Publications

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Selected Publications by SCSB Faculty

Last Updated December 2022

2022

  • Schein CH, Rafael G, Baker WS, Anaya ES, Schmidt JG, Weaver SC, Negi S, Braun W. PCP consensus protein/peptide alphavirus antigens stimulate broad spectrum neutralizing antibodies. Peptides. 2022 Nov;157:170844. doi: 10.1016/j.peptides.2022.170844.
  • Schein CH, Negi SS, Braun W. Still SDAPing Along: 20 Years of the Structural Database of Allergenic Proteins. Front Allergy. 2022 Mar 22;3:863172. doi: 10.3389/falgy.2022.863172.
  • Negi SS, Schein CH, Braun W. Regional and temporal coordinated mutation patterns in SARS-CoV-2 spike protein revealed by a clustering and network analysis. Sci Rep. 2022 Jan 21;12(1):1128. doi: 10.1038/s41598-022-04950-4.
  • Paranjpe MN, Marina VI, Grachev AA, Maviza TP, Tolicheva OA, Paleskava A, Osterman IA, Sergiev PV, Konevega AL, Polikanov YS, Gagnon MG. Insights into the molecular mechanism of translation inhibition by the ribosome-targeting antibiotic thermorubin. Nucleic Acids Res. 2022 Dec 22:gkac1189. doi: 10.1093/nar/gkac1189.
  • Basu RS, Sherman MB, Gagnon MG. Compact IF2 allows initiator tRNA accommodation into the P site and gates the ribosome to elongation. Nat Commun. 2022 Jun 13;13(1):3388. doi: 10.1038/s41467-022-31129-2.
  • Seely SM, Gagnon MG. Mechanisms of ribosome recycling in bacteria and mitochondria: a structural perspective. RNA Biol. 2022;19(1):662-677. doi: 10.1080/15476286.2022.2067712.
  • Wang X, Mayorga-Flores M, Bien KG, Bailey AO, Iwahara J. DNA-mediated proteolysis by neutrophil elastase enhances binding activities of the HMGB1 protein. J Biol Chem. 2022 Nov;298(11):102577. doi: 10.1016/j.jbc.2022.102577.
  • Yu B, Wang X, Iwahara J. Measuring Local Electrostatic Potentials Around Nucleic Acids by Paramagnetic NMR Spectroscopy. J Phys Chem Lett. 2022 Oct 27;13(42):10025-10029. doi: 10.1021/acs.jpclett.2c02623.
  • Yu B, Bien KG, Wang T, Iwahara J. Diffusion NMR-based comparison of electrostatic influences of DNA on various monovalent cations. Biophys J. 2022 Sep 20;121(18):3562-3570. doi: 10.1016/j.bpj.2022.06.022.
  • Bigman LS, Iwahara J, Levy Y. Negatively Charged Disordered Regions are Prevalent and Functionally Important Across Proteomes. J Mol Biol. 2022 Jul 30;434(14):167660. doi: 10.1016/j.jmb.2022.167660.
  • Wang X, Yu B, Iwahara J. Slow Rotational Dynamics of Cytosine NH2 Groups in Double-Stranded DNA. Biochemistry. 2022 Jul 19;61(14):1415-1418. doi: 10.1021/acs.biochem.2c00299.
  • Yu B, Bien KG, Pletka CC, Iwahara J. Dynamics of Cations around DNA and Protein as Revealed by 23Na Diffusion NMR Spectroscopy. Anal Chem. 2022 Feb 8;94(5):2444-2452. doi: 10.1021/acs.analchem.1c04197.
  • Yu B, Pletka CC, Iwahara J. Protein Electrostatics Investigated through Paramagnetic NMR for Nonpolar Groups. J Phys Chem B. 2022 Mar 24;126(11):2196-2202. doi: 10.1021/acs.jpcb.1c10930.
  • Mon KKZ, Si Z, Chan-Park MB, Kenney LJ. Polyimidazolium Protects against an Invasive Clinical Isolate of Salmonella Typhimurium. Antimicrob Agents Chemother. 2022 Oct 18;66(10):e0059722. doi: 10.1128/aac.00597-22.
