Structural snapshots of R-loop formation by a type I-C CRISPR Cascade

O’Brien, RE, Bravo JPK, Ramos D, Hibshman GN, Wright JT, Taylor DW. Structural snapshots of R-loop formation by a type I-C CRISPR Cascade. Molecular Cell (2023). doi: 10.1016/j.molcel.2023.01.024

Molecular Cell

RNA targeting unleashes indiscriminate
nuclease activity of CRISPR–Cas12a2

Bravo JPK, Hallmark T, Naegle B, Beisel CL, Jackson RN, Taylor DW. RNA targeting unleashes indiscriminate nuclease activity of CRISPR–Cas12a2. Nature (2023). doi: 10.1038/s41586-022-05560-w


A single 2′-O-methylation of ribosomal RNA gates assembly of a functional ribosome

Yelland JN, Bravo JPK, Black JB, Taylor DW, Johnson, AW. A single 2′-O-methylation of ribosomal RNA gates assembly of a functional ribosome. Nature Structural & Molecular Biology. (2022). doi: 10.1038/s41594-022-00891-8


Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex

McCafferty CL, Papoulas O, Jordan MA, Hoogerbrugge G, Nichols C, Pigino G, Taylor DW, Wallingford JB, Marcotte EM. eLife. (2022).


Constructing next-generation CRISPR–Cas tools from structural blueprints

Bravo JPK, Hibshman GN, Taylor DW. Current Opinion in Biotechnology. (2022). doi: 10.1016/j.copbio.2022.102839.


The protein organization of a red blood cell

Sae-Lee W, McCafferty CL, Verbeke EJ, Havugimana PC, Papoulas O, McWhite CD, Houser JR, Vanuytsel K, Murphy GJ, Drew K, Emili A, Taylor DW, Marcotte EM. Cell Rep. (2022) 40(3):111103. doi: 10.1016/j.celrep.2022.111103.  


Cross Seeding Controls AB Fibril Populations and Resulting Functions

Lucas MJ, Pan HS, Verbeke EJ, Partipilo G, Helfman EC, Kann L, Keitz BK, Taylor DW, Webb LJ. J Phys Chem B. 2022 Mar 24;126(11):2217-2229. doi: 10.1021/acs.jpcb.1c09995. Epub 2022 Mar 11.


Structural basis for broad anti-phage immunity by DISARM

Bravo, J.P.K., Aparicio-Maldonado, C., Nobrega, F.L. et al. Structural basis for broad anti-phage immunity by DISARM. Nat Commun 13, 2987 (2022). doi: 10.1038/s41467-022-30673-1.

Pubmed Nature Comms

Structural rearrangements allow nucleic acid discrimination by type I-D Cascade

Schwartz, E.A., McBride, T.M., Bravo, J.P.K. et al. Structural rearrangements allow nucleic acid discrimination by type I-D Cascade. Nat Commun 13, 2829 (2022).

PubMed Nature Comms

Structural basis for mismatch surveillance by CRISPR–Cas9

Bravo, J.P.K., Liu, MS., Hibshman, G.N. et al. Structural basis for mismatch surveillance by CRISPR–Cas9. Nature (2022). doi: 10.1016/10.1038/s41586-022-04470-1. PMID: 35236982.

PubMed Nature

Remdesivir is a delayed translocation inhibitor of SARS CoV-2 replication

Bravo JPK, Dangerfield TL, Taylor DW, Johnson KA. Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication. Mol Cell. 2021 Apr 1;81(7):1548-1552.e4. doi: 10.1016/j.molcel.2021.01.035. Epub 2021 Jan 28. PMID: 33631104; PMCID: PMC7843106.


SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation

Steens JA, Zhu Y, Taylor DW, Bravo JPK, Prinsen SHP, Schoen CD, Keijser BJF, Ossendrijver M, Hofstra LM, Brouns SJJ, Shinkai A, van der Oost J, Staals RHJ. SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation. Nat Commun. 2021 Aug 19;12(1):5033. doi: 10.1038/s41467-021-25337-5. PMID: 34413302; PMCID: PMC8376896.


