Jose Rodriguez
Websites:
Publications:
Konieczny KA, Rai R, Rodriguez JA, García-Garibay MA. Single-Crystal-to-Single-Crystal Radical-Ion Chain Reactions under the Electron Microscope: A Chemical Design to Repurpose Electron Beam Damage. J Am Chem Soc. 2025 Dec 03; 147(48):44285-44292. view on PubMed
Eremin DB, Jha KK, Delgadillo DA, Zhang H, Foxman SH, Johnson SN, Vlahakis NW, Cascio D, Lavallo V, Rodríguez JA, Nelson HM. Spatially Aware Diffraction Mapping Enables Fully Autonomous MicroED. J Am Chem Soc. 2025 Nov 19; 147(46):42299-42310. view on PubMed
Pang EZ, Zhao B, Flowers C, Oroudjeva E, Winter JB, Pandey V, Sawaya MR, Wohlschlegel J, Loo JA, Rodriguez JA, Clarke SG. Structural basis for L-isoaspartyl-containing protein recognition by the human PCMTD1 cullin-RING E3 ubiquitin ligase. J Biol Chem. 2025 11; 301(11):110735. view on PubMed
Vlahakis NW, Flowers CW, Liu M, Agdanowski MP, Johnson S, Summers JA, Jacobs LMC, Keyser C, Russell P, Rose SL, Orlans J, Adhami N, Chen Y, Sawaya MR, Basu S, de Sanctis D, Chen Y, Wakatsuki S, Nelson HM, Loo JA, Tang Y, Rodriguez JA. Combining MicroED and native mass spectrometry for structural discovery of enzyme-small molecule complexes. Proc Natl Acad Sci U S A. 2025 Aug 05; 122(31):e2503780122. view on PubMed
Taylor LJ, Sawaya MR, Westover JB, Wang C, Jimenez F, Muñoz AJ, Whitelegge J, Gowen BB, Helguera GF, Castells-Graells R, Rodriguez JA. In situ insights into antibody-mediated neutralization of a pre-fusion Junin virus glycoprotein complex. Cell Rep. 2025 Jul 22; 44(7):115971. view on PubMed
Flores MD, Sawaya MR, Boyer DR, Zink S, Tovmasyan S, Saucedo A, Richards LS, Zee CT, Cardenas J, Fioriti L, Rodriguez JA. Structural insights into functional regulation of the human CPEB3 prion by an amyloid-forming segment. Structure. 2025 Aug 07; 33(8):1314-1324.e5. view on PubMed
Salas-Ambrosio P, Vexler S, P Sivasankaran R, Vlahakis N, Lai RS, Johnson C, Baas-Maynard SI, Min DS, Lower H, Doyle AG, Tang Y, Rodriguez JA, Chen IA, Read de Alaniz J, Maynard HD. Biosourced Functional Hydroxybenzoate-co-Lactide Polymers with Antimicrobial Activity. J Am Chem Soc. 2025 Jun 04; 147(22):19230-19238. view on PubMed
Liu M, Zang X, Vlahakis NW, Rodriguez JA, Ohashi M, Tang Y. Enzymatic combinatorial synthesis of E-64 and related cysteine protease inhibitors. Nat Chem Biol. 2025 Nov; 21(11):1783-1793. view on PubMed
Saha A, Mecklenburg M, Pattison AJ, Brewster AS, Rodriguez JA, Ercius P. Imaging the Progression of Radiolytic Damage in Molecular Crystals with Scanning Nanobeam Electron Diffraction. Phys Rev Lett. 2025 Apr 11; 134(14):146101. view on PubMed
Vlahakis N, Clauss A, Rodriguez JA. Accounting for electron-beam-induced warping of molecular nanocrystals in MicroED structure determination. IUCrJ. 2025 Mar 01; 12(Pt 2):223-238. view on PubMed
Vlahakis NW, Flowers CW, Liu M, Agdanowski M, Johnson S, Summers JA, Keyser C, Russell P, Rose S, Orlans J, Adhami N, Chen Y, Sawaya MR, Basu S, de Sanctis D, Wakatsuki S, Nelson HM, Loo JA, Tang Y, Rodriguez JA. Combining MicroED and native mass spectrometry for structural discovery of enzyme-biosynthetic inhibitor complexes. bioRxiv. 2025 Feb 26. view on PubMed
