NMRFAM Publications (2005-2009)
To get free copies of publications use the PMCID links to PubMed Central
Papers citing NMRFAM published after the proposal was submitted:
1. Bean, G. J., Flickinger, S. T., Westler, W. M., McCully, M. E., Sept, D., Weibel, D. B. & Amann, K. J. (2009) A22 disrupts the bacterial actin cytoskeleton by directly binding and inducing a low-affinity state in MreB, Biochemistry. 22, 4852-7.
2. Gruber, T. D., Borrok, M. J., Westler, W. M., Forest, K. T. & Kiessling, L. L. (2009) Ligand Binding and Substrate Discrimination by UDP-Galactopyranose Mutase, J Mol Biol. In press. [PMCID: PMC Journal- In process]
3. Kim, J. H., Füzéry, A. K., Tonelli, M.,Ta, D. T., Westler, W. M., Vickery, L.E. & Markley, J. L. (2009) Structure and Dynamics of the Iron-Sulfur Cluster Assembly Scaffold Protein IscU and its Interaction with the Cochaperone HscB, Biochemistry. 48, 6062-71. [PMCID - in process]
4. Lee, W., Westler, W. M., Bahrami, A., Eghbalnia, H. R. & Markley, J. L., (2009) PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy, Bioinformatics. Advance Access, doi: 10.1093/bioinformatics/btp345. [PMCID: PMC2645676]
5. Liu, L., Westler, W. M., Wang, X., den Boon, J. A., Diaz, A., Steinberg, H. A. & Ahlquist, P. (2009) An Amphipathic α-Helix Controls Multiple Roles of Brome Mosaic Virus Protein 1a in RNA Replication Complex Assembly and Function, PLoS Pathog. 5(3): e1000351. [PMCID: PMC2654722]
6. Makino, S-i, Goren, M. A., Fox, B. G. & Markley, J. L., “Cell-free protein synthesis technology in NMR high-throughput structure determination,” in “Cell-free Expression Systems”, Methods in Molecular Biology (K. Takai and Y. Endo, Eds.), The Humana Press Inc., in press.
7. Markley, J. L., Aceti, D. J., Bingman, C. A., Fox, B. G., Frederick, R. O., Makino, S., Nichols, K. W., Phillips, G. N. Jr., Primm, J. G., Sahu, S., Vojtik, F. C., Volkman, B. F., Wrobel, R. L. & Zolnai, Z. (2009) The Center for Eukaryotic Structural Genomics, J Struct Funct Genomics. 10, 165-179. [PMCID - in process]
8. Montelione, G. T., Arrowsmith, C., Girvin, M. E., Kennedy, M. A., Markley, J. L., Powers, R., Prestegard, J. H. & Szyperski, T. (2009) Unique Opportunities for NMR Methods in Structural Genomics, J Struct Funct Genomics. 10, 101-106. [PMCID - in process]
9. Park, S., Chen, W., Cierpicki, T., Tonelli, M., Cai, X., Speck, N.A. & Bushweller, J. H. (2009) Structure of the AML1-ETO eTAFH domain-HEB peptide complex and its contribution to AML1-ETO activity, Blood. 113, 3558-67. [PMCID:PMC2668852]
10. Popovych, N., Tzeng, S. R., Tonelli, M., Ebright, R. H. & Kalodimos, C. G. (2009) Structural basis for cAMP-mediated allosteric control of the catabolite activator protein, Proc Natl Acad Sci USA. 106, 6927-32. [PMCID: PMC2678429]
11. Wang, L. & Markley, J. L. (2009) Empirical Correlation Between Protein Backbone 15N and 13C Secondary Chemical Shifts and its Application to Nitrogen Chemical Shift Re-referencing, J. Biomol. NMR. 44, 95-99 (2009). [PMCID - in process]
Publications from 2005-2007 that cite NMRFAM:
1. Aceti, D. J., Bitto, E., Yakunin, A. F., Proudfoot, M., Bingman, C. A., Frederick, R. O., Sreenath, H. K., Vojtik, F. C., R, L. W., Fox, B. G., Markley, J. L. & Phillips, G. N., Jr. (2008) Structural and functional characterization of a novel phosphatase from the Arabidopsis thaliana gene locus At1g05000, Proteins 73, 241-53
2. Ahn, H. C., Juranic, N., Macura, S. & 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, 4398-404. [PMCID: PMC2533276]
3. Ahn, H. C., Le, Y. T., Nagchowdhuri, P. S., Derose, E. F., Putnam-Evans, C., London, R. E., Markley, J. L. & Lim, K. H. (2006) NMR characterizations of an amyloidogenic conformational ensemble of the PI3K SH3 domain, Protein Sci. 15, 2552-7. [PMCID: PMC2242406]
4. Allerdings, E., Ralph, J., Schatz, P. F., Gniechwitz, D., Steinhart, H. & Bunzel, M. (2005) Isolation and structural identification of diarabinosyl 8-O-4-dehydrodiferulate from maize bran insoluble fibre, Phytochemistry. 66, 113-24.
