2023

• Negi SS, Schein CH, Braun W. The updated Structural Database of Allergenic Proteins (SDAP 2.0) provides 3D models for allergens and incorporated bioinformatics tools. J Allergy Clin Immunol Glob. 2023 Aug 11;2(4):100162. doi: 10.1016/j.jacig.2023.100162.
• Canon N, Schein CH, Braun W, Negi SS, Chen X, Kulis MD, Kim EH, Pathy V, Pozzoli M, Liu W, Dreskin SC. Alanine Scanning of the Unstructured Region of Ara h 2 and of a Related Mimotope Reveals Critical Amino Acids for IgE Binding. Mol Nutr Food Res. 2023 Sep 14:e2300134. doi: 10.1002/mnfr.202300134.
• Rosado AM, Zhang Y, Choi HK, Chen Y, Ehrlich SM, Jin F, Grakoui A, Evavold BD, Zhu C. Memory in repetitive protein–protein interaction series. APL Bioengineering. 2023, 7:016102. doi.org/10.1063/5.0130805.
• Seely SM, Parajuli NP, De Tarafder A, Ge X, Sanyal S, Gagnon MG. Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome. Nat Commun. 2023 Aug 3;14(1):4666. doi: 10.1038/s41467-023-40416-5.
• 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. 2023 Jan 11;51(1):449-462. doi: 10.1093/nar/gkac1189.
• Iwahara J, Pettitt BM, Yu B. Direct measurements of biomolecular electrostatics through experiments. Curr Opin Struct Biol. 2023 Oct;82:102680. doi: 10.1016/j.sbi.2023.102680.
• Yu B, Iwahara J. Analyzing paramagnetic NMR data on target DNA search by proteins using a discrete-state kinetic model for translocation. Biopolymers. 2023 May 31:e23553. doi: 10.1002/bip.23553.
• Wang X, Bigman LS, Greenblatt HM, Yu B, Levy Y, Iwahara J. Negatively charged, intrinsically disordered regions can accelerate target search by DNA-binding proteins. Nucleic Acids Res. 2023 Jun 9;51(10):4701-4712. doi: 10.1093/nar/gkad045.
• Yu B, Wang X, Wang T, Iwahara J. DNA base order parameter determination without influence of chemical exchange. Methods. 2023 Feb;210:1-9. doi: 10.1016/j.ymeth.2022.12.004.
• Shetty D, Kenney LJ. A pH-sensitive switch activates virulence in Salmonella. Elife. 2023 Sep 14;12:e85690. doi: 10.7554/eLife.85690.
• Oh D, Liu X, Sheetz MP, Kenney LJ. Small, Dynamic Clusters of Tir-Intimin Seed Actin Polymerization. Small. 2023 Aug 30:e2302580. doi: 10.1002/smll.202302580.
• Sonani RR, Esteves NC, Horton AA, Kelly RJ, Sebastian AL, Wang F, Kreutzberger MAB, Leiman PG, Scharf BE, Egelman EH. Neck and capsid architecture of the robust Agrobacterium phage Milano. Commun Biol. 2023 Sep 8;6(1):921. doi: 10.1038/s42003-023-05292-1.
• Yeh SC, Strilets T, Tan WL, Castillo D, Medkour H, Rey-Cadilhac F, Serrato-Pomar IM, Rachenne F, Chowdhury A, Chuo V, Azar SR, Singh MK, Hamel R, Missé D, Kini RM, Kenney LJ, Vasilakis N, Marti-Renom MA, Nir G, Pompon J, Garcia-Blanco MA. The anti-immune dengue subgenomic flaviviral RNA is present in vesicles in mosquito saliva and is associated with increased infectivity. PLoS Pathog. 2023 Mar 30;19(3):e1011224. doi: 10.1371/journal.ppat.1011224.
• Flores V, Farabella I, Nir G. Genome-wide tracing to decipher nuclear organization. Curr Opin Cell Biol. 2023 Jun;82:102175. doi: 10.1016/j.ceb.2023.102175.