Vlahakis N, Qu S, Richards LS, Moraes LS, Cascio D, Nelson HM, Rodriguez JA. Fast event-based electron counting for small-molecule structure determination by MicroED. Acta Crystallogr C Struct Chem. 2025 Mar 01; 81(Pt 3):116-130. view on PubMed
Chiang CY, Ohashi M, Le J, Chen PP, Zhou Q, Qu S, Bat-Erdene U, Hematian S, Rodriguez JA, Houk KN, Guo Y, Loo JA, Tang Y. Copper-dependent halogenase catalyses unactivated C-H bond functionalization. Nature. 2025 Feb; 638(8049):126-132. view on PubMed
Konieczny KA, Paul I, Rodriguez JA, Garcia-Garibay MA. From Beam Damage to Massive Reaction Amplification under the Electron Microscope: An Ionization-Induced Chain Reaction in Crystals of a Dewar Benzene. ACS Cent Sci. 2024 Dec 25; 10(12):2346-2352. view on PubMed
de Moraes LS, Burch JE, Delgadillo DA, Rodriguez IH, Mai H, Smith AG, Caille S, Walker SD, Wurz RP, Cee VJ, Rodriguez JA, Gostovic D, Quasdorf K, Nelson HM. Structural Elucidation and Absolute Stereochemistry for Pharma Compounds Using MicroED. Org Lett. 2024 Aug 23; 26(33):6944-6949. view on PubMed
Vlahakis N, Holton J, Sauter NK, Ercius P, Brewster AS, Rodriguez JA. 3D Nanocrystallography and the Imperfect Molecular Lattice. Annu Rev Phys Chem. 2024 Jun; 75(1):483-508. view on PubMed
Yang KC, Rivera Mirabal DM, Garcia RV, Vlahakis NW, Nguyen PH, Mengel SD, Mecklenburg M, Rodriguez JA, Shell MS, Hawker CJ, Segalman RA. Crystallization-Induced Flower-like Superstructures via Peptoid Helix Assembly. ACS Macro Lett. 2024 Apr 16; 13(4):423-428. view on PubMed
Glynn C, Rodriguez JA, Hyman BT. The structural line between prion and "prion-like": Insights from prion protein and tau. Curr Opin Neurobiol. 2024 Jun; 86:102857. view on PubMed
Miller JE, Agdanowski MP, Dolinsky JL, Sawaya MR, Cascio D, Rodriguez JA, Yeates TO. AlphaFold-assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography. Acta Crystallogr D Struct Biol. 2024 Apr 01; 80(Pt 4):270-278. view on PubMed
Daugird TA, Shi Y, Holland KL, Rostamian H, Liu Z, Lavis LD, Rodriguez J, Strahl BD, Legant WR. Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment. bioRxiv. 2023 Nov 13. view on PubMed
Richards LS, Flores MD, Zink S, Schibrowsky NA, Sawaya MR, Rodriguez JA. Cryo-EM structure of a human LECT2 amyloid fibril reveals a network of polar ladders at its core. Structure. 2023 11 02; 31(11):1386-1393.e3. view on PubMed
Richards LS, Flores MD, Millán C, Glynn C, Zee CT, Sawaya MR, Gallagher-Jones M, Borges RJ, Usón I, Rodriguez JA. Fragment-Based Ab Initio Phasing of Peptidic Nanocrystals by MicroED. ACS Bio Med Chem Au. 2023 Apr 19; 3(2):201-210. view on PubMed
Richards LS, Flores MD, Zink S, Schibrowsky NA, Sawaya MR, Rodriguez JA. Cryo-EM Structure of a Human LECT2 Amyloid Fibril Reveals a Network of Polar Ladders at its Core. bioRxiv. 2023 Feb 11. view on PubMed
