Coordination of phage genome degradation versus host genome protection by a bifunctional restriction-modification enzyme visualized by CryoEM

Authors: Shen, Betty W., Quispe, Joel D., Luyten, Yvette, McGough, Benjamin E., Morgan, Richard D., Stoddard, Barry L.

Source: In Structure 3 June 2021 29(6):521-530

Design of pseudosymmetric protein hetero-oligomers.

Authors: Kibler, Ryan D., Lee, Sangmin, Kennedy, Madison A., Wicky, Basile I. M., Lai, Stella M., Kostelic, Marius M., Carr, Ann, Li, Xinting, Chow, Cameron M., Nguyen, Tina K., Carter, Lauren, Wysocki, Vicki H., Stoddard, Barry L., Baker, David

Source: Nature Communications; 12/18/2024, Vol. 15 Issue 1, p1-12, 12p

Subject Terms: LIFE sciences, CYTOLOGY, CELL communication, BIOENGINEERING, BIOCHEMISTRY, PROTEIN engineering

Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition

Authors: Lambert, Abigail R., Hallinan, Jazmine P., Werther, Rachel, Głów, Dawid, Stoddard, Barry L.

Source: In Structure 7 July 2020 28(7):760-775

Computational Thermostabilization of an Enzyme

Authors: Korkegian, Aaron, Black, Margaret E., Baker, David, Stoddard, Barry L.

Source: Science, 2005 May 01. 308(5723), 857-860.

Access URL: https://www.jstor.org/stable/3841942

Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

Authors: Kuhlman, Brian, Dantas, Gautam, Ireton, Gregory C., Varani, Gabriele, Stoddard, Barry L., Baker, David

Source: Science, 2003 Nov . 302(5649), 1364-1368.

Access URL: https://www.jstor.org/stable/3835603

Time-resolved macromolecular crystallography.

Authors: Galburt, Eric A., Stoddard, Barry L.

Source: Physics Today; July 2001, Vol. 54 Issue 7, p33-39, 7p

Orbital Steering in the Catalytic Power of Enzymes: Small Structural Changes with Large Catalytic Consequences

Authors: Mesecar, Andrew D., Stoddard, Barry L., Koshland, Daniel E.

Source: Science, 1997 Jul 01. 277(5323), 202-206.

Access URL: https://www.jstor.org/stable/2893564

Capturing the Structure of a Catalytic RNA Intermediate: The Hammerhead Ribozyme

Authors: Scott, William G., Murray, James B., Stoddard, Barry L., Klug, Aaron

Source: Science, 1996 Dec . 274(5295), 2065-2069.

Access URL: https://www.jstor.org/stable/2891358

Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity

Authors: Lambert, Abigail R., Hallinan, Jazmine P., Shen, Betty W., Chik, Jennifer K., Bolduc, Jill M., Kulshina, Nadia, Robins, Lori I., Kaiser, Brett K., Jarjour, Jordan, Havens, Kyle, Scharenberg, Andrew M., Stoddard, Barry L.

Source: In Structure 7 June 2016 24(6):862-873

The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease

Authors: Shen, Betty W., Lambert, Abigail, Walker, Bradley C., Stoddard, Barry L., Kaiser, Brett K.

Source: In Journal of Molecular Biology 16 January 2016 428(1):206-220

CRISPR in Nucleic Acids Research: the sequel.

Authors: Sale, Julian E, Stoddard, Barry L

Source: Nucleic Acids Research; 4/24/2024, Vol. 52 Issue 7, p3489-3492, 4p

A Computationally Designed Inhibitor of an Epstein-Barr Viral Bcl-2 Protein Induces Apoptosis in Infected Cells

Authors: Procko, Erik, Berguig, Geoffrey Y., Shen, Betty W., Song, Yifan, Frayo, Shani, Convertine, Anthony J., Margineantu, Daciana, Booth, Garrett, Correia, Bruno E., Cheng, Yuanhua, Schief, William R., Hockenbery, David M., Press, Oliver W., Stoddard, Barry L., Stayton, Patrick S., Baker, David

Source: In Cell 19 June 2014 157(7):1644-1656

Computational protein design enables a novel one-carbon assimilation pathway

Authors: Siegel, Justin B., Lee Smith, Amanda, Poust, Sean, Wargacki, Adam J., Bar-Even, Arren, Louw, Catherine, Shen, Betty W., Eiben, Christopher B., Tran, Huu M., Noor, Elad, Gallaher, Jasmine L., Bale, Jacob, Yoshikuni, Yasuo, Gelb, Michael H., Keasling, Jay D., Stoddard, Barry L., Lidstrom, Mary E., Baker, David

Source: Proceedings of the National Academy of Sciences of the United States of America, 2015 Mar . 112(12), 3704-3709.

Access URL: https://www.jstor.org/stable/26462142

The structural basis of mRNA recognition and binding by yeast pseudouridine synthase PUS1.

Authors: Grünberg, Sebastian, Doyle, Lindsey A., Wolf, Eric J., Dai, Nan, Corrêa Jr., Ivan R., Yigit, Erbay, Stoddard, Barry L.

Source: PLoS ONE; 11/8/2023, Vol. 18 Issue 11, p1-24, 24p

Subject Terms: PSEUDOURIDINE, RNA modification & restriction, MESSENGER RNA, CATALYTIC RNA, TRANSFER RNA, NON-coding RNA

TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins

Authors: Doyle, Erin L., Stoddard, Barry L., Voytas, Daniel F., Bogdanove, Adam J.

Source: In Trends in Cell Biology August 2013 23(8):390-398

TAL effectors: function, structure, engineering and applications

Authors: Mak, Amanda Nga-Sze, Bradley, Philip, Bogdanove, Adam J, Stoddard, Barry L

Source: In Current Opinion in Structural Biology February 2013 23(1):93-99

Redesign of extensive protein—DNA interfaces of meganucleases using iterative cycles of in vitro compartmentalization

Authors: Takeuchi, Ryo, Choi, Michael, Stoddard, Barry L.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2014 Mar . 111(11), 4061-4066.

Access URL: https://www.jstor.org/stable/23770983

De novo design of knotted tandem repeat proteins.

Authors: Doyle, Lindsey A., Takushi, Brittany, Kibler, Ryan D., Milles, Lukas F., Orozco, Carolina T., Jones, Jonathan D., Jackson, Sophie E., Stoddard, Barry L., Bradley, Philip

Source: Nature Communications; 10/24/2023, Vol. 14 Issue 1, p1-17, 17p

Subject Terms: X-ray crystallography, TANDEM repeats, KNOT theory, PROTEIN engineering, PROTEIN folding, PROTEIN structure

The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target

Authors: Mak, Amanda Nga-Sze, Bradley, Philip, Cernadas, Raul A., Bogdanove, Adam J., Stoddard, Barry L.

Source: Science, 2012 Feb 01. 335(6069), 716-719.

Access URL: http://dx.doi.org/10.1126/science.1216211

Tapping natural reservoirs of homing endonucleases for targeted gene modification

Authors: Takeuchi, Ryo, Lambert, Abigail R., Mak, Amanda Nga-Sze, Jacoby, Kyle, Dickson, Russell J., Gloor, Gregory B., Scharenberg, Andrew M., Edgell, David R., Stoddard, Barry L.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2011 Aug 01. 108(32), 13077-13082.

Access URL: https://www.jstor.org/stable/27979147