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Items: 1 to 50 of 68


Development of potent inhibitors of the human microsomal epoxide hydrolase.

Barnych B, Singh N, Negrel S, Zhang Y, Magis D, Roux C, Hua X, Ding Z, Morisseau C, Tantillo DJ, Siegel JB, Hammock BD.

Eur J Med Chem. 2020 Mar 13;193:112206. doi: 10.1016/j.ejmech.2020.112206. [Epub ahead of print]


A Benchmark for Homomeric Enzyme Active Site Structure Prediction Highlights the Importance of Accurate Modeling of Protein Symmetry.

Contreras SC, Bertolani SJ, Siegel JB.

ACS Omega. 2019 Dec 19;4(27):22356-22362. doi: 10.1021/acsomega.9b02636. eCollection 2019 Dec 31.


Engineering a nicotinamide mononucleotide redox cofactor system for biocatalysis.

Black WB, Zhang L, Mak WS, Maxel S, Cui Y, King E, Fong B, Sanchez Martinez A, Siegel JB, Li H.

Nat Chem Biol. 2020 Jan;16(1):87-94. doi: 10.1038/s41589-019-0402-7. Epub 2019 Nov 25.


Toward Development of Fluorescence-Quenching-Based Biosensors for Drought Stress in Plants.

Sharmah A, Kraus M, Cutler SR, Siegel JB, Brady SM, Guo T.

Anal Chem. 2019 Dec 17;91(24):15644-15651. doi: 10.1021/acs.analchem.9b03751. Epub 2019 Nov 21.


A new benchmark illustrates that integration of geometric constraints inferred from enzyme reaction chemistry can increase enzyme active site modeling accuracy.

Bertolani SJ, Siegel JB.

PLoS One. 2019 Apr 4;14(4):e0214126. doi: 10.1371/journal.pone.0214126. eCollection 2019.


β-Glucosidase Discovery and Design for the Degradation of Oleuropein.

Guggenheim KG, Crawford LM, Paradisi F, Wang SC, Siegel JB.

ACS Omega. 2018 Nov 30;3(11):15754-15762. doi: 10.1021/acsomega.8b02169. Epub 2018 Nov 20.


Repurposing Citizen Science Games as Software Tools for Professional Scientists.

Cooper S, Sterling ALR, Kleffner R, Silversmith WM, Siegel JB.

FDG. 2018 Aug;2018. pii: 39. doi: 10.1145/3235765.3235770.


X-ray-Mediated Release of Molecules and Engineered Proteins from Nanostructure Surfaces.

Su M, Guggenheim KG, Lien J, Siegel JB, Guo T.

ACS Appl Mater Interfaces. 2018 Sep 26;10(38):31860-31864. doi: 10.1021/acsami.8b13117. Epub 2018 Sep 13.


The Zinc Linchpin Motif in the DNA Repair Glycosylase MUTYH: Identifying the Zn2+ Ligands and Roles in Damage Recognition and Repair.

Nuñez NN, Khuu C, Babu CS, Bertolani SJ, Rajavel AN, Spear JE, Armas JA, Wright JD, Siegel JB, Lim C, David SS.

J Am Chem Soc. 2018 Oct 17;140(41):13260-13271. doi: 10.1021/jacs.8b06923. Epub 2018 Oct 8.


Predicting Productive Binding Modes for Substrates and Carbocation Intermediates in Terpene Synthases-Bornyl Diphosphate Synthase as a Representative Case.

O'Brien TE, Bertolani SJ, Zhang Y, Siegel JB, Tantillo DJ.

ACS Catal. 2018 Apr 6;8(4):3322-3330. doi: 10.1021/acscatal.8b00342. Epub 2018 Mar 8.


Changing Face: A Key Residue for the Addition of Water by Sclareol Synthase.

Jia M, O'Brien TE, Zhang Y, Siegel JB, Tantillo DJ, Peters RJ.

ACS Catal. 2018 Apr 6;8(4):3133-3137. doi: 10.1021/acscatal.8b00121. Epub 2018 Mar 8.


Combination of type II fatty acid biosynthesis enzymes and thiolases supports a functional β-oxidation reversal.