Glynn C, Hernandez E, Gallagher-Jones M, Miao J, Sigurdson CJ, Rodriguez JA. Structural consequences of sequence variation in mammalian prion β2α2 loop segments. Front Neurosci. 2022; 16:960322. view on PubMed
Sawaya MR, Hughes MP, Rodriguez JA, Riek R, Eisenberg DS. The expanding amyloid family: Structure, stability, function, and pathogenesis. Cell. 2021 09 16; 184(19):4857-4873. view on PubMed
Ferrero S, Flores MD, Short C, Vazquez CA, Clark LE, Ziegenbein J, Zink S, Fuentes D, Payes C, Batto MV, Collazo M, García CC, Abraham J, Cordo SM, Rodriguez JA, Helguera G. Antibody-Based Inhibition of Pathogenic New World Hemorrhagic Fever Mammarenaviruses by Steric Occlusion of the Human Transferrin Receptor 1 Apical Domain. J Virol. 2021 08 10; 95(17):e0186820. view on PubMed
Zee CT, Saha A, Sawaya MR, Rodriguez JA. Ab Initio Determination of Peptide Structures by MicroED. Methods Mol Biol. 2021; 2215:329-348. view on PubMed
Gallagher-Jones M, Rodriguez JA. Structures from the Mesophase: MicroED Targets Crystals Extracted from LCP. Structure. 2020 10 06; 28(10):1084-1086. view on PubMed
Richards LS, Millán C, Miao J, Martynowycz MW, Sawaya MR, Gonen T, Borges RJ, Usón I, Rodriguez JA. Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER. Acta Crystallogr D Struct Biol. 2020 Aug 01; 76(Pt 8):703-712. view on PubMed
Thompson MC, Yeates TO, Rodriguez JA. Advances in methods for atomic resolution macromolecular structure determination. F1000Res. 2020; 9. view on PubMed
Glynn C, Sawaya MR, Ge P, Gallagher-Jones M, Short CW, Bowman R, Apostol M, Zhou ZH, Eisenberg DS, Rodriguez JA. Cryo-EM structure of a human prion fibril with a hydrophobic, protease-resistant core. Nat Struct Mol Biol. 2020 05; 27(5):417-423. view on PubMed
Gallagher-Jones M, Bustillo KC, Ophus C, Richards LS, Ciston J, Lee S, Minor AM, Rodriguez JA. Atomic structures determined from digitally defined nanocrystalline regions. IUCrJ. 2020 May 01; 7(Pt 3):490-499. view on PubMed
Griner SL, Seidler P, Bowler J, Murray KA, Yang TP, Sahay S, Sawaya MR, Cascio D, Rodriguez JA, Philipp S, Sosna J, Glabe CG, Gonen T, Eisenberg DS. Structure-based inhibitors of amyloid beta core suggest a common interface with tau. Elife. 2019 10 15; 8. view on PubMed
Glynn C, Rodriguez JA. Data-driven challenges and opportunities in crystallography. Emerg Top Life Sci. 2019 Aug 16; 3(4):423-432. view on PubMed
Zee CT, Glynn C, Gallagher-Jones M, Miao J, Santiago CG, Cascio D, Gonen T, Sawaya MR, Rodriguez JA. Homochiral and racemic MicroED structures of a peptide repeat from the ice-nucleation protein InaZ. IUCrJ. 2019 Mar 01; 6(Pt 2):197-205. view on PubMed
Gallagher-Jones M, Ophus C, Bustillo KC, Boyer DR, Panova O, Glynn C, Zee CT, Ciston J, Mancia KC, Minor AM, Rodriguez JA. Nanoscale mosaicity revealed in peptide microcrystals by scanning electron nanodiffraction. Commun Biol. 2019; 2:26. view on PubMed
Jones CG, Martynowycz MW, Hattne J, Fulton TJ, Stoltz BM, Rodriguez JA, Nelson HM, Gonen T. The CryoEM Method MicroED as a Powerful Tool for Small Molecule Structure Determination. ACS Cent Sci. 2018 Nov 28; 4(11):1587-1592. view on PubMed
