Publications

Selected Publications by SCSB Faculty

Last Updated August 2020

2020

  • Gottipati K, Woodson M, Choi KH. Membrane binding and rearrangement by chikungunya virus capping enzyme nsP1 Virology. 2020;544:31–41. doi:10.1016/j.virol.2020.02.006.
  • Bujalowski PJ, Bujalowski W, Choi KH. Identification of the viral RNA promoter stem loop A (SLA)-binding site on Zika virus polymerase NS5. Sci Rep. 2020;10(1):13306. doi:10.1038/s41598-020-70094-y.
  • Patterson, E. I., Khanipov, K., Swetnam, D. M., Walsdorf, S., Kautz, T. F., Thangamani, S., Fofanov, Y., & Forrester, N. L. Measuring Alphavirus Fidelity Using Non-Infectious Virus Particles. Viruses, 2020;12(5), 546. https://doi.org/10.3390/v12050546.
  • Aguirre JE, Beswick EJ, Grim C, Uribe G, Tafoya M, Chacon Palma G, Samedi V, McKee R, Villeger R, Fofanov Y, Cong Y, Yochum G, Koltun W, Powell D, Pinchuk IV. Matrix metalloproteinases cleave membrane-bound PD-L1 on CD90+ (myo-)fibroblasts in Crohn's disease and regulate Th1/Th17 cell responses. Int Immunol. 2020, 32(1):57-68. doi: 10.1093/intimm/dxz060.
  • Zhou D, Tanzawa T, Lin J, Gagnon MG. Structural basis for ribosome recycling by RRF and tRNA. Nat Struct Mol Biol. 2020, 27(1):25-32. doi: 10.1038/s41594-019-0350-7.
  • Nepravishta R, Pletka CC, Iwahara J. Racemic phosphorothioate as a tool for NMR investigations of protein-DNA complexes. J Biomol NMR. 2020;10.1007/s10858-020-00333-x. doi:10.1007/s10858-020-00333-x.
  • Yu B, Pletka CC, Iwahara J. NMR Observation of Intermolecular Hydrogen Bonds between Protein Tyrosine Side-Chain OH and DNA Phosphate Groups. J Phys Chem B. 2020, doi: 10.1021/acs.jpcb.9b10987.
  • Nepravishta R, Yu B, Iwahara J. Hydrogen-exchange kinetics studied through analysis of self-decoupling of nuclear magnetic resonance. J Magn Reson. 2020;312:106687. doi:10.1016/j.jmr.2020.106687.
  • Pletka CC, Nepravishta R, Iwahara J. Detecting Counterion Dynamics in DNA-Protein Association. Angew Chem Int Ed Engl. 2020, 59(4):1465-1468. doi: 10.1002/anie.201910960.
  • Kenney LJ, Anand GS. EnvZ/OmpR Two-Component Signaling: An Archetype System That Can Function Noncanonically. EcoSal Plus. 2020;9(1):10.1128/ecosalplus.ESP-0001-2019. doi:10.1128/ecosalplus.ESP-0001-2019.
  • Ge, P., Scholl, D., Prokhorov, N. S., Avaylon, J., Shneider, M. M., Browning, C., Buth, S. A., Plattner, M., Chakraborty, U., Ding, K., Leiman, P. G., Miller, J. F., & Zhou, Z. H. Action of a minimal contractile bactericidal nanomachine. Nature, 2020;580(7805), 658–662. https://doi.org/10.1038/s41586-020.
  • Giraldo MI, Xia H, Aguilera-Aguirre L, Hage A, van Tol S, Shan C, Xie X, Sturdevant GL, Robertson SJ, McNally KL, Meade-White K, Azar SR, Rossi SL, Maury W, Woodson M, Ramage H, Johnson JR, Krogan NJ, Morais MC, Best SM, Shi PY, Rajsbaum R. Envelope protein ubiquitination drives entry and pathogenesis of Zika virus. Nature. 2020 Jul 8. doi: 10.1038/s41586-020-2457-8.
  • Tan TY, Fibriansah G, Kostyuchenko VA, Ng TS, Lim XX, Zhang S, Lim XN, Wang J, Shi J, Morais MC, Corti D, Lok SM. Capsid protein structure in Zika virus reveals the flavivirus assembly process. Nat Commun. 2020;11(1):895. doi:10.1038/s41467-020-14647-9.