  • Jacob H, Geng H, Shetty D, Halow N, Kenney LJ, Nakano MM. Distinct Interaction Mechanism of RNA Polymerase and ResD at Proximal and Distal Subsites for Transcription Activation of Nitrite Reductase in Bacillus subtilis. J Bacteriol. 2022 Feb 15;204(2):e0043221. doi: 10.1128/JB.00432-21.
  • Mascibroda LG, Shboul M, Elrod ND, Colleaux L, Hamamy H, Huang KL, Peart N, Singh MK, Lee H, Merriman B, Jodoin JN, Sitaram P, Lee LA, Fathalla R, Al-Rawashdeh B, Ababneh O, El-Khateeb M, Escande-Beillard N, Nelson SF, Wu Y, Tong L, Kenney LJ, Roy S, Russell WK, Amiel J, Reversade B, Wagner EJ. INTS13 variants causing a recessive developmental ciliopathy disrupt assembly of the Integrator complex. Nat Commun. 2022 Oct 13;13(1):6054. doi: 10.1038/s41467-022-33547-8.
  • Fraser A, Sokolova ML, Drobysheva AV, Gordeeva JV, Borukhov S, Jumper J, Severinov KV, Leiman PG. Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase. Nat Commun. 2022 Jun 20;13(1):3526. doi: 10.1038/s41467-022-31214-6.
  • Nussinov R, Jang H, Nir G, Tsai CJ, Cheng F. Open Structural Data in Precision Medicine. Annu Rev Biomed Data Sci. 2022 Apr 28. doi: 10.1146/annurev-biodatasci-122220-012951.
  • Qadota H, McPherson A, Corbitt R, Dackowski EK, Matsunaga Y, Oberhauser AF, Benian GM. Genetic analysis suggests a surface of PAT-4 (ILK) that interacts with UNC-112 (kindlin). G3 (Bethesda). 2022 Jul 6;12(7):jkac117. doi: 10.1093/g3journal/jkac117.
  • Workman RJ, Gorle S, Pettitt BM. Effects of Conformational Constraint on Peptide Solubility Limits. J Phys Chem B. 2022 Dec 15;126(49):10510-10518. doi: 10.1021/acs.jpcb.2c06458.
  • Chen C, Yu B, Yousefi R, Iwahara J, Pettitt BM. Assessment of the Components of the Electrostatic Potential of Proteins in Solution: Comparing Experiment and Theory. J Phys Chem B. 2022 Jun 13. doi: 10.1021/acs.jpcb.2c01611.
  • Chen C, Pettitt BM. The Effects of Flexibility on dsDNA–dsDNA Interactions. Life. 2022;12(5):699; doi: 10.3390/life12050699.
  • Dutta AK, Sepuru KM, Rösgen J, Rajarathnam K. Characterizing Thermodynamics of Protein-Glycosaminoglycan Interactions Using Isothermal Titration Calorimetry. Methods Mol Biol. 2022;2303:307-317. doi: 10.1007/978-1-0716-1398-6_25.
  • Joseph PRB, Sepuru KM, Poluri KM, Rajarathnam K. Solution NMR Spectroscopy for Characterizing Protein-Glycosaminoglycan Interactions. Methods Mol Biol. 2022;2303:13-23. doi: 10.1007/978-1-0716-1398-6_2.
  • Gallardo CM, Nguyen AT, Routh AL, Torbett BE. Selective ablation of 3' RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts. Nucleic Acids Res. 2022 Sep 23;50(17):e98. doi: 10.1093/nar/gkac516.
  • Yeung J, Routh AL. ViReMaShiny: an interactive application for analysis of viral recombination data. Bioinformatics. 2022 Sep 15;38(18):4420-4422. doi: 10.1093/bioinformatics/btac522.
  • Sotcheff SL, Chen JY, Elrod N, Cao J, Jaworski E, Kuyumcu-Martinez MN, Shi PY, Routh AL. Zika Virus Infection Alters Gene Expression and Poly-Adenylation Patterns in Placental Cells. Pathogens. 2022 Aug 18;11(8):936. doi: 10.3390/pathogens11080936.
