Superfund Research Program

Research Translation

Research Translation Coordinator: Justin B. Siegel
Grant Number: P42ES004699
Funding Period: 2005-2023

Project-Specific Links

Publications

2022

• King E, Cui Y, Aspacio D, Nicklen F, Zhang L, Maxel S, Luo R, Siegel JB, Aitchison E, Li H. 2022. Engineering embden-meyerhof-parnas glycolysis to generate noncanonical reducing power. ACS Catal 12(14):8582-8592. doi:10.1021/acscatal.2c01837
• King E, Maxel S, Zhang Y, Kenney KC, Cui Y, Luu E, Siegel JB, Weiss GA, Luo R, Li H. 2022. Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase. Nat Commun 13(1):7282. doi:10.1038/s41467-022-35021-x PMID:36435948 PMCID:PMC9701214
• Zhang L, King E, Black WB, Heckmann CM, Wolder A, Cui Y, Nicklen F, Siegel JB, Luo R, Paul CE, Li H. 2022. Directed evolution of phosphite dehydrogenase to cycle noncanonical redox cofactors via universal growth selection platform. Nat Commun 13(1):5021. doi:10.1038/s41467-022-32727-w PMID:36028482 PMCID:PMC9418148

2021

• Denish PR, Fenger J, Powers R, Sigurdson GT, Grisanti L, Guggenheim KG, Laporte S, Li J, Kondo T, Magistrato A, Moloney MP, Riley M, Rusishvili M, Ahmadiani N, Baroni S, Dangles O, Giusti M, Collins TM, Didzbalis J, Yoshida K, Siegel JB, Robbins RJ. 2021. Discovery of a natural cyan blue: A unique food-sourced anthocyanin could replace synthetic brilliant blue. Sci Adv 7:doi:10.1126/sciadv.abe7871 PMID:33827818 PMCID:PMC8026139
• Leman JK, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow KA, Ben-Aharon Z, Farrell D, Fell JS, Hansen WA, Harmalkar A, Jeliazkov JR, Kuenze G, Krys JD, Ljubetic A, Loshbaugh AL, Maguire J, Moretti R, Mulligan VK, Nance ML, Nguyen PT, O'Conchuir S, Roy Burman SS, Samanta R, Smith S, Teets FD, Tiemann JK, Watkins A, Woods H, Yachnin BJ, Bahl CD, Bailey-Kellogg C, Baker D, Das R, DiMaio F, Khare SD, Kortemme T, Labonte JW, Lindorff-Larsen K, Meiler J, Schief W, Schueler-Furman O, Siegel JB, Stein A, Yarov-Yarovoy V, Kuhlman B, Leaver-Fay A, Gront D, Gray JJ, Bonneau R. 2021. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nat Commun 12:doi:10.1038/s41467-021-27222-7 PMID:34845212 PMCID:PMC8630030

