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B-cell epitopes: Discontinuity and conformational analysis.

Ferdous S, Kelm S, Baker TS, Shi J, Martin ACR.

Mol Immunol. 2019 Oct;114:643-650. doi: 10.1016/j.molimm.2019.09.014. Epub 2019 Sep 20.


Cryo-EM Structures of a Group II Intron Reverse Splicing into DNA.

Haack DB, Yan X, Zhang C, Hingey J, Lyumkis D, Baker TS, Toor N.

Cell. 2019 Jul 25;178(3):612-623.e12. doi: 10.1016/j.cell.2019.06.035.


Self-Assembly of a Designed Nucleoprotein Architecture through Multimodal Interactions.

Subramanian RH, Smith SJ, Alberstein RG, Bailey JB, Zhang L, Cardone G, Suominen L, Chami M, Stahlberg H, Baker TS, Tezcan FA.

ACS Cent Sci. 2018 Nov 28;4(11):1578-1586. doi: 10.1021/acscentsci.8b00745. Epub 2018 Nov 15.


A novel FAS mutation with variable expressivity in a family with unicentric and idiopathic multicentric Castleman disease.

Baker TS, Gambino KJ, Schriefer L, Lim JY, Steinberg KM, Fajgenbaum DC, Martín García-Sancho A, Byun M.

Blood Adv. 2018 Nov 13;2(21):2959-2963. doi: 10.1182/bloodadvances.2018023911. No abstract available.


Atomic structures of enterovirus D68 in complex with two monoclonal antibodies define distinct mechanisms of viral neutralization.

Zheng Q, Zhu R, Xu L, He M, Yan X, Liu D, Yin Z, Wu Y, Li Y, Yang L, Hou W, Li S, Li Z, Chen Z, Li Z, Yu H, Gu Y, Zhang J, Baker TS, Zhou ZH, Graham BS, Cheng T, Li S, Xia N.

Nat Microbiol. 2019 Jan;4(1):124-133. doi: 10.1038/s41564-018-0275-7. Epub 2018 Nov 5.


Discovery and structural characterization of a therapeutic antibody against coxsackievirus A10.

Zhu R, Xu L, Zheng Q, Cui Y, Li S, He M, Yin Z, Liu D, Li S, Li Z, Chen Z, Yu H, Que Y, Liu C, Kong Z, Zhang J, Baker TS, Yan X, Hong Zhou Z, Cheng T, Xia N.

Sci Adv. 2018 Sep 19;4(9):eaat7459. doi: 10.1126/sciadv.aat7459. eCollection 2018 Sep.


Sub-2 Å Ewald curvature corrected structure of an AAV2 capsid variant.

Tan YZ, Aiyer S, Mietzsch M, Hull JA, McKenna R, Grieger J, Samulski RJ, Baker TS, Agbandje-McKenna M, Lyumkis D.

Nat Commun. 2018 Sep 7;9(1):3628. doi: 10.1038/s41467-018-06076-6.


Cryo-EM Elucidation of the Structure of Bacteriophage P22 Virions after Genome Release.

McNulty R, Cardone G, Gilcrease EB, Baker TS, Casjens SR, Johnson JE.

Biophys J. 2018 Mar 27;114(6):1295-1301. doi: 10.1016/j.bpj.2018.01.026.


Mono-Substituted Hydrocarbon Diastereomer Combinations Reveal Stapled Peptides with High Structural Fidelity.

McWhinnie FS, Sepp K, Wilson C, Kunath T, Hupp TR, Baker TS, Houston DR, Hulme AN.

Chemistry. 2018 Feb 9;24(9):2094-2097. doi: 10.1002/chem.201705983. Epub 2018 Jan 19.


Atomic Resolution Structure of the Oncolytic Parvovirus LuIII by Electron Microscopy and 3D Image Reconstruction.

