» Thomas J. Magliery
» Research
» News
» Publications
» People
» Links

Department of Chemistry & Biochemistry
The Ohio State University
1043 Evans Laboratory
100 West 18th Ave.
Columbus, Ohio 43210-1185
(614) 247-8425 office
(614) 292-1685 fax
magliery@chemistry.ohio-state.edu

Copyright © 2005-2012, Thomas J. Magliery. All rights reserved. No part of this website may be reproduced without explicit written permission from the author.

 
» Publications

Pubmed SearchPublicationsPatentsMixed Codons Worksheet

Pubmed Search: Magliery

Publications

Wang F, Sen S, Zhang Y, Ahmad I, Zhu X, Wilson IA, Smider VV, Magliery TJ, Schultz PG. (2013) "Somatic hypermutation maintains antibody thermodynamic stability during affinity maturation," Proc. Natl. Acad. Sci. U.S.A., doi:10.1073/pnas.1301810110. PDF+SI (Early Edition)

Durani, V. & Magliery, T.J. (2013) "Protein Engineering and Stabilization from Sequence Statistics: Variation and Co-Variation Analysis," Meth. Enzymol., 523: 237-256. doi:10.1016/B978-0-12-394292-0.00011-4. PDF

Muthukrishnan, S.; Shete, V.S.; Sanan, T.T.; Vyas, S.; Oottikkal, S.; Porter, L.M.; Magliery, T.J. & Hadad, C.M. (2012) "Mechanistic insights into the hydrolysis of organophosphorus compounds by paraoxonase-1: Exploring the limits of substrate tolerance in a promiscuous enzyme," J. Phys. Org. Chem., accepted, doi:10.1002/poc.3002. PDFSupporting Info

Durani, V.; Sullivan, B.J. & Magliery, T.J. (2012) "Simplifying protein expression with ligation-free, traceless and tag-switching plasmids," Protein Expr. Purif., 85: 9-17, doi:10.1016/j.pep.2012.06.007. PDFSupporting Info

Sullivan, B.J.; Nguyen, T.; Durani, V.; Mathur, D.; Rojas, S.; Thomas, M.; Syu, T. & Magliery, T.J. (2012) "Stabilizing proteins from sequence statistics: The interplay of conservation and correlation in triosephosphate isomerase stability," J. Mol. Biol., 420: 384-399, doi:10.1016/j.jmb.2012.04.025. PDFSupporting Info

Sarkar, M.; Harsch, C.K.; Matic, G.T.; Hoffman, K.; Norris III, J.R.; Otto, T.C.; Lenz, D.E.; Cerasoli, D.M. & Magliery, T.J. (2012) "Solubilization and humanization of paraoxonase-1," J. Lipids, 2012: Article ID 610937, 13 pages, doi:10.1155/2012/610937. PDF

Sullivan, B.J.; Durani, V. & Magliery, T.J. (2011) "Triosephosphate Isomerase by Consensus Design: Dramatic Differences in Physical Properties and Activity of Related Variants," J. Mol. Biol., 413: 195-208, doi:10.1016/j.jmb.2011.08.001. PDFSupporting Info

Magliery, T.J.; Lavinder, J.J. & Sullivan, B.J. (2011) "Protein stability by number: high-throughput and statistical approaches to one of protein science's most difficult problems," Curr. Opin. Chem. Biol. 15: 443-451, doi:10.1016/j.cbpa.2011.03.015. PDF

Nie, L.; Lavinder, J.J.; Sarkar, M.; Stephany, K. & Magliery, T.J. (2011) "Synthetic approach to stop-codon scanning mutagenesis," J. Am. Chem. Soc. 133: 6177-6186, doi:10.1021/ja106894g. PDFSupporting Info

Hari, S.B.; Byeon, C.; Lavinder, J.J. & Magliery, T.J. (2010) "Cysteine-free rop: A four-helix bundle core mutant has wild-type stability and structure but dramatically different unfolding kinetics," Protein Sci. 19: 670-679, doi:10.1002/pro.342. PDFSupporting Info

Nadaud, P.S.; Sarkar, M.; Wu, B.; MacPhee, C.E.; Magliery, T.J. & Jaroniec, C.P. (2009) "Expression and purification of a recombinant amyloidogenic peptide from transthyretin for solid-state NMR spectroscopy," Protein Expr. Purif. 70: 101-108, doi:10.1016/j.pep.2009.09.017. PDF