Clomburg JM, Contreras SC, Chou A, Siegel JB, Gonzalez R.

Metab Eng. 2018 Jan;45:11-19. doi: 10.1016/j.ymben.2017.11.003. Epub 2017 Nov 13.


Elucidating Substrate Promiscuity within the FabI Enzyme Family.

Freund GS, O'Brien TE, Vinson L, Carlin DA, Yao A, Mak WS, Tagkopoulos I, Facciotti MT, Tantillo DJ, Siegel JB.

ACS Chem Biol. 2017 Sep 15;12(9):2465-2473. doi: 10.1021/acschembio.7b00400. Epub 2017 Aug 31.


Systematic Functional Analysis of Active-Site Residues in l-Threonine Dehydrogenase from Thermoplasma volcanium.

Desjardins M, Mak WS, O'Brien TE, Carlin DA, Tantillo DJ, Siegel JB.

ACS Omega. 2017 Jul 7;2(7):3308-3314. doi: 10.1021/acsomega.7b00519. eCollection 2017 Jul 31.


Thermal stability and kinetic constants for 129 variants of a family 1 glycoside hydrolase reveal that enzyme activity and stability can be separately designed.

Carlin DA, Hapig-Ward S, Chan BW, Damrau N, Riley M, Caster RW, Bethards B, Siegel JB.

PLoS One. 2017 May 22;12(5):e0176255. doi: 10.1371/journal.pone.0176255. eCollection 2017.


Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta.

Kleffner R, Flatten J, Leaver-Fay A, Baker D, Siegel JB, Khatib F, Cooper S.

Bioinformatics. 2017 Sep 1;33(17):2765-2767. doi: 10.1093/bioinformatics/btx283.


Engineering a Thermostable Keto Acid Decarboxylase Using Directed Evolution and Computationally Directed Protein Design.

Soh LMJ, Mak WS, Lin PP, Mi L, Chen FY, Damoiseaux R, Siegel JB, Liao JC.

ACS Synth Biol. 2017 Apr 21;6(4):610-618. doi: 10.1021/acssynbio.6b00240. Epub 2017 Jan 11.


Comparative analyses of ubiquitin-like ATG8 and cysteine protease ATG4 autophagy genes in the plant lineage and cross-kingdom processing of ATG8 by ATG4.

Seo E, Woo J, Park E, Bertolani SJ, Siegel JB, Choi D, Dinesh-Kumar SP.

Autophagy. 2016 Nov;12(11):2054-2068. Epub 2016 Aug 19.


Mechanistically informed predictions of binding modes for carbocation intermediates of a sesquiterpene synthase reaction.

O'Brien TE, Bertolani SJ, Tantillo DJ, Siegel JB.

Chem Sci. 2016 Jul 1;7(7):4009-4015. doi: 10.1039/c6sc00635c. Epub 2016 Mar 21.


Corrigendum: Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway.

Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D, Liao JC, Siegel JB.

Nat Commun. 2016 Jun 7;7:11912. doi: 10.1038/ncomms11912. No abstract available.


Computational Introduction of Catalytic Activity into Proteins.

Bertolani SJ, Carlin DA, Siegel JB.

Methods Mol Biol. 2016;1414:213-31. doi: 10.1007/978-1-4939-3569-7_13.


Erratum: Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2-dehydrogenase.

Lucas JE, Siegel JB.

Protein Sci. 2016 Mar;25(3):769-70. doi: 10.1002/pro.2882. No abstract available.


Kinetic Characterization of 100 Glycoside Hydrolase Mutants Enables the Discovery of Structural Features Correlated with Kinetic Constants.

Carlin DA, Caster RW, Wang X, Betzenderfer SA, Chen CX, Duong VM, Ryklansky CV, Alpekin A, Beaumont N, Kapoor H, Kim N, Mohabbot H, Pang B, Teel R, Whithaus L, Tagkopoulos I, Siegel JB.

PLoS One. 2016 Jan 27;11(1):e0147596. doi: 10.1371/journal.pone.0147596. eCollection 2016.


Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway.

Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D, Liao JC, Siegel JB.