Pittman N, Misseldine A, Geilen L, Halder S, Smith JK, Kurian J, Chipman P, Janssen M, Mckenna R, Baker TS, D'Abramo A Jr, Cotmore S, Tattersall P, Agbandje-McKenna M.

Viruses. 2017 Oct 30;9(11). pii: E321. doi: 10.3390/v9110321.


Crystal Structures of Two Immune Complexes Identify Determinants for Viral Infectivity and Type-Specific Neutralization of Human Papillomavirus.

Li Z, Wang D, Gu Y, Song S, He M, Shi J, Liu X, Wei S, Li J, Yu H, Zheng Q, Yan X, Baker TS, Zhang J, McLellan JS, Li S, Xia N.

MBio. 2017 Sep 26;8(5). pii: e00787-17. doi: 10.1128/mBio.00787-17.


Atomic structures of Coxsackievirus A6 and its complex with a neutralizing antibody.

Xu L, Zheng Q, Li S, He M, Wu Y, Li Y, Zhu R, Yu H, Hong Q, Jiang J, Li Z, Li S, Zhao H, Yang L, Hou W, Wang W, Ye X, Zhang J, Baker TS, Cheng T, Zhou ZH, Yan X, Xia N.

Nat Commun. 2017 Sep 11;8(1):505. doi: 10.1038/s41467-017-00477-9.


Discovery of a junctional epitope antibody that stabilizes IL-6 and gp80 protein:protein interaction and modulates its downstream signaling.

Adams R, Burnley RJ, Valenzano CR, Qureshi O, Doyle C, Lumb S, Del Carmen Lopez M, Griffin R, McMillan D, Taylor RD, Meier C, Mori P, Griffin LM, Wernery U, Kinne J, Rapecki S, Baker TS, Lawson AD, Wright M, Ettorre A.

Sci Rep. 2017 Jan 30;7:37716. doi: 10.1038/srep37716.


Cryo-electron Microscopy Reconstruction and Stability Studies of the Wild Type and the R432A Variant of Adeno-associated Virus Type 2 Reveal that Capsid Structural Stability Is a Major Factor in Genome Packaging.

Drouin LM, Lins B, Janssen M, Bennett A, Chipman P, McKenna R, Chen W, Muzyczka N, Cardone G, Baker TS, Agbandje-McKenna M.

J Virol. 2016 Sep 12;90(19):8542-51. doi: 10.1128/JVI.00575-16. Print 2016 Oct 1.


The C-Terminal Arm of the Human Papillomavirus Major Capsid Protein Is Immunogenic and Involved in Virus-Host Interaction.

Li Z, Yan X, Yu H, Wang D, Song S, Li Y, He M, Hong Q, Zheng Q, Zhao Q, Gu Y, Zhang J, Janssen ME, Cardone G, Olson NH, Baker TS, Li S, Xia N.

Structure. 2016 Jun 7;24(6):874-85. doi: 10.1016/j.str.2016.04.008.


Self-assembly of coherently dynamic, auxetic, two-dimensional protein crystals.

Suzuki Y, Cardone G, Restrepo D, Zavattieri PD, Baker TS, Tezcan FA.

Nature. 2016 May 19;533(7603):369-73. doi: 10.1038/nature17633. Epub 2016 May 2.


Fluorescent Protein-Tagged Sindbis Virus E2 Glycoprotein Allows Single Particle Analysis of Virus Budding from Live Cells.

Jose J, Tang J, Taylor AB, Baker TS, Kuhn RJ.

Viruses. 2015 Nov 27;7(12):6182-99. doi: 10.3390/v7122926.


Adeno-associated virus serotype 1 (AAV1)- and AAV5-antibody complex structures reveal evolutionary commonalities in parvovirus antigenic reactivity.

Tseng YS, Gurda BL, Chipman P, McKenna R, Afione S, Chiorini JA, Muzyczka N, Olson NH, Baker TS, Kleinschmidt J, Agbandje-McKenna M.

