Publications
Galburt, E., Pelletier, J., Wilson G., and Stoddard, B. L. (2002) "Structure of a tRNA repair enzyme and molecular biology workhorse, T4 polynucleotide kinase" Structure 10 (9): 1249 - 1260.
Liu, M., Shen, B. W., Nakaya, S., Pratt, K. P., Fujikawa, K., Davie, E. W., Stoddard, B. L., and Thompson, A. R. (2000) "Hemophilic factor VIII C1 and C2 domain missense mutations and their modeling to the 1.5 angstrom human C2 domain crystal structure" Blood 96 (3): 979 - 987.
Heath, P. J., Stephens, K., Monnat, R. and Stoddard, B. L. (1997) "Structure of the I-CreI intron-encoded endonuclease: a novel fold that binds and cleaves a long DNA target sequence" Nature Structural Biology 4 (6) 468-476.
The first Laue data collected at SSRL. Later used in Bolduc, J., Dyer, D., Lee, M., Scott, W. G., Singer, P., Sweet, R. M., Koshland, D. E. Jr. and Stoddard, B. L. (1995) "Mutagenesis and laue structures of enzyme intermediates: isocitrate dehydrogenase" Science 268: 1312 - 1318.
Galburt, E., and Stoddard, B. L. (2001) "Time-resolved macromolecular crystallography" Physics Today July: pg. 33 - 39.
Spiegel, P. C., Jacquemin, M., St. Remy, J. -M., Stoddard, B. L. and Pratt, K. P. (2001) "Structure of a factor VIII C2 domain/IgG4K Fab complex: identification of an inhibitory antibody epitope on the surface of Factor VIII" Blood 98 (1): 13 - 19.
Eastberg, J., Pelletier, J.., and Stoddard, B. L. (2004) "Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase" Nuc. Acids Research 32 (2) 653 - 660.
Spiegel, P. C., Murphy, P. and Stoddard, B. L. (2004) "Surface-exposed hemophilic mutations across the Factor VIII C2 domain have variable effects on stability and binding activities" J. Biol. Chem. 279 (51): 53691 - 53698.
Scalley-Kim, M., McConnell-Smith, A., and Stoddard, B. L. (2007) "Coevolution of homing endonuclease specificity and its host target sequence" J. Mol. Biol. 372 (5): 1305 - 1319.
Jurica, M. S. and Stoddard, B. L. "Homing endonucleases: structure, function and evolution" Cellular and Molecular Life Sciences (1999) " 55: 1304 - 1326.
Bolduc, J. M., Spiegel, P. C., Chatterjee, P., Brady, K. L., Downing, M. EW., Caprara, M. G., Waring, R. B. and Stoddard, B. L.(2003) "Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor" Genes and Development 17: 2875-2888.
Norimichi, N., Norimichi, Y., Sussman, D., Klein, D. and Stoddard, B. L. (2009) "Recognition of a common rDNA target site by analogous archael LAGLIDADG and eukaryal His-Cys box homing endonucleases isoschizomers" Nucleic Acids Research 36 (22): 6988 - 6998.
Publications by Project
Homing endonucleases (Meganucleases), Maturases, and TAL effectors
Hydrolases, Phospatases, Kinases
General Enzymology / Time-Resolved Crystallography
Nucleic Acid Synthesis, Salvage and Modification Enzymes
Most recent publications
Ennist NM, Wang S, Kennedy MA, et al. Stoddard BL, Romero E, Hunter CN, Baker D. " De novo design of proteins housing excitonically coupled chlorophyll special pairs" (2024) Nat Chem Biol. 20 (7):906-915. doi: 10.1038/s41589-024-01626-0. PMID: 38831036; PMCID: PMC11213709. Coordinates: 7UNH 7UNI 7UNJ
Kibler RD, Lee S, Kennedy MA, Wicky BIM, Lai SM, Kostelic MM, Carr A, Li X, Chow CM, Nguyen TK, Carter L, Wysocki VH, Stoddard BL, Baker D. Design of pseudosymmetric protein hetero-oligomers. Nat Commun. 2024 Dec 18;15(1):10684. doi: 10.1038/s41467-024-54913-8. PMID: 39695145; PMCID: PMC11655659 Coordinates: 8E0L 8E0M 8E0N 8E0O 8E12
Lee S, Kibler RD, Ahn G, Hsia Y, Borst AJ, Philomin A, Kennedy MA, Huang B, Stoddard B, Baker D. Four-component protein nanocages designed by programmed symmetry breaking. Nature. 2024 Dec 18. doi: 10.1038/s41586-024-07814-1. Epub ahead of print. PMID: 39695226 Coordinates: 8FLX
Lambert, A.R., Hallinan, J.P., Werther, R., Glow, D., and Stoddard, B.L. (2020) “Optimization of protein thermostability and exploitation of recognition behavior to engineer altered protein-DNA recognition” Structure epub ahead of print. doi: 10.1016/j.str.2020.04.009. PMID 32359399 Coordinates: 3QQY 6UVW 6UWG 6UW0 6UWH 6UWJ 6UWK
Niyonzima, N., Lambert, A. R., Werther, R., De Silva, F. H., Roychoudhury, P., Greninger, AL, Stone, D., Stoddard, B. L. and Jerome, K. R. (2017) "Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analyses" Protein Engineering Design and Selection 30 (7):503-522. PMID 28873986 Coordinates: 5V0Q, 5T8D
Moffett, H. F., Coon, M. E., Radteke, S., McKnight, L., Stephan, S. B., McKnight, L., Lambert, A. R., Stoddard, B. L., Kiem, H. -P. and Matthias, S. (2017) "Hit-and-run programming of CAR-T cells using mRNA nanocarriers" Nature Communications 8 (1): 389. doi: 10.1038/s41467-017-00505-8. PMID 28855514
Werther, R., Hallinan, J. P., Lambert, A., Jarjour, J., Havens, K, Galizi, R., Windbichler, N., Crisanti, A., Nolan, T. and Stoddard, B.L. (2017) "Crystallographic analyses illustrate significant plasticity and efficient recoding of meganuclease target specificity" Nuc. Acids Res. 45 (14):8621-8634. PMID 28637173 Coordinates: 5THG 5T2H 5T8D 5T2N 5T2O
Rinaldi, F., Doyle, L. A., Stoddard, B. L. and Bogdanove, A. (2017) "The effect of increasing numbers of repeats on TAL effector binding specificity" Nucleic Acids Research 45 (11):6960-6970. PMID 28460076
Lambert AR, Hallinan JP, Shen BW, Chik JK, Bolduc JM, Kulshina N, Robins LI, Kaiser BK, Jarjour J, Havens K, Scharenberg AM and Stoddard BL. (2016) "Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity." Structure 24 (6): 862 - 873. PMID 27133026 Coordinates: 4YIT 4YIS 4YHX 4Z1X 4LQ0 5ESP 5E5O 4Z20 4Z1Z
Shen, B. W., Walker, B., Lambert, A., Stoddard, B.L., and Kaiser, B.K. (2015) "The structural basis of asymmetry in DNA binding and cleavage as exemplified by the I-SmaMI LAGLIDADG meganuclease" J. Mol. Biol. 428 (1): 206 - 220. PMID 26705195 Coordinates: 5E5P 5E5O 4LOX 5ES5 5E63 5E67
Galizi R, Doyle LA, Menichelli M, Bernardini F, Deredec A, Burt A, Stoddard BL, Windbichler N, Crisanti A. (2014) "A synthetic sex ratio distortion system for the control of the human malaria mosquito" Nature Communications 5: 3977. PMID 24914045
Takeuchi, R., Choi, M., and Stoddard, B.L. (2014) "Redesign of extensive protein-DNA interfaces of meganucleases using iterative cycles of in vitro compartmentalization" PNAS USA 111 (11): 4061 - 4066. PMID 24591643
