Publications

Constructing next-generation CRISPR–Cas tools from structural blueprints

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

COIBT

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. https://doi.org/10.1016/j.celrep.2022.111103.  

Pubmed

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.

Pubmed

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). https://doi.org/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). https://doi.org/10.1038/s41467-022-30402-8

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.

PubMed

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.

PubMed

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.

PubMed

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..

PubMed

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.

PubMed

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

PubMed

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

PubMed

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

PubMed

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 

PubMed

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

PubMed

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 

PubMed

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

PubMed 

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

PubMed 

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.

PubMed

Kinetic Characterization of Cas9 Enzymes

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

PubMed
                

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.

PubMed
              

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.

PubMed
              

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.

PubMed
               

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.

PubMed

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.

PubMed
               


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.

PubMed
               

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.

PubMed

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.

PubMed

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.

PubMed

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.

PubMed

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.

PubMed

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.

PubMed

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.

PubMed

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.

PubMed

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.

PubMed

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. 

PubMed

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.

PubMed

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.

PubMed

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.

PubMed

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.

PubMed

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.  

PubMed

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.

PubMed

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.  

PubMed

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.

PubMed

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