Publications

Vidal Ceballos A., Díaz A. J. A., Preston J. M., Vairamon C., Shen C., Koder R. L., Elbaum-Garfinkle S. Liquid to solid transition of elastin condensates. PNAS 2022 119 (37) e2202240119

A Ebrahim*, BT Riley*, D Kumaran, B Andi, MR Fuchs, S McSweeney, DA Keedy (* contributed equally). “The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (Mpro).” Accepted to IUCrJ (2022). Also available as a bioRxiv preprint (2021)

Marcink, T.C., Kicmal, T., Armbruster, E., Zhang, Z., Zipursky, G., Golub, K.L., Idris, M., Khao, J., Drew-Bear, J., McGill, G. Gallagher, T., Porotto, M., des Georges A., Moscona, A., 2022. Intermediates in SARS-CoV-2 spike–mediated cell entry. Science Advances, 8(33), p.eabo3153.

E.L. Cheng, I.I. Cardle, N. Kacherovsky, H. Bansia, T. Wang, Y. Zhou, J. Raman, A. Yen, D. Gutierrez, S.J. Salipante, A. des Georges, M.C. Jensen, S.H. Pun, Discovery of a Transferrin Receptor 1-Binding Aptamer and Its Application in Cancer Cell Depletion for Adoptive T-Cell Therapy Manufacturing, Journal of the American Chemical Society, 2022, 144(30), 13851-13864.

G. A. Soliman, R. R. Abzalimov, Y. He. MTORC1 and MTORC2 Complexes Regulate the Untargeted Metabolomics and Amino Acid Metabolites Profile through Mitochondrial Bioenergetic Functions in Pancreatic Beta Cells. Nutrients, 2022, 14 (15), 3022. DOI: https://doi.org/10.3390/nu14153022.

Y. X. Chen, K. Veerasammy, J. Yin, T. Choetso, T. Zhong, M. A. Choudhury, C. Weng, E. Xu, M. A. Hein, R. Abzalimov, Y. He. Sample Preparation for Rapid Lipid Analysis in Drosophila Brain Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging. JoVE (Journal of Visualized Experiments), 2022, No. 185, e63930. DOI: https://doi.org/10.3791/63930.

H. Wang, Z.-L. Liu, J. Lao, S. Zhang, R. Abzalimov, T. Wang, and X. Chen, High Energy and Power Density Peptidoglycan Muscles through Super-Viscous Nanoconfined Water, Advanced Science, 2022, https://doi.org/10.1002/advs.202104697.

Assembly mechanism of early Hsp90-Cdc37-kinase complexes. Keramisanou D, Vasantha Kumar MV, Boose N, Abzalimov RR, Gelis I. Sci Adv. 2022 Mar 18;8(11):eabm9294. doi: 10.1126/sciadv.abm9294. Epub 2022 Mar 16. PMID: 35294247 Free PMC article.

J. Yin, E. Spillman, E.S. Cheng, J. Short, Y. Chen, J. Lei, M. Gibbs, J.S. Rosenthal, C. Sheng, Y.X. Chen, K. Veerasammy, T. Choetso, R.R. Abzalimov, B. Wang, C. Han, Y. He, Q. Yuan. Brain-specific lipoprotein receptors interact with astrocyte derived apolipoprotein and mediate neuron-glia lipid shuttling. Nature Commun. 2021, PMID: 33893307

J. Yin, E. Spillman, E. S. Cheng, J. Short, Y. Chen, J. Lei, M. Gibbs, J. S. Rosenthal, C. Sheng, Y. X. Chen, K. Veerasammy, T. Choetso, R. Abzalimov, B. Wang, C. Han, Y. He, Q. Yuan. Brain-Specific Lipoprotein Receptors Interact with Astrocyte Derived Apolipoprotein and Mediate Neuron-Glia Lipid Shuttling. Nature Communications, 2021, 12 (1), 2408. DOI: https://doi.org/10.1038/s41467-021-22751-7.

J. Hart and K. Gardner. Lighting the way: Recent insights into the structure and regulation of phototropin blue light receptors. J. Biol. Chem., 2021.  DOI:10.1016/j.jbc.2021.100594

X. Xu et al. Fragile protein folds: Sequence and environmental factors affecting the equilibrium of two interconverting, stably folded protein conformations. Magn. Reson., 2021. DOI:10.5194/mr-2-63-2021

J. LaBelle et al. TAEL 2.0: An improved optogenetic expression system for zebrafish. Zebrafish, 2021. DOI:10.1089/zeb.2020.1951

X. Xu et al. Volume and compressibility differences between two stably folded protein conformations revealed by high pressure NMR. Biophys J, 2021. DOI:10.1016/j.bpj.2020.12.034

