Member Publications

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114 Member Publications for July 2023

Automated identification of chalcogen bonds in AlphaFold protein structure database files: is it possible?
1. Front Mol Biosci - published July 24, 2023
2. Carugo O, Djinović-Carugo K
Identification and characterisation of anti-IL-13 inhibitory single domain antibodies provides new insights into receptor selectivity and attractive opportunities for drug discovery.
1. Front Immunol - published July 24, 2023
2. Walker K, Baravalle R, Holyfield R, Kalms J, Wright H, Seewooruthun C, Muskett FW, Scott-Tucker A, Merritt A, Henry A, Lawson ADG, Hall G, Prosser C, Carr MD
A PAM of the α(1A)-Adrenergic receptor rescues biomarker, long-term potentiation, and cognitive deficits in Alzheimer's disease mouse models without effects on blood pressure.
1. Curr Res Pharmacol Drug Discov - published July 14, 2023
2. Papay RS, Stauffer SR, Perez DM
Diverse modes of regulating methyltransferase activity by histone ubiquitination.
1. Curr Opin Struct Biol - published July 8, 2023
2. Fields JK, Hicks CW, Wolberger C
Optimized reaction coordinates for analysis of enhanced sampling.
1. J Chem Phys - published July 7, 2023
2. Widmer J, Langini C, Vitalis A, Caflisch A
Principles of human pre-60S biogenesis.
1. Science - published July 7, 2023
2. Vanden Broeck A, Klinge S
Structural insights into RNA bridging between HIV-1 Vif and antiviral factor APOBEC3G.
1. Nat Commun - published July 7, 2023
2. Kouno T, Shibata S, Shigematsu M, Hyun J, Kim TG, Matsuo H, Wolf M
Cryo-EM structure of the chain-elongating E3 ubiquitin ligase UBR5.
1. EMBO J - published July 6, 2023
2. Hodáková Z, Grishkovskaya I, Brunner HL, Bolhuis DL, Belačić K, Schleiffer A, Kotisch H, Brown NG, Haselbach D
Acquired secondary HER2 mutations enhance HER2/MAPK signaling and promote resistance to HER2 kinase inhibition in breast cancer.
1. Cancer Res - published July 5, 2023
2. Marin A, Mamun AA, Patel H, Akamatsu H, Ye D, Sudhan DR, Eli L, Marcelain K, Brown BP, Meiler J, Arteaga CL, Hanker AB
Novel Association of the NOTCH Pathway Regulator MIB1 Gene With the Development of Bicuspid Aortic Valve.
1. JAMA Cardiol - published July 5, 2023
2. Tessler I, Albuisson J, Piñeiro-Sabarís R, Verstraeten A, Kamber Kaya HE, Siguero-Álvarez M, Goudot G, MacGrogan D, Luyckx I, Shpitzen S, Levin G, Kelman G, Reshef N, Mananet H, Holdcraft J, Muehlschlegel JD, Peloso GM, Oppenheim O, Cheng C, Mazzella JM, Andelfinger G, Mital S, Eriksson P, Billon C, Heydarpour M, Dietz HC, Jeunemaitre X, Leitersdorf E, Sprinzak D, Blacklow SC, Body SC, Carmi S, Loeys B, de la Pompa JL, Gilon D, Messas E, Durst R
CT With CTA Versus MRI in Patients Presenting to the Emergency Department With Dizziness: Analysis Using Propensity Score Matching.
1. AJR Am J Roentgenol - published July 5, 2023
2. Tu LH, Navaratnam D, Melnick E, Forman HP, Venkatesh AK, Malhotra A, Yaesoubi R, Sureshanand S, Sheth KN, Mahajan A
Designed ankyrin repeat proteins for detecting prostate-specific antigen expression in vivo.
1. RSC Chem Biol - published July 5, 2023
2. Gut M, Dreier B, Furler S, Sobek J, Plückthun A, Holland JP
Correction: Oligomeric states of ASC specks regulate inflammatory responses by inflammasome in the extracellular space.
1. Cell Death Discov - published July 4, 2023
2. Yu TG, Cha JS, Kim G, Sohn YK, Yoo Y, Kim U, Song JJ, Cho HS, Kim HS
Quantitative analysis of The High Yield Hydrolysis of Kelp by Laminarinase and Alginate Lyase.
1. Chembiochem - published July 4, 2023
2. Takasuka T, Kim H, Deng K, Bianchetti CM, Yamashita K, Beebe ET, Bergeman LF, Vander Meulen KA, Deutsch S, Ralph J, Adams PD, Northen TR, Fox BG
Chopped! Newfound GSDMD cleavage facilitates tolerance to food allergens.
1. Trends Immunol - published July 4, 2023
2. Healy LB, Du G, Wu H
DNA-PK is activated by SIRT2 deacetylation to promote DNA double-strand break repair by non-homologous end joining.