Boissel, S., Jarjour, J., Astrakhan, A., Adey, A., Shendure, J., Stoddard, B. L. Certo, M. T., Baker, D. and Scharenberg, A. (2014) "MegaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering” Nucleic Acids Research 42(4):2591-601. PMID 24285304
Chan, Y- S., Takeuchi, R., Jarjour, J., Huen, D., Stoddard, B. L. and Russell, S. (2013) “The design and in vivo evaluation of I-OnuI based enzymes for HEG gene drive” PLOS One 8 (9): e74254. PMID 24040217
Metzger, M. J., Stoddard, B. L. and Monmat, R. J. Jr. (2013) “PARP-mediated repair, homologous recombination and backup non-homologous end-joining like repair of single strand nicks” DNA Repair 12 (7): 529 – 534. PMID 23684799
Baxter, S., Lambert, A. R., Kuhar, R., Jarjour, J., Kulshina, N., Parmeggiani, F., Danaher, P., Gano, J., Baker, D., Stoddard, B. L., and Scharenberg, A. M. (2012) "Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases" Nuc. Acids Res. 40 (16): 7985 - 8000. PMID 22684507
Taylor, G. K., Petrucci, L. H., Lambert, A. R., Baxter, S. K., Jarjour, J. and Stoddard, B. L. (2012) "LAHEDES: the LAGLIDADG homing endonuclease database and engineering server" Nucleic Acids Research 40 (W1): W110 - W116. PMID 22570419 Webserver: http://www.homingendonuclease.net
Kaiser, B. K. and Stoddard, B. L. (2011) "DNA recognition and transcriptional regulation by the WhiA sporulation factor" Scientific Reports (Nature Press) 1: 156. PMID 22355671
Jacoby, K., Metzger, M., Shen, B. W., Certo, M. T. Jarjour, J., Stoddard, B. L. and Scharenberg, A. M. (2012) "Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space" Nuc. Acids Res. 40 (11): 4954 - 4964. PMID 22334611 Coordinates: 3UVF
Mak, A. N., Bradley, P., Cernadas, R. A., Bogdanove, A. J., and Stoddard, B. L. (2012) "The crystal structure of TAL effector PthXo1 bound to its DNA target" Science 335: 716 - 719. PMID 22223736 Coordinates: 3UGM
Taylor, G.K., Heiter, D. F., Pietrokovski, S. and Stoddard, B.L. (2011) "Activity, specificity and structure of I-Bth0305I: a representative of a new homing endonuclease family" Nuc. Acids Res. 39 (22): 9705 - 9719. PMID 21890897 Coordinates: 3R3P
Takeuchi, R., Lambert, A. R., Mak, A. N., Jacoby, K., Dickson, R. J., Gloor, G. B., Scharenberg, A. M., Edgell, D. R. and Stoddard, B. L. (2011) "Tapping natural reservoirs of homing endonucleases for targeted gene modification" PNAS USA108(32):13077 - 13082. PMID 21784983 Coordinates: 3QQY 3R7P
Metzger, M. J., McConnell-Smith, A., Stoddard, B. L. and Miller, A. D. (2011) "Single strand nicks induce homologous recombination with less toxicity than double-strand breaks using an AAV template" Nuc. Acids Research 39 (3): 926 - 935. PMID 20876694
Ashworth, J., Taylor, G.K., Havranek, J.J., Quadri, S.A. Stoddard, B.L. and Baker, D. (2010) "Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs" Nuc. Acids Res. 38 (16) 5601 - 5608. PMID 2-435674 Coordinates: 3mip 3mis 3ko2
Thyme, S., Takeuchi, R., Jarjour, J., Scharenberg, A., Stoddard, B. L. and Baker, D. (2009) "Exploitation of homing endonuclease binding energy for catalysis and design" Nature 461: 1300 - 1304. PMID 19865174
Kaiser, B. K., Clifton, M. C., Shen, B. W. and Stoddard, B. L. (2009) "The structure of a bacterial DUF199 / WhiA protein: domestication of an invasive endonuclease" Structure 1368 - 1376. PMID 19836336 Coordinates: 13hi 13hj
Jarjour, J., West-Foyle, H., Certo, M. T., Hubert, C. G. Doyle, L., Getz, M. M. Stoddard, B. L. and Scharenberg, A. M. (2009) "High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display" Nucleic Acids Research 2009 Sept. 8. PMID 19740766.
Dassa, B., London, N., Stoddard, B. L. Schueler-Furman, O. and Pietrokovski, S. (2009) "Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family" Nucleic Acids Research 37 (8):2560-73. PMID 19264795
McConnell-Smith, A., Takeuchi, R., Pellenz, S., Davis, L., Maizels, N., Monnat, R. J. Jr., and Stoddard, B. L. (2009) "Generation of a nicking enzyme that stimulates site-specific gene conversion from the I-AniI LAGLIDADG homing endonuclease" PNAS USA 106 (13): 5099 - 5104. PMID 19276110
Li, H., Pellenz, S., Ulge, U., Stoddard, B. L. and Monnat, R. J. Jr. (2009) "Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins" Nucleic Acids Research 37 (5): 1650 - 1662. PMID 19153140 Coordinates: 3fd2
Takeuchi R, Certo M, Caprara MG, Scharenberg AM, and Stoddard BL. (2009) "Optimization of the in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation" 37 (3): 877 - 890. PMID 19103658 Coordinates: 3eh8
Zhao, L., Pellenz, S. and Stoddard, B. L. (2009) "Activity and specificity of the bacterial PD-(D/E)XK homing endonuclease I-Ssp6803I" J. Mol. Biol. 385 (5): 1498 - 1510. PMID 19038269
Nomura, N., Nomura, Y., Sussman, D., Klein, D. and Stoddard, B. L. (2008) "Recognition of a common rDNA target site by analogous archael LAGLIDADG and eukaryal His-Cys box homing endonucleases isoschizomers" Nucleic Acids Research 36(22): 6988 - 6998. PMID 18400177 Coordinates: 3e54
Eastberg, J. H., McConnell-Smith, A., Zhao, L., Ashworth, J., Shen, B. W. and Stoddard, B. L. (2007) "The thermodynamics of DNA target site recognition by homing endonucleases" Nuc. Acids Res. 35 (21) 7209 - 7221. PMID 17947319
Scalley-Kim, M., McConnell-Smith, A. and Stoddard, B. L. (2007) "Coevolution of homing endonuclease specificity and its host target sequence" J. Mol. Biol. 372 (5): 1305 - 1319. PMID 17720189 Coordinates: 2qoj
Eastberg, J., Monnat, R. J. Jr., and Stoddard, B. L. (2007) “Mutability of the ββα-metal HNH nuclease active site: substitution of a deprotonation mechanism” Biochemistry 46 (24): 7215 - 7225. PMID 17416660 Coordinates: 2o6m
Volna, P., Jarjour, J., Baxter,S., Roffler, S. R., Monnat, R. J. Jr., Stoddard, B. L. and Scharenberg, A. M. (2007) "Flow cytometric analysis of DNA binding and cleavage by cell surface-displayed homing endonucleases" Nucleic Acids Res. 35 (8): 2748 - 2758. PMID 17426121
Zhao, L, Boncora, R., Shub, D. and Stoddard, B. L. (2007) “The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD(D/E)XK motif” EMBO Journal 26: 2432 - 2442. PMID 17410205 Coordinates: 2ost
Rosen, L. E., Morrison, H. A., Masri, S., Brown, M. J., Springstubb, B., Sussman, D., Stoddard, B. L. and Seligman, L. M. (2006) "Homing endonuclease I-CreI derivatives with novel DNA target specificities" Nuc. Acids Res. 34 (17): 4791 - 800. PMID 16971456 Coordinates: 2i3p 2i3q