Otto, T.C.; Harsh, C.K.; Yeung, D.T.; Magliery, T.J.; Cerasoli, D.M. & Lenz, D.E. (2009) "Dramatic difference in organophosphorpus hydrolase activity between huam and chimeric recombinant mammalian paraoxonase-1 enzymes," Biochemistry 48: 10416-10422, doi:10.1021/bi901161b. PDFSupporting Info

Gambin, Y.; Schug, A.; Lemke, E.A.; Lavinder, J.J.; Ferreon, A.C.; Magliery, T.J.; Onuchic, J.N.; Deniz, A.A. (2009) "Direct single-molecule observation of a protein living in two opposed native structures," Proc. Natl. Acad. Sci. U.S.A.106: 10153-10158, doi:10.1073/pnas.0904461106. PDFSupporting Info

Lavinder, J.J.; Hari, S.B.; Sullivan, B.J. & Magliery, T.J. (2009) "High-throughput thermal scanning: a general, rapid dye-binding thermal shift screen for protein engineering," J. Am. Chem. Soc., 131: 3794-3795, doi:10.1021/ja8049063. PDFSupporting Info

MolBioSyst_eiSarkar, M & Magliery, T.J. (2008) "Re-engineering a split-GFP reassembly screen to examine RING-domain interactions between BARD1 and BRCA1 mutants observed in cancer patients," Mol. BioSyst. 4: 599-605, doi:10.1039/b802481b. PDF

Chin, J.W. & Magliery, T.J. (2005) "Protein expression by expansion of the genetic code." In Encyclopedia of Molecular Cell Biology and Molecular Medicine, 2nd ed., Vol. 11,ed. Meyers, R.A. Wiley-VCH: Weinheim, Germany, pp. 45-58.

Magliery, T.J. & Regan, L. (2006) “Reassembled GFP: detecting protein-protein interactions and protein expression patterns.” In Green Fluorescent Protein: Properties, Applications, and Protocols, 2nd ed., eds. Chalfie, M. & Kain, S., John Wiley & Sons: Hoboken, NJ, pp. 391-405. Click here to buy the book. PDF

Magliery, T.J. & Regan, L. (2005) “Sequence variation in ligand binding sites in proteins,” BMC Bioinformatics 6: 240, doi:10.1186/1471-2105-6-240. PDFSupporting Info

Magliery, T.J. (2005) “Unnatural protein engineering: producing proteins with unnatural amino acids,” Med. Chem. Rev. Online 2: 303-323. PDF

Magliery, T.J.; Wilson, C.G.M.; Pan, W.; Mishler, D.; Ghosh, I.; Hamilton, A.D. & Regan, L. (2005) “Detecting protein-protein interactions with a green fluorescent protein fragment reassembly trap: scope and mechanism,” J. Am. Chem. Soc. 127: 146-157 PDFSupporting Info

Wilson, C.G.M.; Magliery, T.J. & Regan, L. (2004) "Detecting protein-protein interactions with GFP-fragment reassembly," Nat. Methods 1: 255-262. PDF Supporting NoteSupporting Figure

Magliery, T.J. & Regan, L. (2004) “Beyond consensus: statistical free energies reveal hidden interactions in the design of a TPR motif,” J. Mol. Biol. 343: 731-745. PDF Supporting Info

Magliery, T.J. & Regan, L. (2004) “Library approaches to biophysical problems” (editorial overview), Eur. J. Biochem. 271: 1593-1594. PDF

Magliery, T.J. & Regan, L. (2004) “Combinatorial approaches to protein structure and stability,” Eur. J. Biochem. 271: 1595-1608. PDF

 

Magliery, T.J. & Regan, L. (2004) “A cell-based screen for function of the four-helix bundle protein Rop: A new tool for combinatorial experiments in biophysics,” Protein Eng. Des. Select. 17: 77-83. PDF

Magliery, T.J. & Liu, D.R. (2004) “Expanding the genetic code in vitro and in vivo.” In The Genetic Code and the Origin of Life, ed. Ribas de Pouplana, L. Landes Bioscience: Georgetown, TX, pp. 221-249.

