Structures and Publications

NMRFAM Publications 2006
	Ahn, H.-C., Juranic, N., Macura, S., and Markley, J. L. (2006) Three-dimensional structure of the water-insoluble protein crambin in dodecylphosphocholine micelles and its minimal solvent-exposed surface. J. Am. Chem. Soc. 128, 4398-4404. [Abstract] [PDBs 1YV8, 1YVA, 2EYA, 2EYB, 2EYC, 2EYD]
	Cornilescu, G., Hadley, E.B., Woll, M.G., Markley, J.L., Gellman, S.H., Cornilescu, C.C., (2006) Solution structure of a small protein containing a fluorinated side chain in the core. Protein Sci., 16, 14-19. [Abstract] [PDB 2JM0] [BMRB 15000]
	Cornilescu, G.,Vinarov, D.A., Tyler, E.M., Markley, J.L., Cornilescu, C.C., (2006) Solution structure of a single-domain thiosulfate sulfurtransferase from Arabidopsis thaliana. Protein Sci., 15, 2836-2841. [Abstract] [PDB 1TQ1] [BMRB 6240]
	Cui, Q., Thorgersen, M. P., Westler, W. M., Markley, J. L., and Downs, D. M. (2006) Solution structure of YggX: a prokaryotic protein involved in Fe(II) trafficking. Proteins 62, 578-586. [Abstract] [PDB 1XS8]
	Dmitriev, O., Tsivkovskii, R., Abildgaard, F., Morgan, C. T., Markley, J. L., and Lutsenko, S. (2006) Solution Structure of the N-Domain of Wilson Disease Protein, Unique Nucleotide-Binding Environment and Effects of Disease Mutations. Proc. Natl. Acad. Sci. USA, 103, 5302-5307. [Abstract] [PDB 2ARF]
	Gáspári, Z., Szenthe, B., Patthy, A., Westler, W. M., Gráf, L., and Perczel, A. (2006) Local binding with globally distributed changes in a small protease inhibitor upon enzyme binding. FEBS J. 273, 1831-1842. [Abstract]
	Zornetzer, G. A., White, R. D, Markley, J. L., and Fox, B. G. (2006) Preparation of Isotopically Labeled Spinach Acyl-Acyl Carrier Protein for NMR Structural Studies. Protein Expr. Purif. 46, 446-55. [Abstract]
	Zornetzer, G. A., Fox, B. G., and Markley, J. L. (2006) Solution Structures of Spinach Acyl Carrier Protein with Decanoate and Stearate. Biochemistry, 45, 5217-5227. [Abstract] [PDBs 2FVA, 2FVE, 2FVF, 2AVA]