  • Gaziova I, Moncrief T, Christian CJ, Villarreal M, Powell S, Lee H, Qadota H, White MA, Benian GM, Oberhauser AF. Mutational Analysis of the Structure and Function of the Chaperoning Domain of UNC-45B. Biophys J. 2020 Jul 22:S0006-3495(20)30562-2. doi: 10.1016/j.bpj.2020.07.012.
  • Qadota H, Moody JC, Lesanpezeshki L, Moncrief T, Kitzler D, Bhat PD, Vanapalli SA, Oberhauser AF, Benian GM. A Region of UNC-89 (Obscurin) Lying between Two Protein Kinase Domains Is a Highly Elastic Spring Required for Proper Sarcomere Organization. J Mol Biol. 2020 Aug 7;432(17):4799-4814. doi: 10.1016/j.jmb.2020.06.024.
  • Goldson TM, Turner KL, Huang Y, Carlson GE, Caggiano EG, Oberhauser AF, Fennewald SM, Burdick MM, Resto VA. Nucleolin mediates the binding of cancer cells to L-selectin under conditions of lymphodynamic shear stress. Am J Physiol Cell Physiol. 2020, 318(1):C83-C93. doi: 10.1152/ajpcell.00035.2019.
  • Drake JA, Pettitt BM. Physical Chemistry of the Protein Backbone: Enabling the Mechanisms of Intrinsic Protein Disorder. J Phys Chem B. 2020 Jun 4;124(22):4379-4390. doi: 10.1021/acs.jpcb.0c02489.
  • Lai CL, Chen C, Ou SC, Prentiss M, Pettitt BM. Interactions between identical DNA double helices. Phys Rev E. 2020 Mar;101(3-1):032414. doi: 10.1103/PhysRevE.101.032414.
  • Seckfort D, Lynch GC, Pettitt BM. The lac repressor hinge helix in context: The effect of the DNA binding domain and symmetry. Biochim Biophys Acta Gen Subj. 2020, 1864(4):129538. doi: 10.1016/j.bbagen.2020.129538.
  • Bores C, Pettitt BM. Structure and the role of filling rate on model dsDNA packed in a phage capsid. Physical Review E. 2020, 101, 012406. doi: 10.1103/PhysRevE.101.012406.
  • Rajarathnam K, Desai UR. Structural Insights Into How Proteoglycans Determine Chemokine-CXCR1/CXCR2 Interactions: Progress and Challenges. Front Immunol. 2020 Apr 24;11:660. doi: 10.3389/fimmu.2020.00660.
  • Coon JI, Jain S, Sepuru KM, Chung Y, Mohankumar K, Rajarathnam K, Jain SK. Lyophilization of human amniotic fluid is feasible without affecting biological activity. Pediatr Res. 2020 Apr;87(5):847-852. doi: 10.1038/s41390-019-0632-0.
  • Kautz TF, Jaworski E, Routh A, Forrester NL. A Low Fidelity Virus Shows Increased Recombination during the Removal of an Alphavirus Reporter Gene. Viruses. 2020 Jun 19;12(6):660. doi: 10.3390/v12060660.
  • Sotcheff S, Routh A. Understanding Flavivirus Capsid Protein Functions: The Tip of the Iceberg. Pathogens. 2020, 9(1):E42. doi: 10.3390/pathogens9010042.
  • Zhou Y, Routh A. Mapping RNA-capsid interactions and RNA secondary structure within virus particles using next-generation sequencing. Nucleic Acids Res. 2020, 48(2):e12. doi: 10.1093/nar/gkz1124.
  • Venkannagari H, Kasper JM, Misra A, Rush SA, Fan S, Lee H, Sun H, Seshadrinathan S, Machius M, Hommel JD, Rudenko G. Highly Conserved Molecular Features in IgLONs Contrast Their Distinct Structural and Biological Outcomes. J Mol Biol. 2020 Jul 22:S0022-2836(20)30461-7. doi: 10.1016/j.jmb.2020.07.014.