• Enazy SA, Kirschen GW, Vincent K, Yang J, Saada J, Shah M, Oberhauser AF, Bujalowski PJ, Motamedi M, Salama SA, Kilic G, Rytting E, Borahay MA. PEGylated Polymeric Nanoparticles Loaded with 2-Methoxyestradiol for the Treatment of Uterine Leiomyoma in a Patient-Derived Xenograft Mouse Model. J Pharm Sci. 2023 Sep;112(9):2552-2560. doi: 10.1016/j.xphs.2023.07.018.
• Martin SCT, Qadota H, Oberhauser AF, Hardin J, Benian GM. FARL-11 (STRIP1/2) is required for sarcomere and sarcoplasmic reticulum organization in C. elegans. Mol Biol Cell. 2023 Aug 1;34(9):ar86. doi: 10.1091/mbc.E23-03-0083.
• Odunuga OO, Oberhauser AF. Beyond Chaperoning: UCS Proteins Emerge as Regulators of Myosin-Mediated Cellular Processes. Subcell Biochem. 2023;101:189-211. doi: 10.1007/978-3-031-14740-1_7.
• Huang C, Pettitt BM. Parameter Dependence of the Solubility Limit for Disodium Phosphate. J Phys Chem B. 2023 Oct 12;127(40):8690-8696. doi: 10.1021/acs.jpcb.3c05343.
• Lazennec G, Rajarathnam K, Richmond A. CXCR2 chemokine receptor - a master regulator in cancer and physiology. Trends Mol Med. 2023 Oct 21:S1471-4914(23)00218-6. doi: 10.1016/j.molmed.2023.09.003.
• Sawant KV, Sepuru KM, Penaranda B, Lowry E, Garofalo RP, Rajarathnam K. Chemokine Cxcl1-Cxcl2 heterodimer is a potent neutrophil chemoattractant. J Leukoc Biol. 2023 Aug 25:qiad097. doi: 10.1093/jleuko/qiad097.
• Thompson S, Pang CY, Sepuru KM, Cambier S, Hellyer TP, Scott J, Simpson AJ, Proost P, Kirby JA, Rajarathnam K, Sheerin NS, Ali S. Nitration of chemokine CXCL8 acts as a natural mechanism to limit acute inflammation. Cell Mol Life Sci. 2023 Jan 9;80(1):35. doi: 10.1007/s00018-022-04663-x.
• Pomin VH, Rajarathnam K. NMR Methods for Characterization of Glycosaminoglycan-Chemokine Interactions. Methods Mol Biol. 2023;2597:143-157. doi: 10.1007/978-1-0716-2835-5_12.
• Sung PY, Zhou Y, Kao CC, Aburigh AA, Routh A, Roy P. A multidisciplinary approach to the identification of the protein-RNA connectome in double-stranded RNA virus capsids. Nucleic Acids Res. 2023 Apr 18:gkad274. doi: 10.1093/nar/gkad274.
• Sotcheff S, Zhou Y, Yeung J, Sun Y, Johnson JE, Torbett BE, Routh AL. ViReMa: a virus recombination mapper of next-generation sequencing data characterizes diverse recombinant viral nucleic acids. Gigascience. 2023 Mar 20;12:giad009. doi: 10.1093/gigascience/giad009.
• Schindewolf C, Lokugamage K, Vu MN, Johnson BA, Scharton D, Plante JA, Kalveram B, Crocquet-Valdes PA, Sotcheff S, Jaworski E, Alvarado RE, Debbink K, Daugherty MD, Weaver SC, Routh AL, Walker DH, Plante KS, Menachery VD. SARS-CoV-2 Uses Nonstructural Protein 16 To Evade Restriction by IFIT1 and IFIT3. J Virol. 2023 Feb 28;97(2):e0153222. doi: 10.1128/jvi.01532-22.
• S, Lu Z, Resua Rojas M, Penndorf P, Bailey AO, Russell WK, Machius M, Ren G, Takahashi H, Rudenko G. Designer molecules of the synaptic organizer MDGA1 reveal 3D conformational control of biological function. J Biol Chem. 2023 Apr;299(4):104586. doi: 10.1016/j.jbc.2023.104586.
• Lee H, Chofflet N, Liu J, FanKureel SK, Blair B, Sheetz MP. Recent Advancement in Elimination Strategies and Potential Rejuvenation Targets of Senescence. Adv Biol (Weinh). 2023 Oct 19:e2300461. doi: 10.1002/adbi.202300461.