5. Allerdings, E., Ralph, J., Steinhart, H. & Bunzel, M. (2006) Isolation and structural identification of complex feruloylated heteroxylan side-chains from maize bran, Phytochemistry. 67, 1276-86.
6. Andjus, R. K., Dzakula, Z., Markley, J. L. & Macura, S. (2005) Brain Energetics and Tolerance to Anoxia in Deep Hypothermia, Ann N Y Acad Sci. 1048, 10-35.
7. Assadi-Porter, F. M., Abildgaard, F., Blad, H., Cornilescu, C. C. & Markley, J. L. (2005) Brazzein, a small, sweet protein: effects of mutations on its structure, dynamics and functional properties, Chem Senses. 30 Suppl 1, i90-i91.
8. Assadi-Porter, F. M., Patry, S. & Markley, J. L. (2008) Efficient and rapid protein expression and purification of small high disulfide containing sweet protein brazzein in E. coli, Protein Expr Purif. 58, 263-8. [PMCID: PMC2374762]
9. Assadi-Porter, F. M., Tonelli, M., Maillet, E., Hallenga, K., Benard, O., Max, M. & Markley, J. L. (2008) Direct NMR detection of the binding of functional ligands to the human sweet receptor, a heterodimeric family 3 GPCR, J Am Chem Soc. 130, 7212-3.
10. Assadi-Porter, F. M., Tonelli, M., Radek, J. T., Cornilescu, C. C. & Markley, J. L. (2008) How Sweet It Is: Detailed Molecular and Functional Studies of Brazzein, a Sweet Protein and Its Analogs in Sweetness and Sweeteners, Biology, Chemisty and Psychophysics (ACS Symposium Series 979) (Weerasinghe, D. K. & DuBois, G. E., eds) pp. 560-572, American Chemical Society, Washington DC.
11. Bae, E., Reiter, N. J., Bingman, C. A., Kwan, S. S., Lee, D., Phillips, G. N., Jr., Butcher, S. E. & Brow, D. A. (2007) Structure and interactions of the first three RNA recognition motifs of splicing factor prp24, J Mol Biol. 367, 1447-58. [PMCID: PMC1939982]
12. Bahrami, A., Assadi, A., Markley, J. L. & Eghbalnia, H. (2009) Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy, PLoS Comp. Biol. 5(3), e1000307. [PMCID: PMC2645676]
13. Berman, H., Henrick, K., Nakamura, H. & Markley, J. L. (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data, Nucleic Acids Res. 35, D301-3. [PMCID: PMC1669775]
14. Binder, J. B., Guzei, I. A. & Raines, R. T. (2007) Salicylaldimine ruthenium alkylidene complexes: Metathesis catalysts tuned for protic solvents, Advanced Synthesis & Catalysis. 349, 395-404.
15. Binder, J. B., Blank, J. J. & Raines, R. T. (2007) Olefin metathesis in homogeneous aqueous media catalyzed by conventional ruthenium catalysts, Org Lett. 9, 4885-8. [PMCID: PMC2532671]
16. Bitto, E., Bingman, C. A., Allard, S. T., Wesenberg, G. E., Aceti, D. J., Wrobel, R. L., Frederick, R. O., Sreenath, H., Vojtik, F. C., Jeon, W. B., Newman, C. S., Primm, J., Sussman, M. R., Fox, B. G., Markley, J. L. & Phillips, G. N., Jr. (2005) The structure at 2.4 A resolution of the protein from gene locus At3g21360, a putative Fe(II)/2-oxoglutarate-dependent enzyme from Arabidopsis thaliana, Acta Cryst
Sect F Struct Biol Cryst Commun. 61, 469-72. [PMCID: PMC1952295]
17. Blad, H., Reiter, N. J., Abildgaard, F., Markley, J. L. & Butcher, S. E. (2005) Dynamics and metal ion binding in the U6 RNA intramolecular stem-loop as analyzed by NMR, J Mol Biol. 353, 540-55.
18. Bunzel, M., Ralph, J., Funk, C. & Steinhart, H. (2005) Structural elucidation of new ferulic acid-containing phenolic dimers and trimers isolated from maize bran, Tetrahedron Letters. 46, 5845-5850.
19. Bunzel, M. & Ralph, J. (2006) NMR characterization of lignins isolated from fruit and vegetable insoluble dietary fiber, J Agric Food Chem. 54, 8352-61.
20. Burnette, R. R. & Weinhold, F. (2006) Determination of the conformation of 2-hydroxy- and 2-aminobenzoic acid dimers using 13C NMR and density functional theory/natural bond order analysis: the central importance of the carboxylic acid carbon, J Phys Chem A. 110, 8832-9.