1. Nucleic Acids Res - published July 3, 2023
2. Head PE, Kapoor-Vazirani P, Ganji NP, Zhang H, Rath SK, Luong NC, Haji-Seyed-Javadi R, Sesay F, Wang SY, Duong DM, Daddacha W, Minten EV, Song B, Danelia D, Liu X, Li S, Ortlund EA, Seyfried NT, Smalley DM, Wang Y, Deng X, Dynan WS, El-Rayes B, Davis AJ, Yu DS
A DNA-encoded chemical library based on chiral 4-amino-proline enables stereospecific isozyme-selective protein recognition.
1. Nat Chem - published July 3, 2023
2. Oehler S, Lucaroni L, Migliorini F, Elsayed A, Prati L, Puglioli S, Matasci M, Schira K, Scheuermann J, Yudin D, Jia M, Ban N, Bushnell D, Kornberg R, Cazzamalli S, Neri D, Favalli N, Bassi G
An engineered hypercompact CRISPR-Cas12f system with boosted gene-editing activity.
1. Nat Chem Biol - published July 3, 2023
2. Wu T, Liu C, Zou S, Lyu R, Yang B, Yan H, Zhao M, Tang W
Targeting the Spike Receptor Binding Domain Class V Cryptic Epitope by an Antibody with Pan-Sarbecovirus Activity.
1. J Virol - published July 3, 2023
2. Jensen JL, Sankhala RS, Dussupt V, Bai H, Hajduczki A, Lal KG, Chang WC, Martinez EJ, Peterson CE, Golub ES, Rees PA, Mendez-Rivera L, Zemil M, Kavusak E, Mayer SV, Wieczorek L, Kannan S, Doranz BJ, Davidson E, Yang ES, Zhang Y, Chen M, Choe M, Wang L, Gromowski GD, Koup RA, Michael NL, Polonis VR, Rolland M, Modjarrad K, Krebs SJ, Joyce MG
Human TRMT2A methylates tRNA and contributes to translation fidelity.
1. Nucleic Acids Res - published July 3, 2023
2. Witzenberger M, Burczyk S, Settele D, Mayer W, Welp LM, Heiss M, Wagner M, Monecke T, Janowski R, Carell T, Urlaub H, Hauck SM, Voigt A, Niessing D
Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions.
1. Nat Methods - published July 3, 2023
2. Mészáros B, Hatos A, Palopoli N, Quaglia F, Salladini E, Van Roey K, Arthanari H, Dosztányi Z, Felli IC, Fischer PD, Hoch JC, Jeffries CM, Longhi S, Maiani E, Orchard S, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Pritisanac I, Tenorio L, Viennet T, Tompa P, Vranken W, Tosatto SCE, Davey NE
Editorial overview: Evolution of antiviral defense.
1. Curr Opin Microbiol - published July 3, 2023
2. Kranzusch PJ
Genome- and metabolome-guided discovery of marine BamA inhibitors revealed a dedicated darobactin halogenase.
1. Cell Chem Biol - published July 3, 2023
2. Böhringer N, Kramer JC, de la Mora E, Padva L, Wuisan ZG, Liu Y, Kurz M, Marner M, Nguyen H, Amara P, Yokoyama K, Nicolet Y, Mettal U, Schäberle TF
Utility of Exome Sequencing for Diagnosis in Unexplained Pediatric-Onset Epilepsy.
1. JAMA Netw Open - published July 3, 2023
2. Koh HY, Smith L, Wiltrout KN, Podury A, Chourasia N, D'Gama AM, Park M, Knight D, Sexton EL, Koh JJ, Oby B, Pinsky R, Shao DD, French CE, Shao W, Rockowitz S, Sliz P, Zhang B, Mahida S, Moufawad El Achkar C, Yuskaitis CJ, Olson HE, Sheidley BR, Poduri AH, BCH Neurology Referral and Phenotyping Group
Author Correction: Molecular basis for integrin adhesion receptor binding to p21-activated kinase 4 (PAK4).
1. Commun Biol - published July 3, 2023
2. Ha BH, Yigit S, Natarajan N, Morse EM, Calderwood DA, Boggon TJ
Push-pull mechanics of E-cadherin ectodomains in biomimetic adhesions.
1. Biophys J - published July 3, 2023
2. Nagendra K, Izzet A, Judd NB, Zakine R, Friedman L, Harrison OJ, Pontani LL, Shapiro L, Honig B, Brujic J
SARS-CoV-2 Omicron BA.1 breakthrough infection drives late remodeling of the memory B cell repertoire in vaccinated individuals.
1. Immunity - published July 3, 2023
2. Sokal A, Barba-Spaeth G, Hunault L, Fernández I, Broketa M, Meola A, Fourati S, Azzaoui I, Vandenberghe A, Lagouge-Roussey P, Broutin M, Roeser A, Bouvier-Alias M, Crickx E, Languille L, Fournier M, Michel M, Godeau B, Gallien S, Melica G, Nguyen Y, Canoui-Poitrine F, Pirenne F, Megret J, Pawlotsky JM, Fillatreau S, Reynaud CA, Weill JC, Rey FA, Bruhns P, Mahévas M, Chappert P
Class I histone deacetylase complex: Structure and functional correlates.
