Member Publications

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131 Member Publications for November 2021

Engineered Metal-Binding Sites to Probe Protein Folding Transition States: Psi Analysis.
1. Methods Mol Biol - published November 30, 2021
2. Baxa MC, Sosnick TR
NLRP3 cages revealed by full-length mouse NLRP3 structure control pathway activation.
1. Cell - published November 30, 2021
2. Andreeva L, David L, Rawson S, Shen C, Pasricha T, Pelegrin P, Wu H
Cyclodextrins for structural and functional studies of mechanosensitive channels.
1. J Struct Biol X - published November 24, 2021
2. Zhang Y, Angiulli G, Martinac B, Cox CD, Walz T
Rapid relaxation of pandemic restrictions after vaccine rollout favors growth of SARS-CoV-2 variants: A model-based analysis.
1. PLoS One - published November 24, 2021
2. Van Egeren D, Stoddard M, Novokhodko A, Rogers MS, Joseph-McCarthy D, Zetter B, Chakravarty A
Classification and Characteristics of Mesenchymal Stem Cells and Its Potential Therapeutic Mechanisms and Applications against Ischemic Stroke.
1. Stem Cells Int - published November 19, 2021
2. Gong P, Zhang W, He Y, Wang J, Li S, Chen S, Ye Q, Li M
De novo identification of mammalian ciliary motility proteins using cryo-EM.
1. Cell - published November 11, 2021
2. Gui M, Farley H, Anujan P, Anderson JR, Maxwell DW, Whitchurch JB, Botsch JJ, Qiu T, Meleppattu S, Singh SK, Zhang Q, Thompson J, Lucas JS, Bingle CD, Norris DP, Roy S, Brown A
Relating cellular signaling timescales to single-molecule kinetics: A first-passage time analysis of Ras activation by SOS.
1. Proc Natl Acad Sci U S A - published November 9, 2021
2. Huang WYC, Alvarez S, Kondo Y, Kuriyan J, Groves JT
Extended antibody-framework-to-antigen distance observed exclusively with broad HIV-1-neutralizing antibodies recognizing glycan-dense surfaces.
1. Nat Commun - published November 9, 2021
2. Lee M, Changela A, Gorman J, Rawi R, Bylund T, Chao CW, Lin BC, Louder MK, Olia AS, Zhang B, Doria-Rose NA, Zolla-Pazner S, Shapiro L, Chuang GY, Kwong PD
The chemotherapeutic CX-5461 primarily targets TOP2B and exhibits selective activity in high-risk neuroblastoma.
1. Nat Commun - published November 9, 2021
2. Pan M, Wright WC, Chapple RH, Zubair A, Sandhu M, Batchelder JE, Huddle BC, Low J, Blankenship KB, Wang Y, Gordon B, Archer P, Brady SW, Natarajan S, Posgai MJ, Schuetz J, Miller D, Kalathur R, Chen S, Connelly JP, Babu MM, Dyer MA, Pruett-Miller SM, Freeman BB 3rd, Chen T, Godley LA, Blanchard SC, Stewart E, Easton J, Geeleher P
Multifaceted N-degron recognition and ubiquitylation by GID/CTLH E3 ligases.
1. J Mol Biol - published November 9, 2021
2. Chrustowicz J, Sherpa D, Teyra J, Siong Loke M, Popowicz G, Basquin J, Sattler M, Rajan Prabu J, Sidhu SS, Schulman BA
Effector-mediated membrane disruption controls cell death in CBASS antiphage defense.
1. Mol Cell - published November 9, 2021
2. Duncan-Lowey B, McNamara-Bordewick NK, Tal N, Sorek R, Kranzusch PJ
Mechanisms of Nucleosome Reorganization by PARP1.
1. Int J Mol Sci - published November 9, 2021
2. Maluchenko NV, Nilov DK, Pushkarev SV, Kotova EY, Gerasimova NS, Kirpichnikov MP, Langelier MF, Pascal JM, Akhtar MS, Feofanov AV, Studitsky VM
Electron Microscopy Techniques for Investigating Structure and Composition of Hair-Cell Stereociliary Bundles.
1. Front Cell Dev Biol - published November 8, 2021
2. Ivanchenko MV, Indzhykulian AA, Corey DP
Structural insights into the interactions of Polycomb Repressive Complex 2 with chromatin.
1. Biochem Soc Trans - published November 8, 2021
2. Iragavarapu AG, Yao L, Kasinath V
An Open Drug Discovery Competition: Experimental Validation of Predictive Models in a Series of Novel Antimalarials.
1. J Med Chem - published November 8, 2021
2. Tse EG, Aithani L, Anderson M, Cardoso-Silva J, Cincilla G, Conduit GJ, Galushka M, Guan D, Hallyburton I, Irwin BWJ, Kirk K, Lehane AM, Lindblom JCR, Lui R, Matthews S, McCulloch J, Motion A, Ng HL, Öeren M, Robertson MN, Spadavecchio V, Tatsis VA, van Hoorn WP, Wade AD, Whitehead TM, Willis P, Todd MH
Computational redesign of a fluorogen activating protein with Rosetta.
1. PLoS Comput Biol - published November 8, 2021
2. Bozhanova NG, Harp JM, Bender BJ, Gavrikov AS, Gorbachev DA, Baranov MS, Mercado CB, Zhang X, Lukyanov KA, Mishin AS, Meiler J
DIALS as a toolkit.
1. Protein Sci - published November 8, 2021
2. Winter G, Beilsten-Edmands J, Devenish N, Gerstel M, Gildea RJ, McDonagh D, Pascal E, Waterman DG, Williams BH, Evans G
Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption.
1. PLoS Pathog - published November 8, 2021
2. Ren W, Lan J, Ju X, Gong M, Long Q, Zhu Z, Yu Y, Wu J, Zhong J, Zhang R, Fan S, Zhong G, Huang A, Wang X, Ding Q
Sumoylation of the human histone H4 tail inhibits p300-mediated transcription by RNA polymerase II in cellular extracts.