21. Borrok, M. J., Kiessling, L. L. & Forest, K. T. (2007) Conformational changes of glucose/galactose-binding protein illuminated by open, unliganded, and ultra-high-resolution ligand-bound structures, Protein Sci. 16, 1032-41. [PMCID: PMC2206672]
22. Chae, Y. K., Lee, K. & 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.
23. Chen, K. M., Harjes, E., Gross, P. J., Fahmy, A., Lu, Y., Shindo, K., Harris, R. S. & Matsuo, H. (2008) Structure of the DNA deaminase domain of the HIV-1 restriction factor APOBEC3G, Nature. 452, 116-9.
24. Chiellini, G., Grzywacz, P., Plum, L. A., Barycki, R., Clagett-Dame, M. & DeLuca, H. F. (2008) Synthesis and biological properties of 2-methylene-19-nor-25-dehydro-1alpha-hydroxyvitamin D(3)-26,23-lactones–weak agonists, Bioorg Med Chem. 16, 8563-73.
25. Cornilescu, G., Bahrami, A., Tonelli, M., Markley, J. L. & Eghbalnia, H. R. (2007) HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections, J. Biomol. NMR. 38, 341-351.
26. Cornilescu, G., Hadley, E. B., Woll, M. G., Markley, J. L., Gellman, S. H. & Cornilescu, C. C. (2007) Solution structure of a small protein containing a fluorinated side chain in the core, Protein Sci. 16, 14-9. [PMCID: PMC2222841]
27. Cornilescu, C. C., Porter, F. W., Zhao, K. Q., Palmenberg, A. C. & Markley, J. L. (2008) NMR structure of the mengovirus Leader protein zinc-finger domain, FEBS Lett. 582, 896-900.
28. Cornilescu, G., Ulijasz, A. T., Cornilescu, C. C., Markley, J. L. & Vierstra, R. D. (2008) Solution Structure of a Cyanobacterial Phytochrome GAF Domain in the Red-Light-Absorbing Ground State, J Mol Biol. 383, 403-413. [PMCID: PMC Journal-in Process]
29. Cui, Q., Thorgersen, M. P., Westler, W. M., Markley, J. L. & Downs, D. M. (2006) Solution structure of YggX: a prokaryotic protein involved in Fe(II) trafficking, Proteins. 62, 578-86.
30. Cui, Q., Lewis, I. A., Hegeman, A. D., Anderson, M. E., Li, J., Schulte, C. F., Westler, W. M., Eghbalnia, H. R., Sussman, M. R. & Markley, J. L. (2008) Metabolite identification via the Madison Metabolomics Consortium Database, Nat Biotechnol. 26, 162-4.
31. Davis, J. H., Tonelli, M., Scott, L. G., Jaeger, L., Williamson, J. R. & 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.
32. Davis, J. H., Foster, T. R., Tonelli, M. & Butcher, S. E. (2007) Role of metal ions in the tetraloop-receptor complex as analyzed by NMR, RNA. 13, 76-86. [PMCID: PMC1705752]
33. Ding, Z., Lee, G. I., Liang, X., Gallazzi, F., Arunima, A. & Van Doren, S. R. (2005) PhosphoThr peptide binding globally rigidifies much of the FHA domain from Arabidopsis receptor kinase-associated protein phosphatase, Biochemistry. 44, 10119-34.
34. Dmitriev, O., Tsivkovskii, R., Abildgaard, F., Morgan, C. T., Markley, J. L. & Lutsenko, S. (2006) Solution structure of the N-domain of Wilson disease protein: Distinct nucleotide-binding environment and effects of disease mutations, Proc Natl Acad Sci U S A. 103, 5302-7. [PMCID: PMC1459350]
35. Dmitriev, O. Y. & Fillingame, R. H. (2007) The rigid connecting loop stabilizes hairpin folding of the two helices of the ATP synthase subunit c, Protein Sci. 16, 2118-22. [PMCID: PMC2204134]
36. Dmitriev, O. Y., Freedman, K. H., Hermolin, J. & Fillingame, R. H. (2008) Interaction of transmembrane helices in ATP synthase subunit a in solution as revealed by spin label difference NMR, Biochim Biophys Acta. 1777, 227-37. [PMCID: PMC2276983]
37. Dobson, N., Dantas, G., Baker, D. & Varani, G. (2006) High-resolution structural validation of the computational redesign of human U1A protein, Structure. 14, 847-56.
38. Eghbalnia, H. R., Bahrami, A., Tonelli, M., Hallenga, K. & Markley, J. L. (2005) High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection, J Am Chem Soc. 127, 12528-36.
39. Eghbalnia, H. R., Bahrami, A., Wang, L., Assadi, A. & Markley, J. L. (2005) Probabilistic Identification of Spin Systems and their Assignments including Coil-Helix Inference as Output (PISTACHIO), J. Biomol. NMR. 32, 219-33.
40. Eghbalnia, H. R., Wang, L., Bahrami, A., Assadi, A. & 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.
41. Eichmuller, C. & Skrynnikov, N. R. (2005) A new amide proton R1rho experiment permits accurate characterization of microsecond time-scale conformational exchange, J Biomol NMR. 32, 281-93.