Nat Commun. 2015 Nov 24;6:10005. doi: 10.1038/ncomms10005. Erratum in: Nat Commun. 2016 Jun 07;7:11912.


Engineering of Kuma030: A Gliadin Peptidase That Rapidly Degrades Immunogenic Gliadin Peptides in Gastric Conditions.

Wolf C, Siegel JB, Tinberg C, Camarca A, Gianfrani C, Paski S, Guan R, Montelione G, Baker D, Pultz IS.

J Am Chem Soc. 2015 Oct 14;137(40):13106-13. doi: 10.1021/jacs.5b08325. Epub 2015 Sep 29.


Mechanistic Analysis of an Engineered Enzyme that Catalyzes the Formose Reaction.

Poust S, Piety J, Bar-Even A, Louw C, Baker D, Keasling JD, Siegel JB.

Chembiochem. 2015 Sep 7;16(13):1950-1954. doi: 10.1002/cbic.201500228. Epub 2015 Jul 27.


Computational protein design enables a novel one-carbon assimilation pathway.

Siegel JB, Smith AL, Poust S, Wargacki AJ, Bar-Even A, Louw C, Shen BW, Eiben CB, Tran HM, Noor E, Gallaher JL, Bale J, Yoshikuni Y, Gelb MH, Keasling JD, Stoddard BL, Lidstrom ME, Baker D.

Proc Natl Acad Sci U S A. 2015 Mar 24;112(12):3704-9. doi: 10.1073/pnas.1500545112. Epub 2015 Mar 9.


Biocatalytic conversion of ethylene to ethylene oxide using an engineered toluene monooxygenase.

Carlin DA, Bertolani SJ, Siegel JB.

Chem Commun (Camb). 2015 Feb 11;51(12):2283-5. doi: 10.1039/c4cc08802f.


Computational enzyme design: transitioning from catalytic proteins to enzymes.

Mak WS, Siegel JB.

Curr Opin Struct Biol. 2014 Aug;27:87-94. doi: 10.1016/ Epub 2014 Jul 5. Review.


Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase.

Preiswerk N, Beck T, Schulz JD, Milovník P, Mayer C, Siegel JB, Baker D, Hilvert D.

Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):8013-8. doi: 10.1073/pnas.1401073111. Epub 2014 May 20.


Expanding the product profile of a microbial alkane biosynthetic pathway.

Harger M, Zheng L, Moon A, Ager C, An JH, Choe C, Lai YL, Mo B, Zong D, Smith MD, Egbert RG, Mills JH, Baker D, Pultz IS, Siegel JB.

ACS Synth Biol. 2013 Jan 18;2(1):59-62. doi: 10.1021/sb300061x. Epub 2012 Sep 26.


Janus: prediction and ranking of mutations required for functional interconversion of enzymes.

Addington TA, Mertz RW, Siegel JB, Thompson JM, Fisher AJ, Filkov V, Fleischman NM, Suen AA, Zhang C, Toney MD.

J Mol Biol. 2013 Apr 26;425(8):1378-89. doi: 10.1016/j.jmb.2013.01.034. Epub 2013 Feb 6.


Computational design of an α-gliadin peptidase.

Gordon SR, Stanley EJ, Wolf S, Toland A, Wu SJ, Hadidi D, Mills JH, Baker D, Pultz IS, Siegel JB.

J Am Chem Soc. 2012 Dec 19;134(50):20513-20. doi: 10.1021/ja3094795. Epub 2012 Dec 5.


Increased Diels-Alderase activity through backbone remodeling guided by Foldit players.

Eiben CB, Siegel JB, Bale JB, Cooper S, Khatib F, Shen BW, Players F, Stoddard BL, Popovic Z, Baker D.

Nat Biotechnol. 2012 Jan 22;30(2):190-2. doi: 10.1038/nbt.2109.


Improvement of a potential anthrax therapeutic by computational protein design.

Wu SJ, Eiben CB, Carra JH, Huang I, Zong D, Liu P, Wu CT, Nivala J, Dunbar J, Huber T, Senft J, Schokman R, Smith MD, Mills JH, Friedlander AM, Baker D, Siegel JB.