1. Elife - published November 8, 2021
2. Leonen CJA, Shimada M, Weller CE, Nakadai T, Hsu PL, Tyson EL, Mishra A, Shelton PMM, Sadilek M, Hawkins RD, Zheng N, Roeder RG, Chatterjee C
Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data.
1. Nat Biomed Eng - published November 8, 2021
2. Rashid R, Chen YA, Hoffer J, Muhlich JL, Lin JR, Krueger R, Pfister H, Mitchell R, Santagata S, Sorger PK
Asymmetric requirement of Dpp/BMP morphogen dispersal in the Drosophila wing disc.
1. Nat Commun - published November 8, 2021
2. Matsuda S, Schaefer JV, Mii Y, Hori Y, Bieli D, Taira M, Plückthun A, Affolter M
Structure of the human Meckel-Gruber protein Meckelin.
1. Sci Adv - published November 5, 2021
2. Liu D, Qian D, Shen H, Gong D
Mapping the catalytic conformations of an assembly-line polyketide synthase module.
1. Science - published November 5, 2021
2. Cogan DP, Zhang K, Li X, Li S, Pintilie GD, Roh SH, Craik CS, Chiu W, Khosla C
Modular polyketide synthase contains two reaction chambers that operate asynchronously.
1. Science - published November 5, 2021
2. Bagde SR, Mathews II, Fromme JC, Kim CY
The Caenorhabditis elegans Patched domain protein PTR-4 is required for proper organization of the precuticular apical extracellular matrix.
1. Genetics - published November 5, 2021
2. Cohen JD, Cadena Del Castillo CE, Serra ND, Kaech A, Spang A, Sundaram MV
Biomechanical Performance of BoneHelix^® Compared with Elastic Stable Intramedullary Nailing (ESIN) in a Pediatric Tibia Fracture Model.
1. Life (Basel) - published November 5, 2021
2. Brandes LL, Nicolini LF, Greven J, Lichte P, Stopinski TT, Sattler M, Hildebrand F, Pishnamaz M
Identification of Novel and Recurrent Variants in MYO15A in Ashkenazi Jewish Patients With Autosomal Recessive Nonsyndromic Hearing Loss.
1. Front Genet - published November 4, 2021
2. Booth KT, Hirsch Y, Vardaro AC, Ekstein J, Yefet D, Quint A, Weiden T, Corey DP
Discovery and Preclinical Characterization of BIIB091, a Reversible, Selective BTK Inhibitor for the Treatment of Multiple Sclerosis.
1. J Med Chem - published November 4, 2021
2. Hopkins BT, Bame E, Bajrami B, Black C, Bohnert T, Boiselle C, Burdette D, Burns JC, Delva L, Donaldson D, Grater R, Gu C, Hoemberger M, Johnson J, Kapadnis S, King K, Lulla M, Ma B, Marx I, Magee T, Meissner R, Metrick CM, Mingueneau M, Murugan P, Otipoby KL, Polack E, Poreci U, Prince R, Roach AM, Rowbottom C, Santoro JC, Schroeder P, Tang H, Tien E, Zhang F, Lyssikatos J
Rapid assessment of SARS-CoV-2 evolved variants using virus-like particles.
1. Science - published November 4, 2021
2. Syed AM, Taha TY, Tabata T, Chen IP, Ciling A, Khalid MM, Sreekumar B, Chen PY, Hayashi JM, Soczek KM, Ott M, Doudna JA
Sensory transduction is required for normal development and maturation ofcochlear inner hair cell synapses.
1. Elife - published November 4, 2021
2. Lee J, Kosuke Kawai K, Holt JR, Geleoc G
A recurrent SHANK3 frameshift variant in Autism Spectrum Disorder.
1. NPJ Genom Med - published November 4, 2021
2. Loureiro LO, Howe JL, Reuter MS, Iaboni A, Calli K, Roshandel D, Pritišanac I, Moses A, Forman-Kay JD, Trost B, Zarrei M, Rennie O, Lau LYS, Marshall CR, Srivastava S, Godlewski B, Buttermore ED, Sahin M, Hartley D, Frazier T, Vorstman J, Georgiades S, Lewis SME, Szatmari P, Bradley CAL, Tabet AC, Willems M, Lumbroso S, Piton A, Lespinasse J, Delorme R, Bourgeron T, Anagnostou E, Scherer SW
Conformational dynamics of auto-inhibition in the ER calcium sensor STIM1.
1. Elife - published November 3, 2021
2. van Dorp S, Qiu R, Choi UB, Wu MM, Yen M, Kirmiz M, Brunger AT, Lewis RS
Hydrolytically Stable Maleimide-End-Functionalized Polymers for Site-Specific Protein Conjugation.
1. Bioconjug Chem - published November 3, 2021
2. Wright TA, Rahman MS, Bennett C, Johnson MR, Fischesser H, Ram N, Tyler A, Page RC, Konkolewicz D
A look at the lives of lipids.
1. Curr Opin Chem Biol - published November 3, 2021
2. Baskin JM, Seeliger JC
RTN4/NoGo-receptor binding to BAI adhesion-GPCRs regulates neuronal development.
1. Cell - published November 3, 2021
2. Wang J, Miao Y, Wicklein R, Sun Z, Wang J, Jude KM, Fernandes RA, Merrill SA, Wernig M, Garcia KC, Südhof TC
Click chemistry-enabled CRISPR screening reveals GSK3 as a regulator of PLD signaling.
1. Proc Natl Acad Sci U S A - published November 3, 2021
2. Bumpus TW, Huang S, Tei R, Baskin JM
Molecular structure of an open human K_ATP channel.
1. Proc Natl Acad Sci U S A - published November 3, 2021
2. Zhao C, MacKinnon R
Translesion polymerase eta both facilitates DNA replication and promotes increased human genetic variation at common fragile sites.
1. Proc Natl Acad Sci U S A - published November 3, 2021
2. Twayana S, Bacolla A, Barreto-Galvez A, De-Paula RB, Drosopoulos WC, Kosiyatrakul ST, Bouhassira EE, Tainer JA, Madireddy A, Schildkraut CL
Structure and Dynamics of the Guanidine-II Riboswitch from Escherichia coli by NMR Spectroscopy and Small-angle X-ray Scattering (SAXS).