Isolation of the Buchnera aphidicola flagellum basal body complexes from the Buchnera membrane

Schepers MJ, Yelland JN, Moran NA, Taylor DW. Isolation of the Buchnera aphidicola flagellum basal body complexes from the Buchnera membrane. PLoS One. 2021 May 10;16(5):e0245710. doi: 10.1371/journal.pone.0245710. PMID: 33970928; PMCID: PMC8109811.


Improving integrative 3D modeling into low- to medium-resolution electron microscopy structures with evolutionary couplings

McCafferty CL, Taylor DW, Marcotte EM. Improving integrative 3D modeling into low- to medium-resolution electron microscopy structures with evolutionary couplings. Protein Sci. 2021 May;30(5):1006-1021. doi: 10.1002/pro.4067. Epub 2021 Apr 9. PMID: 33759266; PMCID: PMC8040867..


Structure of a type IV CRISPR-Cas ribonucleoprotein complex

Zhou Y, Bravo JPK, Taylor HN, Steens JA, Jackson RN, Staals RHJ, Taylor DW. Structure of a type IV CRISPR-Cas ribonucleoprotein complex. iScience. 2021 Feb 17;24(3):102201. doi: 10.1016/j.isci.2021.102201. PMID: 33733066; PMCID: PMC7937560.


Diverse CRISPR-Cas Complexes Require Independent Translation of Small and Large Subunits from a Single Gene

T.M. McBride, E.A. Schwartz, A. Kumar, D.W. Taylor, P.C. Fineran, R.D. Fagerlund. Mol Cell. 2020 Dec 17;80(6):971-979.e7. doi: 10.1016/j.molcel.2020.11.003. Epub 2020 Nov 27. PMID: 33248026


Structural basis for assembly of non-canonical small subunits into type I-C Cascade

R.E. O’Brien, I.C. Santos, D. Wrapp, J.P.K. Bravo, E.A. Schwartz, J.S. Brodbelt , D.W. Taylor. Nat Commun. 2020 Nov 23;11(1):5931. doi: 10.1038/s41467-020-19785-8. PMID: 33230133


Simplified geometric representations of protein structures identify complementary interaction interfaces

C.L. McCafferty, E.M. Marcotte, D.W. Taylor. Proteins. 2020 Nov 2. doi: 10.1002/prot.26020. PMID: 33140424


Engineered CRISPR/Cas9 enzymes improve discrimination by slowing DNA cleavage to allow release of off-target DNA.

M.S. Liu, S. Gong, H.H. Yu, K. Jung, K.A. Johnson, D.W. Taylor. Nat Commun. 2020 Jul 17;11(1):3576. doi: 10.1038/s41467-020-17411-1. PMID: 32681021 


Functionalized Mesoporous Silicas Direct Structural Polymorphism of Amyloid-β Fibrils

M.J. Lucas, H.S. Pan, E.J. Verbeke, L.I. Webb, D.W. Taylor, B.K. Keitz. Langmuir. 2020 Jul 7;36(26):7345-7355. doi: 10.1021/acs.langmuir.0c00827. Epub 2020 Jun 16. PMID: 32482072


Separating distinct structures of multiple macromolecular assemblies from cryo-EM projections.

E.J. Verbeke, Y. Zhou, A.P. Horton, A.L. Mallam, D.W. Taylor, E.M. Marcotte. J Struct Biol. 2020 Jan 1;209(1):107416. doi: 10.1016/j.jsb.2019.107416. Epub 2019 Nov 11. PMID: 31726096 


Structural Biology in the Multi-Omics Era

C.L. McCafferty, E.J. Verbeke, E.M. Marcotte, D.W. Taylor. J Chem Inf Model. 2020 May 26;60(5):2424-2429. doi: 10.1021/acs.jcim.9b01164. Epub 2020 Mar 10. PMID: 32129623


The final cut: Cas9 editing

D.W. Taylor. Nat Struct Mol Biol. 2019 Aug;26(8):669-670. doi: 10.1038/s41594-019-0267-1.