Spiegel, P. C., Chevalier, B., Sussman, D., Turmel, M., Lemieux, and Stoddard, B. L. (2006) "The structure of I-CeuI homing endonuclease: evolving asymmetric DNA recognition from a symmetric protein scaffold" Structure 14 (5): 869 - 880. PMID 16698548 Coordinates: 2ex5
Ashworth, J., Havranek, J. J., Duarte, C. M., Sussman, D., Monnat, R. J. Jr., Stoddard, B. L. and Baker, D. (2006) "Computational redesign of endonuclease DNA binding and cleavage specificity" Nature 441: 656 - 659. (Also listed under "protein engineering" below) PMID 16738662 Coordinates: 2fld
Landthaler, M., Shen, B.W., Stoddard, B. L. and Shub, D.A. (2006) "Two phage intron-encoded endonucleases with homologous DNA recognition sequences but distinct DNA specificities" J. Mol. Biol. 358 (4): 1137 - 1151. PMID 16569414
Chevalier, B., Sussman, D., Otis, C., Noel, A. -J., Turmel, M., Lemieux, C., Stephens, K., Monnat, R. J. Jr. and Stoddard, B. L. (2004) "Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing endonuclease " Biochemistry 43: 14015 - 14026. PMID 15518550 Coordinates: 1t9j 1t9i
Sussman, D., Chadsey, M., Fauce, S., Engel, A., Bruett, A., Monnat, R. J. Jr., Stoddard, B. L. and Seligman, L. (2004) "Isolation and characterization of new homing endonuclease specificities at individual target site positions" J. Mol. Biol. 342 (1): 31 - 41. PMID 15313605 Coordinates: 1uoc 1uod
Shen, B. W., Landthaler, M., Shub, D. A. and Stoddard, B. L. (2004) "DNA binding and cleavage by the HNH homing endonuclease I-HmuI" J. Mol. Biol. 342 (1): 34 - 56. PMID 15313606 Coordinates: 1u3e
Bakhrat, A., Jurica, M. S., Stoddard, B. L. and Raveh, D. (2004) "Homology modeling and mutational analysis of HO endonuclease of yeast" Genetics 166: 721 - 728. PMID 15020462
Bolduc, J. M., Spiegel, P. C., Chatterjee, P., Brady, K. L., Downing, M. EW., Caprara, M. G., Waring, R. B. and Stoddard, B. L. (2003) "Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor" Genes and Development 17: 2875-2888. PMID 1463397 Coordinates: 1p8k
Chevalier, B., Turmel, M., Lemieux, C., Monnat, R. J. Jr. and Stoddard, B. L. (2003) "Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI" J. Mol. Biol. 329: 253 - 269. PMID 12758074 Coordinates: 1m5x 1n3e 1n3f
Chevalier, B., Kortemme, T., Chadsey, M., Baker, D., Monnat, R. J. Jr. and Stoddard, B. L. (2002) "Design, activity and structure of a highly specific artificial endonuclease" Molecular Cell 10 :895 - 905. (Also listed under "protein engineering" below) PMID 12419232 Coordinates: 1mow
Chevalier, B., Monnat, R. J. Jr. and Stoddard, B. L. (2001) "The homing endonuclease I-CreI uses three metals, one of which is shared between two active sites" Nature Structural Biology 8 (4): 312 - 316. PMID 11276249 Coordinates: 1g9y 1g9z
Galburt, E., Jurica, M., Chevalier, B., Erho, D., Tang, W., Monnat, R. J. Jr., and Stoddard, B. L. (2000) "Conformational changes and cleavage by the homing endonuclease I-PpoI: a critical role for a leucine residue in the active site" J. Mol. Biol. 300(4): 877 - 887. PMID 10891275 Coordinates: 1evw 1evx
Galburt, E., Chevalier, B., Tang, W., Jurica, M. S., Flick, K. E., Monnat, R. J. Jr., and Stoddard, B. L. (1999) "A novel endonuclease mechanism directly visualized for I-PpoI" Nature Structural Biology 6: 1096 - 1099. PMID 10581547 Coordinates: 1cqy 1czo
Jurica, M. S., Monnat, R. J. Jr. and Stoddard, B. L. (1998) "DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI" Molecular Cell 2: 469 - 476. PMID 9665136 Coordinates: 1bp7
Flick, K.E., Jurica, M. S., Monnat, R. J. Jr., and Stoddard, B. L. (1998) "DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI" Nature 394: 96 - 101. PMID 9665136 Coordinates: 1a74 1a73 1ipp
Flick, K.E., McHugh, D., Heath, J.D., Stephens, K.M., Monnat, R.J. Jr., and Stoddard, B.L. (1997) "Crystallization and preliminary X-ray studies of I-PpoI: a nuclear, intron-encoded homing endonuclease from Physarum polycephalum" Protein Science 6: 2677 - 2680. PMID 9416623
Heath, P. J., Stephens, K., Monnat, R. and Stoddard, B. L. (1997) "Structure of the I-CreI intron-encoded endonuclease: a novel fold that binds and cleaves a long DNA target sequence" Nature Structural Biology 4 (6) 468-476. PMID 9187655 Coordinates: 1af5
Stephens, K., Monnat, R. Heath, P.J. and Stoddard, B. L. (1997) "Crystallization and preliminary x-ray characterization of I-CreI: an intron-encoded restriction endonuclease" Proteins 28: 137 - 139. PMID 9144800
Shen, B.W., Doyle, L.A., Werther, R., Westburg, A.A., Bies, D. P., Walter, S. I., Luyten, Y.A., Morgan, R.D., Stoddard, B.L. and Kaiser, B. K. (2023) "Structure, substrate binding and activity of a unique AAA+ protein: the BrxL phage restriction factor" Nucleic Acids Res. 51 (8): 3513 - 3528. PUBMED 36794719 Coordinates: 8EIL 8EMC 8EMH
Kennedy, M., Hosford, C., Azumaya C., Luyten, Y., Chen, M., Morgan, R.D., and Stoddard, B.L. (2023) "Structures, activity and mechanism of the type IIS restriction endonuclease PaqCI" Nucleic Acids Res. 51 (9): 4467 - 4487. PUBMED 36987874. Coordinates: 8EM1 8EPX
Luyten YA, Hausman DE, Young JC, Doyle LA, Higashi KM, Ubilla-Rodriguez NC, Lambert AR, Arroyo CS, Forsberg KJ, Morgan RD, Stoddard BL, Kaiser BK. (2022) Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system. Nucleic Acids Res. doi: 10.1093/nar/gkac311. Epub ahead of print. PMID: 35511079. Coordinates: 7T8K 7T8L
Forsberg KJ, Schmidtke DT, Werther R, Uribe RV, Hausman D, Sommer MOA, Stoddard BL, Kaiser BK, Malik HS. (2021) The novel anti-CRISPR AcrIIA22 relieves DNA torsion in target plasmids and impairs SpyCas9 activity. PLoS Biol. 19 (10) :e3001428. doi: 10.1371/journal.pbio.3001428. PMID: 34644300; PMCID: PMC8545432. Coordinates: 7JTA
Shen BW, Quispe JD, Luyten Y, McGough BE, Morgan RD, Stoddard BL. (2021) "Coordination of phage genome degradation versus host genome protection by a bifunctional restriction-modification enzyme visualized by CryoEM." Structure. 2021 Jun 3;29(6):521-530.e5. doi: 10.1016/j.str.2021.03.012. Epub 2021 Apr 6. PMID: 33826880; PMCID: PMC8178248. Coordinates: 7LO5 7LVV
Forsberg KJ, Bhatt IV, Schmidtke DT, Javanmardi K, Dillard KE, Stoddard BL, Finkelstein IJ, Kaiser BK, Malik HS (2019) “Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome” eLife Sep 10;8. pii: e46540. doi: 10.7554/eLife.46540. PMID 31502535.