1. Chembiochem - published November 3, 2021
2. Schamber T, Binas O, Schlundt A, Wacker A, Schwalbe H
A molecular mechanism for the generation of ligand-dependent differential outputs by the epidermal growth factor receptor.
1. Elife - published November 3, 2021
2. Huang Y, Ognjenovic J, Karandur D, Miller K, Merk A, Subramaniam S, Kuriyan J
Neuropilin 1 regulates bone marrow vascular regeneration and hematopoietic reconstitution.
1. Nat Commun - published November 3, 2021
2. Termini CM, Pang A, Fang T, Roos M, Chang VY, Zhang Y, Setiawan NJ, Signaevskaia L, Li M, Kim MM, Tabibi O, Lin PK, Sasine JP, Chatterjee A, Murali R, Himburg HA, Chute JP
Ribosome Profiling Reveals Novel Regulation of C9ORF72 GGGGCC Repeat-Containing RNA Translation.
1. RNA - published November 3, 2021
2. van 't Spijker HM, Stackpole EE, Almeida S, Katsara O, Liu B, Shen K, Schneider RJ, Gao FB, Richter JD
The active site region plays a critical role in Na⁺ binding to thrombin.
1. J Biol Chem - published November 3, 2021
2. Pelc LA, Koester SK, Kukla CR, Chen Z, Di Cera E
SepA Enhances Shigella Invasion of Epithelial Cells by Degrading Alpha-1 Antitrypsin and Producing a Neutrophil Chemoattractant.
1. mBio - published November 2, 2021
2. Meza-Segura M, Birtley JR, Maldonado-Contreras A, Mueller C, Simin KJ, Stern LJ, McCormick BA
A broadly cross-reactive antibody neutralizes and protects against sarbecovirus challenge in mice.
1. Sci Transl Med - published November 2, 2021
2. Martinez DR, Schäfer A, Gobeil S, Li D, De la Cruz G, Parks R, Lu X, Barr M, Stalls V, Janowska K, Beaudoin E, Manne K, Mansouri K, Edwards RJ, Cronin K, Yount B, Anasti K, Montgomery SA, Tang J, Golding H, Shen S, Zhou T, Kwong PD, Graham BS, Mascola JR, Montefiori DC, Alam SM, Sempowski GD, Khurana S, Wiehe K, Saunders KO, Acharya P, Haynes BF, Baric RS
The tumor suppressor activity of DLC1 requires the interaction of its START domain with Phosphatidylserine, PLCD1, and Caveolin-1.
1. Mol Cancer - published November 2, 2021
2. Sanchez-Solana B, Wang D, Qian X, Velayoudame P, Simanshu DK, Acharya JK, Lowy DR
Structural basis of glycan276-dependent recognition by HIV-1 broadly neutralizing antibodies.
1. Cell Rep - published November 2, 2021
2. Cottrell CA, Manne K, Kong R, Wang S, Zhou T, Chuang GY, Edwards RJ, Henderson R, Janowska K, Kopp M, Lin BC, Louder MK, Olia AS, Rawi R, Shen CH, Taft JD, Torres JL, Wu NR, Zhang B, Doria-Rose NA, Cohen MS, Haynes BF, Shapiro L, Ward AB, Acharya P, Mascola JR, Kwong PD
Molecular and structural basis of olfactory sensory neuron axon coalescence by Kirrel receptors.
1. Cell Rep - published November 2, 2021
2. Wang J, Vaddadi N, Pak JS, Park Y, Quilez S, Roman CA, Dumontier E, Thornton JW, Cloutier JF, Özkan E
Crystal structure of the Tspan15 LEL domain reveals a conserved ADAM10 binding site.
1. Structure - published November 2, 2021
2. Lipper CH, Gabriel KH, Seegar TCM, Dürr KL, Tomlinson MG, Blacklow SC
Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation.
1. Cancer Cell - published November 2, 2021
2. Duraiswamy J, Turrini R, Minasyan A, Barras D, Crespo I, Grimm AJ, Casado J, Genolet R, Benedetti F, Wicky A, Ioannidou K, Castro W, Neal C, Moriot A, Renaud-Tissot S, Anstett V, Fahr N, Tanyi JL, Eiva MA, Jacobson CA, Montone KT, Westergaard MCW, Svane IM, Kandalaft LE, Delorenzi M, Sorger PK, Färkkilä A, Michielin O, Zoete V, Carmona SJ, Foukas PG, Powell DJ Jr, Rusakiewicz S, Doucey MA, Dangaj Laniti D, Coukos G
Disrupting Roquin-1 interaction with Regnase-1 induces autoimmunity and enhances antitumor responses.
1. Nat Immunol - published November 2, 2021
2. Behrens G, Edelmann SL, Raj T, Kronbeck N, Monecke T, Davydova E, Wong EH, Kifinger L, Giesert F, Kirmaier ME, Hohn C, de Jonge LS, Pisfil MG, Fu M, Theurich S, Feske S, Kawakami N, Wurst W, Niessing D, Heissmeyer V
Structure of the human SAGA coactivator complex.
1. Nat Struct Mol Biol - published November 2, 2021
2. Herbst DA, Esbin MN, Louder RK, Dugast-Darzacq C, Dailey GM, Fang Q, Darzacq X, Tjian R, Nogales E
Crystal structure of the potato leafroll virus coat protein and implications for viral assembly.
1. J Struct Biol - published November 2, 2021
2. Adams MC, Schiltz CJ, Heck ML, Chappie JS
Colloidal Aggregators in Biochemical SARS-CoV-2 Repurposing Screens.
1. J Med Chem - published November 2, 2021
2. O'Donnell HR, Tummino TA, Bardine C, Craik CS, Shoichet BK
Evidence for an Enzyme-Catalyzed Rauhut-Currier Reaction during the Biosynthesis of Spinosyn A.