Pryor A, Rana A, Xu R, Rodriguez JA, Yang Y, Gallagher-Jones M, Jiang H, Kanhaiya K, Nathanson M, Park J, Kim S, Kim S, Nam D, Yue Y, Fan J, Sun Z, Zhang B, Gardner DF, Dias CSB, Joti Y, Hatsui T, Kameshima T, Inubushi Y, Tono K, Lee JY, Yabashi M, Song C, Ishikawa T, Kapteyn HC, Murnane MM, Heinz H, Miao J. Single-shot 3D coherent diffractive imaging of core-shell nanoparticles with elemental specificity. Sci Rep. 2018 05 29; 8(1):8284. view on PubMed
Guenther EL, Cao Q, Trinh H, Lu J, Sawaya MR, Cascio D, Boyer DR, Rodriguez JA, Hughes MP, Eisenberg DS. Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregation. Nat Struct Mol Biol. 2018 06; 25(6):463-471. view on PubMed
Hattne J, Shi D, Glynn C, Zee CT, Gallagher-Jones M, Martynowycz MW, Rodriguez JA, Gonen T. Analysis of Global and Site-Specific Radiation Damage in Cryo-EM. Structure. 2018 05 01; 26(5):759-766.e4. view on PubMed
Hughes MP, Sawaya MR, Boyer DR, Goldschmidt L, Rodriguez JA, Cascio D, Chong L, Gonen T, Eisenberg DS. Atomic structures of low-complexity protein segments reveal kinked β sheets that assemble networks. Science. 2018 02 09; 359(6376):698-701. view on PubMed
Gallagher-Jones M, Glynn C, Boyer DR, Martynowycz MW, Hernandez E, Miao J, Zee CT, Novikova IV, Goldschmidt L, McFarlane HT, Helguera GF, Evans JE, Sawaya MR, Cascio D, Eisenberg DS, Gonen T, Rodriguez JA. Sub-ångström cryo-EM structure of a prion protofibril reveals a polar clasp. Nat Struct Mol Biol. 2018 02; 25(2):131-134. view on PubMed
Krotee P, Griner SL, Sawaya MR, Cascio D, Rodriguez JA, Shi D, Philipp S, Murray K, Saelices L, Lee J, Seidler P, Glabe CG, Jiang L, Gonen T, Eisenberg DS. Common fibrillar spines of amyloid-β and human islet amyloid polypeptide revealed by microelectron diffraction and structure-based inhibitors. J Biol Chem. 2018 02 23; 293(8):2888-2902. view on PubMed
Mogul R, Vaishampayan P, Bashir M, McKay CP, Schubert K, Bornaccorsi R, Gomez E, Tharayil S, Payton G, Capra J, Andaya J, Bacon L, Bargoma E, Black D, Boos K, Brant M, Chabot M, Chau D, Cisneros J, Chu G, Curnutt J, DiMizio J, Engelbrecht C, Gott C, Harnoto R, Hovanesian R, Johnson S, Lavergne B, Martinez G, Mans P, Morales E, Oei A, Peplow G, Piaget R, Ponce N, Renteria E, Rodriguez V, Rodriguez J, Santander M, Sarmiento K, Scheppelmann A, Schroter G, Sexton D, Stephenson J, Symer K, Russo-Tait T, Weigel B, Wilhelm MB. Microbial Community and Biochemical Dynamics of Biological Soil Crusts across a Gradient of Surface Coverage in the Central Mojave Desert. Front Microbiol. 2017; 8:1974. view on PubMed
Pryor A, Yang Y, Rana A, Gallagher-Jones M, Zhou J, Lo YH, Melinte G, Chiu W, Rodriguez JA, Miao J. GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging. Sci Rep. 2017 09 05; 7(1):10409. view on PubMed
Rodriguez JA, Jiang L, Eisenberg DS. Toward the Atomic Structure of PrPSc. Cold Spring Harb Perspect Biol. 2017 Sep 01; 9(9). view on PubMed
Rodriguez JA, Eisenberg DS, Gonen T. Taking the measure of MicroED. Curr Opin Struct Biol. 2017 10; 46:79-86. view on PubMed