Shen, B.W., Doyle, L., Bradley, P., Heiter, D.F., Lunnen, K.D. Wilson, G. G., and Stoddard, B.L. (2019) "Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI" Nucleic Acids Research 47(1):450-467 . doi: 10.1093/nar/gky1059. PMID 3035313. Coordinates: 6EG7 6M9G 6MAG 6MAF
Shen BW, Heiter DF, Lunnen KD, Wilson GG, Stoddard BL. (2017) "DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target." Nucleic Acids Res. 45 (3):1516-1528. PMID 27913730 Coordinates: 5TGQ 5TGX 5TH3
Shen, B. W., Xu, D., Chan, S. H., Zheng, Y., Shu, Z., Xu, S. -Y., and Stoddard, B. L. (2011) "Characterization and crystal structure of the type IIG restriction endonuclease RM.BpuSI" Nucleic Acids Research 39 (18):8223-36. PMID 21724614 Coordinates: 3S1S
Mak, A., Lambert, A.R. and Stoddard, B.L. (2010) "Folding, DNA recognition and function of GIY-YIG endonucleases: crystal structures of R.Eco29kI" Structure epub ahead of print PMID 20800503. Coordinates: 3mx1 3mx4 3nic
Shen, B.W., Heiter, D., Wilson, G. and Stoddard, B.L. (2010) "Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI" Structure 18 (6): 734 - 743. PMID 20541511 Coordinates: 3ldy 3m7k
Lambert, A. R., Sussman, D., Shen, B. W., Nix, J., Maunus, R., Samuelson, J., Xu, S. -Y., and Stoddard, B. L. (2008) "Structures of the rare cutting restriction endonuclease NotI revieal a novel metal binding fold involved in DNA recognition" Structure 16: 558 - 569. PMID 18400177 Coordinates: 3bvq 3c25
Hydrolases, Phosphatases and Kinases
Perraud., A. -L., Takanishi, C., Shen, B. W., Kang, S., Smith, M. K., Schmitz, C., Knowles, H. M., Ferraris, D., Li, Weixing, Zhang, J., Stoddard, B. L. and Scharenberg, A. M. (2005) "Accumulation of free ADP-ribose from mitochondria mediates oxidative stress-induced gating of TRPM2 cation channels" J. Biol. Chem. 280 (7): 6138 - 6148. PMID 15561722
Eastberg, J., Pelletier, J., and Stoddard, B. L. (2004) "Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase" Nucleic Acids Research 32 (2): 653 - 660. PMID 14754987 Coordinates: 1rc8 1rpz 1rrc
Shen, B. W., Perraud, A. -L., Scharenberg, A. M and Stoddard, B. L. (2003) "The crystal structure and mutational analysis of human NUDT9" J. Mol. Biol. 332(2):385-98. PMID 12948489 Coordinates: 1qvj 1q33
Perraud, A. -L., Shen, B., Dunn, C. A., Rippe, K., Smith, M. K., Bessman, M. J., Stoddard, B. L. and Scharenberg, A. M. (2003) "NUDT9, a member of the nudix hydrolase family, is an evolutionarily conserved mitochondrial ADP-ribose pyrophosphatase" J. Biol. Chem. 278 (3): 1794 - 1801. PMID 12427752
Galburt, E., Pelletier, J., Wilson G., and Stoddard, B. L. (2002) "Structure of a tRNA repair enzyme and molecular biology workhorse, T4 polynucleotide kinase" Structure 10 (9): 1249 - 1260. PMID 12220496 Coordinates: 1ltq
Blood Coagulation Factors
Shen, B. W., Spiegel, P.C., Chang, C. -H., Huh, J. -W., Lee, J. -S., Kim, J., Kim, Y. -H. and Stoddard, B. L. (2008) "Tertiary structure and domain organization of coagulation factor VIII" Blood 111 (3): 1240 - 1247. PMID 17965321 Coordinates: 1r7e
Spiegel, P. C. and Stoddard, B. L. (2004) "Surface-exposed hemophilic mutations across the factor VIII C2 domain have variable effects on stability and binding activities" J. Biol. Chem. 279 (51): 53691 - 53698. PMID 15471879
Spiegel, P.C., Kaiser, S. M., Simon, J. and Stoddard, B. L. (2004) "Disruption of protein-membrane binding and identification of small molecule inhibitors of coagulation factor VIII" Chemistry and Biology 11 (10): 1413 - 1422. PMID 15489168
Spiegel, P. C., Jacquemin, M., St. Remy, J. -M., Stoddard, B. L. and Pratt, K. P. (2001) "Structure of a factor VIII C2 domain/IgG4K Fab complex: identification of an inhibitory antibody epitope on the surface of Factor VIII" Blood 98(1): 13 - 19. PMID 11418455 Coordinates: 1iqd
Liu, M., Shen, B. W., Nakaya, S., Pratt, K. P., Fujikawa, K., Davie, E. W., Stoddard, B. L., and Thompson, A. R. (2000) "Hemophilic factor VIII C1 and C2 domain missense mutations and their modeling to the 1.5 angstrom human C2 domain crystal structure" Blood 96 (3): 979 - 987. PMID 10910913
Pratt, K. P., Shen, B. W., Takeshima, K., Davie, E. W., Fujikawa, K. and Stoddard, B. L. (1999) "Structure of the C2 domain of human factor VIII at 1.5 angstrom resolution" Nature 402: 439 - 442. PMID 10586887 Coordinates: 1d7p
General Mechanistic Enzymology
Bond, C., Jurica, M. S., Mesecar, A. and Stoddard, B. L. (2000) "Determinants of allosteric activation of yeast pyruvate kinase and identification of novel effectors using computational screening" Biochemistry 39: 15333 - 15343. PMID 11112519
Bond, C. J., Huang, J. -Y., Hajduk, R., Heath, P. J., Flick, K. E., and Stoddard, B. L. (2000) "Cloning, sequence and crystallographic structure of recombinant iron superoxide dismutase from Pseudomonas ovalis" Acta Cryst D56 1359 - 1366. PMID 11053832 Coordinates: 1dt0
Bryant, M. D., Flick, K. E., Koduri, R. S., Wilton, D. C., Stoddard, B. L., and Gelb, M. H. (1999) "1,3-dioxane-4,6-dione-5-carboxamide-based inhibitors of human group IIA phospholipase A2: X-ray structure of the complex and interfacial selection of inhibitors from a structural library" Bioorg. & Med. Chem. Letters 9: 1097 - 1102. PMID 10328292
Jurica, M. S., Heath, P. J., Shi, W., Mesecar, A., and Stoddard, B. L. (1998) "The allosteric regulation of pyruvate kinase by fructose-1,6-bis-phosphate" Structure 6 (2) 195 - 210. PMID 2202599 Coordinates: 1a3x 1a3w
Stoddard, B. L., Cohen, B., Brubaker, M., Mesecar, A. and Koshland, D. E. Jr. (1998) "Millisecond Laue structures of an enzyme product complex using photocaged substrate analogues" Nature Structural Biology 5 (10): 891 - 897. PMID 9783749 Coordinates: 1bl5
