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Faculty Publications in Academic Year 2021-2022

Faculty Publications in Academic Year 2021-2022

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  1.   Amankwaa B, Schoborg T, and Labrador M (2021) Drosophila insulator proteins form in-vivo liquid-liquid phase separating condensates. Life Science Alliance. Jul 19;5(12):e202201536. doi: 10.26508/lsa.202201536. PMID: 35853678 
  2.   Apte MS and Joshi AS. Membrane curvature, lipids, and cytoskeleton: Recipe for nascent lipid droplet formation. Bioessays. (2022) Jul 13; e2200038
  3.   Bensing, B, Stubbs H, Agarwal R, Yamakawa I, Luong K, Solakyildirim K, Yu H, Hadadianpour A, Castro A, Fialkowski, K, Morrison K, Wawrzak Z, Chen X, Lebrilla C, Baudry J, Smith JC, Sullam P, Iverson T. (2022) Origins of glycan selectivity in streptococcal Siglec-like adhesins suggest mechanisms of receptor adaptation. Nature Communications 13(1):2753, doi:10.1038/s41467-022-30509-y.
  4.   Bogati B, N Wadsworth, F Barrera, EM Fozo. (2022) Improved Growth of Escherichia coli in Aminoglycoside Antibiotics by the zor-orz Toxin-Antitoxin System. Journal of Bacteriology 204 (1), e00407-21
  5.   Brady NT, S Qian, J Nguyen, HM O’Neill, BD Bruce (2022) Small angle neutron scattering and lipidomic analysis of a native, trimeric PSI-SMALP from a thermophilic cyanobacteria. Biochimica et Biophysica Acta (BBA)-Bioenergetics 1863 (7), 148596
  6.   Campbell BF, Hercyk BS, Williams AR; Miguel ES; Young HG; Das ME (2022) Cdc42 GTPase activating proteins Rga4 and Rga6 coordinate septum synthesis and membrane trafficking at the division plane during cytokinesis. Traffic. DOI: 10.1111/tra.12864
  7.   Das P, Shen T, McCord RP (2022) Characterizing the variation in chromosome structure ensembles in the context of the nuclear microenvironment. PLoS Computational Biology 18: e1010392
  8.   Davis MM, R Lamichhane, BD Bruce (2021) Elucidating protein translocon dynamics with single-molecule precision. Trends in Cell Biology 31 (7), 569-583
  9.   DeGennaro, D., Urquidi Camacho, R. A., Zhang, L., Shpak, E.D. (2022) Initiation of aboveground organ primordia depends on combined action of auxin, ERECTA family genes, and PINOID. Plant Physiology, kiac288
  10.   Doppler D, MT Rabbani, R Letrun, J Cruz Villarreal, DH Kim, S Gandhi, …Bruce BD … Ros A. (2022) Co-flow injection for serial crystallography at X-ray free-electron lasers. Journal of Applied Crystallography 55 (1)
  11.   Fernandez E, Lohry D, Dompreh B, T Shen (2022) Allostery and dynamics in nuclear hormone receptor transactivation FEBS OPEN BIO 12, 248-249
  12.   Glaser J, Sedova A, Galanie S, Kneller D, Davidson R, Maradzike, E, Del Galdo S, Labbe A, Hsu D, Agarwal R, Bykov D, Tharrington A, Parks J, Smith D, Daidone I, Coates L, Kovalevsky A, Smith JC. (2022) Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor. ACS Publications. ACS Pharmacol. Transl.Sci. 2022, 5, 4, 255-265. doi:10.1021/acsptsci.200026.
  13.   Golloshi R, Playter C, Freeman TF, Das P, Raines TI, Garretson JH, Thurston D, McCord RP (2022) Constricted migration is associated with stable 3D genome structure differences in cancer cells. EMBO Reports: e52149
  14.   Gray ALH, Sawaya MR, Acharyya D, Lou J, Edington E, Best MD, Prosser RA, Eisenberg D, Do TD (2022) Atomic View of an Amyloid Dodecamer Exhibiting Selective Cellular Toxic Vulnerability in Acute Brain Slices. Prot. Sci. 2022:1-12. 
  15.   Gumbart JC, Ferreira JL, Hwang H, Hazel AJ, Parks JM, Smith JC, Zgurskaya HI, Bebby M. (2021) Lpp positions peptidoglycan an the AcrA-TolC interface in the AcrAB-TolC multidrug efflux pump. Biophysical Journal 120, no.18:3973-3982.