2020

• Barnych B, Singh N, Negrel S, Zhang Y, Magis D, Roux C, Hua X, Ding Z, Morisseau C, Tantillo DJ, Siegel JB, Hammock BD. 2020. Development of potent inhibitors of the human microsomal epoxide hydrolase. Eur J Med Chem 193:doi:10.1016/j.ejmech.2020.112206 PMID:32203787
• Cui Y, Allmon SD, Siegel JB. 2020. Functional characterization and reclassification of an enzyme previously proposed to be a limonoidUDP-glucosyltransferase. Journal of the Science of Food and Agriculture 9:doi:10.1002/jsfa.10547 PMID:32483918 PMCID:PMC7920543
• Huang P, Chu SK, Frizzo HN, Connolly MP, Caster RW, Siegel JB. 2020. Evaluating protein engineering thermostability prediction tools using an independently generated dataset. ACS Omega 5:6487-6493. doi:10.1021/acsomega.9b04105 PMID:32258884 PMCID:PMC7114132
• Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang P, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib F, Khramushin A, King IC, Kleffner R, Koepnick B, Kortemme T, Kuenze G, Kuhlman B, Kuroda D, Labonte JW, Lai JK, Lapidoth G, Leaver-Fay A, Lindert S, Linsky T, London N, Lubin JH, Lyskov S, Maguire J, Malmstrom L, Marcos E, Marcu O, Marze NA, Meiler J, Moretti R, Mulligan VK, Nerli S, Norn C, O'Conchuir S, Ollikainen N, Ovchinnikov S, Pacella MS, Pan X, Park H, Pavlovicz RE, Pethe M, Pierce BG, Pilla KB, Raveh B, Renfrew PD, Burma SS, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furman O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel JB, Silva D, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RY, Watkins A, Zimmerman L, Bonneau R. 2020. Macromolecular modeling and design in Rosetta: Recent methods and frameworks. Nat Methods 16:doi:10.1038/s41592-020-0848-2 PMID:32483333
• Mak WS, Wang X, Arenas R, Cui Y, Bertolani SJ, Deng W, Tagkopoulos I, Wilson D, Siegel JB. 2020. Discovery, Design, and Structural Characterization of Alkane-Producing Enzymes across the Ferritin-like Superfamily. Biochemistry 59:3834-3843. doi:10.1021/acs.biochem.0c00665 PMID:32935984
• Park S, Doherty EE, Xie Y, Padyana AK, Fang F, Zhang Y, Karki A, Lebrilla CB, Siegel JB, Beal PA. 2020. High-throughput mutagenesis reveals unique structural features of human ADAR1. Nat Commun 11:5130. doi:10.1038/s41467-020-18862-2 PMID:33046702 PMCID:PMC7550611
• Zhang Y, Prach LM, O'Brien TE, DiMaio F, Prigozhin DM, Corn JE, Alber T, Siegel JB, Tantillo DJ. 2020. Crystal structure and mechanistic molecular modeling studies of Mycobacterium tuberculosis diterpene cyclase Rv3377c. Biochemistry 59:4507-4515. doi:10.1021/acs.biochem.0c00762 PMID:33182997

2019

• Bertolani SJ, Siegel JB. 2019. A new benchmark illustrates that integration of geometric constraints inferred from enzyme reaction chemistry can increase enzyme active site modeling accuracy. PLoS One 14:15. doi:10.1371/journal.pone.0214126 PMID:30947258 PMCID:PMC6448891
• Black WB, Zhang L, Mak WS, Maxel S, Cui Y, King E, Fong B, Sanchez Martinez A, Siegel JB, Li H. 2019. Engineering a nicotinamide mononucleotide redox cofactor system for biocatalysis. Nat Chem Biol 16:87-94. doi:10.1038/s41589-019-0402-7 PMID:31768035

2017

• Vasylieva N, Barnych B, Wan D, El-Sheikh EA, Nguyen HM, Wulff H, McMahen R, Strynar M, Gee SJ, Hammock BD. 2017. Hydroxy-fipronil is a new urinary biomarker of exposure to fipronil. Environ Int 103:91-98. doi:10.1016/j.envint.2017.03.012 PMID:28343720 PMCID:PMC5432128

2015

• Vasylieva N, Ahn K, Barnych B, Gee SJ, Hammock BD. 2015. Development of an immunoassay for the detection of the phenylpyrazole insecticide fipronil. Environ Sci Technol 49(16):10038-10047. doi:10.1021/acs.est.5b01005 PMID:26196357 PMCID:PMC4605820

2010

• Jorgenson BC, Young TM. 2010. Formulation effects and the off-target transport of pyrethroid insecticides from urban hard surfaces. Environ Sci Technol 44(13):4951-4957. doi:10.1021/es100094f PMID:20524665 PMCID:PMC2927978
• Rose TE, Morisseau C, Liu J, Inceoglu B, Jones PD, Sanborn JR, Hammock BD. 2010. 1-Aryl-3-(1-acylpiperidin-4-yl)urea inhibitors of human and murine soluble epoxide hydrolase: structure-activity relationships, pharmacokinetics, and reduction of inflammatory pain. J Med Chem 53(19):7067-7075. doi:10.1021/jm100691c PMID:20812725 PMCID:PMC3285450