Kazemi M, Sorzano COS, Carazo JM, des Georges A, Abrishami V, Vargas J. ENRICH: A fast method to improve the quality of flexible macromolecular reconstructions. Prog Biophys Mol Biol. 2021 Jan 12;. doi:10.1016/j.pbiomolbio.2021.01.001

M.A. Beckwith, T. Erazo-Colon, B.A. Johnson. RING NMR dynamics: software for analysis of multiple NMR relaxation experiments. J Biomol NMR, 2020. DOI: 10.1007/s10858-020-00350-w

W. Aguilar, O. Zacarias, M. Romaine, G. Proni, A.G. Petrovic, R.R. Abzalimov, M.M. Paz, E. Champeil. Synthesis of Oligonucleotides containing the cis‐Interstrand Crosslink Produced by Mitomycins in their Reaction with DNA.Chem. Eur. J., 2020, 1-20.

R.S Fisher, S. Elbaum-Garfinkle. Tunable multiphase dynamics of arginine and lysine liquid condensates. Nat Commun, 2020, 11, 4628.

A. Dashti, G. Mashayekhi, M. Shekhar, D. Ben Hail, S. Salah, P. Schwander, A. des Georges, A. Singharoy, J. Frank, A. Ourmazd. Retrieving functional pathways of biomolecules from single-particle snapshots. Nature Communications, 2020, 11, no. 1 : 1-14.

T. C. Marcink, T. Wang, A. des Georges, M. Porotto, A. Moscona. Human parainfluenza virus fusion complex glycoproteins imaged in action on authentic viral surfaces. PLoS pathogens, 2020, 16, no. 9: e1008883.

T.C. Marcink, E. Yariv, K. Rybkina, V. Más, F. T. Bovier, A. des Georges, A. L. Greninger et al. Hijacking the Fusion Complex of Human Parainfluenza Virus as an Antiviral Strategy. Mbio, 2020, 11, no. 1.

X. Xu, R. Godoy-Ruiz, K. A. Adipietro, C. Peralta, D. Ben-Hail, K. M. Varney, M. E. Cook et al. Structure of the cell-binding component of the Clostridium difficile binary toxin reveals a di-heptamer macromolecular assembly. Proceedings of the National Academy of Sciences, 2020, 117, no. 2: 1049-1058.

A.H. Nguyen, A. R. B. Thomsen, T. J. Cahill, R. Huang, L. Huang, T. Marcink, O. B. Clarke, A. des Georges et al. Structure of an endosomal signaling GPCR–G protein–β-arrestin megacomplex. Nature structural & molecular biology, 2019, 26, no. 12: 1123-1131.

J. Marchant, M.F. Summers and B.A. Johnson. Assigning NMR spectra of RNA, peptides and small organic molecules using molecular network visualization software. J Biomol NMR, 2019, 73, 525–529. DOI:10.1007/s10858-019-00271-3

S. Elbaum-Garfinkle. Matter over mind: Liquid phase separation and neurodegeneration. J. Biol. Chem, 2019, In Press

I. Dikiy, U. R. Edupuganti, R. R. Abzalimov, P. P. Borbat, M. Srivastava, J. H. Freed, K. H. Gardner. Insights into histidine kinase activation mechanisms from the monomeric blue light sensor. Proc. Natl. Acad. Sci., 2019, EL346. DOI: 10.1073/pnas.1813586116.

D.A. Keedy. Journey to the center of the protein: allostery from multitemperature multiconformer X-­ray crystallography. Acta Cryst D, 2019, 75:123-137. PMID: 30821702.

L.C. Montemiglio, C. Testi, P. Ceci, E. Falvo, M. Pitea, C. Savino, A. Arcovito, G. Peruzzi, P. Baiocco, F. Mancia, A. Boffi, A. des Georges, B. Vallone. Cryo-EM structure of the human ferritin-transferrin receptor 1 complex. Nat Commun. 2019, 10(1), 1121. DOI: 10.1038/s41467-019-09098-w.

A. Dashti, D.B. Hail, G. Mashayekhi, P. Schwander, A. des Georges, J. Frank, A. Ourmazd (co-corresponding author). Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots. 2019, bioRxiv: 291922 (pre-print)

I. Dikiy, L. Clark, K. H. Gardner, D. M. Rosenbaum. Isotopic labeling of integral membrane proteins for study by solution NMR relaxation methods. Methods Enzymol., 2019, 614, 37-65.

J. Chase, A. Catalano, A. J. Noble, E. T. Eng, P. DB Olinares, K. Molloy, D. Pakotiprapha, A. des Georges, et al. Mechanisms of opening and closing of the bacterial replicative helicase. Elife, 2018, 7: e41140.

