, Hoh SW, Hou J, Hung L, Igaev M, Joseph AP, Kihara D, Kumar D, Mittal S, Monastyrskyy B, Olek M, Palmer CM, Patwardhan A, Perez A, Pfab J, Pintilie GD, Richardson JS, Rosenthal PB, Sarkar D, Schäfer LU, Schmid MF, Schröder GF, Shekhar M, Si D, Singharoy A, Terashi G, Terwilliger TC, Vaiana A, Wang L, Wang Z, Wankowicz SA, Williams CJ, Winn M, Wu T, Yu X, Zhang K, Berman HM, Chiu W
Nature Methods, 2021
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Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates
Barad BA, Liu L, Diaz RE, Basillo R, Van Dyken SJ, Locksley RM, Fraser JS
Protein Science, 2020


Temperature-Jump Solution X-ray Scattering Reveals Distinct Motions in a Dynamic Enzyme
Thompson MC, Barad BA, Wolff AM, Cho HS, Schotte F, Schwarz DMC, Anfinrud P, Fraser JS
Nature Chemistry, 2019


Synthetic essentiality of metabolic regulator PDHK1 in PTEN-deficient cells and cancers
Chatterjee N, Pazarentzos E, Mayekar MK, Gui P, Allegakoen DV, Hrustanovic G, Olivas V, Lin L, Verschueren E, Johnson JR, Hofree M, Yan JJ, Newton BW, Dollen JV, Earnshaw CH, Flanagan J, Chan E, Asthana S, Ideker T, Wu W, Suzuki J, Barad BA, Kirichok Y, Fraser J*, Weiss WA, Krogan NJ, Tulpule A, Sabnis AJ, Bivona TG
Cell Reports, 2019
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XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction
Thomaston JL, Woldeyes RA, Nakane T, Yamashita A, Tanaka T, Koiwai K, Brewster AS, Barad BA, Chen Y, Lemmin T, Uervirojnangkoorn M, Arima T, Kobayashi J, Masuda T, Suzuki M, Sugahara M, Sauter NK, Tanaka R, Nureki O, Tono K, Joti Y, Nango E, Iwata S, Yumoto F, Fraser JS, DeGrado WF
PNAS, 2017
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Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta
Wang RYR, Song Y, Barad BA, Cheng Y, Fraser JS, DiMaio F
eLife, 2016
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Determination of Ubiquitin fitness landscapes under different chemical stresses in a classroom setting
Mavor D, Barlow KA, Thompson S, Barad BA, Bonny AR, Cario CL, Gaskins G, Liu Z, Deming L, Axen SD, Caceres E, Chen W, Cuesta A, Gate R, Green EM, Hulce KR, Ji W, Kenner LR, Mensa B, Morinishi LS, Moss SM, Mravic M, Muir RK, Niekamp S, Nnadi CI, Palovcak E, Poss EM, Ross TD, Salcedo E, See S, Subramaniam M, Wong AW, Li J, Thorn KS, Conchúir SÓ, Roscoe BP, Chow ED, DeRisi JL, Kortemme T, Bolon DN, Fraser JS
eLife, 2016


EMRinger: Side-chain-directed model and map validation for 3D electron cryomicroscopy
Barad BA, Echols N, Wang RYR, Cheng Y, DiMaio F, Adams PD, Fraser JS
Nature Methods, 2015
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