Cohen, B. E., Stoddard, B. L. and Koshland, D. E. Jr. (1997) "Caged NADP and NAD. "Synthesis and characterization of functionally distinct caged compounds." Biochemistry 36: 9035 - 9044. PMID 9220992
Mesecar, A., Stoddard, B. L. and Koshland, D. E. Jr. (1997) "Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences" Science 277: 202 - 206. PMID 9211842 Coordinates: 1ai3 1ai2
Scott, W. G., Stoddard, B. L. and Klug, A. (1996) "Capturing structures of catalytic RNA intermediates: the hammerhead ribozyme" Science 274: 2065 - 2069. PMID 8953035
Stoddard, B. L., Dean, A. and Bash, P. A. (1996) "Combining Laue diffraction and molecular dynamics to study enzyme intermediates: formation of a Michaelis complex" Nature Struct. Biol. 3 (7): 590 - 594. PMID 8673502
Brubaker, M., Dyer, D. H., Stoddard, B. L. and Koshland, D. E. Jr. (1995) "Synthesis, kinetics, and structural studies of a photolabile caged isocitrate: a catalytic trigger for isocitrate dehydrogenase" (1996) Biochemistry 35: 2854 - 2864. PMID 8608121
O'Hara, P., Goodwin, P. and Stoddard, B. L. (1995) "Determination of substrate diffusion rates in protein crystals by optical microspectrophotometry using CCD video analysis" J. Appl. Cryst. 28: 829 - 833.
Stoddard, B. L. and Farber, G. K. (1995) "Direct measurement of steady-state kinetic constants in the enzyme crystal" Structure 3: 991 - 996. PMID 8590009
Bolduc, J., Dyer, D., Lee, M., Scott, W. G., Singer, P., Sweet, R. M., Koshland, D. E. Jr. and Stoddard, B. L. (1995) "Mutagenesis and laue structures of enzyme intermediates: isocitrate dehydrogenase" Science 268: 1312 - 1318. PMID 7761851 Coordinates: 1ide 1idc
Lee, M., Klein, O. D., Bolduc, J., Dyer, D. H., Stoddard, B. L. and Koshland, D. E. Jr. (1995) "The role of the catalytic residues Lysine 230 and Tyrosine 160 in the NADP+-dependent isocitrate dehyrogenase" Biochemistry 34: 378 - 384. PMID 7819221
Nucleic Acid Synthesis, Salvage and Modification Enzymes
Gruenberg, S., Doyle, L.A., Wolf, E.J., Dan, N., Corrêa, I.R. Jr., Yigit, E., and Stoddard, B.L. (2023) “The structural basis of mRNA recognition and binding by yeast pseudouridine synthetase PUS-1” PLoS One Published online 09-Nov (doi https://doi.org/10.1371/journal.pone.0291267) Coordinates: 7R9F 7R9G
Fuchita, M., Ardiani, A., Zhao, L., Serve, K., Stoddard, B. L. and Black, M.E. (2009) "Bacterial Cytosine Deaminase Mutants Created by Molecular Engineering Show Improved 5FC-Mediated Cell Killing In Vitro and In Vivo" Cancer Research 69 (11): 4791-9. PMID 19487291 Coordinates: 3g77
Murphy, P., Bolduc, J., Gallaher, J., Stoddard, B. L. and Baker, D. (2009) "Alteration of enzyme specificity by computational loop remodeling and design" PNAS USA 106 (23): 9215-20. (Also listed under "protein engineering" below). PMID 18291415 Coordinates: 3eol
Stolworthy, T.S., Korkegian, A. M., Willmon, C. L., Ardiani, A., Cundiff, J., Stoddard, B. L. and Black, M.E. (2008) "Yeast cytosine deaminase mutants with increased thermostability impart sensitivity to 5-fluorocytosine" J. Mol. Biol 377 (3): 854 - 869.
Korkegian, A., Baker, D. and Stoddard, B. L. (2005) "Computational thermostabilization of an enzyme" Science 308: 857 - 860 (Also listed under "protein engineering" below). PMID 15879217 Coordinates: 2o3k 1ysb 1ysd
Mahan, S. D., Ireton, G. C., Stoddard, B. L. and Black, M. E. (2004) “Random mutagenesis and selection of Escherichia colo cytosine deaminase for cancer gene therapy” Protein Engineering and Design 17 (8): 225 – 633. (Also listed under "protein engineering" below). PMID 15381761 Coordinates: 1r9y 1ra5 1r9z 1rak 1r9x 1ra0
Mahan, S. D., Ireton, G. C., Stoddard, B. L. and Black, M. E. (2004) "Alanine-Scanning Mutagenesis Reveals a Cytosine Deaminase Mutant with Altered Substrate Preference" Biochemistry 43: 8957 - 8964. PMID 15248753
Ireton, G. and Stoddard, B. L. (2004) "Microseed matrix screening to improve crystals of yeast cytosine deaminase" Acta Cryst D 60: 601 - 605. PMID 14993707 Coordinates: 1rb7
Ireton, G., Black, M. and Stoddard, B. L. (2003) "The 1.14 Å crystal structure of yeast cytosine deaminase: evolution of nucleotide salvage enzymes and implications for genetic chemotherapy" Structure 11(8): 961 - 972. PMID 12905827 Coordinates: 1ox7 1p6o
Ireton, G., McDermitt, G., Black, M. and Stoddard, B. L. (2002) "The structure of Escherichia coli cytosine deaminase" J. Mol. Biol. 315(4): 687 - 697. PMID 11812140 Coordinates: 1k6w 1k70
Ireton, G., Black, M., and Stoddard, B. L. (2001) "Crystallization and prelminary X-ray analysis of bacterial cytosine deaminase" Acta Cryst D 57: 1643 - 1645. PMID 11679731
Shen, B. W., Dyer, D. H., Huang, J. -Y., D'Ari, L., Rabinowitz, J., and Stoddard, B. L. (1998) "The crystal structure of a bacterial bifunctional 5,10-methylene tetrahydrofolate cyclohydrolase/dehydrogenase" Protein Science 8(6) 1342 - 1349. PMID 10386884 Coordinates: 1b0a
Cheung, E., D'Ari, L., Rabinowitz, J. C., Dyer, D. H. and Stoddard, B. L. (1997) "Purification, crystallization, and preliminary x-ray studies of a bifunctional 5,10-methenyl/methylene tetrahydrofolate cyclohydrolase/dehydrogenase from Escherichia coli" Proteins 27: 322 - 324. PMID 9061797
D'Ari, L., Cheung, E., Rabinowitz, J., Bolduc, J. and Stoddard, B. L. (1997) "Purification, crystallization, and preliminary x-ray Data for 10-formyl-tetrahydrofolate synthetase from Clostridium acidi-urici" Proteins 27: 319 - 321. PMID 9061796
Protein Engineering
(Please note that some of these papers are also listed under their respective biological functions, above.)