NMRFAM Publications 2005
	Assadi-Porter, F. M., Abildgaard, F., Blad, H., Cornilescu, C. C., and Markley, J. L. (2005) Brazzein, a small sweet protein: effects of mutations on its structure, dynamics, and functional properties. Chemical Senses 30 Suppl. 1: i90-i91. [Abstract]
	Blad, H., Reiter, N. J., Abildgaard, F., Markley, J. L., and. Butcher, S. E. (2005) Dynamics in the U6 RNA intramolecular stem loop: II. NMR analysis of metal binding and conformational exchange on the microsecond time scale. J. Mol. Biol. 353, 540-555. [Abstract]
	Chae, Y. K., Lee, K., and Markley, J. L. (2005) ¹H, ¹⁵N and ¹³C resonance assignments of a protein involved in the autophagy process, At4g21980.1 from Arabidopsis thaliana. J. Biomol. NMR 32, 337. [Abstract]
	Davis, J. H., Tonelli, M., Scott, L. G., Jaeger, L., Williamson, J. R., and Butcher, S. E. (2005) RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex. J. Mol. Biol. 351, 371-82. [Abstract] [PDB 2ADT]
	Eghbalnia, H. R., Bahrami, A., Wang, L., Assadi, A., and Markley, J. L. (2005) Probabilistic Identification of Spin Systems and their Assignments including Coil-Helix Inference as Output (PISTACHIO). J. Biomol. NMR 32, 219-233. Probabilistic Identification of Spin Systems and their Assignments including Coil-Helix Inference as Output (PISTACHIO). [Abstract]
	Eghbalnia, H. R., Bahrami, A., Tonelli, M. , Hallenga, K., and Markley, J. L. (2005) High Resolution Iterative Frequency Identification for NMR (HIFI-NMR) as a General Strategy for Multidimensional Data Collection. J. Am. Chem. Soc 127, 12528-12536. [Abstract]
	Eghbalnia, H. R., Wang, L., Bahrami, A., Assadi, A., and Markley, J. L. (2005) Protein Energetic Conformational Analysis from NMR Chemical Shifts (PECAN) and its use in Determining Secondary Structural Elements. J. Biomol. NMR 32, 71-81. [Abstract]
	Lin, I-J., Gebel, E. B., Machonkin, T. E., Westler, W. M., and Markley, J. L. (2005) Changes in hydrogen bond strengths explain variations in the reduction potentials in a series of rubredoxin mutants. Proc. Natl. Acad. Sci. USA 102, 14581-14586. [Abstract]
	Machonkin, T. E., Westler, W. M., and Markley, J. L. (2005) Paramagnetic NMR Spectroscopy and Density Functional Calculations in the Analysis of the Geometric and Electronic Structures of Iron-Sulfur Proteins. Inorg. Chem. 44, 779-797. [Abstract]
	Markley, J. L. (2005) Protein Solution Structure in Three Days or Less?. The Scientist 19, 36-40.
	Nederveen, A. J., Doreleijers, J. F., Vranken, W., Miller, Z., Spronk, C. A., Nabuurs, S. B., Guntert, P., Livny, M., Markley, J. L., Nilges, M., Ulrich, E. L., Kaptein, R., and Bonvin, A. M. (2005) RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins 59, 662-72.
	Oldfield, C. J., Ulrich, E. L., Cheng, Y. G., Dunker, A. K., and Markley, J. L. (2005) Addressing the Intrinsic Disorder Bottleneck in Structural Proteomics. Proteins 59, 444-453. [Abstract]
	Sicinska, W., Westler, W. M., and DeLuca, H. F. (2005) NMR assignments of tryptophan residue in apo and holo LBD-rVDR. Proteins 61, 461-467 (2005). [Abstract]
	Singh, S., Cornilescu, C. C., Tyler, R. C., Cornilescu, G., Tonelli, M., Lee, M. S., and Markley, J. L. (2005) Solution Structure of a Late Embryogenesis Abundant (LEA) Protein from Arabidopsis thaliana, a Cellular Stress Related Protein. Protein Sci. 14, 2601-2609. [Abstract] [PDB 1XO8] [BMRB 6339]