B. Johnson. From Raw Data to Protein Backbone: Chemical Shifts Using NMRFx Processing and NMRViewJ Analysis. Methods in Molecular Biology, 2018. DOI: 10.1007/978-1-4939-7386-6_13

B. B. Minsky, R. R. Abzalimov, C. Niu, Y. Zhao, Z. Kirsch, P. L. Dubin, S. N. Savinov, I. A. Kaltashov. Mass spectrometry reveals a multi-faceted role of glycosaminoglycan chains in factor Xa inactivation by antithrombin. Biochemistry, 2018. DOI: 10.1021/acs.biochem.8b00199.

L. Calisti, M.C. Trabuco, A. Boffi, C. Testi, L.C. Montemiglio, A. des Georges, et al. Engineered ferritin for lanthanide binding. PLoS ONE, 2018, 13, 8, e0201859. DOI: 10.1371/journal.pone.0201859

D.A. Keedy, Z.B. Hill, J.T. Biel, E. Kang, T.J. Rettenmaier, J. Brandao-Neto, N.M. Pearce, F. von Delft, J.A. Wells, J.S. Fraser. An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering. eLife, 2018. DOI: 10.7554/eLife.36307.

A. J. Noble, V. P. Dandey, H. Wei, J. Brasch, J. Chase, P. Acharya, G. Scarpin M. Rapp, E. T. Eg, W. J. Rice, A. Cheng, C. Negro, L. Shapiro, P.D. Kwong, D. Jeruzalmi, A. des Georges, C. Potter, B. Carragher. Routine single particle CryoEM sample and grid characterization by tomography. eLife, 2018, 7, e34257. DOI: 10.7554/eLife.34257

A. Losi, K. H. Gardner, A. Möglich. Blue-light receptors for optogenetics. Chem. Rev., 2018. DOI: 10.1021/acs.chemrev.8b00163

G. Santulli, D. Lewis, A. des Georges, A. R. Marks, J. Frank. Ryanodine receptor structure and function in health and disease. Membrane Protein Complexes: Structure and Function, 2018, 329-352. DOI: 10.1007/978-981-10-7757-9_11

S.T. Glantz, E.E. Berlew, Z. Jaber, B.S. Schuster, K. H. Gardner, B.Y. Chow. Directly light-regulated binding of RGS-LOV photoreceptors to anionic membrane phospholipids. Proc. Natl. Acad. Sci., 2018, 115, E7720-E7727.

L. Clark, I. Dikiy, D. M. Rosenbaum, K. H. Gardner. On the use of Pichia pastoris for isotopic labeling of human GPCRs for NMR studies. J. Biomol. NMR, 2018, 71, 203-211.

A. Ceballos, C.J. McDonald, S. Elbaum-Garfinkle. Methods and Strategies to Quantify Liquid Phase Separation of Disordered Proteins. Methods in Enzymology, 2018, 611:31-50.

Y. Hashem, A. des Georges, J. Fu, S.N. Buss, F. Jossinet, A. Jobe, Q. Zhang, H.Y. Liao, R.A. Grassucci, C. Bajaj, E. Westhof, S. Madison-Antenucci, J. Frank. High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Series in Structural Biology Single-Particle Cryo-Electron Microscopy, pp. 456-462. DOI: 10.1142/9789813234864_0047

A. des Georges, O.B. Clarke, R. Zalk, Q. Yuan, K.J. Condon, R.A. Grassucci, W.A. Hendrickson, A.R. Marks, J. Frank. Structural Basis for Gating and Activation of RyR1. Series in Structural Biology Single-Particle Cryo-Electron Microscopy, pp. 497-515. DOI: 10.1142/9789813234864_0051

A. Reade, L.B. Motta-Mena, K.H. Gardner, D.Y. Stanier, O.D. Weiner, S. Woo. TAEL: A zebrafish-optimized optogenetic gene expression system with fine spatial and temporal control. Development, 2017.  DOI:  10.1242/dev.139238

L. Clark, I. Dikiy, K. Chapman, K.E. Rödström, J. Aramini, M. LeVine, G. Khelashvili, S.G.F. Rasmussen, K.H. Gardner, D.M. Rosenbaum. Ligand modulation of sidechain dynamics in a wild-type human GPCR. eLife, 2017. DOI: 10.7554/eLife.28505

V. de Turris, M.C. Trabuco, G. Peruzzi, A. Boffi, C. Testi, B. Vallone, L.C. Montemiglio, A. Des Georges, L. Calisti, I. Benni, A. Bonamore, P. Baiocco. Humanized archaeal ferritin as a tool for cell targeted delivery. Nanoscale, Volume 9, Issue 2, Pages 647-655. DOI: 10.1039/C6NR07129E

Y. Zhao, R.R. Abzalimov, I.A. Kaltashov. Interactions of Intact Unfractionated Heparin with Its Client Proteins Can Be Probed Directly Using Native Electrospray Ionization Mass Spectrometry. Analytical ChemI, 2016, 88, 1711-1718.

