Search Results - "Shen, Betty W"

Increased Diels-Alderase activity through backbone remodeling guided by Foldit players by Eiben, Christopher B, Siegel, Justin B, Bale, Jacob B, Cooper, Seth, Khatib, Firas, Shen, Betty W, Players, Foldit, Stoddard, Barry L, Popovic, Zoran, Baker, David

“…Baker and colleagues have already shown that protein folding can be turned into an online game played by nonscientists. Now, Foldit players tackle the problem…”
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Computational protein design enables a novel one-carbon assimilation pathway by 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

“…We describe a computationally designed enzyme, formolase (FLS), which catalyzes the carboligation of three one-carbon formaldehyde molecules into one…”
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Control of repeat-protein curvature by computational protein design by Park, Keunwan, Shen, Betty W, Parmeggiani, Fabio, Huang, Po-Ssu, Stoddard, Barry L, Baker, David

“…Leucine-rich repeats (LRRs) can form horseshoe-like structures with different curvatures in nature. A computational approach now allows the design of 12 new…”
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A Computationally Designed Inhibitor of an Epstein-Barr Viral Bcl-2 Protein Induces Apoptosis in Infected Cells by 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

“…Because apoptosis of infected cells can limit virus production and spread, some viruses have co-opted prosurvival genes from the host. This includes the…”
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The tertiary structure and domain organization of coagulation factor VIII by Shen, Betty W., Spiegel, Paul Clint, Chang, Chong-Hwan, Huh, Jae-Wook, Lee, Jung-Sik, Kim, Jeanman, Kim, Young-Ho, Stoddard, Barry L.

“…Factor VIII (fVIII) is a serum protein in the coagulation cascade that nucleates the assembly of a membrane-bound protease complex on the surface of activated…”
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Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer by Berger, Stephanie, Procko, Erik, Margineantu, Daciana, Lee, Erinna F, Shen, Betty W, Zelter, Alex, Silva, Daniel-Adriano, Chawla, Kusum, Herold, Marco J, Garnier, Jean-Marc, Johnson, Richard, MacCoss, Michael J, Lessene, Guillaume, Davis, Trisha N, Stayton, Patrick S, Stoddard, Barry L, Fairlie, W Douglas, Hockenbery, David M, Baker, David

“…Many cancers overexpress one or more of the six human pro-survival BCL2 family proteins to evade apoptosis. To determine which BCL2 protein or proteins block…”
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Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity by 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.

“…LAGLIDADG meganucleases are DNA cleaving enzymes used for genome engineering. While their cleavage specificity can be altered using several protein engineering…”
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Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces by Hallinan, Jazmine P., Doyle, Lindsey A., Shen, Betty W., Gewe, Mesfin M., Takushi, Brittany, Kennedy, Madison A., Friend, Della, Roberts, James M., Bradley, Philip, Stoddard, Barry L.

“…Circular tandem repeat proteins (‘cTRPs’) are de novo designed protein scaffolds (in this and prior studies, based on antiparallel two-helix bundles) that…”
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Unusual Target Site Disruption by the Rare-Cutting HNH Restriction Endonuclease PacI by Shen, Betty W., Heiter, Daniel F., Chan, Siu-Hong, Wang, Hua, Xu, Shuang-Yong, Morgan, Richard D., Wilson, Geoffrey G., Stoddard, Barry L.

“…The crystal structure of the rare-cutting HNH restriction endonuclease PacI in complex with its eight-base-pair target recognition sequence 5′-TTAATTAA-3′ has…”
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Structure of the C2 domain of human factor VIII at 1.5  resolution by Stoddard, Barry L, Pratt, Kathleen P, Shen, Betty W, Takeshima, Kazuya, Davie, Earl W, Fujikawa, Kazuo

“…Human factor VIII is a plasma glycoprotein that has a critical role in blood coagulation. Factor VIII circulates as a complex with von Willebrand factor. After…”
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The Crystal Structure and Mutational Analysis of Human NUDT9 by Shen, Betty W., Perraud, Anne-Laure, Scharenberg, Andrew, Stoddard, Barry L.