	Singh, S., Tonelli, M., Tyler, R. C., Bahrami, A., Lee, M. S., and Markley, J. L. (2005) Three-dimensional structure of the AAH26994.1 protein from Mus musculus, a putative eukaryotic Urm1. Protein Sci. 14, 2095-2102. [Abstract] [PDB 1XO3]
	Song, J. Tyler, R.C., Lee, M.S., Tyler, E. M., Markley, J. L. (2005) Solution structure of isoform 1 of Roadblock/LC7, a light chain in the dynein complex. J. Mol. Biol. 354, 1043-1051. [Abstract] [PDB 1XOY]
	Song, J., Tyler, R. C., Wrobel, R. L., Frederick, R. O., Vojtek, F. C., Jeon, W. B., Lee, M. S., and Markley, J. L. (2005) Solution structure of At3g04780.1-des15, an Arabidopsis thaliana ortholog of the C-terminal domain of human thioredoxin-like protein. Protein Sci. 14, 1059-1063. [Abstract] [PDB 1Y4O]
	Song, J., Zhao, Q., Lee, M. S., and Markley, J. L. (2005) ¹H, ¹⁵N and ¹³C resonance assignments of the putative Bet v 1 family protein At1g24000.1 from Arabidopsis thaliana. J. Biomol. NMR 32, 335. [Abstract]
	Staple, D. W., and Butcher, S. E. (2005) Solution structure and thermodynamic investigation of the HIV-1 frameshift inducing element. J. Mol. Biol. 349, 1011-23. [Abstract] [PDB 1Z2J]
	Tyler, R.C., Aceti, D.J., Bingman, C.A., Cornilescu, C.C., Fox, B.G., Frederick, R.O., Jeon, W.B., Lee, M.S., Newman, C.S., Peterson, F.C., Phillips, G.N., Jr., Shahan, M.N., Singh, S., Song, J., Sreenath, H., Tyler, E.M., Ulrich, E.L., Vinarov, D.A., Vojtek, F.C., Volkman, B.F., Wrobel, R.L., Zhao, Q., and Markley, J.L. (2005) Comparison of cell-based and cell-free protocols for producing target proteins from the Arabidopsis thaliana genome for structural studies. Proteins 59, 633-643. [Abstract]
	Tyler, R. C., Sreenath, H K., Aceti, D. J., Bingman, C A., Singh, S., Markley, J. L., and Fox, B. G. (2005) Auto-Induction Medium for the Production of [U-¹⁵N]- and [U-¹³C, U-¹⁵N]-labeled Proteins for NMR Screening and Structure Determination. Protein Exp Purif 40, 268-278. [Abstract] [PDB 1XO8, 1X09]
	Uchida, K., Markley, J. L., and Kainosho, M. (2005) Carbon-13 NMR method for the detection of correlated hydrogen exchange at adjacent backbone peptide amides and its application to hydrogen exchange in five anti-parallel b-strands within the hydrophobic core of Streptomyces subtilisin inhibitor (SSI). Biochemistry 44, 11811-11820. [Abstract]
	Vinarov, D. A. and Markley, J. L. (2005) High-Throughput Automated Platform for NMR-Based Structural Proteomics. Expert Review of Proteomics 2, 49-55 (2005). [Abstract]
	Vranken, W. F., Boucher, W., Stevens, T. J., Fogh, R. H., Pajon, A., Llinas, M., Ulrich, E. L., Markley, J. L., Ionides, J., and Laue, E. D. (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59, 687-96. [Abstract]
	Wang, L., Eghbalnia, H. R., Bahrami, A., and Markley, J. L. (2005) Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications. J. Biomol. NMR 32, 13-22. [Abstract]
	Yao, H., and Sem, D. S. (2005) Cofactor fingerprinting with STD NMR to characterize proteins of unknown function: identification of a rare cCMP cofactor preference. FEBS Lett. 579, 661-6. [Abstract]
	Zhao, Q., Song, J., Jin, Z., Danilova, V., Hellekant, G., and Markley, J.L. (2005) Structural and Functional Consequences of Inserting Two Residues into a Solvent-Exposed Loop of the Sweet Protein Brazzein. Biochem. Biophys. Res. Commun. 325, 256-263. [Abstract]