PMID: 31285603


Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome.

Y. Zhou, S. Musalgaonkar, A.W. Johnson, D.W. Taylor. (2019) Nature Communications 10, 958.


Kinetic Characterization of Cas9 Enzymes

M. Liu, S. Gong, H.H. Yu, D.W. Taylor, K.A. Johnson. (2019)  Methods Enzymol. 616, 289-311.


Supercharging enables organized assembly of synthetic biomolecules

A.J. Simon, Y. Zhou, V. Ramasubraman, J. Glaser, A. Pothukuchy, J. Gerberich, J. Leggere, B.R. Morrow,  J. Golihar, C..Jung, S.C. Glotzer, D.W. Taylor, A.D. Ellington. (2019) Nature Chemistry 11, 204-212.


Electron microscopy snapshots of single particles from single cells

X. Yi, E.J. Verbeke, Y. Chang, D.J. Dickinson, D.W. Taylor. (2019) J. Biol. Chem. 294, 1602-1608.


Classification of single particles from human cell extract reveals distinct structures

E.J. Verbeke, A.L. Mallam, K. Drew, E.M. Marcotte, D.W. Taylor. (2018) Cell Reports 24, 359-368.


Cas4 dependent prespacer processing ensures high-fidelity processing of CRISPR arrays

H. Lee, Y. Zhou, D.W. Taylor, D. Sashital. (2018) Mol. Cell 70, 48-58.


DNA unwinding is the primary determinant of CRISPR- Cas9 activity

S. Gong, H.H. Yu, K.A. Johnson, D.W. Taylor. (2018) Cell Reports 22, 359-371-851.


DNA targeting by a minimal CRISPR RNA-guided Cascade

M.L. Hochstrasser, D.W. Taylor, J.E. Kornfeld, E. Nogales, J.A. Doudna. (2016) Mol. Cell 63, 840-851.


Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs

W.S.V. Yip, H. Shigematsu, D.W. Taylor, S.J Baserga. (2016) Nucl. Acids Res. E pub 24 Jun 2016.


Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage

F. Jiang, D.W. Taylor, J.S. Chen, J.E. Kornfeld, K. Zhou, A.J. Thompson, E. Nogales, J.A. Doudna. (2016) Science. 351, 867-871.


Antigenic and cryo-electron microscopy structure analysis of a chimeric sapovirus capsid

N. Miyazaki, D.W. Taylor, G.S. Hansman, K. Murata. (2016) J Virol. 90, 2664-2675.


A Single a Helix Drives Extensive Remodeling of the Protaesome Lid and Completion of Regulatory Particle Assembly

R.J. Tomko Jr., D.W. Taylor, Z.A. Chen, H.W. Wang, J. Rappsilber, M. Hochstrasser. (2015) Cell 163, 432-444.


Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning

D.W. Taylor, Y. Zhu, R.H.J. Staals, J.E. Kornfeld, A. Shinkai, J. van der Oost, E. Nogales, J.A. Doudna. (2015) Science 348, 581-585.


Rational design of a split-Cas9 enzyme complex

A.V. Wright, S.H. Sternberg, D.W. Taylor, B.T. Staahl, J.A. Bardales, J.E. Kornfeld, J.A. Doudna. (2015) Proc. Nat. Acad. Sci112, 2984-2989.