1. J Am Chem Soc - published November 2, 2021
2. Choi SH, Jeon B, Kim N, Wu HH, Ko TP, Ruszczycky MW, Isiorho EA, Liu YN, Keatinge-Clay AT, Tsai MD, Liu HW
Cellular origins of dsRNA, their recognition and consequences.
1. Nat Rev Mol Cell Biol - published November 2, 2021
2. Chen YG, Hur S
Molecular basis for the evolved instability of a human G-protein coupled receptor.
1. Cell Rep - published November 2, 2021
2. Chamness LM, Zelt NB, Harrington HR, Kuntz CP, Bender BJ, Penn WD, Ziarek JJ, Meiler J, Schlebach JP
Sequential immunization of macaques elicits heterologous neutralizing antibodies targeting the V3-glycan patch of HIV-1 Env.
1. Sci Transl Med - published November 2, 2021
2. Escolano A, Gristick HB, Gautam R, DeLaitsch AT, Abernathy ME, Yang Z, Wang H, Hoffmann MAG, Nishimura Y, Wang Z, Koranda N, Kakutani LM, Gao H, Gnanapragasam PNP, Raina H, Gazumyan A, Cipolla M, Oliveira TY, Ramos V, Irvine DJ, Silva M, West AP Jr, Keeffe JR, Barnes CO, Seaman MS, Nussenzweig MC, Martin MA, Bjorkman PJ
Glucose metabolism and pyruvate carboxylase enhance glutathione synthesis and restrict oxidative stress in pancreatic islets.
1. Cell Rep - published November 2, 2021
2. Fu A, van Rooyen L, Evans L, Armstrong N, Avizonis D, Kin T, Bird GH, Reddy A, Chouchani ET, Liesa-Roig M, Walensky LD, Shapiro AMJ, Danial NN
Glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein.
1. J Virol - published November 2, 2021
2. Zhang S, Go EP, Ding H, Anang S, Kappes JC, Desaire H, Sodroski JG
The encapsulin from Thermotoga maritima is a flavoprotein with a symmetry matched ferritin-like cargo protein.
1. Sci Rep - published November 2, 2021
2. LaFrance BJ, Cassidy-Amstutz C, Nichols RJ, Oltrogge LM, Nogales E, Savage DF
Binding of Natural Peptide Ligands to the Neuropeptide Y5 Receptor.
1. Angew Chem Int Ed Engl - published November 2, 2021
2. Rudolf S, Kaempf K, Vu O, Meiler J, Beck-Sickinger AG, Coin I
Golgi membrane protein Erd1 Is essential for recycling a subset of Golgi glycosyltransferases.
1. Elife - published November 2, 2021
2. Sardana R, Highland CM, Straight BE, Chavez CF, Fromme JC, Emr SD
ANTH domains within CALM, HIP1R, and Sla2 recognize ubiquitin internalization signals.
1. Elife - published November 2, 2021
2. Pashkova N, Gakhar L, Yu L, Schnicker NJ, Minard AY, Winistorfer S, Johnson IE, Piper RC
Structural basis for ligand reception by anaplastic lymphoma kinase.
1. Nature - published November 2, 2021
2. Li T, Stayrook SE, Tsutsui Y, Zhang J, Wang Y, Li H, Proffitt A, Krimmer SG, Ahmed M, Belliveau O, Walker IX, Mudumbi KC, Suzuki Y, Lax I, Alvarado D, Lemmon MA, Schlessinger J, Klein DE
Mechanism for the activation of the anaplastic lymphoma kinase receptor.
1. Nature - published November 2, 2021
2. Reshetnyak AV, Rossi P, Myasnikov AG, Sowaileh M, Mohanty J, Nourse A, Miller DJ, Lax I, Schlessinger J, Kalodimos CG
Comparison of the immunogenicity of BNT162b2 and CoronaVac COVID-19 vaccines in Hong Kong.
1. Respirology - published November 2, 2021
2. Mok CKP, Cohen CA, Cheng SMS, Chen C, Kwok KO, Yiu K, Chan TO, Bull M, Ling KC, Dai Z, Ng SS, Lui GC, Wu C, Amarasinghe GK, Leung DW, Wong SYS, Valkenburg SA, Peiris M, Hui DS
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging.
1. Nat Methods - published November 2, 2021
2. Schapiro D, Sokolov A, Yapp C, Chen YA, Muhlich JL, Hess J, Creason AL, Nirmal AJ, Baker GJ, Nariya MK, Lin JR, Maliga Z, Jacobson CA, Hodgman MW, Ruokonen J, Farhi SL, Abbondanza D, McKinley ET, Persson D, Betts C, Sivagnanam S, Regev A, Goecks J, Coffey RJ, Coussens LM, Santagata S, Sorger PK
Structures of tweety homolog proteins TTYH2 and TTYH3 reveal a Ca²⁺-dependent switch from intra- to intermembrane dimerization.
1. Nat Commun - published November 2, 2021
2. Li B, Hoel CM, Brohawn SG
Clostridioides difficile toxins: mechanisms of action and antitoxin therapeutics.
1. Nat Rev Microbiol - published November 2, 2021
2. Kordus SL, Thomas AK, Lacy DB
A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses.
1. Emerg Microbes Infect - published November 2, 2021
2. Wang P, Casner RG, Nair MS, Yu J, Guo Y, Wang M, Chan JF, Cerutti G, Iketani S, Liu L, Sheng Z, Chen Z, Yuen KY, Kwong PD, Huang Y, Shapiro L, Ho DD
Structural evolution of a DNA repair self-resistance mechanism targeting genotoxic secondary metabolites.
1. Nat Commun - published November 2, 2021
2. Mullins EA, Dorival J, Tang GL, Boger DL, Eichman BF
Cryo-EM structures and biochemical insights into heterotrimeric PCNA regulation of DNA ligase.
1. Structure - published November 2, 2021
2. Sverzhinsky A, Tomkinson AE, Pascal JM
Relaxed Substrate Requirements of Sterol 14α-Demethylase from Naegleria fowleri Are Accompanied by Resistance to Inhibition.