Krotee P, Rodriguez JA, Sawaya MR, Cascio D, Reyes FE, Shi D, Hattne J, Nannenga BL, Oskarsson ME, Philipp S, Griner S, Jiang L, Glabe CG, Westermark GT, Gonen T, Eisenberg DS. Atomic structures of fibrillar segments of hIAPP suggest tightly mated β-sheets are important for cytotoxicity. Elife. 2017 01 03; 6. view on PubMed
Luria-Pérez R, Helguera G, Rodríguez JA. Antibody-mediated targeting of the transferrin receptor in cancer cells. Bol Med Hosp Infant Mex. 2016 Nov - Dec; 73(6):372-379. view on PubMed
Colletier JP, Sawaya MR, Gingery M, Rodriguez JA, Cascio D, Brewster AS, Michels-Clark T, Hice RH, Coquelle N, Boutet S, Williams GJ, Messerschmidt M, DePonte DP, Sierra RG, Laksmono H, Koglin JE, Hunter MS, Park HW, Uervirojnangkoorn M, Bideshi DK, Brunger AT, Federici BA, Sauter NK, Eisenberg DS. De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure. Nature. 2016 11 03; 539(7627):43-47. view on PubMed
Rodriguez JA, Ivanova MI, Sawaya MR, Cascio D, Reyes FE, Shi D, Sangwan S, Guenther EL, Johnson LM, Zhang M, Jiang L, Arbing MA, Nannenga BL, Hattne J, Whitelegge J, Brewster AS, Messerschmidt M, Boutet S, Sauter NK, Gonen T, Eisenberg DS. Structure of the toxic core of α-synuclein from invisible crystals. Nature. 2015 Sep 24; 525(7570):486-90. view on PubMed
Rodriguez JA, Xu R, Chen CC, Huang Z, Jiang H, Chen AL, Raines KS, Pryor A, Nam D, Wiegart L, Song C, Madsen A, Chushkin Y, Zontone F, Bradley PJ, Miao J. Three-dimensional coherent X-ray diffractive imaging of whole frozen-hydrated cells. IUCrJ. 2015 Sep 01; 2(Pt 5):575-83. view on PubMed
Rodriguez JA. Accessible atomic structures from sub-micron protein crystals. Acta Crystallogr A Found Adv. 2015 Jul; 71(Pt 4):351-2. view on PubMed
Xu R, Jiang H, Song C, Rodriguez JA, Huang Z, Chen CC, Nam D, Park J, Gallagher-Jones M, Kim S, Kim S, Suzuki A, Takayama Y, Oroguchi T, Takahashi Y, Fan J, Zou Y, Hatsui T, Inubushi Y, Kameshima T, Yonekura K, Tono K, Togashi T, Sato T, Yamamoto M, Nakasako M, Yabashi M, Ishikawa T, Miao J. Single-shot three-dimensional structure determination of nanocrystals with femtosecond X-ray free-electron laser pulses. Nat Commun. 2014 Jun 05; 5:4061. view on PubMed
Miao J, Rodriguez JA. Phasing tiny crystals. IUCrJ. 2014 Jan 01; 1(Pt 1):3-4. view on PubMed
Rodriguez JA, Xu R, Chen CC, Zou Y, Miao J. Oversampling smoothness: an effective algorithm for phase retrieval of noisy diffraction intensities. J Appl Crystallogr. 2013 Apr 01; 46(Pt 2):312-318. view on PubMed
Daniels TR, Delgado T, Rodriguez JA, Helguera G, Penichet ML. The transferrin receptor part I: Biology and targeting with cytotoxic antibodies for the treatment of cancer. Clin Immunol. 2006 Nov; 121(2):144-58. view on PubMed
Ng PP, Helguera G, Daniels TR, Lomas SZ, Rodriguez JA, Schiller G, Bonavida B, Morrison SL, Penichet ML. Molecular events contributing to cell death in malignant human hematopoietic cells elicited by an IgG3-avidin fusion protein targeting the transferrin receptor. Blood. 2006 Oct 15; 108(8):2745-54. view on PubMed