1. Proc Natl Acad Sci U S A - published July 2, 2023
2. Wang X, Wang Y, Liu S, Zhang Y, Xu K, Ji L, Kornberg RD, Zhang H
Nonsteroidal anti-inflammatory drugs sensitize epithelial cells to Clostridioides difficile toxin-mediated mitochondrial damage.
1. Sci Adv - published July 2, 2023
2. Soto Ocaña J, Bayard NU, Hart JL, Thomas AK, Furth EE, Lacy DB, Aronoff DM, Zackular JP
Contemporary human H3N2 influenza a viruses require a low threshold of suitable glycan receptors for efficient infection.
1. Glycobiology - published July 2, 2023
2. Spruit CM, Sweet IR, Maliepaard JCL, Bestebroer T, Lexmond P, Qiu B, Damen MJA, Fouchier RAM, Reiding KR, Snijder J, Herfst S, Boons GJ, de Vries RP
Antiviral HIV-1 SERINC restriction factors disrupt virus membrane asymmetry.
1. Nat Commun - published July 2, 2023
2. Leonhardt SA, Purdy MD, Grover JR, Yang Z, Poulos S, McIntire WE, Tatham EA, Erramilli SK, Nosol K, Lai KK, Ding S, Lu M, Uchil PD, Finzi A, Rein A, Kossiakoff AA, Mothes W, Yeager M
Structures of channelrhodopsin paralogs in peptidiscs explain their contrasting K(+) and Na(+) selectivities.
1. Nat Commun - published July 2, 2023
2. Morizumi T, Kim K, Li H, Govorunova EG, Sineshchekov OA, Wang Y, Zheng L, Bertalan É, Bondar AN, Askari A, Brown LS, Spudich JL, Ernst OP
Peptide Macrocyclization Guided by Reversible Covalent Templating.
1. Chemistry - published July 2, 2023
2. Maier JM, Valenzuela SA, Stok AV, Menta AK, Shimizu Y, Ngo PH, Ellington AD, Anslyn EV
Tackling FGFR3-driven bladder cancer with a promising synergistic FGFR/HDAC targeted therapy.
1. NPJ Precis Oncol - published July 2, 2023
2. Wang Z, Muthusamy V, Petrylak DP, Anderson KS
Purine-ifying uric acid by gut microbes.
1. Cell Chem Biol - published July 2, 2023
2. Grelska A, Sharan D, Light SH
Arena: Rapid and Accurate Reconstruction of Full Atomic RNA Structures From Coarse-grained Models.
1. J Mol Biol - published July 2, 2023
2. Perry ZR, Pyle AM, Zhang C
Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants.
1. Sci Adv - published July 2, 2023
2. Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke TR Jr, Levy RM, Hughes SH, Craigie R, Lyumkis D
Designing an effective malaria vaccine targeting Plasmodium vivax Duffy-binding protein.
1. Trends Parasitol - published July 2, 2023
2. Dickey TH, Tolia NH
Identification of small molecule antivirals against HTLV-1 by targeting the hDLG1-Tax-1 protein-protein interaction.
1. Antiviral Res - published July 2, 2023
2. Maseko SB, Brammerloo Y, Van Molle I, Sogues A, Martin C, Gorgulla C, Plant E, Olivet J, Blavier J, Ntombela T, Delvigne F, Arthanari H, El Hajj H, Bazarbachi A, Van Lint C, Salehi-Ashtiani K, Remaut H, Ballet S, Volkov AN, Twizere JC
RAD51C-XRCC3 structure and cancer patient mutations define DNA replication roles.
1. Nat Commun - published July 2, 2023
2. Longo MA, Roy S, Chen Y, Tomaszowski KH, Arvai AS, Pepper JT, Boisvert RA, Kunnimalaiyaan S, Keshvani C, Schild D, Bacolla A, Williams GJ, Tainer JA, Schlacher K
Two point mutations in protocadherin-1 disrupt hantavirus recognition and afford protection against lethal infection.
1. Nat Commun - published July 2, 2023
2. Slough MM, Li R, Herbert AS, Lasso G, Kuehne AI, Monticelli SR, Bakken RR, Liu Y, Ghosh A, Moreau AM, Zeng X, Rey FA, Guardado-Calvo P, Almo SC, Dye JM, Jangra RK, Wang Z, Chandran K
Identification of in vivo metabolites of Citri Sarcodactylis Fructus by UHPLC-Q/Orbitrap HRMS.
1. Phytochem Anal - published July 2, 2023
2. Deng F, Li XM, Gong QQ, Zheng ZX, Zeng L, Zhang MJ, Duan TY, Liu X, Zhang MZ, Guo DL
Discovery and development of novel substituted monohydrazides as potent antifungal agents.