NMRFAM Publication List 2004
	Borbat, P. P., Davis, J. H., Butcher, S. E., and Freed, J. H. (2004) Measurement of large distances in biomolecules using double-quantum filtered refocused electron spin-echoes. J. Am. Chem. Soc. 126, 7746-7. [Abstract] [PDB 1QC0]
	S. E. Butcher and M. Wickens, (2004) STAR-studded circuitry. Nat. Struct. Mol. Biol. 11, 2-3. [Abstract]
	Chae, Y. K., Im, H., Zhao, Q., Doelling, J. H., Vierstra, R. D., and Markley, J. L. (2004) Prevention of Aggregation after Refolding by balanced Stabilization-Destabilization: Production of the Arabidopsis thaliana Protein At4g21980 (APG8a) for NMR Structure Determination. Protein Prod.Purif. 34, 280-283. [Abstract]
	Cornilescu, G., Cornilescu, C. C., Zhao, Q., Frederick, R. O., Peterson, F. C., Thao, S., and Markley, J. L. (2004) Solution structure of a homodimeric hypothetical protein, At5g22580, a structural genomics target from Arabidopsis thaliana. J. Biomol. NMR 29, 387-390. [Abstract] [PDB 1RJJ]
	Dmitriev, O. Y., Abildgaard, F., Markley, J. L., and Fillingame, R. H. (2004) Backbone 1H, 15N and 13C assignments for the subunit a of the E.coli ATP synthase. J. Biomol. NMR 29, 439-440. [Abstract]
	Dmitriev, O. Y., Altendorf, K., and Fillingame, R. H. (2004) Subunit a of the E. coli ATP synthase: reconstitution and high resolution NMR with protein purified in a mixed polarity solvent. FEBS Letters 556, 35-38. [Abstract]
	Fischer, M. H., Yu, N., Gray, G. R., Ralph, J., Anderson, L., and Marlett, J. A. (2004) The gel-forming polysaccharide of psyllium husk (Plantago ovata Forsk). Carbohydr. Res. 339, 2009-17. [Abstract]
	Laurence, J. S., Hallenga, K., and Stauffacher, C. V. (2004) 1H, 15N, 13C resonance assignments of the human protein tyrosine phosphatase PRL-1. J. Biomol. NMR 29, 417-8. [Abstract]
	Lytle, B., Peterson, F. C., Qiu, S. H., Luo, M., Zhao, Q., Markley, J. L., and Volkman, B. F. (2004) Solution structure of a ubiquitin-like domain from tubulin-binding cofactor B. J. Biol. Chem. 279, 46787-93. [Abstract] [PDB 1T0Y]
	Machonkin, T. E., Westler, W. M., and Markley, J. L. (2004) Strategy for the study of paramagnetic proteins with slow electronic relaxation rates by nmr spectroscopy: application to oxidized human [2Fe-2S] ferredoxin. J. Am. Chem. Soc. 126, 5413-26. [Abstract]
	Park, I. Y., Eidsness, M. K., Lin, I. J., Gebel, E. B., Youn, B., Harley, J. L., Machonkin, T. E., Frederick, R. O., Markley, J. L., Smith, E. T., Ichiye, T., and Kang, C. (2004) Crystallographic studies of V44 mutants of Clostridium pasteurianum rubredoxin: effects of side-chain size on reduction potential. Proteins 57, 618-25. [Abstract]
	Parsons, L. M., Yeh, D. C., and Orban, J. (2004) Solution structure of the highly acidic protein HI1450 from Haemophilus influenzae, a putative double-stranded DNA mimic. Proteins 54, 375-83. [Abstract] [PDB 1NNV]
	Ralph, J., and Lu, F. (2004) Cryoprobe 3D NMR of acetylated ball-milled pine cell walls. Org Biomol. Chem. 2, 2714-5. [Abstract]
	Reiter, N. J., Blad, H., Abildgaard, F., and Butcher, S. E. (2004) Dynamics in the U6 RNA intramolecular stem-loop: a base flipping conformational change. Biochemistry 43, 13739-47. [[Abstract] [PDB 1SYZ]
	Sashital, D. G., Cornilescu, G., McManus, C. J., Brow, D. A., and Butcher, S. E. (2004) U2-U6 RNA folding reveals a group II intron-like domain and a four-helix junction. Nat. Struct. Mol. Biol. 11, 1237-42. [Abstract] [PDB 1XHP]
	Sigel, R. S., Sashital, D. G., Abramovitz, D. L., Palmer, A. G., Butcher, S. E., and Pyle, A. M. (2004) The solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif. Nat. Struct. Mol. Biol. 11, 187-92. [Abstract] [PDB 1R2P]
	Song, J., Zhao, Q., Thao, S., Frederick, R. O., and Markley, J. L. (2004) Letter to the Editor: Solution Structure of a Calmodulin-Like Calcium-Binding Domain from Arabidopsis thaliana. J. Biomol. NMR 30, 451-6. [Abstract] [PDB 1T1Z]
	Song, J., Vinarov, D., Tyler, E. M., Shahan, M. N., Tyler, R. C., and Markley, J. L. (2004) Hypothetical protein At2g24940.1 from Arabidopsis thaliana has a cytochrome b5 like fold. J. Biomol. NMR 30, 215-8. [Abstract] [PDB 1TOG]
	Skjeldal, L., Peterson, F. C., Moe, L. A., Pikus, J. D., Doreleijers, J. F., Volkman, B. F., Westler, W. M., and Markley, J. L. (2004) Solution Structure of T4moC, the Rieske Ferredoxin Component of the Toluene 4-Monooxygenase Complex. J. Biol. Inorg. Chem. 9, 945-53. [Abstract] [PDB 1SJG]
	Sugimori, N., Torizawa, T., Aceti, D. J., Thao, S., Markley, J. L., and Kainosho, M. (2004) 1H, 13C and 15N backbone assignments of a 32 kDa bypothetical protein from Arabidopsis thaliana , At3g16450.1. J.Biol.NMR. 30, 357-8. [Abstract]
	Vinarov, D. A., Lytle, B. L., Peterson, F. C., Tyler, E. M., Volkman, B. F., and Markley, J. L. (2004) Cell-free protein production and labeling protocol for NMR-based structural proteomics. Nat. Methods 1, 149-153. [Abstract]
	Zhao, Q., Frederick, R., Seder, K., Thao, S., Sreenath, H., Peterson, F., Volkman, B. F., Markley, J. L., and Fox, B. G. (2004) Production in two-liter beverage bottles of proteins for NMR structure determination labeled with either 15N- or 13C-15N. J Struct Funct Genomics 5, 87-93.

Structures and Publications

NMRFAM Publications 2006

NMRFAM Publications 2005

NMRFAM Publication List 2004

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