1. J Med Chem - published November 2, 2021
2. Hargrove TY, Wawrzak Z, Rachakonda G, Nes WD, Villalta F, Guengerich FP, Lepesheva GI
Structural insights into proteolytic activation of the human Dispatched1 transporter for Hedgehog morphogen release.
1. Nat Commun - published November 2, 2021
2. Li W, Wang L, Wierbowski BM, Lu M, Dong F, Liu W, Li S, Wang P, Salic A, Gong X
Genetically encoded photo-switchable molecular sensors for optoacoustic and super-resolution imaging.
1. Nat Biotechnol - published November 2, 2021
2. Mishra K, Fuenzalida-Werner JP, Pennacchietti F, Janowski R, Chmyrov A, Huang Y, Zakian C, Klemm U, Testa I, Niessing D, Ntziachristos V, Stiel AC
Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks.
1. Nat Commun - published November 2, 2021
2. Koehler Leman J, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetič A, Loshbaugh AL, Maguire J, Moretti R, Mulligan VK, Nance ML, Nguyen PT, Ó Conchúir S, Roy Burman SS, Samanta R, Smith ST, Teets F, Tiemann JKS, Watkins A, Woods H, Yachnin BJ, Bahl CD, Bailey-Kellogg C, Baker D, Das R, DiMaio F, Khare SD, Kortemme T, Labonte JW, Lindorff-Larsen K, Meiler J, Schief W, Schueler-Furman O, Siegel JB, Stein A, Yarov-Yarovoy V, Kuhlman B, Leaver-Fay A, Gront D, Gray JJ, Bonneau R
Structure, dynamics, and function of SrnR, a transcription factor for nickel-dependent gene expression.
1. Metallomics - published November 2, 2021
2. Mazzei L, Musiani F, Żerko S, Koźminski W, Cianci M, Beniamino Y, Ciurli S, Zambelli B
Discovery of highly reactive self-splicing group II introns within the mitochondrial genomes of human pathogenic fungi.
1. Nucleic Acids Res - published November 2, 2021
2. Liu T, Pyle AM
Physiological and pharmacological modulation of BAX.
1. Trends Pharmacol Sci - published November 2, 2021
2. Spitz AZ, Gavathiotis E
Chromosome segregation in Archaea: SegA- and SegB-DNA complex structures provide insights into segrosome assembly.
1. Nucleic Acids Res - published November 2, 2021
2. Yen CY, Lin MG, Chen BW, Ng IW, Read N, Kabli AF, Wu CT, Shen YY, Chen CH, Barillà D, Sun YJ, Hsiao CD
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation.
1. Nucleic Acids Res - published November 2, 2021
2. Quaglia F, Mészáros B, Salladini E, Hatos A, Pancsa R, Chemes LB, Pajkos M, Lazar T, Peña-Díaz S, Santos J, Ács V, Farahi N, Fichó E, Aspromonte MC, Bassot C, Chasapi A, Davey NE, Davidović R, Dobson L, Elofsson A, Erdős G, Gaudet P, Giglio M, Glavina J, Iserte J, Iglesias V, Kálmán Z, Lambrughi M, Leonardi E, Longhi S, Macedo-Ribeiro S, Maiani E, Marchetti J, Marino-Buslje C, Mészáros A, Monzon AM, Minervini G, Nadendla S, Nilsson JF, Novotný M, Ouzounis CA, Palopoli N, Papaleo E, Pereira PJB, Pozzati G, Promponas VJ, Pujols J, Rocha ACS, Salas M, Sawicki LR, Schad E, Shenoy A, Szaniszló T, Tsirigos KD, Veljkovic N, Parisi G, Ventura S, Dosztányi Z, Tompa P, Tosatto SCE, Piovesan D
GLYCO: a tool to quantify glycan shielding of glycosylated proteins.
1. Bioinformatics - published November 2, 2021
2. Lee M, Reveiz M, Rawi R, Kwong PD, Chuang GY
Biochemical basis for an interaction between SNX27 and the flexible SNX1 N-terminus.
1. Adv Biol Regul - published November 2, 2021
2. Chandra M, Collins BM, Jackson LP
mTORC1 Promotes ARID1A Degradation and Oncogenic Chromatin Remodeling in Hepatocellular Carcinoma.
1. Cancer Res - published November 1, 2021
2. Zhang S, Zhou YF, Cao J, Burley SK, Wang HY, Zheng XFS
The hypervariable region of atlastin-1 is a site for intrinsic and extrinsic regulation.
1. J Cell Biol - published November 1, 2021
2. Kelly CM, Byrnes LJ, Neela N, Sondermann H, O'Donnell JP
Patterns of Failure in Metastatic Non-Small Cell Lung Cancer Patients After Initiation of Pembrolizumab.
1. Int J Radiat Oncol Biol Phys - published November 1, 2021
2. All S, Iyengar P, Westover KD, Choy H, Rashdan S, Lohrey J, Hughes R, Dowell J, Gerber DE, Vo DT
Molecular Characterization of AMPA-Receptor-Containing Vesicles.
1. Front Mol Neurosci - published November 1, 2021
2. Peters JJ, Leitz J, Oses-Prieto JA, Burlingame AL, Brunger AT
The Q61H mutation decouples KRAS from upstream regulation and renders cancer cells resistant to SHP2 inhibitors.
1. Nat Commun - published November 1, 2021
2. Gebregiworgis T, Kano Y, St-Germain J, Radulovich N, Udaskin ML, Mentes A, Huang R, Poon BPK, He W, Valencia-Sama I, Robinson CM, Huestis M, Miao J, Yeh JJ, Zhang ZY, Irwin MS, Lee JE, Tsao MS, Raught B, Marshall CB, Ohh M, Ikura M
A Slam-dependent hemophore contributes to heme acquisition in the bacterial pathogen Acinetobacter baumannii.
1. Nat Commun - published November 1, 2021
2. Bateman TJ, Shah M, Ho TP, Shin HE, Pan C, Harris G, Fegan JE, Islam EA, Ahn SK, Hooda Y, Gray-Owen SD, Chen W, Moraes TF
John D. Westbrook Jr (1957-2021).