1. RSC Med Chem - published July 2, 2023
2. Thamban Chandrika N, Green KD, Spencer AC, Tsodikov OV, Garneau-Tsodikova S
Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct.
1. Sci Rep - published July 2, 2023
2. Kosno M, Currie SL, Kumar A, Xing C, Rosen MK
ER membrane curvature and ubiquitin as drivers of ER-phagy.
1. Dev Cell - published July 2, 2023
2. Hoyer MJ, Harper JW
Expulsion mechanism of the substrate-translocating subunit in ECF transporters.
1. Nat Commun - published July 2, 2023
2. Thangaratnarajah C, Nijland M, Borges-Araújo L, Jeucken A, Rheinberger J, Marrink SJ, Souza PCT, Paulino C, Slotboom DJ
Structural homology screens reveal host-derived poxvirus protein families impacting inflammasome activity.
1. Cell Rep - published July 2, 2023
2. Boys IN, Johnson AG, Quinlan MR, Kranzusch PJ, Elde NC
Oligomerization-mediated activation of a short prokaryotic Argonaute.
1. Nature - published July 2, 2023
2. Shen Z, Yang XY, Xia S, Huang W, Taylor DJ, Nakanishi K, Fu TM
A highly potent human neutralizing antibody prevents vertical transmission of Rift Valley fever virus in a rat model.
1. Nat Commun - published July 2, 2023
2. McMillen CM, Chapman NS, Hoehl RM, Skvarca LB, Schwarz MM, Handal LS, Crowe JE Jr, Hartman AL
Protein target highlights in CASP15: Analysis of models by structure providers.
1. Proteins - published July 2, 2023
2. Alexander LT, Durairaj J, Kryshtafovych A, Abriata LA, Bayo Y, Bhabha G, Breyton C, Caulton SG, Chen J, Degroux S, Ekiert DC, Erlandsen BS, Freddolino PL, Gilzer D, Greening C, Grimes JM, Grinter R, Gurusaran M, Hartmann MD, Hitchman CJ, Keown JR, Kropp A, Kursula P, Lovering AL, Lemaitre B, Lia A, Liu S, Logotheti M, Lu S, Markússon S, Miller MD, Minasov G, Niemann HH, Opazo F, Phillips GN Jr, Davies OR, Rommelaere S, Rosas-Lemus M, Roversi P, Satchell K, Smith N, Wilson MA, Wu KL, Xia X, Xiao H, Zhang W, Zhou ZH, Fidelis K, Topf M, Moult J, Schwede T
Direct Mass Spectrometry-Based Detection and Antibody Sequencing of Monoclonal Gammopathy of Undetermined Significance from Patient Serum: A Case Study.
1. J Proteome Res - published July 2, 2023
2. Peng W, den Boer MA, Tamara S, Mokiem NJ, van der Lans SPA, Bondt A, Schulte D, Haas PJ, Minnema MC, Rooijakkers SHM, van Zuilen AD, Heck AJR, Snijder J
Study of drug resistance-associated genetic mutations, and phylo-genetic analysis of HCV in the Province of Sindh, Pakistan.
1. Sci Rep - published July 2, 2023
2. Faiz S, Irfan M, Farooq S, Khan IA, Iqbal H, Wahab AT, Shakeel M, Gong P, Iftner T, Choudhary MI
Immunopeptidome profiling of human coronavirus OC43-infected cells identifies CD4 T-cell epitopes specific to seasonal coronaviruses or cross-reactive with SARS-CoV-2.
1. PLoS Pathog - published July 2, 2023
2. Becerra-Artiles A, Nanaware PP, Muneeruddin K, Weaver GC, Shaffer SA, Calvo-Calle JM, Stern LJ
Exposure of iPSC-derived human microglia to brain substrates enables the generation and manipulation of diverse transcriptional states in vitro.
1. Nat Immunol - published July 2, 2023
2. Dolan MJ, Therrien M, Jereb S, Kamath T, Gazestani V, Atkeson T, Marsh SE, Goeva A, Lojek NM, Murphy S, White CM, Joung J, Liu B, Limone F, Eggan K, Hacohen N, Bernstein BE, Glass CK, Leinonen V, Blurton-Jones M, Zhang F, Epstein CB, Macosko EZ, Stevens B
Deploying synthetic coevolution and machine learning to engineer protein-protein interactions.
1. Science - published July 2, 2023
2. Yang A, Jude KM, Lai B, Minot M, Kocyla AM, Glassman CR, Nishimiya D, Kim YS, Reddy ST, Khan AA, Garcia KC
Human astrovirus capsid protein releases a membrane lytic peptide upon trypsin maturation.
1. J Virol - published July 2, 2023
2. Ykema M, Ye K, Xun M, Harper J, Betancourt-Solis MA, Arias CF, McNew JA, Tao YJ
Lectin-Seq: A method to profile lectin-microbe interactions in native communities.