  16.   Hintzen JCJ, Ma H, Deng H, Witecka A, Andersen SB, Drozak J, Guo H, Qian P, Li H, Mecinović, J (2022). Histidine methyltransferase SETD3 methylates structurally diverse histidine mimics in actin. Protein Science, 31(5). doi:10.1002/pro.4305
  17.   Hintzen JCJ, Ma H, Deng H, Witecka A, Andersen SB, Drozak J, Guo H, Qian P, Li H, Mecinović, J (2022). Histidine methyltransferase SETD3 methylates structurally diverse histidine mimics in actin. Protein Science, 31(5). doi:10.1002/pro.4305
  18.   J Liu, HME Willems, EA Sansevere, S Allert, KS Barker, DJ Lowes, … Barrera FN, ….Peters BM. (2021)A variant ECE1 allele contributes to reduced pathogenicity of Candida albicans during vulvovaginal candidiasis. PLoS pathogens 17 (9), e1009884
  19.   Joshi AS. Peroxisomal membrane contact sites in yeasts. Frontiers in Cell and Developmental Biology. (2021). November 19; 9:735031.
  20.   Kumar P, J Lynch, B Song, H Ling, F Barrera, K Kisslinger, H Zhang, … (2022) Light–matter coupling in large-area van der Waals superlattices. Nature nanotechnology 17 (2), 182-189
  21.   Leus I, Weeks J, Bonifay V, Shen Y, Yang L, Cooper C, Nash D, Duerfeldt A, Smith JC, Parks J, Rybenkov V, Zgurskaya H. (2022) Property space mapping of Pseudomonas aeruginosa permeability to small molecules. Scientific Reports Sci Rep 12, 8220 doi:10.1038/s41598-022-12376-1.
  22.   Li J, Xie JF, Godec A, Weninger K, Liu C, Smith JC, Hong L. (2022) Non-ergodicity of a globular protein extending beyond its functional timescale. Chemical Science Issue 33, 2022 doi:10.1039/D2SC03069A.
  23.   Liang L, Wang YY, Bhagia S, Sethuraman V, Yang Z, Meng X, Bryant N, Petridis L, Smith JC, Pingali S, Gallego N, Pu Y, Evans B, O’Neill H, Davison B, Ragauskas A. (2022) Chemical and Morphological Structure of Transgenic Switchgrass Organosolv Lignin Extracted by Ethanol, Tetrahydrofuran, and y-Valerolactone Pretreatments. ACS Publications ACS Sustainable Chem. Eng. 2022, 10, 28, 9041-9052 doi:10.1021/acssuschemeng.2c00948.
  24.   Liu SH, Xiao Z, Mishra S, Mitchell J, Smith JC, Quarles D, Petridis L. (2022) Identification of Small-Molecule Inhibitors of Fibroblast Growth Factor 23 Signaling via In Silico Hot Spot Prediction and Molecular Docking to a-Klotho. ACS Publications J.Chem. Inf. Model. 2022, 62, 15, 3627-3637 doi:10.1021/acs.jcim.2c00633.
  25.   Lohry D, Stevens T, Shen T, Fernandez E. (2021) Interactions Between Intrinsically Disordered Domains of Nuclear Receptors and DNA Studied with Single-Molecule Optical Tweezers, Computational Simulations, and Cell Assays. FASEB JOURNAL 35
  26.   Lokdarshi, A. and von Arnim, A.G. (2022). Review: Emerging roles of the signaling network of the protein kinase GCN2 in the plant stress response. Plant Science 320:111280.  doi: https://doi.org/10.1016/j.plantsci.2022.111280. PMC pre ID” NIHMS 1800014″
  27.   Lokdarshi, A., von Arnim, A.G., and Akuoko, T.K. (2022). Modulation of GCN2 activity under excess light stress by osmoprotectants and amino acids. Plant Signaling & Behavior (in press). https://doi.org/10.1080/15592324.2022.2115747 .
  28.   Lou J, JA Schuster, FN Barrera, MD Best  (2022) ATP-Responsive Liposomes via Screening of Lipid Switches Designed to Undergo Conformational Changes upon Binding Phosphorylated Metabolites. Journal of the American Chemical Society 144 (8), 3746-3756
  29.   McAdam S. A. M., Chater C.C., Shpak E.D., Raissig, M.T., Dow G. J. (2021) Linking Stomatal Development and Physiology: From Stomatal Models to Non-Model Species and Crops. Frontiers in Plant Science 12, 2094
  30.   McCord RP, Taipale M, Teichmann S, Vorhees R, Wan Y, Dekker C, Sanjana NE. (2022) Voices on technology: The molecular biologists’ ever-expanding toy box. Molecular Cell. 82(2):221-226. doi: 10.1016/j.molcel.2021.12.025.