  • Vu MN, Lokugamage KG, Plante JA, Scharton D, Bailey AO, Sotcheff S, Swetnam DM, Johnson BA, Schindewolf C, Alvarado RE, Crocquet-Valdes PA, Debbink K, Weaver SC, Walker DH, Russell WK, Routh AL, Plante KS, Menachery VD. QTQTN motif upstream of the furin-cleavage site plays a key role in SARS-CoV-2 infection and pathogenesis. Proc Natl Acad Sci U S A. 2022 Aug 9;119(32):e2205690119. doi: 10.1073/pnas.2205690119.
  • Zhou Y, Sotcheff SL, Routh AL. Next-generation sequencing: A new avenue to understand viral RNA-protein interactions. J Biol Chem. 2022 Apr 9;298(5):101924. doi: 10.1016/j.jbc.2022.101924.
  • Wang S, Sotcheff SL, Gallardo CM, Jaworski E, Torbett BE, Routh AL. Covariation of viral recombination with single nucleotide variants during virus evolution revealed by CoVaMa. Nucleic Acids Res. 2022 Jan 8:gkab1259. doi: 10.1093/nar/gkab1259.
  • Kumar A, Aglyamova G, Yim YY, Bailey AO, Lynch HM, Powell RT, Nguyen ND, Rosenthal Z, Zhao WN, Li Y, Chen J, Fan S, Lee H, Russell WK, Stephan C, Robison AJ, Haggarty SJ, Nestler EJ, Zhou J, Machius M, Rudenko G. Chemically targeting the redox switch in AP1 transcription factor ΔFOSB. Nucleic Acids Res. 2022 Sep 9;50(16):9548-9567. doi: 10.1093/nar/gkac710.
  • Jain K, Kanchanawong P, Sheetz MP, Zhou X, Cai H, Changede R. Ligand functionalization of titanium nanopattern enables the analysis of cell-ligand interactions by super-resolution microscopy. Nat Protoc. 2022 Oct;17(10):2275-2306. doi: 10.1038/s41596-022-00717-3.
  • Toh PJY, Lai JKH, Hermann A, Destaing O, Sheetz MP, Sudol M, Saunders TE. Optogenetic control of YAP cellular localisation and function. EMBO Rep. 2022 Sep 5;23(9):e54401. doi: 10.15252/embr.202154401.
  • Mukherjee A, Melamed S, Damouny-Khoury H, Amer M, Feld L, Nadjar-Boger E, Sheetz MP, Wolfenson H. α-Catenin links integrin adhesions to F-actin to regulate ECM mechanosensing and rigidity dependence. J Cell Biol. 2022 Aug 1;221(8):e202102121. doi: 10.1083/jcb.202102121.
  • Qin R, Melamed S, Yang B, Saxena M, Sheetz MP, Wolfenson H. Tumor Suppressor DAPK1 Catalyzes Adhesion Assembly on Rigid but Anoikis on Soft Matrices. Front Cell Dev Biol. 2022 Jul 19;10:959521. doi: 10.3389/fcell.2022.959521.
  • Wang YH, Sheetz MP. When PIP2 Meets p53: Nuclear Phosphoinositide Signaling in the DNA Damage Response. Front Cell Dev Biol. 2022 May 13;10:903994. doi: 10.3389/fcell.2022.903994.
  • Oh D, Chen Z, Biswas KH, Bai F, Ong HT, Sheetz MP, Groves JT. Competition for shared downstream signaling molecules establishes indirect negative feedback between EGFR and EphA2. Biophys J. 2022 May 17;121(10):1897-1908. doi: 10.1016/j.bpj.2022.04.015.
  • Wang YH, Ho TLF, Hariharan A, Goh HC, Wong YL, Verkaik NS, Lee MY, Tam WL, van Gent DC, Venkitaraman AR, Sheetz MP, Lane DP. Rapid recruitment of p53 to DNA damage sites directs DNA repair choice and integrity. Proc Natl Acad Sci U S A. 2022 Mar 8;119(10):e2113233119. doi: 10.1073/pnas.2113233119.