  • Li Y, Liu Z, Aglyamova G, Chen J, Chen H, Bhandari M, White MA, Rudenko G, Zhou J. Discovery of phenanthridine analogues as novel chemical probes disrupting the binding of DNA to ΔFosB homodimers and ΔFosB/JunD heterodimers. Bioorg Med Chem Lett. 2020 Aug 15;30(16):127300. doi: 10.1016/j.bmcl.2020.127300.
  • Yin Z, Venkannagaria H, Lynch H, Aglyamova G, Bhandari M, Machius M, Nestler EJ, Robison AJ, Rudenko G. Self-assembly of the bZIP transcription factor ΔFosB. Current Research in Structural Biology. 2020, 2:1-13. doi: 10.1016/j.crstbi.2019.12.001. 
  • Doss BL, Pan M, Gupta M, Grenci G, Mège RM, Lim CT, Sheetz MP, Voituriez R, Ladoux B. Cell response to substrate rigidity is regulated by active and passive cytoskeletal stress. Proc Natl Acad Sci U S A. 2020 Jun 9;117(23):12817-12825. doi: 10.1073/pnas.1917555117.
  • Yang B, Wolfenson H, Chung VY, Nakazawa N, Liu S, Hu J, Huang RY, Sheetz MP. Stopping transformed cancer cell growth by rigidity sensing. Nat Mater. 2020;19(2):239–250. doi:10.1038/s41563-019-0507-0.
  • Shan C, Xia H, Haller SL, Azar SR, Liu Y, Liu J, Muruato AE, Chen R, Rossi SL, Wakamiya M, Vasilakis N, Pei R, Fontes-Garfias CR, Singh SK, Xie X, Weaver SC, Shi PY. A Zika virus envelope mutation preceding the 2015 epidemic enhances virulence and fitness for transmission. Proc Natl Acad Sci U S A. 2020 Aug 3:202005722. doi: 10.1073/pnas.2005722117.
  • Xia H, Xie X, Zou J, Noble CG, Russell WK, Holthauzen LMF, Choi KH, White MA, Shi PY. A cocrystal structure of dengue capsid protein in complex of inhibitor. Proc Natl Acad Sci U S A. 2020 Jul 28;117(30):17992-18001. doi: 10.1073/pnas.2003056117.
  • Baker C, Xie X, Zou J, Muruato A, Fink K, Shi PY. Using recombination-dependent lethal mutations to stabilize reporter flaviviruses for rapid serodiagnosis and drug discovery. EBioMedicine. 2020 Jul;57:102838. doi: 10.1016/j.ebiom.2020.102838.
  • Xie X, Muruato A, Lokugamage KG, Narayanan K, Zhang X, Zou J, Liu J, Schindewolf C, Bopp NE, Aguilar PV, Plante KS, Weaver SC, Makino S, LeDuc JW, Menachery VD, Shi PY. An Infectious cDNA Clone of SARS-CoV-2. Cell Host Microbe. 2020 May 13;27(5):841-848.e3. doi: 10.1016/j.chom.2020.04.004.
  • Muruato AE, Fontes-Garfias CR, Ren P, Garcia-Blanco MA, Menachery VD, Xie X, Shi PY. A high-throughput neutralizing antibody assay for COVID-19 diagnosis and vaccine evaluation. bioRxiv [Preprint]. 2020 May 22:2020.05.21.109546. doi: 10.1101/2020.05.21.109546.
  • Zhang QY, Li XF, Niu X, Li N, Wang HJ, Deng CL, Ye HQ, Huang XY, Chen Q, Xu YP, Dong HL, Li XD, Zhao H, Shi PY, Yuan ZM, Gong P, Fang X, Qin CF, Zhang B. Short direct repeats in the 3'-untranslated region are involved in subgenomic flaviviral RNA production. J Virol. 2020, doi: 10.1128/JVI.01175-19.
  • Sherman MB, Smith HQ, Smith TJ. The Dynamic Life of Virus Capsids. Viruses. 2020 Jun 5;12(6):618. doi: 10.3390/v12060618.