J Biol Chem. 2011 Sep 16;286(37):32586-92. doi: 10.1074/jbc.M111.251041. Epub 2011 Jul 18.


Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.

Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, St Clair JL, Gallaher JL, Hilvert D, Gelb MH, Stoddard BL, Houk KN, Michael FE, Baker D.

Science. 2010 Jul 16;329(5989):309-13. doi: 10.1126/science.1190239.


Tunneled dialysis catheters: pearls and pitfalls.

Siegel JB.

Tech Vasc Interv Radiol. 2008 Sep;11(3):181-5. doi: 10.1053/j.tvir.2008.09.005. Review.


A first-in-human phase I trial of locally delivered human plasmin for hemodialysis graft occlusion.

Shlansky-Goldberg RD, Matsumoto AH, Baumbach GA, Siegel JB, Raabe RD, Murphy TP, Deng C, Ray Dawkins J, Marder VJ.

J Thromb Haemost. 2008 Jun;6(6):944-50. doi: 10.1111/j.1538-7836.2008.02969.x. Epub 2008 Apr 2.


Use of the peripheral cutting balloon to treat hemodialysis-related stenoses.

Vesely TM, Siegel JB.

J Vasc Interv Radiol. 2005 Dec;16(12):1593-603.


Beneath the skin. The workings of a dedicated dialysis vascular access center.

Siegel JB.

Nephrol News Issues. 2003 Jul;17(8):54-7. No abstract available.


Hydrodynamic thrombectomy system versus pulse-spray thrombolysis for thrombosed hemodialysis grafts: a multicenter prospective randomized comparison.

Barth KH, Gosnell MR, Palestrant AM, Martin LG, Siegel JB, Matalon TA, Goodwin SC, Neese PA, Swan TL, Uflacker R.

Radiology. 2000 Dec;217(3):678-84.


Analysis of CD39/ATP diphosphohydrolase (ATPDase) expression in endothelial cells, platelets and leukocytes.

Koziak K, Sévigny J, Robson SC, Siegel JB, Kaczmarek E.

Thromb Haemost. 1999 Nov;82(5):1538-44.


The WuScope technique for endotracheal tube exchange.

Andrews SR, Norcross SD, Mabey MF, Siegel JB.

Anesthesiology. 1999 Mar;90(3):929-30. No abstract available.


Structural elements and limited proteolysis of CD39 influence ATP diphosphohydrolase activity.

Schulte am Esch J 2nd, Sévigny J, Kaczmarek E, Siegel JB, Imai M, Koziak K, Beaudoin AR, Robson SC.

Biochemistry. 1999 Feb 23;38(8):2248-58.


Disseminated intravascular coagulation in association with the delayed rejection of pig-to-baboon renal xenografts.

Ierino FL, Kozlowski T, Siegel JB, Shimizu A, Colvin RB, Banerjee PT, Cooper DK, Cosimi AB, Bach FH, Sachs DH, Robson SC.

Transplantation. 1998 Dec 15;66(11):1439-50.


Expression of human thrombomodulin cofactor activity in porcine endothelial cells.

Kopp CW, Grey ST, Siegel JB, McShea A, Vetr H, Wrighton CJ, Schulte am Esch J 2nd, Bach FH, Robson SC.

Transplantation. 1998 Jul 27;66(2):244-51.


Regulation of monocyte tissue factor activity by allogeneic and xenogeneic endothelial cells.

Kopp CW, Robson SC, Siegel JB, Anrather J, Winkler H, Grey S, Kaczmarek E, Bach FH, Geczy CL.

Thromb Haemost. 1998 Mar;79(3):529-38.


Activation of human platelets by the membrane-expressed A1 domain of von Willebrand factor.

Schulte am Esch J 2nd, Cruz MA, Siegel JB, Anrather J, Robson SC.

Blood. 1997 Dec 1;90(11):4425-37.


Xenogeneic endothelial cells activate human prothrombin.

Siegel JB, Grey ST, Lesnikoski BA, Kopp CW, Soares M, Schulte am Esch J 2nd, Bach FH, Robson SC.

Transplantation. 1997 Sep 27;64(6):888-96.


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