Kibler RD, Lee S, Kennedy MA, Wicky BIM, Lai SM, Kostelic MM, Carr A, Li X, Chow CM, Nguyen TK, Carter L, Wysocki VH, Stoddard BL, Baker D. Design of pseudosymmetric protein hetero-oligomers. Nat Commun. 2024 Dec 18;15(1):10684. doi: 10.1038/s41467-024-54913-8. PMID: 39695145; PMCID: PMC11655659 Coordinates: 8E0L 8E0M 8E0N 8E0O 8E12
Lee S, Kibler RD, Ahn G, Hsia Y, Borst AJ, Philomin A, Kennedy MA, Huang B, Stoddard B, Baker D. Four-component protein nanocages designed by programmed symmetry breaking. Nature. 2024 Dec 18. doi: 10.1038/s41586-024-07814-1. Epub ahead of print. PMID: 39695226 Coordinates: 8FLX
Ennist NM, Wang S, Kennedy MA, et al., Stoddard BL, Romero E, Hunter CN, Baker D. (2024) "De novo design of proteins housing excitonically coupled chlorophyll special pairs" Nat Chem Biol. 20 (7): 906-915. doi: 10.1038/s41589-024-01626-0. PMID: 38831036; PMCID: PMC11213709. Coordinates: 7UNH 7UNI 7UNJ
Glasscock CJ, Pecoraro R, McHugh R, Doyle LA, Chen W, Boivin O, Lonnquist B, Na E, Politanska Y, Haddox HK, Cox D, Norn C, Coventry B, Goreshnik I, Vafeados D, Lee GR, Gordan R, Stoddard BL, DiMaio F, Baker D. (2023) "Computational design of sequence-specific DNA-binding proteins" bioRxiv [Preprint]. doi: 10.1101/2023.09.20.558720. PMID: 37790440; PMCID: PMC10542524. Coordinates: 8TAC
Kibler RD, Lee S, Kennedy MA, Wicky BIM, Lai SM, Kostelic MM, Li X, Chow CM, Carter L, Wysocki VH, Stoddard BL, Baker D. (2023) "Stepwise design of pseudosymmetric protein hetero-oligomers" bioRxiv [Preprint]. doi: 10.1101/2023.04.07.535760. PMID: 37066191; PMCID: PMC10104133. Coordinates: 8E12 8E0O 8E0N 8E0M 8E0L 8FLX
Malhi H, Homad LJ, Wan YH, Poudel B, Fiala B, Borst AJ, Wang JY, Walkey C, Price J, Wall A, Singh S, Moodie Z, Carter L, Handa S, Correnti CE, Stoddard BL, Veesler D, Pancera M, Olson J, King NP, McGuire AT. (2022) "Immunization with a self-assembling nanoparticle vaccine displaying EBV gH/gL protects humanized mice against lethal viral challenge" Cell Rep Med. 3 (6):100658. doi: 10.1016/j.xcrm.2022.100658. PMID: 35705092; PMCID: PMC9245003.
Hallinan JP, Doyle LA, Shen BW, Gewe MM, Takushi B, Kennedy MA, Friend D, Roberts JM, Bradley P, Stoddard BL.(2021) Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces. Commun Biol. 4 (1): 1240. doi: 10.1038/s42003-021-02766-y. PMID: 34716407; PMCID: PMC8556268. Coordinates: 6XR1 6XR2 7RDR
Klima JC, Doyle LA, Lee JD, Rappleye M, Gagnon LA, Lee MY, Barros EP, Vorobieva AA, Dou J, Bremner S, Quon JS, Chow CM, Carter L, Mack DL, Amaro RE, Vaughan JC, Berndt A, Stoddard BL, Baker D. (2021) "Incorporation of sensing modalities into de novo designed fluorescence-activating proteins" Nature Comm. 12 (1): 856. doi: 10.1038/s41467-020-18911-w. Coordinates: 6OHH
Lambert, A.R., Hallinan, J.P., Werther, R., Glow, D., and Stoddard, B.L. (2020) “Optimization of protein thermostability and exploitation of recognition behavior to engineer altered protein-DNA recognition” Structure epub ahead of print. doi: 10.1016/j.str.2020.04.009. PMID 32359399. Coordinates: 3QQY 6UVW 6UWG 6UW0 6UWH 6UWJ 6UWK
Correnti, C.E., Hallinan, J. P., Doyle, L. A., Ruff, R. O, Jaeger-Ruckstuhl, C. A., Xu, Y., Shen, B. W., Qu, A., Polkinghorn, C., Friend, D. J., Bandaranayake, A.D., Riddell, S. R., Kaiser, B. K., Stoddard,B. L. and Bradley, P. (2020) "Engineering and functionalization of large circular tandem repeat protein nanoparticles" Nature Structural and Molecular Biology 27 (4): 342 – 350. PMID 32203491
Day AL, Greisen P, Doyle L, Schena A, Stella N, Johnsson K, Baker D, Stoddard B. (2018) "Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold" Protein Engineering 31 (10):375-387. doi: 10.1093/protein/gzy031 PMID 30566669. Coordinates: 5IEN 5IEO 5IEP
Dou, J., Vorobieva, A., Sheffler, W., Doyle, L., Park, H., Bick, M. J., Mao, B., Foight, G. W., Lee, M. Y., Carter, L., Sankaran, B., Ovchinnikov, S., Marcos, E., Huang, P. -S., Vaughan, J. C., Stoddard, B. L. and Baker, D. “De novo design of a fluorescence-activating beta-barrel” Nature 561: 485 – 491. PubMed 30209393 Coordinates: 6D0T 6CZG 6CZH 6CZI 6CZJ
Dou, J., Doyle, L., Greisen, P., Schena, A., Park, H., Johnsson, K., Stoddard, B.L., and Baker, D. (2017) "Sampling and energy evaluation challenges in ligand binding protein design" Protein Science Oct 4. doi 10.1002/pro.3317. PMID 28980354 Coordinates: 5IER 5IF6
Berger S, Procko E, Margineantu D, Lee EF, Shen BW, Zelter A, Silva DA, Chawla K, Herold MJ, Garnier JM, Johnson R, MacCoss MJ, Lessene G, Davis TN, Stayton PS, Stoddard BL, Fairlie WD, Hockenbery DM, Baker D. (2016) "Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer" eLife Nov 2;5. pii: e20352. doi: 10.7554/eLife.20352. PMID 27805565 Coordinates: 5JSB 5JSN
King, I.C., Gleixner, J., Doyle, L., Kusin, A., Hunt, J. F., Xiao, R., Montelione, G. T., Stoddard, B. L. , Dimaio, F. and Baker, D. (2015) "Precise assembly of complex beta sheet topologies from de novo designed building blocks" eLife doi: 10.7554/eLife.11012. [Epub ahead of print]. PMID 26650357 Coordinates: 5CW9
Doyle, L. A., Hallinan, J. P., Bolduc, J. M., Stoddard, B. L. and Bradley, P. (2015) "Rational design of alpha-helical tandem repeat proteins with closed architectures" Nature 528: 585 - 588. PMID 26675735 Coordinates: 4YXX 4YXY 4YXZ 4YY2 4YY5 5BYO
Siegel, J. B., Smith, A. L., Poust, S., Wargacki, A. J., Bar-Even, A., Louw, C., Shen, B. W., Eiben, C. B., Tran, H. M., Noor, E., Gallaher, J., Bale, J., Yoshikuni, Y., Gelb, M. H., Keasling, J. D., Stoddard, B. L., Lidstrom, M. E., and Baker, D. (2015) "Computational enzyme design enables a novel one-carbon assimiliation pathway" PNAS USA 112 (12): 3704-3709. PMID 25775555 Coordinates: 4QPZ 4QQ8