1. Sci Adv - published July 2, 2023
2. McPherson RL, Isabella CR, Walker RL, Sergio D, Bae S, Gaca T, Raman S, Nguyen LTT, Wesener DA, Halim M, Wuo MG, Dugan A, Kerby R, Ghosh S, Rey FE, Dhennezel C, Pishchany G, Lensch V, Vlamakis H, Alm EJ, Xavier RJ, Kiessling LL
The new world of RNA diagnostics and therapeutics.
1. J Exp Clin Cancer Res - published July 2, 2023
2. Blandino G, Dinami R, Marcia M, Anastasiadou E, Ryan BM, Palcau AC, Fattore L, Regazzo G, Sestito R, Loria R, Díaz Méndez AB, Cappelletto MC, Pulito C, Monteonofrio L, Calin GA, Sozzi G, Cheong JK, Aharonov R, Ciliberto G
Diverse p120RasGAP interactions with doubly phosphorylated partners EphB4, p190RhoGAP and Dok1.
1. J Biol Chem - published July 2, 2023
2. Vish KJ, Stiegler AL, Boggon TJ
FUBP1 is a general splicing factor facilitating 3' splice site recognition and splicing of long introns.
1. Mol Cell - published July 2, 2023
2. Ebersberger S, Hipp C, Mulorz MM, Buchbender A, Hubrich D, Kang HS, Martínez-Lumbreras S, Kristofori P, Sutandy FXR, Llacsahuanga Allcca L, Schönfeld J, Bakisoglu C, Busch A, Hänel H, Tretow K, Welzel M, Di Liddo A, Möckel MM, Zarnack K, Ebersberger I, Legewie S, Luck K, Sattler M, König J
Distinct types of multicellular aggregates in Pseudomonas aeruginosa liquid cultures.
1. NPJ Biofilms Microbiomes - published July 2, 2023
2. Melaugh G, Martinez VA, Baker P, Hill PJ, Howell PL, Wozniak DJ, Allen RJ
Potent cross-neutralization of respiratory syncytial virus and human metapneumovirus through a structurally conserved antibody recognition mode.
1. Cell Host Microbe - published July 2, 2023
2. Wen X, Suryadevara N, Kose N, Liu J, Zhan X, Handal LS, Williamson LE, Trivette A, Carnahan RH, Jardetzky TS, Crowe JE Jr
Cryo-EM structure of a RAS/RAF recruitment complex.
1. Nat Commun - published July 2, 2023
2. Park E, Rawson S, Schmoker A, Kim BW, Oh S, Song K, Jeon H, Eck MJ
Allosteric Modulation of Cytochrome P450 Enzymes by the NADPH Cytochrome P450 Reductase FMN-containing domain.
1. J Biol Chem - published July 2, 2023
2. Burris-Hiday SD, Scott EE
Structural insight into G-protein chaperone-mediated maturation of a bacterial adenosylcobalamin-dependent mutase.
1. J Biol Chem - published July 2, 2023
2. Vaccaro FA, Faber DA, Andree GA, Born DA, Kang G, Fonseca DR, Jost M, Drennan CL
Functional analyses of single nucleotide polymorphic variants of the DNA glycosylase NEIL1 present in sub-Saharan African populations.
1. DNA Repair (Amst) - published July 2, 2023
2. Zuckerman JT, Minko IG, Kant M, Jaruga P, Stone MP, Dizdaroglu M, McCullough AK, Lloyd RS
A standard data format for 3DED/MicroED.
1. Structure - published July 2, 2023
2. Waterman DG, Frisina N, Owen CD, Winter G, Nunes P
Arabinose- and xylose-modified analogs of 2',3'-cGAMP act as STING agonists.
1. Cell Chem Biol - published July 2, 2023
2. Xie W, Lama L, Yang X, Kuryavyi V, Bhattacharya S, Nudelman I, Yang G, Ouerfelli O, Glickman JF, Jones RA, Tuschl T, Patel DJ
Zinc finger 1 of the RING E3 ligase, RNF125, interacts with the E2 to enhance ubiquitylation.
1. Structure - published July 2, 2023
2. Middleton AJ, Barzak FM, Fokkens TJ, Nguyen K, Day CL
Structure determination of a DNA crystal by MicroED.
1. Structure - published July 2, 2023
2. Haymaker A, Bardin AA, Gonen T, Martynowycz MW, Nannenga BL
TMEM63 proteins function as monomeric high-threshold mechanosensitive ion channels.
1. Neuron - published July 2, 2023
2. Zheng W, Rawson S, Shen Z, Tamilselvan E, Smith HE, Halford J, Shen C, Murthy SE, Ulbrich MH, Sotomayor M, Fu TM, Holt JR
Design Optimization and Mechanical Properties of SiC Particle Reinforced Ti-Based Metallic Glass Matrix Composite.