42. Eichmuller, C. & Skrynnikov, N. R. (2007) Observation of microsecond time-scale protein dynamics in the presence of Ln3+ ions: application to the N-terminal domain of cardiac troponin C, J Biomol NMR. 37, 79-95.
43. Fenwick, M. K. & Oswald, R. E. (2008) NMR spectroscopy of the ligand-binding core of ionotropic glutamate receptor 2 bound to 5-substituted willardiine partial agonists, J Mol Biol. 378, 673-85. [PMCID: PMC2467514]
44. Fraser, C. M., Thompson, M. G., Shirley, A. M., Ralph, J., Schoenherr, J. A., Sinlapadech, T., Hall, M. C. & Chapple, C. (2007) Related Arabidopsis serine carboxypeptidase-like sinapoylglucose acyltransferases display distinct but overlapping substrate specificities, Plant Physiol. 144, 1986-99. [PMCID: PMC1949888]
45. Frederick, R. O., Bergeman, L., Blommel, P. G., Bailey, L. J., McCoy, J. G., Song, J., Meske, L., Bingman, C. A., Riters, M., Dillon, N. A., Kunert, J., Yoon, J. W., Lim, A., Cassidy, M., Bunge, J., Aceti, D. J., Primm, J. G., Markley, J. L., Phillips, G. N., Jr. & Fox, B. G. (2007) Small-scale, semi-automated purification of eukaryotic proteins for structure determination, J Struct Funct Genomics 8, 153-166. [PMCID: PMC2668602]
46. Fuzery, A. K., Tonelli, M., Ta, D. T., Cornilescu, G., Vickery, L. E. & Markley, J. L. (2008) Solution structure of the iron-sulfur cluster cochaperone HscB and its binding surface for the iron-sulfur assembly scaffold protein IscU, Biochemistry. 47, 9394-404. [PMCID: PMC2627783]
47. Gao, F., Mer, G., Tonelli, M., Hansen, S. B., Burghardt, T. P., Taylor, P. & Sine, S. M. (2006) Solution NMR of acetylcholine binding protein reveals agonist-mediated conformational change of the C-loop, Mol Pharmacol. 70, 1230-5.
48. Gorres, K. L., Edupuganti, R., Krow, G. R. & Raines, R. T. (2008) Conformational preferences of substrates for human prolyl 4-hydroxylase, Biochemistry. 47, 9447-55.
49. Griffith, B. R., Krepel, C., Fu, X., Blanchard, S., Ahmed, A., Edmiston, C. E. & Thorson, J. S. (2007) Model for antibiotic optimization via neoglycosylation: synthesis of liponeoglycopeptides active against VRE, J Am Chem Soc. 129, 8150-5.
50. Grzywacz, P., Plum, L. A., Sicinski, R. R., Clagett-Dame, M. & DeLuca, H. F. (2007) Methyl substitution of the 25-hydroxy group on 2-methylene-19-nor-1alpha,25-dihydroxyvitamin D3 (2MD) reduces potency but allows bone selectivity, Arch Biochem Biophys. 460, 274-84.
51. Guo, L. W., Assadi-Porter, F. M., Grant, J. E., Wu, H., Markley, J. L. & Ruoho, A. E. (2007) One-step purification of bacterially expressed recombinant transducin alpha-subunit and isotopically labeled PDE6 gamma-subunit for NMR analysis, Protein Expr Purif. 51, 187-97.
52. Hamma, T., Reichow, S. L., Varani, G. & Ferre-D’Amare, A. R. (2005) The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs, Nat Struct Mol Biol. 12, 1101-7.
53. Haquin, S., Oeuillet, E., Pajon, A., Harris, M., Jones, A. T., van Tilbeurgh, H., Markley, J. L., Zolnai, Z. & Poupon, A. (2008) Data management in structural genomics: an overview, Methods Mol Biol. 426, 49-79.
54. Hegeman, A. D., Schulte, C. F., Cui, Q., Lewis, I. A., Huttlin, E. L., Eghbalnia, H., Harms, A. C., Ulrich, E. L., Markley, J. L. & Sussman, M. R. (2007) Stable isotope assisted assignment of elemental compositions for metabolomics, Anal Chem 79, 6912-21.
55. Henrick, K., Feng, Z., Bluhm, W. F., Dimitropoulos, D., Doreleijers, J. F., Dutta, S., Flippen-Anderson, J. L., Ionides, J., Kamada, C., Krissinel, E., Lawson, C. L., Markley, J. L., Nakamura, H., Newman, R., Shimizu, Y., Swaminathan, J., Velankar, S., Ory, J., Ulrich, E. L., Vranken, W., Westbrook, J., Yamashita, R., Yang, H., Young, J., Yousufuddin, M. & Berman, H. M. (2008) Remediation of the protein data bank archive, Nucleic Acids Res. 36, D426-33. [PMCID: PMC2238854]
56. Hodges, J. A. & Raines, R. T. (2005) Stereoelectronic and steric effects in the collagen triple helix: toward a code for strand association, J Am Chem Soc. 127, 15923-32.