  • Sherman MB, Guenther R, Reade R, Rochon D, Sit T, Smith TJ. Near-Atomic-Resolution Cryo-Electron Microscopy Structures of Cucumber Leaf Spot Virus and Red Clover Necrotic Mosaic Virus: Evolutionary Divergence at the Icosahedral Three-Fold Axes. J Virol. 2020, 94(2):e01439-19. doi: 10.1128/JVI.01439-19.
  • Alcott CE, Yalamanchili HK, Ji P, van der Heijden ME, Saltzman A, Elrod N, Lin A, Leng M, Bhatt B, Hao S, Wang Q, Saliba A, Tang J, Malovannaya A, Wagner EJ, Liu Z, Zoghbi HY. Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylation. Elife. 2020 Apr 22;9:e50895. doi: 10.7554/eLife.50895.
  • Yalamanchili HK, Alcott CE, Ji P, Wagner EJ, Zoghbi HY, Liu Z. PolyA-miner: accurate assessment of differential alternative poly-adenylation from 3'Seq data using vector projections and non-negative matrix factorization. Nucleic Acids Res. 2020 Jul 9;48(12):e69. doi: 10.1093/nar/gkaa398.
  • Weng T, Huang J, Wagner EJ, Ko J, Wu M, Wareing NE, Xiang Y, Chen NY, Ji P, Molina JG, Volcik KA, Han L, Mayes MD, Blackburn MR, Assassi S. Downregulation of CFIm25 amplifies dermal fibrosis through alternative polyadenylation. J Exp Med. 2020, 217(2):e20181384. doi: 10.1084/jem.20181384.
  • Eastwood G, Sang RC, Lutomiah J, Tunge P, Weaver SC. Sylvatic Mosquito Diversity in Kenya-Considering Enzootic Ecology of Arboviruses in an Era of Deforestation. Insects. 2020 Jun 3;11(6):342. doi: 10.3390/insects11060342.
  • Ribeiro GS, Hamer GL, Diallo M, Kitron U, Ko AI, Weaver SC. Influence of herd immunity in the cyclical nature of arboviruses. Curr Opin Virol. 2020;40:1–10. doi:10.1016/j.coviro.2020.02.004.
  • Kaelber JT, Jiang W, Weaver SC, Auguste AJ, Chiu W. Arrangement of the Polymerase Complexes inside a Nine-Segmented dsRNA Virus. Structure. 2020;S0969-2126(20)30011-3. doi:10.1016/j.str.2020.01.011.
  • Bergren NA, Haller S, Rossi SL, Seymour RL, Huang J, Miller AL, Bowen RA, Hartman DA, Brault AC, Weaver SC. "Submergence" of Western equine encephalitis virus: Evidence of positive selection argues against genetic drift and fitness reductions. PLoS Pathog. 2020;16(2):e1008102. doi:10.1371/journal.ppat.1008102.
  • Weaver SC. Incrimination of mosquito vectors. Nat Microbiol. 2020, 5(2):232-233. doi: 10.1038/s41564-019-0665-5.
  • Ahmed A, Dietrich I, LaBeaud AD, Lindsay SW, Musa A, Weaver SC. Risks and Challenges of Arboviral Diseases in Sudan: The Urgent Need for Actions. Viruses. 2020, 12(1):E81. doi: 10.3390/v12010081.
  • Pacheco LD, Weaver SC, Saade GR. Zika Virus Infection - After the Pandemic. N Engl J Med. 2020, 382(2):e3. doi: 10.1056/NEJMc1914974.
  • Jain N, Blauch LR, Szymanski MR, Das R, Tang SKY, Yin YW, Fire AZ. Transcription polymerase-catalyzed emergence of novel RNA replicons. Science. 2020 Apr 10;368(6487):eaay0688. doi: 10.1126/science.aay0688.
  • Singh A, Pandey M, Nandakumar D, Raney KD, Yin YW, Patel SS. Excessive excision of correct nucleotides during DNA synthesis explained by replication hurdles. EMBO J. 2020;39(6):e103367. doi:10.15252/embj.2019103367.
  • Anderson AP, Luo X, Russell W, Yin YW. Oxidative damage diminishes mitochondrial DNA polymerase replication fidelity. Nucleic Acids Res. 2020, 48(2):817-829. doi: 10.1093/nar/gkz1018.