• Wang YH, Sheetz MP. Transcription-independent functions of p53 in DNA repair pathway selection. Bioessays. 2023 Jan;45(1):e2200122. doi: 10.1002/bies.202200122.
• Conrad JW, Sowers ML, Yap DY, Cherryhomes E, Pettitt BM, Khanipov K, Sowers LC. Transition Mutations in the hTERT Promoter Are Unrelated to Potential i-motif Formation in the C-Rich Strand. Biomolecules. 2023 Aug 25;13(9):1308. doi: 10.3390/biom13091308.
• Sowers ML, Conrad JW, Chang-Gu B, Cherryhomes E, Hackfeld LC, Sowers LC. DNA Base Excision Repair Intermediates Influence Duplex-Quadruplex Equilibrium. Molecules. 2023 Jan 18;28(3):970. doi: 10.3390/molecules28030970.
• Baljinnyam T, Conrad JW, Sowers ML, Chang-Gu B, Herring JL, Hackfeld LC, Zhang K, Sowers LC. Characterization of a Novel Thermostable DNA Lyase Used To Prepare DNA for Next-Generation Sequencing. Chem Res Toxicol. 2023 Feb 20;36(2):162-176. doi: 10.1021/acs.chemrestox.2c00172.
• 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. 2023 Feb;601(4):763-782. doi: 10.1113/JP283836.
• Reyna RA, Walker J, Mitchell B, Shinde DP, Plante JA, Weaver SC, Plante KS. Vaccination against SARS-CoV-2 Does Not Protect against the Development of Anosmia in a Hamster Model. Vaccines (Basel). 2023 Oct 5;11(10):1564. doi: 10.3390/vaccines11101564.
• Campos RK, Rossi SL, Tesh RB, Weaver SC. Zoonotic mosquito-borne arboviruses: Spillover, spillback, and realistic mitigation strategies. Sci Transl Med. 2023 Oct 18;15(718):eadj2166. doi: 10.1126/scitranslmed.adj2166.
• Powers AM, Williamson LE, Carnahan RH, Crowe JE Jr, Hyde JL, Jonsson CB, Nasar F, Weaver SC. Developing a Prototype Pathogen Plan and Research Priorities for the Alphaviruses. J Infect Dis. 2023 Oct 18;228(Suppl 6):S414-S426. doi: 10.1093/infdis/jiac326.
• Machado RRG, Walker JL, Scharton D, Rafael GH, Mitchell BM, Reyna RA, de Souza WM, Liu J, Walker DH, Plante JA, Plante KS, Weaver SC. Immunogenicity and efficacy of vaccine boosters against SARS-CoV-2 Omicron subvariant BA.5 in male Syrian hamsters. Nat Commun. 2023 Jul 17;14(1):4260. doi: 10.1038/s41467-023-40033-2.
• Reyna RA, Weaver SC. Sequelae and Animal Modeling of Encephalitic Alphavirus Infections. Viruses. 2023 Jan 28;15(2):382. doi: 10.3390/v15020382.
• Caston RA, Fortini P, Chen K, Bauer J, Dogliotti E, Yin YW, Demple B. Maintenance of Flap Endonucleases for Long-Patch Base Excision DNA Repair in Mouse Muscle and Neuronal Cells Differentiated In Vitro. Int J Mol Sci. 2023 Aug 12;24(16):12715. doi: 10.3390/ijms241612715.
• Herrmann GK, Yin YW. The Role of Poly(ADP-ribose) Polymerase 1 in Nuclear and Mitochondrial Base Excision Repair. Biomolecules. 2023 Jul 31;13(8):1195. doi: 10.3390/biom13081195.
• Park J, Herrmann GK, Mitchell PG, Sherman MB, Yin YW. Polγ coordinates DNA synthesis and proofreading to ensure mitochondrial genome integrity. Nat Struct Mol Biol. 2023 Jun;30(6):812-823. doi: 10.1038/s41594-023-00980-2.
• Park J, Baruch-Torres N, Yin YW. Structural and Molecular Basis for Mitochondrial DNA Replication and Transcription in Health and Antiviral Drug Toxicity. Molecules. 2023 Feb 14;28(4):1796. doi: 10.3390/molecules28041796.