57. Horng, J. C., Hawk, A. J., Zhao, Q., Benedict, E. S., Burke, S. D. & Raines, R. T. (2006) Macrocyclic scaffold for the collagen triple helix, Org Lett. 8, 4735-8.
58. Horng, J. C. & Raines, R. T. (2006) Stereoelectronic effects on polyproline conformation, Protein Sci. 15, 74-83. [PMCID: PMC2242370]
59. Horng, J. C., Kotch, F. W. & Raines, R. T. (2007) Is glycine a surrogate for a D-amino acid in the collagen triple helix?, Protein Sci. 16, 208-15. [PMCID: PMC2203290]
60. Jewell, C. M., Fuchs, S. M., Flessner, R. M., Raines, R. T. & Lynn, D. M. (2007) Multilayered films fabricated from an oligoarginine-conjugated protein promote efficient surface-mediated protein transduction, Biomacromolecules. 8, 857-63. [PMCID: PMC2527465]
61. Johnson, R. J., Chao, T. Y., Lavis, L. D. & Raines, R. T. (2007) Cytotoxic ribonucleases: the dichotomy of Coulombic forces, Biochemistry. 46, 10308-16.
62. Johnson, R. J., Lin, S. R. & Raines, R. T. (2007) Genetic selection reveals the role of a buried, conserved polar residue, Protein Sci. 16, 1609-16. [PMCID: PMC2203362]
63. Johnson, R. J., McCoy, J. G., Bingman, C. A., Phillips, G. N., Jr. & Raines, R. T. (2007) Inhibition of human pancreatic ribonuclease by the human ribonuclease inhibitor protein, J Mol Biol. 368, 434-49. [PMCID: PMC1993901]
64. Juranic, N., Dannenberg, J. J., Cornilescu, G., Salvador, P., Atanasova, E., Ahn, H. C., Macura, S., Markley, J. L. & Prendergast, F. G. (2008) Structural dependencies of protein backbone 2JNC’ couplings, Protein Sci. 17, 768-76. [PMCID: PMC2271174]
65. Kalia, J. & Raines, R. T. (2006) Reactivity of intein thioesters: appending a functional group to a protein, Chembiochem. 7, 1375-83.
66. Kalia, J. & Raines, R. T. (2008) Hydrolytic stability of hydrazones and oximes, Angew Chem Int Ed Engl. 47, 7523-6.
67. Kieken, F., Jovic, M., Naslavsky, N., Caplan, S. & Sorgen, P. L. (2007) EH domain of EHD1, J Biomol NMR. 39, 323-9.
68. Kitamura, A., Jardine, P. J., Anderson, D. L., Grimes, S. & Matsuo, H. (2008) Analysis of intermolecular base pair formation of prohead RNA of the phage phi29 DNA packaging motor using NMR spectroscopy, Nucleic Acids Res. 36, 839-48. [PMCID: PMC2241910]
69. Kotch, F. W., Guzei, I. A. & Raines, R. T. (2008) Stabilization of the collagen triple helix by O-methylation of hydroxyproline residues, J Am Chem Soc. 130, 2952-3.
70. Kurt, N. & Cavagnero, S. (2008) Nonnative helical motif in a chaperone-bound protein fragment, Biophys J. 94, L48-50. [PMCID: PMC2267123]
71. Lavis, L. D., Chao, T. Y. & Raines, R. T. (2006) Latent blue and red fluorophores based on the trimethyl lock, Chembiochem. 7, 1151-4.
72. Lavis, L. D., Chao, T. Y. & Raines, R. T. (2006) Fluorogenic label for biomolecular imaging, ACS Chem Biol. 1, 252-60.
73. Lavis, L. D., Rutkoski, T. J. & Raines, R. T. (2007) Tuning the pK(a) of fluorescein to optimize binding assays, Anal Chem. 79, 6775-82.
74. Lee, H., Lee, B. P. & Messersmith, P. B. (2007) A reversible wet/dry adhesive inspired by mussels and geckos, Nature. 448, 338-41.
75. Levine, M. N., Lavis, L. D. & Raines, R. T. (2008) Trimethyl lock: a stable chromogenic substrate for esterases, Molecules. 13, 204-11.
76. Lewis, I. A., Schommer, S. C., Hodis, B., Robb, K. A., Tonelli, M., Westler, W. M., Sussman, M. R. & Markley, J. L. (2007) Method for determining molar concentrations of metabolites in complex solutions from two-dimensional (1)h-(13)c NMR spectra, Anal Chem. 79, 9385-90. [PMCID: PMC2533272]
77. Lewis, I. A., Shortreed, M. R., Hegeman, A. D. & Markley, J. L. (2008) Novel NMR and MS approaches to metabolomics in Handbook of Metabolomics (Fan, T. & Lane, A., eds).