Park K, Shen BW, Parmeggiani F, Huang PS, Stoddard BL, Baker D. (2015) "Control of repeat-protein curvature by computational protein design" Nature Struct. Mol. Biol. Jan 12. doi: 10.1038/nsmb.2938. [Epub ahead of print] PMID 25580576 Coordinates: 4R6G 4R5C 4R58 4R5D 4R6F
Procko E, Berguig GY, Shen BW, Song Y, Frayo S, Convertine AJ, Margineantu D, Booth G, Correia BE, Cheng Y, Schief WR, Hockenbery DM, Press OW, Stoddard BL, Stayton PS, and Baker D. (2014) "A computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells" Cell 157 (7): 1644 - 1656. PMID 24949974 Coordinates: 4OYD
Mills, J., Khare, S., Bolduc, J., Forouhar, F., Lew, S., Seetharaman, J., Tong, L., Stoddard, B. L. and Baker, D. (2013) “Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy” J. Am. Chem. Soc. 135(36):13393 – 13399. PMID 23924187) Coordinates: 4IXO 4IWW
Tinberg, C., Khare, S.D., Dou, J., Doyle, L., Nelson, J., Schena, A., Johnsson, K., Stoddard, B. L. and Baker, D. “Computational Design of Ligand Binding Proteins with High Affinity and Selectivity” (2013) Nature 501: 212 – 216. (PMID 24005320) Coordinates: 4J8T 4J9A
Khare, S.D., Kipnis, Y., Greisen, P.J., Takeuchi, R., Ashani, Y., Goldsmith, M., Song, Y., Gallaher, J.L., Silman, Il., Leader, H., Sussman, J.L., Stoddard, B.L., Tawfik, D.S., and Baker, D. (2012) "Computational redesign of a mononuclease zinc metalloenzyme for organophosphate hydrolysis" Nature Chem. Biol. 8 (3):294-300 PMID 22306579 Coordinates: 3T1G
Eiben, C.B., Siegel, J.B., Bale, J.B., Cooper, S., Khatib, F., Shen, B.W., Payers, F., Stoddard, B.L. Popovic, Z., and Baker, D. (2012) "Increased Diels-Alderase activity through backbone remodeling guided by FoldIt players" Nature Biotech. 30(2): 190 - 192. PMID 22267011 Coordinates: 3UOS
Wang, L., Althoff, E. A., Bolduc, J., Moody, J., Lassila, J. K., Giger, L., Hilvert, D., Stoddard, B.L. and Baker, D. (2012) "Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design" J. Mol. Biol. 15 (3): 615 - 625. PMID 22075445 Coordinates: 3UD6 3NXF 3O6Y
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. (2010) "Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction" Science 329: 309 - 313. PMID 20647463 Coordinates: 3i1c
Murphy, P., Bolduc, J., Gallaher, J., Stoddard, B. L. and Baker, D. (2009) "Alteration of enzyme specificity by computational loop remodeling and design" PNAS USA 106 (23):9215-20. (Also listed under "nucleotide salvage and synthesis enzymes" above). PMID 18291415 Coordinates: 3e0l
Jiang, L, Althoff, E. A., Clemente, F. R., Doyle, L., Rothlisberger, D., Zanghellini, A., Gallaher, J. L., Betker, J. L., Tanaka, F., Barbas, C. F., Hilvert, D., Houk, K. N., Stoddard, B. L. and Baker, D. (2008) "De Novo computational design of retro-aldol enzymes" Science 319 : 1387 - 1391. PMID 18323453 Coordinates: 3b5v 3b5l
Dantas, G., Watters, A.L., Lunde, B. M., Eletr, Z. M., Isern, N.G., Roseman, T., Lipfert, J., Doniach, S., Tompa, M., Kuhlman, B., Stoddard, B. L., Varani, G. and Baker, D. (2006) "Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution" J. Mol. Biol. 362 (5): 1004 - 1024. PMID 16949611 Coordinates (NMR from Varani Lab): 2GJH
Joachimiak, L.A., Kortemme, T., Stoddard, B. L., and Baker, D. (2006) "Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface" J. Mol. Biol. 361 (1): 195-208. PMID 16831445 Coordinates: 2erh
Ashworth, J., Havranek, J. J., Duarte, C. M., Sussman, D., Monnat, R. J. Jr., Stoddard, B. L. and Baker, D. (2006) "Computational redesign of endonuclease DNA binding and cleavage specificity" Nature 441: 656 - 659. (Also listed under "intron-encoded proteins" above) PMID 16738662 Coordinates: 2fld
Korkegian, A., Baker, D. and Stoddard, B. L. (2005) "Computational thermostabilization of an enzyme catalyst" Science 308: 857 - 860 (Also listed under "nucleotide synthesis and salvage enzymes" above). PMID 15879217 Coordinates: 2o3k 1ysb 1ysd
Mahan, S. D., Ireton, G. C., Stoddard, B. L. and Black, M. E. (2004) “Directed evolution and selection of bacterial cytosine deaminase with altered substrate specificity towards 5-fluorocytosine” Protein Engineering and Design 17 (8): 225 – 633. (Also listed under "nucleotide synthesis and salvage enzymes" above). PMID 15381761 Coordinates: 1r9y 1ra5 1r9z 1rak 1r9x 1ra0
Kortemme, T., Joachimiak, L. A., Bullock, A. N., Stoddard, B. L. and Baker, D. (2004) "Computational redesign of protein-protein interaction specificity" Nature Structural and Molecular Biology 11: 371 - 379. PMID 15034550 Coordinates: 1ujz
Kuhlman, B., Dantas, G., Ireton, G. C., Varani, G., Stoddard, B. L. and Baker, D. (2003) "Design of a novel globular protein fold with atomic accuracy" Science 302: 1364 - 1368. PMID 14631033 Coordinates: 1qys
Chevalier, B., Kortemme, T., Chadsey, M., Baker, D., Monnat, R. J. Jr. and Stoddard, B. L. (2002) "Design, activity and structure of a highly specific artificial endonuclease" Molecular Cell 10 : 895 - 905 (Also listed under "intron-encoded proteins" above). PMID 12419232 Coordinates: 1mow
Reviews, Commentaries, and Editorials
Sale, JE and Stoddard, BL (2024) Editorial: CRISPR in Nucleic Acids Research: the sequel” Nucleic Acids Res. 52 (7): 3489 – 3492.
Sale, J.E. and Stoddard, B.L. (2024) “Editorial: Fifty years of Nucleic Acids Research” Nucleic Acids Res. 52 (1): 1 – 3.