O. Fatunmbi, R.R. Abzalimov, S.N. Savinov, A. Gershenson, I.A. Kaltashov. Interactions of Haptoglobin with Monomeric Globin Species: Insights from Molecular Modeling and Native Electrospray Ionization Mass Spectrometry. Biochemistry, 2016, 55, 1918-1928.

S.T. Glantz, E.J. Carpenter, M. Melkonian, K.H. Gardner, E.S. Boyden, G.K-S. Wong and B.Y. Chow. Functional and topological diversity of LOV domain photoreceptors. Proc. Natl. Acad. Sci. USA, 2016, 113, E1442-E1451.

F. Corrêa and K.H. Gardner. Basis of mutual domain inhibition in a bacterial signaling switch. Cell Chemical Biology, 2016.

M. Norris, B. Fetler, J. Marchant, B.A. Johnson. NMRFx Processor: a cross-platform NMR data processing program. J Biomol NMR, 2016. DOI:10.1007/s10858-016-0049-6

F. Corrêa, J. Key. B. Kuhlman, K.H. Gardner. Computational repacking of the HIF-2α cavity replaces water-based stabilized core. Structure, 2016. DOI: 10.1016/j.str.2016.08.014

A. des Georges, O.B. Clarke, R. Zalk, Q. Yuan, K.J. Condon, R.A. Grassucci, W.A. Hendrickson, A.R. Marks, J. Frank. Structural Basis for Gating and Activation of RyR1. Cell. 2016 Sep 22;167(1):145-157.e17. doi: 10.1016/j.cell.2016.08.075.

S. Belh, A. Manandhar, G. Huffman, K. Ng, A. Chowdhury, M. Patel, N. Yehya, A. des Georges, S. Loverde, D. Eisele. Counterion interactions in supramolecular self-assembly. Abstracts of Papers of the American Chemical Society, Volume 252.

R. Zalk, O.B. Clarke, A. des Georges, R.A. Grassucci, S. Reiken, F. Mancia, W.A. Hendrickson, J. Frank, A.R. Marks. Structure of a mammalian ryanodine receptor, Nature 517, n. 7532, 2015: 44-49.

V. Ocasio, F. Corrêa and K.H. Gardner. Ligand-induced folding of a two-component signaling receiver domain. Biochemistry, 2015, 54, 1353-1363.

Y.  Guo, T.H. Scheuermann, C.L. Partch, D.R. Tomchick and K.H. Gardner. Coiled-coil coactivators play a structural role mediating interactions in hypoxia inducible factor heterodimerization. J. Biol. Chem., 2015, 290, 7707-7721.

T.H. Scheuermann, D. Stroud, C. Sleet, L. Bayeh, C. Shokri, H. Wang, C.G. Caldwell, J. Longgood, J.B. MacMillan, R.K. Bruick, K.H. Gardner and U.K. Tambar. Isoform-selective and stereoselective inhibition of hypoxia inducible factor-2. J. Med. Chem., 2015, 58, 5930-5941.

S.C. Keane, X. Heng, K. Lu, S. Kharytonchyk, V. Ramakrishnan, G. Carter, S. Barton, A. Hosic, A. Florwick, J. Santos, N.C. Bolden, S. McCowin, D.A. Case, B.A. Johnson, M. Salemi, A.Telesnitsky, M.F. Summers. Structure of the HIV-1 RNA packaging signal, Science, 2015, 348:917-921.

des Georges A, Dhote V, Kuhn L, Hellen CU, Pestova TV, Frank J, Hashem Y. Structure of mammalian eIF3 in the context of the 43S preinitiation complex. Nature. 2015 Sep 24;525(7570):491-5. doi: 10.1038/nature14891. Epub 2015 Sep 7. PubMed PMID: 26344199; PubMed Central PMCID: PMC4719162.

L.B. Motta-Mena, A. Reade, M.J. Mallory, S. Glantz, O.D. Weiner, K.W. Lynch, K.H. Gardner. An optogenetic gene expression system with rapid activation and deactivation kinetics, Nature Chemical Biology, 2014, 10, 196-202.

G. Rivera-Cancel, W.H. Ko, D.R. Tomchick, F. Correa, K.H. Gardner. Full-length structure of a monomeric histidine kinase reveals basis for sensory regulation, Proc. Natl. Acad. Sci., 2014, 111, 17839-17844.