78. Lin, I. J., Gebel, E. B., Machonkin, T. E., Westler, W. M. & Markley, J. L. (2005) Changes in hydrogen-bond strengths explain reduction potentials in 10 rubredoxin variants, Proc Natl Acad Sci U.S.A. 102, 14581-6. [PMCID: PMC1239895]
79. Lin, I. J., Chen, Y., Fee, J. A., Song, J., Westler, W. M. & Markley, J. L. (2006) Rieske protein from Thermus thermophilus: 15N NMR titration study demonstrates the role of iron-ligated histidines in the pH dependence of the reduction potential, J Am Chem Soc. 128, 10672-3.
80. Lytle, B. L., Peterson, F. C., Tyler, E. M., Newman, C. L., Vinarov, D. A., Markley, J. L. & Volkman, B. F. (2006) Solution structure of Arabidopsis thaliana protein At5g39720.1, a member of the AIG2-like protein family, Acta Cryst, Section F: Struct Biol Cryst Commun. 62, 490-3. [PMCID: PMC2243094]
81. Machonkin, T. E., Westler, W. M. & Markley, J. L. (2005) Paramagnetic NMR Spectroscopy and Density Functional Calculations in the Analysis of the Geometric and Electronic Structures of Iron-Sulfur Proteins, Inorganic Chemistry. 44, 779-97.
82. Marcheschi, R. J., Staple, D. W. & Butcher, S. E. (2007) Programmed ribosomal frameshifting in SIV is induced by a highly structured RNA stem-loop, J Mol Biol. 373, 652-63. [PMCID: PMC2080864]
83. Markley, J. L. (2005) NMR-Based Strucutural Proteomics in Spectral Techniques in Proteomics (Sem, D. S., ed) pp. 350-367, CRC Press, Taylor and Francis Group, Boca raton, FL.
84. Markley, J. L., Anderson, M. E., Cui, Q., Eghbalnia, H. R., Lewis, I. A., Hegeman, A. D., Li, J., Schulte, C. F., Sussman, M. R., Westler, W. M., Ulrich, E. L. & Zolnai, Z. (2007) New bioinformatics resources for metabolomics, Pac Symp Biocomput, 157-68.
85. Markley, J. L. (2007) NMR analysis goes nano, Nat Biotechnol. 25, 750-1.
86. Markley, J. L., Ulrich, E. L., Berman, H. M., Henrick, K., Nakamura, H. & Akutsu, H. (2008) BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions, J Biomol NMR. 40, 153-5. [PMCID: PMC2268728]
87. Markley, J. L., Bahrami, A., Eghbalnia, H. R., Peterson, F. C., Ulrich, E. L., Westler, W. M. & Volkman, B. F. (2008) Macromolecular Structure Determination by NMR Spectroscopy In Structural Bioinformatics, 2nd Ed., Gu, J. & Bourne, P. eds., John Wiley, pp. 93-142.
88. Masterson, L. R., Tonelli, M., Markley, J. L. & Veglia, G. (2008) Simultaneous detection and deconvolution of congested NMR spectra containing three isotopically labeled species, J Am Chem Soc. 130, 7818-9. [PMCID: PMC2662704]
89. Phillips, G. N., Jr., Fox, B. G., Markley, J. L., Volkman, B. F., Bae, E., Bitto, E., Bingman, C. A., Frederick, R. O., McCoy, J. G., Lytle, B. L., Pierce, B. S., Song, J. & Twigger, S. N. (2007) Structures of proteins of biomedical interest from the Center for Eukaryotic Structural Genomics, J Struct Funct Genomics 2-3, 73-84
90. Ralph, J., Akiyama, T., Kim, H., Lu, F., Schatz, P. F., Marita, J. M., Ralph, S. A., Reddy, M. S., Chen, F. & Dixon, R. A. (2006) Effects of coumarate 3-hydroxylase down-regulation on lignin structure, J Biol Chem. 281, 8843-53.
91. Ralph, J., Kim, H., Lu, F., Grabber, J. H., Leple, J. C., Berrio-Sierra, J., Derikvand, M. M., Jouanin, L., Boerjan, W. & Lapierre, C. (2008) Identification of the structure and origin of a thioacidolysis marker compound for ferulic acid incorporation into angiosperm lignins (and an indicator for cinnamoyl CoA reductase deficiency), Plant J. 53, 368-79.
92. Reiter, N. J., Maher, L. J., 3rd & Butcher, S. E. (2008) DNA mimicry by a high-affinity anti-NF-kappaB RNA aptamer, Nucleic Acids Res. 36, 1227-36. [PMCID: PMC2275087]
93. Sashital, D. G., Venditti, V., Angers, C. G., Cornilescu, G. & Butcher, S. E. (2007) Structure and thermodynamics of a conserved U2 snRNA domain from yeast and human, RNA. 13, 328-38. [PMCID: PMC1800520]
94. Schwartz, P. A. & Frey, P. A. (2007) 5′-Peroxyadenosine and 5′-peroxyadenosylcobalamin as intermediates in the aerobic photolysis of adenosylcobalamin, Biochemistry. 46, 7284-92. [PMCID: PMC2553253]
95. Shoulders, M. D., Guzei, I. A. & Raines, R. T. (2008) 4-chloroprolines: synthesis, conformational analysis, and effect on the collagen triple helix, Biopolymers. 89, 443-54.