Magliery, T.J.; Pastrnak, M.; Anderson, J.C.; Santoro, S.W.; Meggers, E.; Herberich, B.; Wang, L. & Schultz, P.G. (2003) “Incorporation of unnatural amino acids into proteins.” In Translation Mechanisms, eds. Lapointe, J.; Brakier-Gingras L. Landes Bioscience: Georgetown, TX, pp. 95-114.

Anthony-Cahill, S.J. & Magliery, T.J. (2002) “Expanding the natural repertoire of protein structure and function,” Curr. Pharm. Biotech. 3: 299-315. PDF

Anderson, J.C.; Magliery, T.J. & Schultz, P.G. (2002) “Exploring the limits of codon and anticodon size,” Chem. Biol. 9: 237-244. [See commentary: Landweber, L. (2002) “Custom codons come in threes, fours and fives,” Chem. Biol. 9: 143.] PDFCommentary

Magliery, T.J.; Anderson, J.C. & Schultz, P.G. (2001) "Expanding the genetic code: selection of efficient suppressors of four-base codons and identification of 'shifty' 4-base codons with a library approach in Escherichia coli," J. Mol. Biol. 307: 755-769. PDF

Pastrnak, M.; Magliery, T.J. & Schultz, P.G. (2000) "A new orthogonal suppressor tRNA/aminoacyl-tRNA synthetase pair for evolving an organism with an expanded genetic code," Helv. Chim. Acta 83: 2277-2286. PDF

Wang L.; Magliery, T.J.; Liu, D.R. & Schultz, P.G. (2000) "A new functional suppressor tRNA/aminoacyl-tRNA synthetase pair for the in vivo incorporation of unnatural amino acids into proteins," J. Am. Chem. Soc. 122: 5010-5011. PDF

Liu, D.R.; Magliery, T.J.; Pastrnak, M. & Schultz, P.G. (1997) “Engineering a tRNA and aminoacyl-tRNA synthetase for the site-specific incorporation of unnatural amino acids into proteins in vivo ,” Proc. Natl. Acad. Sci. USA 94: 10092-10097. [See commentary: Schimmel, P. & Söll, D. (1997) “When protein engineering confronts the tRNA world,” Proc. Natl. Acad. Sci. USA 94: 10007-10009.] PDFCommentary

Liu, D.R; Magliery, T.J. & Schultz, P.G. (1997) “Characterization of an 'orthogonal' suppressor tRNA derived from E. coli tRNA2Gln,” Chem. Biol. 4: 685-691. PDF

Magliery, T.J.; Vitellaro, L.K.; Diop, N.K. & Marusak, R.A. (1997) “Fe-EDTA- bis amide and Fe-ADR-925, the iron-bound hydrolysis product of the cardioprotective agent dexrazoxane, cleave DNA via the hydroxyl radical,” Metal Based Drugs, 4: 199-205. PDF

Patents

Schultz, P.; Wang, L.; Anderson, J.C.; Chin, J.; Liu, D.R.; Magliery, T.J.; Meggers, E.L.; Mehl, R.A.; Pastrnak, M.; Santoro, S.W.; Zhang, Z. “Methods and composition for the production of orthogonal tRNA-aminoacyl tRNA synthetase pairs,” Patent Nos. 7,083,970 and 7,354,761.

Schultz, P.; Wang, L.; Anderson, J.C.; Chin, J.; Liu, D.R.; Magliery, T.J.; Meggers, E.L.; Mehl, R.A.; Pastrnak, M.; Santoro, S.W.; Zhang, Z. “In vivo incorporation of unnatural amino acids,” Patent Nos. 7,045,337, 7,368,275 and 7,638,300.

Mixed Codons Worksheet

This Excel worksheet and Visual Basic macro helps plan the library-oriented use of "combinatorial codons" made from equimolar mixes of phosphoramidites. It will both "translate" mixed codons, so that you can see the expected amino acid composition, and it will search for the best mixed codons for a particular set of desired amino acids.

Freeware, but please distribute the whole ZIPped package. You need an archiving tool like WinZip to unpack this file. Written for Microsoft Excel 2002 (XP) for Windows. Seems to work fine on Mac.