  • Yang YA, Nguyen E, Sankara Narayana GHN, Heuzé M, Fu C, Yu H, Mège RM, Ladoux B, Sheetz MP. Local contractions regulate E-cadherin rigidity sensing. Sci Adv. 2022 Jan 28;8(4):eabk0387. doi: 10.1126/sciadv.abk0387.
  • Kurhade C, Zou J, Xia H, Liu M, Yang Q, Cutler M, Cooper D, Muik A, Sahin U, Jansen KU, Ren P, Xie X, Swanson KA, Shi PY. Neutralization of Omicron sublineages and Deltacron SARS-CoV-2 by three doses of BNT162b2 vaccine or BA.1 infection. Emerg Microbes Infect. 2022 Dec;11(1):1828-1832. doi: 10.1080/22221751.2022.2099305.
  • Fang FF, Shi PY. Omicron: a drug developer's perspective. Emerg Microbes Infect. 2022 Dec;11(1):208-211. doi: 10.1080/22221751.2021.2023330.
  • Wang Y, Xie X, Shi PY. Flavivirus NS4B protein: Structure, function, and antiviral discovery. Antiviral Res. 2022 Nov;207:105423. doi: 10.1016/j.antiviral.2022.105423.
  • Liu Y, Liu J, Zou J, Kalveram B, Machado RRG, Ren P, Türeli S, Smith DJ, Weaver SC, Xie X, Shi PY. Cross-neutralization and cross-protection among SARS-CoV-2 viruses bearing different variant spikes. Signal Transduct Target Ther. 2022 Aug 13;7(1):285. doi: 10.1038/s41392-022-01137-1.
  • Liu Y, Zhang X, Liu J, Xia H, Zou J, Muruato AE, Periasamy S, Kurhade C, Plante JA, Bopp NE, Kalveram B, Bukreyev A, Ren P, Wang T, Menachery VD, Plante KS, Xie X, Weaver SC, Shi PY. A live-attenuated SARS-CoV-2 vaccine candidate with accessory protein deletions. Nat Commun. 2022 Jul 27;13(1):4337. doi: 10.1038/s41467-022-31930-z. Erratum in: Nat Commun. 2022 Oct13;13(1):6060.
  • Kurhade C, Zou J, Xia H, Cai H, Yang Q, Cutler M, Cooper D, Muik A, Jansen KU, Xie X, Swanson KA, Shi PY. Neutralization of Omicron BA.1, BA.2, and BA.3 SARS-CoV-2 by 3 doses of BNT162b2 vaccine. Nat Commun. 2022 Jun 23;13(1):3602. doi: 10.1038/s41467-022-30681-1.
  • Liu Y, Liu J, Johnson BA, Xia H, Ku Z, Schindewolf C, Widen SG, An Z, Weaver SC, Menachery VD, Xie X, Shi PY. Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Cell Rep. 2022 May 17;39(7):110829. doi: 10.1016/j.celrep.2022.110829.
  • Xia H, Zou J, Kurhade C, Cai H, Yang Q, Cutler M, Cooper D, Muik A, Jansen KU, Xie X, Swanson KA, Shi PY. Neutralization and durability of 2 or 3 doses of the BNT162b2 vaccine against Omicron SARS-CoV-2. Cell Host Microbe. 2022 Apr 13;30(4):485-488.e3. doi: 10.1016/j.chom.2022.02.015.
  • Liu J, Liu Y, Xia H, Zou J, Weaver SC, Swanson KA, Cai H, Cutler M, Cooper D, Muik A, Jansen KU, Sahin U, Xie X, Dormitzer PR, Shi PY. BNT162b2-elicited neutralization of Delta plus, Lambda, Mu, B.1.1.519, and Theta SARS-CoV-2 variants. NPJ Vaccines. 2022 Apr 8;7(1):41. doi: 10.1038/s41541-022-00462-4.
  • Liu Y, Liu J, Shi PY. SARS-CoV-2 variants and vaccination. Zoonoses (Burlingt). 2022;2(1):6. doi: 10.15212/zoonoses-2022-0001.