1. Materials (Basel) - published July 2, 2023
2. Liu H, Li J, Zhang J, Gong P, Yang W, Zhao L, Wang X
Modeling of ACE2 and antibodies bound to SARS-CoV-2 provides insights into infectivity and immune evasion.
1. JCI Insight - published July 1, 2023
2. Lubin JH, Markosian C, Balamurugan D, Ma MT, Chen CH, Liu D, Pasqualini R, Arap W, Burley SK, Khare SD
Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM.
1. Acta Crystallogr D Struct Biol - published July 1, 2023
2. Herreros D, Krieger JM, Fonseca Y, Conesa P, Harastani M, Vuillemot R, Hamitouche I, Serrano Gutiérrez R, Gragera M, Melero R, Jonic S, Carazo JM, Sorzano COS
Machine learning for classifying narrow-beam electron diffraction data.
1. Acta Crystallogr A Found Adv - published July 1, 2023
2. Matinyan S, Demir B, Filipcik P, Abrahams JP, van Genderen E
rMSA: A Sequence Search and Alignment Algorithm to Improve RNA Structure Modeling.
1. J Mol Biol - published July 1, 2023
2. Zhang C, Zhang Y, Pyle AM
Naturally mutagenic sequence diversity in a human type II topoisomerase.
1. Proc Natl Acad Sci U S A - published July 1, 2023
2. Bandak AF, Blower TR, Nitiss KC, Gupta R, Lau AY, Guha R, Nitiss JL, Berger JM
A deep learning solution for crystallographic structure determination.
1. IUCrJ - published July 1, 2023
2. Pan T, Jin S, Miller MD, Kyrillidis A, Phillips GN Jr
Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein.
1. Nat Struct Mol Biol - published July 1, 2023
2. Zhang J, Tang W, Gao H, Lavine CL, Shi W, Peng H, Zhu H, Anand K, Kosikova M, Kwon HJ, Tong P, Gautam A, Rits-Volloch S, Wang S, Mayer ML, Wesemann DR, Seaman MS, Lu J, Xiao T, Xie H, Chen B
Membrane recruitment of the polarity protein Scribble by the cell adhesion receptor TMIGD1.
1. Commun Biol - published July 1, 2023
2. Thüring EM, Hartmann C, Maddumage JC, Javorsky A, Michels BE, Gerke V, Banks L, Humbert PO, Kvansakul M, Ebnet K
Increased neutralization potency and breadth elicited by a SARS-CoV-2 mRNA vaccine forming virus-like particles.
1. Proc Natl Acad Sci U S A - published July 1, 2023
2. Zhang P, Falcone S, Tsybovsky Y, Singh M, Gopan V, Miao H, Seo Y, Rogers D, Renzi I, Lai YT, Narayanan E, Stewart-Jones G, Himansu S, Carfi A, Fauci AS, Lusso P
Development of a Naked Eye CRISPR-Cas12a and -Cas13a Multiplex Point-of-Care Detection of Genetically Modified Swine.
1. ACS Synth Biol - published July 1, 2023
2. Wang Y, Fu L, Tao D, Han X, Xu B, Deng M, Li S, Zhao C, Li X, Zhao S, Gong P, Yang Y, Khazalwa EM, Ma Y, Ruan J, Li C, Xie S
Structural insights into NMDA receptor pharmacology.
1. Biochem Soc Trans - published July 1, 2023
2. Zhou C, Tajima N
Loss of TDP-43 oligomerization or RNA binding elicits distinct aggregation patterns.
1. EMBO J - published July 1, 2023
2. Pérez-Berlanga M, Wiersma VI, Zbinden A, De Vos L, Wagner U, Foglieni C, Mallona I, Betz KM, Cléry A, Weber J, Guo Z, Rigort R, de Rossi P, Manglunia R, Tantardini E, Sahadevan S, Stach O, Hruska-Plochan M, Allain FH, Paganetti P, Polymenidou M
NCCN Guidelines® Insights: Biliary Tract Cancers, Version 2.2023.
1. J Natl Compr Canc Netw - published July 1, 2023
2. Benson AB, D'Angelica MI, Abrams T, Abbott DE, Ahmed A, Anaya DA, Anders R, Are C, Bachini M, Binder D, Borad M, Bowlus C, Brown D, Burgoyne A, Castellanos J, Chahal P, Cloyd J, Covey AM, Glazer ES, Hawkins WG, Iyer R, Jacob R, Jennings L, Kelley RK, Kim R, Levine M, Palta M, Park JO, Raman S, Reddy S, Ronnekleiv-Kelly S, Sahai V, Singh G, Stein S, Turk A, Vauthey JN, Venook AP, Yopp A, McMillian N, Schonfeld R, Hochstetler C
An ankyrin repeat chaperone targets toxic oligomers during amyloidogenesis.
1. Protein Sci - published July 1, 2023
2. Gupta A, Lu C, Wang F, Chou TF, Shan SO
HIV-1 neutralizing antibodies elicited in humans by a prefusion-stabilized envelope trimer form a reproducible class targeting fusion peptide.