RNA Targeting by the Type 111-A CRISPR-Cas Csm Complex of Thermus thermophilus

R.H.J. Staals, Y. Zhu, D.W. Taylor, J.E. Kornfeld, K. Sharma, A. Barendregt, J.J. Koehorst, M. Vlot, N. Neupane, K. Varossieau, K. Sakamoto, T. Suzuki, N. Dohmae, S. Yokoyama, P.J. Schaap, H. Urlaub, A.J.R. Heck, E. Nogales, J.A. Doudna, A. Shinkai, J. van der Oost. (2014) Mol. Cell 56, 518-530.


CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference

M.L. Hochstrasser, D.W. Taylor, P. Bhat, C.K. Guegler, S.H. Sternberg, E. Nogales, J.A. Doudna. (2014) Proc. Nat. Acad. Sci111, 6618–6623.


Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation

M. Jinek, F. Jiang, D.W. Taylor, S.H. Sternberg, E. Kaya, S.H. Sternberg, E. Ma, C. Anders, M. Hauer, K. Zhou, S. Lin, M. Kaplan, A.T. Iavarone, E. Charpentier, E. Nogales, J.A. Doudna. (2014) Science 343, 1247997.


Structure and activity of an RNA-targeting Type III-B CRISPR-Cas complex in Thermus thermophilus

R.H.J. Staals, Y. Agari, S. Maki-Yonekura, Y. Zhu, D.W. Taylor, E. van Duijn, A. Barendregt, M. Vlot, J.J. Koehorst, K. Sakamoto, A. Masuda, N. Dohmae, P.J. Schaap, J.A. Doudna, A.J.R. Heck, K. Yonekura, J. van der Oost, A. Shinkai. (2013) Mol. Cell 52, 135-145. 


Noncoding Y RNAs as Tethers and Gates: Insights from Bacteria

S.L. Wolin, C. Belair, X. Chen, S. Sim, D.W. Taylor, H.W. Wang. (2013) Noncoding Y RNAs as Tethers and Gates: Insight  RNA Biol. 10, 1602-1608.


Substrate-specific structural rearrangements of human Dicer

D.W. Taylor, E. Ma, H. Shigematsu, M.A. Cianfrocco, C.N. Noland, K. Nagayama, E. Nogales, J.A. Doudna, H.W. Wang. (2013) Nat. Stuct. Mol. Biol. 20, 662-670.


An RNA degradation machine sculpted by Ro auto antigen and noncoding RNA

X. Chen, D.W. Taylor, C.C. Fowler, J.E. Galan, H.W. Wang, S.L. Wolin. (2013) Cell 153, 166-177.


The box C/D sRNP dimeric architecture is conserved across domain Archaea

K.R. Bower-Phipps, D.W. Taylor, H.W. Wang, S.J. Baserga. (2012) RNA 18, 1553-1562.


Structural basis for broad detection of genogroup II noroviruses by a monoclonal antibody that binds to a site occlude in the viral particle

G.S. Hansman, D.W. Taylor, J.S. McLellan, T.J. Smith, I. Georgiev, J.R.H. Tame, S.Y. Park, M. Yamazaki, F. Gondaira, M. Miki, K. Katayama, K. Murata, P.D. Kwong. (2012) J. Virol. 86, 3635-3646.  


Two modes of interaction between the membrane-embedded TARP stargazer’s C-terminal domain and the bilayer visualized by electron crystallography

M.F. Roberts, D.W. Taylor, V.M. Unger. (2011) J. Struct. Biol. 174, 542-551.


A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity

D. Cifuentes, H. Xue, D.W. Taylor, H. Patnode, Y. Mishima, S. Cheloufi, E. Ma, S. Mane, G.J. Hannon, N.D. Lawson, S.A. Wolfe, A.J. Giraldez. (2010) Science 328, 1694-1698.  


Structural insights into RNA processing by the human RISC-loading complex

H.W. Wang, C. Noland, B. Siridechadilok, D.W. Taylor, E. Ma, K. Felderer, J.A. Doudna, E. Nogales. (2009) Nat. Stuct. Mol. Biol. 16, 1148-1153.


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