1. Acta Crystallogr D Struct Biol - published November 1, 2021
2. Zardecki C, Burley SK
Functional differences among the spike glycoproteins of multiple emerging SARS-CoV-2 variants of concern.
1. iScience - published November 1, 2021
2. Wang Q, Nair MS, Anang S, Zhang S, Nguyen H, Huang Y, Liu L, Ho DD, Sodroski JG
Structures of the HER2-HER3-NRG1β complex reveal a dynamic dimer interface.
1. Nature - published November 1, 2021
2. Diwanji D, Trenker R, Thaker TM, Wang F, Agard DA, Verba KA, Jura N
Structural basis and mechanism of activation of two different families of G proteins by the same GPCR.
1. Nat Struct Mol Biol - published November 1, 2021
2. Alegre KO, Paknejad N, Su M, Lou JS, Huang J, Jordan KD, Eng ET, Meyerson JR, Hite RK, Huang XY
Target site selection and remodelling by type V CRISPR-transposon systems.
1. Nature - published November 1, 2021
2. Querques I, Schmitz M, Oberli S, Chanez C, Jinek M
Computed structures of core eukaryotic protein complexes.
1. Science - published November 1, 2021
2. Humphreys IR, Pei J, Baek M, Krishnakumar A, Anishchenko I, Ovchinnikov S, Zhang J, Ness TJ, Banjade S, Bagde SR, Stancheva VG, Li XH, Liu K, Zheng Z, Barrero DJ, Roy U, Kuper J, Fernández IS, Szakal B, Branzei D, Rizo J, Kisker C, Greene EC, Biggins S, Keeney S, Miller EA, Fromme JC, Hendrickson TL, Cong Q, Baker D
The Crystal Structure of Cysteamine Dioxygenase Reveals the Origin of the Large Substrate Scope of This Vital Mammalian Enzyme.
1. Biochemistry - published November 1, 2021
2. Fernandez RL, Elmendorf LD, Smith RW, Bingman CA, Fox BG, Brunold TC
Connecting copper and cancer: from transition metal signalling to metalloplasia.
1. Nat Rev Cancer - published November 1, 2021
2. Ge EJ, Bush AI, Casini A, Cobine PA, Cross JR, DeNicola GM, Dou QP, Franz KJ, Gohil VM, Gupta S, Kaler SG, Lutsenko S, Mittal V, Petris MJ, Polishchuk R, Ralle M, Schilsky ML, Tonks NK, Vahdat LT, Van Aelst L, Xi D, Yuan P, Brady DC, Chang CJ
A modular toolbox to generate complex polymeric ubiquitin architectures using orthogonal sortase enzymes.
1. Nat Commun - published November 1, 2021
2. Fottner M, Weyh M, Gaussmann S, Schwarz D, Sattler M, Lang K
Gain-of-Function Mutations in RPA1 Cause a Syndrome with Short Telomeres and Somatic Genetic Rescue.
1. Blood - published November 1, 2021
2. Sharma R, Sahoo SS, Honda M, Granger SL, Goodings C, Sanchez L, Künstner A, Busch H, Beier F, Pruett-Miller SM, Valentine M, Fernandez AG, Chang TC, Géli V, Churikov D, Hirschi S, Pastor VB, Boerries M, Lauten M, Kelaidi C, Wlodarski MW, Cooper MA, Nicholas SK, Rosenfeld JA, Polychronopoulou S, Kannengiesser C, Saintome C, Niemeyer CM, Revy P, Wold MS, Spies M, Erlacher M, Coulon S, Wlodarski MW
Using quantitative reconstitution to investigate multi-component condensates.
1. RNA - published November 1, 2021
2. Currie SL, Rosen MK
What are the distinguishing features and size requirements of biomolecular condensates and their implications for RNA-containing condensates?
1. RNA - published November 1, 2021
2. Forman-Kay JD, Ditlev JA, Nosella ML, Lee HO
Discovery of a novel pseudo β-hairpin structure of N-truncated amyloid-β for use as a vaccine against Alzheimer's disease.
1. Mol Psychiatry - published November 1, 2021
2. Bakrania P, Hall G, Bouter Y, Bouter C, Beindorff N, Cowan R, Davies S, Price J, Mpamhanga C, Love E, Matthews D, Carr MD, Bayer TA
A transcriptome atlas of the mouse iris at single-cell resolution defines cell types and the genomic response to pupil dilation.
1. Elife - published November 1, 2021
2. Wang J, Rattner A, Nathans J
An aluminum hydroxide:CpG adjuvant enhances protection elicited by a SARS-CoV-2 receptor-binding domain vaccine in aged mice.
1. Sci Transl Med - published November 1, 2021
2. Nanishi E, Borriello F, O'Meara TR, McGrath ME, Saito Y, Haupt RE, Seo HS, van Haren SD, Cavazzoni CB, Brook B, Barman S, Chen J, Diray-Arce J, Doss-Gollin S, De Leon M, Prevost-Reilly A, Chew K, Menon M, Song K, Xu AZ, Caradonna TM, Feldman J, Hauser BM, Schmidt AG, Sherman AC, Baden LR, Ernst RK, Dillen C, Weston SM, Johnson RM, Hammond HL, Mayer R, Burke A, Bottazzi ME, Hotez PJ, Strych U, Chang A, Yu J, Sage PT, Barouch DH, Dhe-Paganon S, Zanoni I, Ozonoff A, Frieman MB, Levy O, Dowling DJ
Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.