1. Cell Rep - published July 1, 2023
2. Wang S, Matassoli F, Zhang B, Liu T, Shen CH, Bylund T, Johnston T, Henry AR, Teng IT, Tripathi P, Becker JE, Changela A, Chaudhary R, Cheng C, Gaudinski M, Gorman J, Harris DR, Lee M, Morano NC, Novik L, O'Dell S, Olia AS, Parchment DK, Rawi R, Roberts-Torres J, Stephens T, Tsybovsky Y, Wang D, Van Wazer DJ, Zhou T, Doria-Rose NA, Koup RA, Shapiro L, Douek DC, McDermott AB, Kwong PD
Viral manipulation of cell polarity signalling.
1. Biochim Biophys Acta Mol Cell Res - published July 1, 2023
2. Javorsky A, Humbert PO, Kvansakul M
Engineering RNA export for measurement and manipulation of living cells.
1. Cell - published July 1, 2023
2. Horns F, Martinez JA, Fan C, Haque M, Linton JM, Tobin V, Santat L, Maggiolo AO, Bjorkman PJ, Lois C, Elowitz MB
Improved HIV-1 neutralization breadth and potency of V2-apex antibodies by in silico design.
1. Cell Rep - published July 1, 2023
2. Holt GT, Gorman J, Wang S, Lowegard AU, Zhang B, Liu T, Lin BC, Louder MK, Frenkel MS, McKee K, O'Dell S, Rawi R, Shen CH, Doria-Rose NA, Kwong PD, Donald BR
The mechanism of the phage-encoded protein antibiotic from ΦX174.
1. Science - published July 1, 2023
2. Orta AK, Riera N, Li YE, Tanaka S, Yun HG, Klaic L, Clemons WM Jr
Cryo-EM structures of full-length integrin αIIbβ3 in native lipids.
1. Nat Commun - published July 1, 2023
2. Adair BD, Xiong JP, Yeager M, Arnaout MA
Development of in-line anoxic small-angle X-ray scattering and structural characterization of an oxygen-sensing transcriptional regulator.
1. J Biol Chem - published July 1, 2023
2. Illava G, Gillilan R, Ando N
Mechanism of RanGTP priming H2A-H2B release from Kap114 in an atypical RanGTP•Kap114•H2A-H2B complex.
1. Proc Natl Acad Sci U S A - published July 1, 2023
2. Jiou J, Shaffer JM, Bernades NE, Fung HYJ, Kikumoto Dias J, D'Arcy S, Chook YM
Impact of misclassified defective proviruses on HIV reservoir measurements.
1. Nat Commun - published July 1, 2023
2. Reeves DB, Gaebler C, Oliveira TY, Peluso MJ, Schiffer JT, Cohn LB, Deeks SG, Nussenzweig MC
Modulation of IL-17 backbone dynamics reduces receptor affinity and reveals a new inhibitory mechanism.
1. Chem Sci - published July 1, 2023
2. Shaw DJ, Waters LC, Strong SL, Schulze MED, Greetham GM, Towrie M, Parker AW, Prosser CE, Henry AJ, Lawson ADG, Carr MD, Taylor RJ, Hunt NT, Muskett FW
Lrp1 is essential for lethal Rift Valley fever hepatic disease in mice.
1. Sci Adv - published July 1, 2023
2. Schwarz MM, Ganaie SS, Feng A, Brown G, Yangdon T, White JM, Hoehl RM, McMillen CM, Rush RE, Connors KA, Cui X, Leung DW, Egawa T, Amarasinghe GK, Hartman AL
Structural basis for specific RNA recognition by the alternative splicing factor RBM5.
1. Nat Commun - published July 1, 2023
2. Soni K, Jagtap PKA, Martínez-Lumbreras S, Bonnal S, Geerlof A, Stehle R, Simon B, Valcárcel J, Sattler M
Analysis of macerated ticks using Boolean logic gating colorimetric isothermal nucleic acid assays for Lyme Borrelia and Ixodes scapularis ticks.
1. Sci Rep - published July 1, 2023
2. Bhadra S, Esteve-Gasent MD, Ellington AD
Neurologic complications in herpes simplex encephalitis: clinical, immunological and genetic studies.
1. Brain - published July 1, 2023
2. Armangue T, Olivé-Cirera G, Martínez-Hernandez E, Rodes M, Peris-Sempere V, Guasp M, Ruiz R, Palou E, González A, Marcos MÁ, Erro ME, Bataller L, Corral-Corral Í, Planagumà J, Caballero E, Vlagea A, Chen J, Bastard P, Materna M, Marchal A, Abel L, Cobat A, Alsina L, Fortuny C, Saiz A, Mignot E, Vanderver A, Casanova JL, Zhang SY, Dalmau J
Bacterial TANGO2 homologs are heme-trafficking proteins that facilitate biosynthesis of cytochromes c.