  • Zou J, Xia H, Xie X, Kurhade C, Machado RRG, Weaver SC, Ren P, Shi PY. Neutralization against Omicron SARS-CoV-2 from previous non-Omicron infection. Nat Commun. 2022 Feb 9;13(1):852. doi: 10.1038/s41467-022-28544-w.
  • Helm EW, Peiper AM, Phillips M, Williams CG, Sherman MB, Kelley T, Smith HQ, Jacobs SO, Shah D, Tatum SM, Iyer N, Grodzki M, Morales Aparicio JC, Kennedy EA, Manzi MS, Baldridge MT, Smith TJ, Karst SM. Environmentally-triggered contraction of the norovirus virion determines diarrheagenic potential. Front Immunol. 2022 Nov 1;13:1043746. doi: 10.3389/fimmu.2022.1043746.
  • Baljinnyam T, Sowers ML, Hsu CW, Conrad JW, Herring JL, Hackfeld LC, Sowers LC. Chemical and enzymatic modifications of 5-methylcytosine at the intersection of DNA damage, repair, and epigenetic reprogramming. PLoS One. 2022 Aug 29;17(8):e0273509. doi: 10.1371/journal.pone.0273509.
  • Hsu CW, Conrad JW, Sowers ML, Baljinnyam T, Herring JL, Hackfeld LC, Hatch SS, Sowers LC. A combinatorial system to examine the enzymatic repair of multiply damaged DNA substrates. Nucleic Acids Res. 2022 Jul 22;50(13):7406-7419. doi: 10.1093/nar/gkac530.
  • Hsu CW, Sowers ML, Baljinnyam T, Herring JL, Hackfeld LC, Tang H, Zhang K, Sowers LC. Measurement of deaminated cytosine adducts in DNA using a novel hybrid thymine DNA glycosylase. J Biol Chem. 2022 Mar;298(3):101638. doi: 10.1016/j.jbc.2022.101638.
  • Wilson C, Mertens TC, Shivshankar P, Bi W, Collum SD, Wareing N, Ko J, Weng T, Naikawadi RP, Wolters PJ, Maire P, Jyothula SS, Thandavarayan RA, Ren D, Elrod ND, Wagner EJ, Huang HJ, Dickey BF, Ford HL, Karmouty-Quintana H. Sine oculis homeobox homolog 1 plays a critical role in pulmonary fibrosis. JCI Insight. 2022 May 23;7(10):e142984. doi:10.1172/jci.insight.142984.
  • LaForce GR, Farr JS, Liu J, Akesson C, Gumus E, Pinkard O, Miranda HC, Johnson K, Sweet TJ, Ji P, Lin A, Coller J, Philippidou P, Wagner EJ, Schaffer AE. Suppression of premature transcription termination leads to reduced mRNA isoform diversity and neurodegeneration. Neuron. 2022 Feb 4:S0896-6273(22)00057-5. doi: 10.1016/j.neuron.2022.01.018.
  • Jones RG 3rd, Dimet-Wiley A, Haghani A, da Silva FM, Brightwell CR, Lim S, Khadgi S, Wen Y, Dungan CM, Brooke RT, Greene NP, Peterson CA, McCarthy JJ, Horvath S, Watowich SJ, Fry CS, Murach KA. A molecular signature defining exercise adaptation with ageing and in vivo partial reprogramming in skeletal muscle. J Physiol. 2022 Dec 19. doi: 10.1113/JP283836.
  • Dungan CM, Brightwell CR, Wen Y, Zdunek CJ, Latham CM, Thomas NT, Zagzoog AM, Brightwell BD, VonLehmden GL, Keeble AR, Watowich SJ, Murach KA, Fry CS. Muscle-Specific Cellular and Molecular Adaptations to Late-Life Voluntary Concurrent Exercise. Function (Oxf). 2022 May 23;3(4):zqac027. doi: 10.1093/function/zqac027.
  • Dimet-Wiley A, Golovko G, Watowich SJ. One-Year Postfracture Mortality Rate in Older Adults With Hip Fractures Relative to Other Lower Extremity Fractures: Retrospective Cohort Study. JMIR Aging. 2022 Mar 16;5(1):e32683. doi: 10.2196/32683.