“…Human ADP-ribose pyrophosphatase NUDT9 belongs to a superfamily of Nudix hydrolases that catabolize potentially toxic compounds in the cell. The enzyme…”
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Structure, substrate binding and activity of a unique AAA+ protein: the BrxL phage restriction factor by Shen, Betty W, Doyle, Lindsey A, Werther, Rachel, Westburg, Abigail A, Bies, Daniel P, Walter, Stephanie I, Luyten, Yvette A, Morgan, Richard D, Stoddard, Barry L, Kaiser, Brett K

“…Abstract Bacteriophage exclusion (‘BREX’) systems are multi-protein complexes encoded by a variety of bacteria and archaea that restrict phage by an unknown…”
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Coordination of phage genome degradation versus host genome protection by a bifunctional restriction-modification enzyme visualized by CryoEM by Shen, Betty W., Quispe, Joel D., Luyten, Yvette, McGough, Benjamin E., Morgan, Richard D., Stoddard, Barry L.

“…Restriction enzymes that combine methylation and cleavage into a single assemblage and modify one DNA strand are capable of efficient adaptation toward novel…”
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Engineering and functionalization of large circular tandem repeat protein nanoparticles by Correnti, Colin E., Hallinan, Jazmine P., Doyle, Lindsey A., Ruff, Raymond O., Jaeger-Ruckstuhl, Carla A., Xu, Yuexin, Shen, Betty W., Qu, Amanda, Polkinghorn, Caley, Friend, Della J., Bandaranayake, Ashok D., Riddell, Stanley R., Kaiser, Brett K., Stoddard, Barry L., Bradley, Philip

“…Protein engineering has enabled the design of molecular scaffolds that display a wide variety of sizes, shapes, symmetries and subunit compositions. Symmetric…”
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Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI by Shen, Betty W, Doyle, Lindsey, Bradley, Phil, Heiter, Daniel F, Lunnen, Keith D, Wilson, Geoffrey G, Stoddard, Barry L

“…Abstract BbvCI, a Type IIT restriction endonuclease, recognizes and cleaves the seven base pair sequence 5′-CCTCAGC-3′, generating 3-base, 5′-overhangs. BbvCI…”
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Crystal structure of human recombinant ornithine aminotransferase by Shen, Betty W, Hennig, Michael, Hohenester, Erhard, Jansonius, Johan N, Schirmer, Tilman

“…Ornithine aminotransferase (OAT), a pyridoxal-5′-phosphate dependent enzyme, catalyses the transfer of the δ-amino group of l-ornithine to 2-oxoglutarate,…”
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The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease by Shen, Betty W., Lambert, Abigail, Walker, Bradley C., Stoddard, Barry L., Kaiser, Brett K.

“…LAGLIDADG homing endonucleases (“meganucleases”) are highly specific DNA cleaving enzymes that are used for genome engineering. Like other enzymes that act on…”
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DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target by Shen, Betty W, Heiter, Daniel F, Lunnen, Keith D, Wilson, Geoffrey G, Stoddard, Barry L

“…R.SwaI, a Type IIP restriction endonuclease, recognizes a palindromic eight base pair (bp) symmetric sequence, 5΄-ATTTAAAT-3΄, and cleaves that target at its…”
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Characterization and crystal structure of the type IIG restriction endonuclease RM.BpuSI by Shen, Betty W., Xu, Derrick, Chan, Siu-Hong, Zheng, Yu, Zhu, Zhenyu, Xu, Shuang-yong, Stoddard, Barry L.

“…A type IIG restriction endonuclease, RM.BpuSI from Bacillus pumilus, has been characterized and its X-ray crystal structure determined at 2.35Å resolution. The…”
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Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space by Jacoby, Kyle, Metzger, Michael, Shen, Betty W, Certo, Michael T, Jarjour, Jordan, Stoddard, Barry L, Scharenberg, Andrew M

“…LAGLIDADG homing endonucleases (LHEs) are a family of highly specific DNA endonucleases capable of recognizing target sequences ≈ 20 bp in length, thus drawing…”
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