1. mBio - published July 1, 2023
2. Han S, Guo K, Wang W, Tao YJ, Gao H
A murine model of hnRNPH2-related neurodevelopmental disorder reveals a mechanism for genetic compensation by Hnrnph1.
1. J Clin Invest - published July 1, 2023
2. Korff A, Yang X, O'Donovan K, Gonzalez A, Teubner BJ, Nakamura H, Messing J, Yang F, Carisey AF, Wang YD, Patni T, Sheppard H, Zakharenko SS, Chook YM, Taylor JP, Kim HJ
Allosteric activation of vinculin by talin.
1. Nat Commun - published July 1, 2023
2. Franz F, Tapia-Rojo R, Winograd-Katz S, Boujemaa-Paterski R, Li W, Unger T, Albeck S, Aponte-Santamaria C, Garcia-Manyes S, Medalia O, Geiger B, Gräter F
RNA target highlights in CASP15: Evaluation of predicted models by structure providers.
1. Proteins - published July 1, 2023
2. Kretsch RC, Andersen ES, Bujnicki JM, Chiu W, Das R, Luo B, Masquida B, McRae EKS, Schroeder GM, Su Z, Wedekind JE, Xu L, Zhang K, Zheludev IN, Moult J, Kryshtafovych A
The peroxidation-derived DNA adduct, 6-oxo-M(1)dG, is a strong block to replication by human DNA polymerase η.
1. J Biol Chem - published July 1, 2023
2. Richie-Jannetta R, Pallan P, Kingsley PJ, Kamdar N, Egli M, Marnett LJ
Interplay of thermodynamics and evolution within the ternary ligand-GPCR-G protein complex.
1. Curr Opin Struct Biol - published July 1, 2023
2. Junker H, Meiler J, Schoeder CT
Advances, Applications, and Perspectives in Small-Angle X-ray Scattering of RNA.
1. Chembiochem - published July 1, 2023
2. Tants JN, Schlundt A
Biphasic JNK-Erk signaling separates the induction and maintenance of cell senescence after DNA damage induced by topoisomerase II inhibition.
1. Cell Syst - published July 1, 2023
2. Netterfield TS, Ostheimer GJ, Tentner AR, Joughin BA, Dakoyannis AM, Sharma CD, Sorger PK, Janes KA, Lauffenburger DA, Yaffe MB
UBR5 forms ligand-dependent complexes on chromatin to regulate nuclear hormone receptor stability.
1. Mol Cell - published July 1, 2023
2. Tsai JM, Aguirre JD, Li YD, Brown J, Focht V, Kater L, Kempf G, Sandoval B, Schmitt S, Rutter JC, Galli P, Sandate CR, Cutler JA, Zou C, Donovan KA, Lumpkin RJ, Cavadini S, Park PMC, Sievers Q, Hatton C, Ener E, Regalado BD, Sperling MT, Słabicki M, Kim J, Zon R, Zhang Z, Miller PG, Belizaire R, Sperling AS, Fischer ES, Irizarry R, Armstrong SA, Thomä NH, Ebert BL
Acetylation of the NS3 helicase by KAT5γ is essential for flavivirus replication.
1. Cell Host Microbe - published July 1, 2023
2. Serman T, Chiang C, Liu G, Sayyad Z, Pandey S, Volcic M, Lee H, Muppala S, Acharya D, Goins C, Stauffer SR, Sparrer KMJ, Gack MU
Loss of SYNCRIP unleashes APOBEC-driven mutagenesis, tumor heterogeneity, and AR-targeted therapy resistance in prostate cancer.
1. Cancer Cell - published July 1, 2023
2. Li X, Wang Y, Deng S, Zhu G, Wang C, Johnson NA, Zhang Z, Tirado CR, Xu Y, Metang LA, Gonzalez J, Mukherji A, Ye J, Yang Y, Peng W, Tang Y, Hofstad M, Xie Z, Yoon H, Chen L, Liu X, Chen S, Zhu H, Strand D, Liang H, Raj G, He HH, Mendell JT, Li B, Wang T, Mu P
SUB1A-1 anchors a regulatory cascade for epigenetic and transcriptional controls of submergence tolerance in rice.
1. PNAS Nexus - published July 1, 2023
2. Lin CC, Lee WJ, Zeng CY, Chou MY, Lin TJ, Lin CS, Ho MC, Shih MC
Serological Survey of Retrovirus and Coronavirus Infections, including SARS-CoV-2, in Rural Stray Cats in The Netherlands, 2020-2022.
1. Viruses - published July 1, 2023
2. Duijvestijn MBHM, Schuurman NNMP, Vernooij JCM, van Leeuwen MAJM, Bosch BJ, van den Brand JMA, Wagenaar JA, van Kuppeveld FJM, Egberink HF, Verhagen JH
Structural basis for membrane-proximal proteolysis of substrates by ADAM10.
1. Cell - published July 1, 2023
2. Lipper CH, Egan ED, Gabriel KH, Blacklow SC