1. Arch Virol - published November 1, 2021
2. Kuhn JH, Adkins S, Agwanda BR, Al Kubrusli R, Alkhovsky SV, Amarasinghe GK, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Basler CF, Bavari S, Beer M, Bejerman N, Bennett AJ, Bente DA, Bergeron É, Bird BH, Blair CD, Blasdell KR, Blystad DR, Bojko J, Borth WB, Bradfute S, Breyta R, Briese T, Brown PA, Brown JK, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Cao M, Casas I, Chandran K, Charrel RN, Cheng Q, Chiaki Y, Chiapello M, Choi IR, Ciuffo M, Clegg JCS, Crozier I, Dal Bó E, de la Torre JC, de Lamballerie X, de Swart RL, Debat H, Dheilly NM, Di Cicco E, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolnik O, Drebot MA, Drexler JF, Dundon WG, Duprex WP, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Elbeaino T, Ergünay K, Ferguson HW, Fooks AR, Forgia M, Formenty PBH, Fránová J, Freitas-Astúa J, Fu J, Fürl S, Gago-Zachert S, Gāo GF, García ML, García-Sastre A, Garrison AR, Gaskin T, Gonzalez JJ, Griffiths A, Goldberg TL, Groschup MH, Günther S, Hall RA, Hammond J, Han T, Hepojoki J, Hewson R, Hong J, Hong N, Hongo S, Horie M, Hu JS, Hu T, Hughes HR, Hüttner F, Hyndman TH, Ilyas M, Jalkanen R, Jiāng D, Jonson GB, Junglen S, Kadono F, Kaukinen KH, Kawate M, Klempa B, Klingström J, Kobinger G, Koloniuk I, Kondō H, Koonin EV, Krupovic M, Kubota K, Kurath G, Laenen L, Lambert AJ, Langevin SL, Lee B, Lefkowitz EJ, Leroy EM, Li S, Li L, Lǐ J, Liu H, Lukashevich IS, Maes P, de Souza WM, Marklewitz M, Marshall SH, Marzano SL, Massart S, McCauley JW, Melzer M, Mielke-Ehret N, Miller KM, Ming TJ, Mirazimi A, Mordecai GJ, Mühlbach HP, Mühlberger E, Naidu R, Natsuaki T, Navarro JA, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Olmedo-Velarde A, Palacios G, Pallás V, Pályi B, Papa A, Paraskevopoulou S, Park AC, Parrish CR, Patterson DA, Pauvolid-Corrêa A, Pawęska JT, Payne S, Peracchio C, Pérez DR, Postler TS, Qi L, Radoshitzky SR, Resende RO, Reyes CA, Rima BK, Luna GR, Romanowski V, Rota P, Rubbenstroth D, Rubino L, Runstadler JA, Sabanadzovic S, Sall AA, Salvato MS, Sang R, Sasaya T, Schulze AD, Schwemmle M, Shi M, Shí X, Shí Z, Shimomoto Y, Shirako Y, Siddell SG, Simmonds P, Sironi M, Smagghe G, Smither S, Song JW, Spann K, Spengler JR, Stenglein MD, Stone DM, Sugano J, Suttle CA, Tabata A, Takada A, Takeuchi S, Tchouassi DP, Teffer A, Tesh RB, Thornburg NJ, Tomitaka Y, Tomonaga K, Tordo N, Torto B, Towner JS, Tsuda S, Tu C, Turina M, Tzanetakis IE, Uchida J, Usugi T, Vaira AM, Vallino M, van den Hoogen B, Varsani A, Vasilakis N, Verbeek M, von Bargen S, Wada J, Wahl V, Walker PJ, Wang LF, Wang G, Wang Y, Wang Y, Waqas M, Wèi T, Wen S, Whitfield AE, Williams JV, Wolf YI, Wu J, Xu L, Yanagisawa H, Yang C, Yang Z, Zerbini FM, Zhai L, Zhang YZ, Zhang S, Zhang J, Zhang Z, Zhou X
Vaccination in a humanized mouse model elicits highly protective PfCSP-targeting anti-malarial antibodies.
1. Immunity - published November 1, 2021
2. Kratochvil S, Shen CH, Lin YC, Xu K, Nair U, Da Silva Pereira L, Tripathi P, Arnold J, Chuang GY, Melzi E, Schön A, Zhang B, Dillon M, Bonilla B, Flynn BJ, Kirsch KH, Kisalu NK, Kiyuka PK, Liu T, Ou L, Pancera M, Rawi R, Reveiz M, Seignon K, Wang LT, Waring MT, Warner J, Yang Y, Francica JR, Idris AH, Seder RA, Kwong PD, Batista FD
Structures of prokaryotic ubiquitin-like protein Pup in complex with depupylase Dop reveal the mechanism of catalytic phosphate formation.
1. Nat Commun - published November 1, 2021
2. Cui H, Müller AU, Leibundgut M, Tian J, Ban N, Weber-Ban E
Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs.
1. J Biol Chem - published November 1, 2021
2. Schilling J, Jost C, Ilie IM, Schnabl J, Buechi O, Eapen RS, Truffer R, Caflisch A, Forrer P
Structural basis of synergistic neutralization of Crimean-Congo hemorrhagic fever virus by human antibodies.
1. Science - published November 1, 2021
2. Mishra AK, Hellert J, Freitas N, Guardado-Calvo P, Haouz A, Fels JM, Maurer DP, Abelson DM, Bornholdt ZA, Walker LM, Chandran K, Cosset FL, McLellan JS, Rey FA
Nickel import and export in the human pathogen Helicobacter pylori, perspectives from molecular modelling.
1. Metallomics - published November 1, 2021
2. Camporesi G, Minzoni A, Morasso L, Ciurli S, Musiani F
Locus-Conserved Circular RNA cZNF292 Controls Endothelial Cell Flow Responses.
1. Circ Res - published November 1, 2021
2. Heumüller AW, Jones AN, Mourão A, Klangwart M, Shi C, Wittig I, Fischer A, Muhly Reinholz M, Buchmann GK, Dieterich C, Potente M, Braun T, Grote P, Jaé N, Sattler M, Dimmeler S
Noncoding RNAs: biology and applications-a Keystone Symposia report.
1. Ann N Y Acad Sci - published November 1, 2021
2. Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen CK, Wilusz JE, Lempradl A, McGeary SE, Wahba L, Pyle AM, Hargrove AE, Simon MD, Marcia M, Przanowska RK, Chang HY, Jaffrey SR, Contreras LM, Chen Q, Shi J, Mendell JT, He L, Song E, Rinn JL, Lalwani MK, Kalem MC, Chuong EB, Maquat LE, Liu X
Structural insights into Ubr1-mediated N-degron polyubiquitination.