J Virol. 2015 Feb;89(3):1794-808. doi: 10.1128/JVI.02710-14. Epub 2014 Nov 19.


Three-dimensional structure of a protozoal double-stranded RNA virus that infects the enteric pathogen Giardia lamblia.

Janssen ME, Takagi Y, Parent KN, Cardone G, Nibert ML, Baker TS.

J Virol. 2015 Jan 15;89(2):1182-94. doi: 10.1128/JVI.02745-14. Epub 2014 Nov 5.


A Real-Time 3D Reconstruction System for Screening Icosahedral Particles Under Different Conditions at the Microscope.

Cardone G, Yan X, Sinkovits RS, Baker TS.

Microsc Microanal. 2013 Aug;19(Suppl 2):764-765. No abstract available.


Creation of a gated antibody as a conditionally functional synthetic protein.

Gunnoo SB, Finney HM, Baker TS, Lawson AD, Anthony DC, Davis BG.

Nat Commun. 2014 Jul 30;5:4388. doi: 10.1038/ncomms5388.


Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tailspike receptor-binding domain.

Parent KN, Tang J, Cardone G, Gilcrease EB, Janssen ME, Olson NH, Casjens SR, Baker TS.

Virology. 2014 Sep;464-465:55-66. doi: 10.1016/j.virol.2014.06.017. Epub 2014 Jul 18.


A novel partitivirus that confers hypovirulence on plant pathogenic fungi.

Xiao X, Cheng J, Tang J, Fu Y, Jiang D, Baker TS, Ghabrial SA, Xie J.

J Virol. 2014 Sep 1;88(17):10120-33. doi: 10.1128/JVI.01036-14. Epub 2014 Jun 25.


OmpA and OmpC are critical host factors for bacteriophage Sf6 entry in Shigella.

Parent KN, Erb ML, Cardone G, Nguyen K, Gilcrease EB, Porcek NB, Pogliano J, Baker TS, Casjens SR.

Mol Microbiol. 2014 Apr;92(1):47-60. doi: 10.1111/mmi.12536. Epub 2014 Mar 6.


Single particle analysis integrated with microscopy: a high-throughput approach for reconstructing icosahedral particles.

Yan X, Cardone G, Zhang X, Zhou ZH, Baker TS.

J Struct Biol. 2014 Apr;186(1):8-18. doi: 10.1016/j.jsb.2014.02.016. Epub 2014 Mar 5.


Dynamic and geometric analyses of Nudaurelia capensis ω virus maturation reveal the energy landscape of particle transitions.

Tang J, Kearney BM, Wang Q, Doerschuk PC, Baker TS, Johnson JE.

J Mol Recognit. 2014 Apr;27(4):230-7. doi: 10.1002/jmr.2354.


Analysis of heavy and light chain sequences of conventional camelid antibodies from Camelus dromedarius and Camelus bactrianus species.

Griffin LM, Snowden JR, Lawson AD, Wernery U, Kinne J, Baker TS.

J Immunol Methods. 2014 Mar;405:35-46. doi: 10.1016/j.jim.2014.01.003. Epub 2014 Jan 18.


Three-dimensional reconstruction of icosahedral particles from single micrographs in real time at the microscope.

Cardone G, Yan X, Sinkovits RS, Tang J, Baker TS.

J Struct Biol. 2013 Sep;183(3):329-341. doi: 10.1016/j.jsb.2013.07.007. Epub 2013 Jul 25.


Capsid antibodies to different adeno-associated virus serotypes bind common regions.

Gurda BL, DiMattia MA, Miller EB, Bennett A, McKenna R, Weichert WS, Nelson CD, Chen WJ, Muzyczka N, Olson NH, Sinkovits RS, Chiorini JA, Zolotutkhin S, Kozyreva OG, Samulski RJ, Baker TS, Parrish CR, Agbandje-McKenna M.