96. Singh, S., Cornilescu, C. C., Tyler, R. C., Cornilescu, G., Tonelli, M., Lee, M. S. & Markley, J. L. (2005) Solution structure of a late embryogenesis abundant protein (LEA14) from Arabidopsis thaliana, a cellular stress-related protein, Protein Sci. 14, 2601-9. [PMCID: PMC2253292]
97. Singh, S., Tonelli, M., Tyler, R. C., Bahrami, A., Lee, M. S. & Markley, J. L. (2005) Three-dimensional structure of the AAH26994.1 protein from Mus musculus, a putative eukaryotic Urm1, Protein Sci. 14, 2095-102. [PMCID: PMC2279321]
98. Singh, S., Hager, M. H., Zhang, C., Griffith, B. R., Lee, M. S., Hallenga, K., Markley, J. L. & Thorson, J. S. (2006) Structural insight into the self-sacrifice mechanism of enediyne resistance, ACS Chem Biol. 1, 451-60.
99. Soellner, M. B., Nilsson, B. L. & Raines, R. T. (2006) Reaction mechanism and kinetics of the traceless Staudinger ligation, J Am Chem Soc. 128, 8820-8.
100. Song, J., Vinarov, D., Tyler, E. M., Shahan, M. N., Tyler, R. C. & Markley, J. L. (2004) Hypothetical protein At2g24940.1 from Arabidopsis thaliana has a cytochrome b5 like fold, J Biomol NMR. 30, 215-8.
101. Song, J., Zhao, Q., Thao, S., Frederick, R. O. & Markley, J. L. (2004) Solution structure of a calmodulin-like calcium-binding domain from Arabidopsis thaliana, J Biomol NMR. 30, 451-6.
102. Song, J., Zhao, Q., Lee, M. S. & 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.
103. 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, 1043-51.
104. Song, J., Tyler, R. C., Wrobel, R. L., Frederick, R. O., Vojtek, F. C., Jeon, W. B., Lee, M. S. & 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 Science. 14, 1059-63. [PMCID: PMC2253455]
105. Song, J., Lee, M. S., Carlberg, I., Vener, A. V. & Markley, J. L. (2006) Micelle-Induced Folding of Spinach Thylakoid Soluble Phosphoprotein of 9 kDa and Its Functional Implications(,), Biochemistry. 45, 15633-15643. [PMCID: PMC2533273]
106. Song, J. & Markley, J. L. (2007) Cautionary tail: the presence of an N-terminal tag on dynein light-chain Roadblock/LC7 affects its interaction with a functional partner, Protein Pept Lett. 14, 265-8.
107. Song, J. & Markley, J. L. (2007) Three-dimensional Structure Determined for a Subunit of Human tRNA Splicing Endonuclease (Sen15) Reveals a Novel Dimeric Fold, J Mol Biol. 366, 155-64. [PMCID: PMC1865571]
108. Song, J., Zhao, K. Q., Newman, C. L., Vinarov, D. A. & Markley, J. L. (2007) Solution structure of human sorting nexin 22, Protein Science. 16, 807-14. [PMCID: PMC2206652]
109. Song, J., Guo, L. W., Muradov, H., Artemyev, N. O., Ruoho, A. E. & Markley, J. L. (2008) Intrinsically disordered gamma-subunit of cGMP phosphodiesterase encodes functionally relevant transient secondary and tertiary structure, Proc Natl Acad Sci U S A. 105, 1505-10. [PMCID: PMC2234174]
110. Song, J., Bettendorff, L., Tonelli, M. & Markley, J. L. (2008) Structural basis for the catalytic mechanism of mammalian 25-kDa thiamine triphosphatase, J Biol Chem. 283, 10939-48. [PMCID: PMC2447667]
111. Song, J., McGivern, J. V., Nichols, K. W., Markley, J. L. & Sheets, M. D. (2008) Structural basis for RNA recognition by a type II poly(A)-binding protein, Proc Natl Acad Sci U S A. 105, 15317-22. [PMCID: PMC2563106]
112. Song, X. J., Simplaceanu, V., Ho, N. T. & Ho, C. (2008) Effector-induced structural fluctuation regulates the ligand affinity of an allosteric protein: binding of inositol hexaphosphate has distinct dynamic consequences for the T and R states of hemoglobin, Biochemistry. 47, 4907-15. [PMCID: PMC2493540]
113. Staple, D. W. & Butcher, S. E. (2005) Solution structure and thermodynamic investigation of the HIV-1 frameshift inducing element, J Mol Biol. 349, 1011-23.