Stoddard, B.L. and Fox, K.R. (2019) "Editorial: Preprints, citations and Nucleic Acids Research" Nucleic Acids Res. 47(1): 1-2. PMID: 30629263
Bogdanove, A.J., Bohm, A., Miller, J.C., Morgan, R.D. and Stoddard, B.L. (2018) "Engineering altered protein-DNA recognition specificity" Nucleic Acids Res. 46(10): 4845-4871. PMID 29718463
Stoddard, B.L., Khvorova, A., Corey, D.R., Dynan, W.S. and Fox, K.R. (2018) "Editorial: Nucleic Acids Research and Nucleic Acid Therapeutics" Nucleic Acids Res. 46 (4): 1563 - 1564. PMID 29506274
Stoddard, B.L. and Fox, K.R. (2016) "Editorial: CRISPR in Nucleic Acids Research" Nucleic Acids Res. 44 (17): 8512. PMID 27382068
Jeltsch, A., Wende, W., Friedhoff, P., and Stoddard, B. L. (2015) "Editorial: Alfred Pingoud (1945 - 2015)" Nucleic Acids Res. 43(16): 7661 - 7663. PMID 26385498
Corey DR, Wise JA, Fox KR, Stoddard BL. (2015) "Editorial: Breakthrough articles: putting science first" Nucleic Acids Research 42(18):11273-4. PMID 25301802
Takeuchi R, Choi M, and Stoddard BL. (2015) "Engineering of customized meganucleases via in vitro compartmentalization and in cellulo optimization" Methods in Molecular Biology 1239: 105-32. PMID 25408403
Dynan, W., Fox, K. and Stoddard, B. L. (2014) " Editorial: NAR surveys the past, present and future of restriction endonucleases" Nucleic Acids Research 42 (1): 1 – 2.
Stoddard, B. L. (2014) "Homing endonucleases from mobile group I introns: discovery to genome engineering" Mobile DNA 5(1): 7 PMID 24589358
Zhao, L. and Stoddard, B. L. (2014) "Rapid determination of homing endonuclease DNA binding specificity profiles" in Methods in Enzymology 1123: 127 - 13.4 PMID 24510265
Doyle, E. L, Stoddard, B. L., Voytas, D. F., and Bodganove, A. J. (2013) "TAL effectors: high adaptable phytobcterial virulence factors and readily engineered DNA-targeting proteins.” Trends Cell Biol. 23 (8): 390-8 PMID 23707478
Mak, A. N. -S., Bradley, P., Bogdanove, P. and Stoddard, B. L. (2013) "TAL effectors: structure, mechanism, engineering and applications" Current Opinions in Structural Biology 23 (1): 93 - 99. PMID 23265998
Taylor, G. K. and Stoddard, B. L. (2012) "Structural, functional and evolutionary relationships between homing endonucleases and proteins from their host organisms" Nuc. Acids Res. 40 (12): 5189 - 5200. PMID 22406833
Stoddard, B.L. (2011) "Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification" Structure 19 (1): 7 - 15. PMID 21220111
Stoddard, B.L. and Belfort, M. (2010) "Social networking by mobile introns and their host genes" Molecular Microbiology 78(1): 1 - 4. PMID 20545861
Chan, S. -H., Stoddard, B. L. and Shuang, X. -U. (2010) "Natural and engineered nicking endonucleases: from cleavage mechanism to engineering of strand-specificity" Nuc. Acids Res. 39 (1): 1 - 18. PMID 20805246
Monnat, R. J. Jr., Scharenberg, A. M. and Stoddard, B. L. (2008) "Progress in engineering homing endonucleases for gene targeting: ten years after structures " Progress in Gene Therapy Volume 3: Autologous and cancer stem cell gene therapy (R. Bertolotti and K. Ozawa, ed.) World Scientific Publishers.
Stoddard, B. L. (2005) "Homing endonuclease structure and function" Quarterly Reviews in Biophysics 38 (1): 49 - 95. PMID 16335743
Chevalier, B., Monnat, R. J. Jr. and Stoddard, B. L. (2005) "The LAGLIDADG homing endonuclease family" in Homing endonucleases and Inteins (Springer Verlag; M. Belfort, V. Derbyshire, D. Wood and B. Stoddard, editors) .
Roberts, R., et al., Stoddard, B. L. et al. (2003) "A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes" Nucl. Acids. Res. 31 (7): 1805 - 1812. PMID 12654995
Galburt, E. and Stoddard, B. L. (2002) "Catalytic mechanisms of restriction and homing endonucleases" Biochemistry 41(47): 13851 - 13860. PMID 12437341
Spiegel, P. C. and Stoddard, B. L. (2002) "Optimization of factor VIII replacement therapy: can structural studies help evade antibody inhibitors?" British Journal of Haematology 119: 310 - 322. PMID 12406063
Chevalier, B. and Stoddard, B. L. (2001) "Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility" Nucleic Acids Research 28(18): 3757-3774. PMID 11557808
Galburt, E., and Stoddard, B. L. (2001) "Time-resolved macromolecular crystallography" Physics Today July: pg. 33 - 39.
Stoddard, B. L. (2001) "Accumulation and trapping of catalytic intermediates for crystallographic structure determination" Methods 24: 125 - 138.
Galburt, E. and Stoddard, B. L. (2000) "Restriction endonucleases: one of these things is not like the others" Nature Structural Biology 7(2): 89 - 91. PMID 10655603
Ren, Z., Bourgeois, D., Helliwell, J. R., Moffat, K., Srajer, V. and Stoddard, B. L. (1999) "Laue Crystallography: Coming of Age" Journal of Synchrotron Radiation 6: 891 - 917.
Gottschling, D. and Stoddard, B. L. (1999) "Telomeres: Structure of a chromosome's aglet" Current Biology 9: R164 - R167. PMID 10074444
Jurica, M. S. and Stoddard, B. L. (1999) "Homing endonucleases: structure, function and evolution" Cellular and Molecular Life Sciences 55: 1304 - 1326. PMID 10487208
Stoddard, B. L., Bolduc, J. M., Dyer, D. H., Scott, W. G. and Sweet, R.M. (1998) "Visualizing enzyme and ribozyme intermediates using fast diffraction and reaction trapping methods" Pure and Applied Chemistry 70 (1): 17 - 23.
Stoddard, B. L. (1998) "New results from time-resolved crystallography" Curr. Opin. Struct. Biol. 8: 612 - 618. PMID 9818266
Jurica, M. S. and Stoddard, B. L. (1998) "Mind your Bs and Rs: Bacterial Chemotaxis, signal transduction, and protein recognition" Structure 6: 809 - 813. PMID 9687374
Stoddard, B. L. and Pietrokovski, S. (1998) "Breaking up is hard to do" Nature Structural Biology 5 (1): 3 - 6. PMID 9437416
Ellman, J., Stoddard, B. L. and Wells, J. (1997) "Combinatorial Thinking in Chemistry and Biology" PNAS USA 94: 2779 - 2782. PMID 9096292
Flick, K. E. and Stoddard, B. L. (1996) "Calcineurin" Current Opinions in Structural Biology 6 (6) 770 - 775. PMID 8994877
Stoddard, B. L. (1996) "Caught in a chemical trap" Nature Structural Biology 3 (11): 907 - 909. PMID 8901863
Stoddard, B. L. (1996) "Intermediate Trapping and Laue X-ray diffraction: potential for enzyme mechanism, dynamics and inhibitor screening" Pharmacology and Therapeutics 70 (3): 215 - 256. PMID 8888067
Stoddard, B. L., Farber, G. K., and Strong, R. K. (1993) "Facts and Fancy of Microgravity Protein Crystallization" Biotechnology and Genetic Engineering Reviews 11: 57 - 77. PMID 7840348
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