J Virol. 2013 Aug;87(16):9111-24. doi: 10.1128/JVI.00622-13. Epub 2013 Jun 12.


Structure of a protozoan virus from the human genitourinary parasite Trichomonas vaginalis.

Parent KN, Takagi Y, Cardone G, Olson NH, Ericsson M, Yang M, Lee Y, Asara JM, Fichorova RN, Baker TS, Nibert ML.

MBio. 2013 Apr 2;4(2). pii: e00056-13. doi: 10.1128/mBio.00056-13.


Three-dimensional structure of victorivirus HvV190S suggests coat proteins in most totiviruses share a conserved core.

Dunn SE, Li H, Cardone G, Nibert ML, Ghabrial SA, Baker TS.

PLoS Pathog. 2013 Mar;9(3):e1003225. doi: 10.1371/journal.ppat.1003225. Epub 2013 Mar 14.


Viruses of Helminthosporium (Cochlioblus) victoriae.

Ghabrial SA, Dunn SE, Li H, Xie J, Baker TS.

Adv Virus Res. 2013;86:289-325. doi: 10.1016/B978-0-12-394315-6.00011-8. Review.


3D structures of fungal partitiviruses.

Nibert ML, Tang J, Xie J, Collier AM, Ghabrial SA, Baker TS, Tao YJ.

Adv Virus Res. 2013;86:59-85. doi: 10.1016/B978-0-12-394315-6.00003-9. Review.


¹⁵N, ¹³C and ¹H resonance assignments and secondary structure determination of a variable heavy domain of a heavy chain antibody.

Prosser CE, Waters LC, Muskett FW, Veverka V, Addis PW, Griffin LM, Baker TS, Lawson AD, Wernery U, Kinne J, Henry AJ, Taylor RJ, Carr MD.

Biomol NMR Assign. 2014 Apr;8(1):113-6. doi: 10.1007/s12104-013-9464-8. Epub 2013 Jan 29.


Atomic model of rabbit hemorrhagic disease virus by cryo-electron microscopy and crystallography.

Wang X, Xu F, Liu J, Gao B, Liu Y, Zhai Y, Ma J, Zhang K, Baker TS, Schulten K, Zheng D, Pang H, Sun F.

PLoS Pathog. 2013 Jan;9(1):e1003132. doi: 10.1371/journal.ppat.1003132. Epub 2013 Jan 17.


Mapping a neutralizing epitope onto the capsid of adeno-associated virus serotype 8.

Gurda BL, Raupp C, Popa-Wagner R, Naumer M, Olson NH, Ng R, McKenna R, Baker TS, Kleinschmidt JA, Agbandje-McKenna M.

J Virol. 2012 Aug;86(15):7739-51. doi: 10.1128/JVI.00218-12. Epub 2012 May 16.


Stepwise molecular display utilizing icosahedral and helical complexes of phage coat and decoration proteins in the development of robust nanoscale display vehicles.

Parent KN, Deedas CT, Egelman EH, Casjens SR, Baker TS, Teschke CM.

Biomaterials. 2012 Aug;33(22):5628-37. doi: 10.1016/j.biomaterials.2012.04.026. Epub 2012 May 8.


Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays.

Brodin JD, Ambroggio XI, Tang C, Parent KN, Baker TS, Tezcan FA.

Nat Chem. 2012 Mar 4;4(5):375-82. doi: 10.1038/nchem.1290.


Structural insight into the unique properties of adeno-associated virus serotype 9.

DiMattia MA, Nam HJ, Van Vliet K, Mitchell M, Bennett A, Gurda BL, McKenna R, Olson NH, Sinkovits RS, Potter M, Byrne BJ, Aslanidi G, Zolotukhin S, Muzyczka N, Baker TS, Agbandje-McKenna M.

J Virol. 2012 Jun;86(12):6947-58. doi: 10.1128/JVI.07232-11. Epub 2012 Apr 11.