  31.   McCord RP, Xu Y, Li H, Das P, San Martin R (2022) SnapShot: Chromosome organization. Molecular Cell 82: 2350-2350 e2351
  32.   Melchionna MV, Gullett JM, Bouveret E, Shrestha HK, Abraham PE, Hettich RL, Alexandre G (2022) Bacterial Homologs of Progestin and AdipoQ Receptors (PAQRs) Affect Membrane Energetics Homeostasis but Not Fluidity. J. Bacteriol. 204(4):e0058321. doi: 10.1128/jb.00583-21.
  33.   Miller G, Ellis J, Sarangarajan R, Parikh A, Rodrigues L, Bruce C, Chand N, Smith S, Richardson K, Vazquez R, Kiebish M, Haneesh C, Granger E, Holtz J, Hinkle J, Narain N, Goodpaster B, Smith JC, Lupu D. (2022) Hypothesis-Agnostic Network-Based Analysis of Real-World Data Suggest Ondansetron is Associated with Lower COVID-19 Any Cause Mortality. Drugs – Real World Outcomes 9, 359-375 doi:10.1007/s40801-022-00303-9.
  34.   Perez I, Berndt S, Agarwal R, Castro A, Vishnivetskiy SA, Smith JC, Sanders CR, Gurevich VV, Iverson TM. (2022) A model for the signal initiation complex between arrestin-3 and the Src family kinase Fgr. Journal of Molecular Biology 434, no. 2: 167400.
  35.   Rajeshwar R, Smith JC. (2022) Structural patterns in class 1 major histocompatibility complex-restricted nonamer peptide binding to T-cell receptors. Proteins Volume 901, Issue 9, p 1645-1654, doi:10.1002/prot.26343.
  36.   Ren WS, Rahman A, Jiang KB, Deng, H, Zhao, YY, Zhang, WJ, Liu K, Qian P, Guo, H. (2022). Unraveling the Origins of Changing Product Specificity Properties of Arginine Methyltransferase PRMT7 by the E181D and E181D/Q329AMutations through QM/MM MD and Free-Energy Simulations. J Chem Theory Comput, 18(4), 2631-2641. doi:10.1021/acs.jctc.1c01219
  37.   Ren WS, Rahman A, Jiang KB, Deng, H, Zhao, YY, Zhang, WJ, Liu K, Qian P, Guo, H. (2022). Unraveling the Origins of Changing Product Specificity Properties of Arginine Methyltransferase PRMT7 by the E181D and E181D/Q329AMutations through QM/MM MD and Free-Energy Simulations. J Chem Theory Comput, 18(4), 2631-2641. doi:10.1021/acs.jctc.1c01219
  38.   Rich Robinson J, Russell A, Mancinin E, Das M. (2021)  Cdc42 reactivation at growth sites is regulated by local cell-cycle-dependent loss of its GTPase-activating protein Rga4 in fission yeast. Journal of Cell Science 134 (19), jcs259291
  39.   S Field, WC Conner, DM Roberts (2021) Arabidopsis calmodulin-like 38 regulates hypoxia-induced autophagy of suppressor of gene silencing 3 bodies. Frontiers in plant science, 1872
  40.   San Martin R, Das P, Dos Reis Marques R, Xu Y, Roberts JM, Sanders JT, Golloshi R, McCord RP. (2022) Chromosome compartmentalization alterations in prostate cancer cell lines model disease progression. Journal of Cell Biology. 221(2):e202104108. doi: 10.1083/jcb.202104108. Epub 2021 Dec 10. PMID: 34889941
  41.   Sanders JT*, Golloshi R*, Das P, Xu Y, Terry PH, Nash DG, Dekker J, McCord RP. (2022) Loops, topologically associating domains, compartments, and territories are elastic and robust to dramatic nuclear volume swelling. Scientific Reports. 2022 12(1):4721. doi: 10.1038/s41598-022-08602-5.
  42.   Semchonok DA, J Mondal, CJ Cooper, K Schlum, M Li, M Amin, … Bruce BD. (2022) Cryo-EM structure of a tetrameric photosystem I from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium. Plant communications 3 (1), 100248
  43.   Simmons, James R., Ran An, Bright Amankwaa, Shannon Zayac, Justin Kemp, Mariano Labrador (2022) Phosphorylated Histone variant γH2Av is associated with Chromatin Insulators in Drosophila. Plos Genetics, Accepted for publication
  44.   Sobe RC, Gilbert C, Vo L, Alexandre G, Scharf BE (2022) FliL and its paralog MotF have distinct roles in the stator activity of the Sinorhizobium meliloti flagellar motor. Mol Microbiol. 2022 Jul 8. doi: 10.1111/mmi.14964. Epub ahead of print. PMID: 35808893.