1. Nature - published November 1, 2021
2. Pan M, Zheng Q, Wang T, Liang L, Mao J, Zuo C, Ding R, Ai H, Xie Y, Si D, Yu Y, Liu L, Zhao M
Physicochemistry of Cereblon Modulating Drugs Determines Pharmacokinetics and Disposition.
1. ACS Med Chem Lett - published November 1, 2021
2. Kong NR, Liu H, Che J, Jones LH
Investigation of bioluminescence-based assays for determination of kinetic parameters for the bifunctional Neisseria meningitidis serogroup W capsule polymerase.
1. BMC Res Notes - published November 1, 2021
2. Sheikhi Moghaddam L, Adegbite A, McCarthy PC
Use of peripheral neutrophil to lymphocyte ratio and peripheral monocyte levels to predict survival in fibrotic hypersensitivity pneumonitis (fHP): a multicentre retrospective cohort study.
1. BMJ Open Respir Res - published November 1, 2021
2. Barratt SL, Creamer AW, Adamali HI, Duckworth A, Fallon J, Fidan S, Nancarrow T, Wollerton R, Steward M, Gooptu B, Gibbons M, Woodhead FA, Scotton C
Distinct conformations of the HIV-1 V3 loop crown are targetable for broad neutralization.
1. Nat Commun - published November 1, 2021
2. Friedrich N, Stiegeler E, Glögl M, Lemmin T, Hansen S, Kadelka C, Wu Y, Ernst P, Maliqi L, Foulkes C, Morin M, Eroglu M, Liechti T, Ivan B, Reinberg T, Schaefer JV, Karakus U, Ursprung S, Mann A, Rusert P, Kouyos RD, Robinson JA, Günthard HF, Plückthun A, Trkola A
Three critical regions of the erythromycin resistance methyltransferase, ErmE, are required for function supporting a model for the interaction of Erm family enzymes with substrate rRNA.
1. RNA - published November 1, 2021
2. Sharkey RE, Herbert JB, McGaha DA, Nguyen V, Schoeffler AJ, Dunkle JA
Kinesin-binding protein remodels the kinesin motor to prevent microtubule binding.
1. Sci Adv - published November 1, 2021
2. Solon AL, Tan Z, Schutt KL, Jepsen L, Haynes SE, Nesvizhskii AI, Sept D, Stumpff J, Ohi R, Cianfrocco MA
HPF1 dynamically controls the PARP1/2 balance between initiating and elongating ADP-ribose modifications.
1. Nat Commun - published November 1, 2021
2. Langelier MF, Billur R, Sverzhinsky A, Black BE, Pascal JM
Identification of gp120 Residue His105 as a Novel Target for HIV-1 Neutralization by Small-Molecule CD4-Mimics.
1. ACS Med Chem Lett - published November 1, 2021
2. Fritschi CJ, Liang S, Mohammadi M, Anang S, Moraca F, Chen J, Madani N, Sodroski JG, Abrams CF, Hendrickson WA, Smith AB 3rd
Controlling long-term SARS-CoV-2 infections can slow viral evolution and reduce the risk of treatment failure.
1. Sci Rep - published November 1, 2021
2. Van Egeren D, Novokhodko A, Stoddard M, Tran U, Zetter B, Rogers MS, Joseph-McCarthy D, Chakravarty A
Design of a population-based longitudinal cohort study of SARS-CoV-2 incidence and prevalence among adults in the San Francisco Bay Area.
1. Ann Epidemiol - published November 1, 2021
2. Lindan CP, Desai M, Boothroyd D, Judson T, Bollyky J, Sample H, Weng Y, Cheng Y, Dahlen A, Hedlin H, Grumbach K, Henne J, Garcia S, Gonzales R, Craik CS, Maldonado Y, Rutherford G
Allelic variants of full-length VAR2CSA, the placental malaria vaccine candidate, differ in antigenicity and receptor binding affinity.
1. Commun Biol - published November 1, 2021
2. Renn JP, Doritchamou JYA, Tentokam BCN, Morrison RD, Cowles MV, Burkhardt M, Ma R, Tolia NH, Fried M, Duffy PE
Rescuing activity of oxygen-damaged pyruvate formate-lyase by a spare part protein.
1. J Biol Chem - published November 1, 2021
2. Andorfer MC, Backman LRF, Li PL, Ulrich EC, Drennan CL
The fission yeast FLCN/FNIP complex augments TORC1 repression or activation in response to amino acid (AA) availability.
1. iScience - published November 1, 2021
2. Calvo IA, Sharma S, Paulo JA, Gulka AOD, Boeszoermenyi A, Zhang J, Lombana JM, Palmieri CM, Laviolette LA, Arthanari H, Iliopoulos O, Gygi SP, Motamedi M
Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials.
1. IUCrJ - published November 1, 2021
2. Herreros D, Lederman RR, Krieger J, Jiménez-Moreno A, Martínez M, Myška D, Strelak D, Filipovic J, Bahar I, Carazo JM, Sanchez COS
Ceramide-1-Phosphate Transfer Protein Promotes Sphingolipid Reorientation Needed for Binding during Membrane Interaction.
1. J Lipid Res - published November 1, 2021
2. Gao YG, McDonald J, Malinina L, Patel DJ, Brown RE
Structure-based design of haloperidol analogues as inhibitors of acetyltransferase Eis from Mycobacterium tuberculosis to overcome kanamycin resistance.
1. RSC Med Chem - published November 1, 2021
2. Punetha A, Green KD, Garzan A, Thamban Chandrika N, Willby MJ, Pang AH, Hou C, Holbrook SYL, Krieger K, Posey JE, Parish T, Tsodikov OV, Garneau-Tsodikova S
Identification of a therapeutic interfering particle-A single-dose SARS-CoV-2 antiviral intervention with a high barrier to resistance.
1. Cell - published November 1, 2021
2. Chaturvedi S, Vasen G, Pablo M, Chen X, Beutler N, Kumar A, Tanner E, Illouz S, Rahgoshay D, Burnett J, Holguin L, Chen PY, Ndjamen B, Ott M, Rodick R, Rogers T, Smith DM, Weinberger LS