Structural evolution of the P22-like phages: comparison of Sf6 and P22 procapsid and virion architectures.

Parent KN, Gilcrease EB, Casjens SR, Baker TS.

Virology. 2012 Jun 5;427(2):177-88. doi: 10.1016/j.virol.2012.01.040. Epub 2012 Mar 3.


Molecular links between the E2 envelope glycoprotein and nucleocapsid core in Sindbis virus.

Tang J, Jose J, Chipman P, Zhang W, Kuhn RJ, Baker TS.

J Mol Biol. 2011 Dec 2;414(3):442-59. doi: 10.1016/j.jmb.2011.09.045. Epub 2011 Oct 4.


Electron Cryo-Microscopy Studies of Helminthosporium victoriae Virus 190S.

Dunn SE, Li H, Nibert ML, Ghabrial SA, Baker TS.

Microsc Microanal. 2011 Jul;17(Suppl 2):134-135. No abstract available.


Virion structure of baboon reovirus, a fusogenic orthoreovirus that lacks an adhesion fiber.

Yan X, Parent KN, Goodman RP, Tang J, Shou J, Nibert ML, Duncan R, Baker TS.

J Virol. 2011 Aug;85(15):7483-95. doi: 10.1128/JVI.00729-11. Epub 2011 May 18.


Controlling and switching the morphology of micellar nanoparticles with enzymes.

Ku TH, Chien MP, Thompson MP, Sinkovits RS, Olson NH, Baker TS, Gianneschi NC.

J Am Chem Soc. 2011 Jun 8;133(22):8392-5. doi: 10.1021/ja2004736. Epub 2011 Apr 4.


Peering down the barrel of a bacteriophage portal: the genome packaging and release valve in p22.

Tang J, Lander GC, Olia AS, Li R, Casjens S, Prevelige P Jr, Cingolani G, Baker TS, Johnson JE.

Structure. 2011 Apr 13;19(4):496-502. doi: 10.1016/j.str.2011.02.010. Erratum in: Structure. 2011 May 11;19(5):748. Olia, Adam [corrected to Olia, Adam S].


The structure of avian polyomavirus reveals variably sized capsids, non-conserved inter-capsomere interactions, and a possible location of the minor capsid protein VP4.

Shen PS, Enderlein D, Nelson CD, Carter WS, Kawano M, Xing L, Swenson RD, Olson NH, Baker TS, Cheng RH, Atwood WJ, Johne R, Belnap DM.

Virology. 2011 Mar 1;411(1):142-52. doi: 10.1016/j.virol.2010.12.005. Epub 2011 Jan 15.


Cryo-reconstructions of P22 polyheads suggest that phage assembly is nucleated by trimeric interactions among coat proteins.

Parent KN, Sinkovits RS, Suhanovsky MM, Teschke CM, Egelman EH, Baker TS.

Phys Biol. 2010 Dec 9;7(4):045004. doi: 10.1088/1478-3975/7/4/045004.


Three-dimensional asymmetric reconstruction of tailed bacteriophage.

Tang J, Sinkovits RS, Baker TS.

Methods Enzymol. 2010;482:185-210. doi: 10.1016/S0076-6879(10)82008-7.


Structural characterization of the dual glycan binding adeno-associated virus serotype 6.

Ng R, Govindasamy L, Gurda BL, McKenna R, Kozyreva OG, Samulski RJ, Parent KN, Baker TS, Agbandje-McKenna M.

J Virol. 2010 Dec;84(24):12945-57. doi: 10.1128/JVI.01235-10. Epub 2010 Sep 22.


Determinants of bacteriophage P22 polyhead formation: the role of coat protein flexibility in conformational switching.

Suhanovsky MM, Parent KN, Dunn SE, Baker TS, Teschke CM.

Mol Microbiol. 2010 Sep;77(6):1568-82. doi: 10.1111/j.1365-2958.2010.07311.x. Epub 2010 Aug 18.

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