  • Murach KA, Dimet-Wiley AL, Wen Y, Brightwell CR, Latham CM, Dungan CM, Fry CS, Watowich SJ. Late-life exercise mitigates skeletal muscle epigenetic aging. Aging Cell. 2022 Jan;21(1):e13527. doi: 10.1111/acel.13527.
  • Uddin MB, Liang Y, Shao S, Palani S, McKelvey M, Weaver SC, Sun K. Type I IFN Signaling Protects Mice from Lethal SARS-CoV-2 Neuroinvasion. Immunohorizons. 2022 Oct 11;6(10):716-721. doi: 10.4049/immunohorizons.2200.
  • Plante JA, Machado RRG, Mitchell BM, Shinde DP, Walker J, Scharton D, McConnell A, Saada N, Liu J, Khan B, Campos RK, Johnson BA, Menachery VD, Levine CB, Ren P, McLellan SLF, Plante KS, Weaver SC. Vaccination Decreases the Infectious Viral Load of Delta Variant SARS-CoV-2 in Asymptomatic Patients. Viruses. 2022 Sep 18;14(9):2071. doi:10.3390/v14092071.
  • Shinde DP, Plante JA, Plante KS, Weaver SC. Yellow Fever: Roles of Animal Models and Arthropod Vector Studies in Understanding Epidemic Emergence. Microorganisms. 2022 Aug 5;10(8):1578. doi: 10.3390/microorganisms10081578.
  • Azar SR, Campos RK, Yun R, Strange T, Rossi SL, Hanley KA, Vasilakis N, Weaver SC. Aedes aegypti Shows Increased Susceptibility to Zika Virus via Both In Vitro and In Vivo Models of Type II Diabetes. Viruses. 2022 Mar 23;14(4):665. doi: 10.3390/v14040665.
  • Liu Y, Liu J, Plante KS, Plante JA, Xie X, Zhang X, Ku Z, An Z, Scharton D, Schindewolf C, Widen SG, Menachery VD, Shi PY, Weaver SC. The N501Y spike substitution enhances SARS-CoV-2 infection and transmission. Nature. 2022 Feb;602(7896):294-299. doi: 10.1038/s41586-021-04245-0.
  • Nielsen MC, Machado RRG, Mitchell BM, McConnell AJ, Saada NI, Weaver SC, Ren P. A Comparison of Seegene Technologies Novaplex SARS-CoV-2 Variants I, II, and IV Assays with Spike Gene Sequencing for Detection of Known Severe Acute Respiratory Syndrome Coronavirus 2 Variants. J Mol Diagn. 2022 Feb 24:S1525-1578(22)00040-X. doi: 10.1016/j.jmoldx.2022.02.001.
  • Weldon CT, Weaver SC, Jacobsen KH. Impact of COVID-19 on the Vector-Borne Disease Research and Applied Public Health Workforce in the United States. Am J Trop Med Hyg. 2022 Feb 22:tpmd211340. doi: 10.4269/ajtmh.21-1340.
  • Clark LE, Clark SA, Lin C, Liu J, Coscia A, Nabel KG, Yang P, Neel DV, Lee H, Brusic V, Stryapunina I, Plante KS, Ahmed AA, Catteruccia F, Young-Pearse TL, Chiu IM, Llopis PM, Weaver SC, Abraham J. VLDLR and ApoER2 are receptors for multiple alphaviruses. Nature. 2022 Feb;602(7897):475-480. doi:10.1038/s41586-021-04326-0. 
  • Pata JD, Yin YW, Lahiri I. Editorial: Nucleic Acid Polymerases: The Two-Metal-Ion Mechanism and Beyond. Front Mol Biosci. 2022 Jul 13;9:948326. doi: 10.3389/fmolb.2022.948326.
  • Park J, Baruch-Torres N, Iwai S, Herrmann GK, Brieba LG, Yin YW. Human Mitochondrial DNA Polymerase Metal Dependent UV Lesion Bypassing Ability. Front Mol Biosci. 2022 Mar 9;9:808036. doi: 10.3389/fmolb.2022.808036.