  45.   Stow EC, An R, Simmons JR, Schoborg TA, Davenport NM and Labrador M. (2022) A Drosophila Insulator Interacting Protein Suppresses Enhancer-Blocking Function and Modulates Replication Timing. Gene doi: 10.1016/j.gene.2022.146208. Epub 2022 Jan 29. PMID: 35092858.
  46.   Tatikonda R, Saharay M, Smith JC, Krishnan M. (2021) Correlated Response of Protein Side Chain Fluctuations and Conformational Entropy to Ligand Binding. Journal of Physical Chemistry B 125(34):9641-9651.
  47.   Teodor AH, LB Thal, S Vijayakumar, M Chan, G Little, BD Bruce. (2021) Photosystem I integrated into mesoporous microspheres has enhanced stability and photoactivity in biohybrid solar cells. Materials Today Bio 11, 100122
  48.   Teodor AH, S Monge, D Aguilar, A Tames, R Nunez, E Gonzalez, …  Bruce BD. (2022) PEDOT-Carbon Nanotube Counter Electrodes and Bipyridine Cobalt (II/III) Mediators as Universally Compatible Components in Bio-Sensitized Solar Cells Using Photosystem I. International Journal of Molecular Sciences 23 (7), 3865
  49.   Thakur, N, Wei, S, Lamichhane, R, Eddy, MT. (2022) Production of Human A2AAR in Lipid Nanodiscs for 19F-NMR and Single-Molecule Fluorescence Spectroscopy. STAR Protocol, 3, 1-32.
  50.   Wei, S, Thakur, N, Ray, AP, Beining, J, Obeng, S, McCurdy, CR, McMahon, LR, Gutiérrez-de-Terán, H, Eddy, MT, and Lamichhane, R (2021) Slow conformational dynamics of the human A2A adenosine receptor are temporally ordered. Structure, 30, 329-337.
  51.   Xiao Z, Liu J, Liu SH, Petridis L, Cai C, Cao L, Wang G, Chin A, Cleveland J, Ikedionwu O, Carrick J, Smith JC, Quarles L. (2022) Novel small molecule FGF23 inhibitors increase serum phosphate and improve skeletal abnormalities in Hyp Mice. Molecular Pharmacology Molpharm-ar-2001-000471, doi:10.1124/molpharm.121.000471.
  52.   Xu Y, Begoli E, McCord RP (2022) sciCAN: Single-cell chromatin accessibility and gene expression data integration via Cycle-consistent Adversarial Network. npj Systems Biology and Applications.
  53.   Xu Y, Das P, McCord RP. (2021) SMILE: Mutual Information Learning for Integration of Single Cell Omics Data. Bioinformatics. Oct 8;btab706. doi: 10.1093/bioinformatics/btab706. Online ahead of print.
  54.   Xu Y, McCord RP (2022) Diagonal integration of multimodal single-cell data: potential pitfalls and paths forward. Nature Communications 13: 3505
  55.   Yaw A, Glass JD, Prosser RA, Caldwell HK (2022) Paternal Cocaine Alters Social Interactions and Oxytocin Receptor Density in First Generation Male Offspring. Neuroscience 485: 65-77. 
  56.   Zagoskin M, Wang J: Programmed DNA elimination: silencing genes and repetitive sequences in somatic cells. Biochem Soc Trans 2021, 49 (5): 1891–1903. https://doi.org/10.1042/BST20190951
  57.   Zagoskin MV*, Wang J*#, Neff AT, Veronezi GMB, Davis RE#: Small RNA pathways in the nematode Ascaris in the absence of piRNAs. Nature Communications. 2022, 13:837. (*co-first authors; # corresponding authors). https://www.nature.com/articles/s41467-022-28482-7
  58.   Zhao YY, Deng H, Rahman A, Xu XL, Qian P, Guo, H. (2022). Computational Study of Methionine Methylation Process Catalyzed by SETD3. Interdisciplinary Sciences: Computational Life Sciences. doi:10.1007/s12539-022-00516-0
  59.   Zhao YY, Deng H, Rahman A, Xu XL, Qian P, Guo, H. (2022). Computational Study of Methionine Methylation Process Catalyzed by SETD3. Interdisciplinary Sciences: Computational Life Sciences. doi:10.1007/s12539-022-00516-0
  60. ZG Beamer, P Routray, WG Choi, MK Spangler, A Lokdarshi, DM Roberts (2021) Aquaporin family lactic acid channel NIP2; 1 promotes plant survival under low oxygen stress in Arabidopsis. Plant Physiology 187 (4), 2262-2278