114. Staple, D. W., Venditti, V., Niccolai, N., Elson-Schwab, L., Tor, Y. & Butcher, S. E. (2008) Guanidinoneomycin B recognition of an HIV-1 RNA helix, Chembiochem. 9, 93-102.
115. Takeda, M., Sugimori, N., Torizawa, T., Terauchi, T., Ono, A. M., Yagi, H., Yamaguchi, Y., Kato, K., Ikeya, T., Jee, J., Guntert, P., Aceti, D. J., Markley, J. L. & Kainosho, M. (2008) Structure of the putative 32 kDa myrosinase-binding protein from Arabidopsis (At3g16450.1) determined by SAIL-NMR, FEBS J. 275, 5873-5884. [PMCID: PMC Journal- in process]
116. Tam, A., Soellner, M. B. & Raines, R. T. (2007) Water-soluble phosphinothiols for traceless staudinger ligation and integration with expressed protein ligation, J Am Chem Soc. 129, 11421-30.
117. Tam, A., Arnold, U., Soellner, M. B. & Raines, R. T. (2007) Protein prosthesis: 1,5-disubstituted[1,2,3]triazoles as cis-peptide bond surrogates, J Am Chem Soc. 129, 12670-1. [PMCID: PMC2531141]
118. Tonelli, M., Masterson, L. R., Hallenga, K., Veglia, G. & Markley, J. L. (2007) Carbonyl carbon label selective (CCLS) (1)H- (15)N HSQC experiment for improved detection of backbone (13)C- (15)N cross peaks in larger proteins, J Biomol NMR. 39, 177-85.
119. Turcotte, R. F. & Raines, R. T. (2008) Interaction of onconase with the human ribonuclease inhibitor protein, Biochem Biophys Res Commun. 377, 512-4.
120. 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. K., Tyler, E. M., Ulrich, E. L., Vinarov, D. A., Vojtik, F. C., Volkman, B. F., Wrobel, R. L., Zhao, Q. & 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, 633-43.
121. Tyler, R. C., Bitto, E., Berndsen, C. E., Bingman, C. A., Singh, S., Lee, M. S., Wesenberg, G. E., Denu, J. M., Phillips, G. N., Jr. & Markley, J. L. (2006) Structure of Arabidopsis thaliana At1g77540 protein, a minimal acetyltransferase from the COG2388 family, Biochemistry. 45, 14325-36. [PMCID: PMC2533278]
122. Tyler, R. C., Sreenath, H. K., Singh, S., Aceti, D. J., Bingman, C. A., Markley, J. L. & 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 Expr Purif. 40, 268-78.
123. Uchida, K., Markley, J. L. & 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 antiparallel beta strands within the hydrophobic core of Streptomyces subtilisin inhibitor (SSI), Biochemistry. 44, 11811-20. [PMCID: PMC2631424]
124. Ulijasz, A. T., Cornilescu, G., von Stetten, D., Kaminski, S., Mroginski, M. A., Zhang, J., Bhaya, D., Hildebrandt, P. & Vierstra, R. D. (2008) Characterization of two thermostable cyanobacterial phytochromes reveals global movements in the chromophore-binding domain during photoconversion, J Biol Chem. 283, 21251-66.
125. Ulrich, E. L., Akutsu, H., Doreleijers, J. F., Harano, Y., Ioannidis, Y. E., Lin, J., Livny, M., Mading, S., Maziuk, D., Miller, Z., Nakatani, E., Schulte, C. F., Tolmie, D. E., Kent Wenger, R., Yao, H. & Markley, J. L. (2008) BioMagResBank, Nucleic Acids Res. 36, D402-8. [PMCID: PMC2238925]
126. Ulyanov, N. B., Mujeeb, A., Du, Z., Tonelli, M., Parslow, T. G. & James, T. L. (2006) NMR structure of the full-length linear dimer of stem-loop-1 RNA in the HIV-1 dimer initiation site, J Biol Chem. 281, 16168-77.
127. Venditti, V., Niccolai, N. & Butcher, S. E. (2008) Measuring the dynamic surface accessibility of RNA with the small paramagnetic molecule TEMPOL, Nucleic Acids Res. 36, e20. [PMCID: PMC2275091]
128. Vinarov, D. A., Loushin Newman, C. L. & Markley, J. L. (2006) Wheat germ cell-free platform for eukaryotic protein production, FEBS Journal. 273, 4160-9.
129. Vinarov, D. A., Newman, C. L., Tyler, E. M., Markley, J. L. & Shahan, M. N. (2006) Wheat germ cell-free expression system for protein production, Curr Protoc Protein Sci. Chapter 5, Unit 5 18.
130. Vugmeyster, L. & McKnight, C. J. (2008) Slow Motions in Chicken Villin Headpiece Subdomain Probed by Cross-correlated NMR Relaxation of Amide NH Bonds in Successive Residues, Biophys J. 95, 5941-50
131. Wang, L., Eghbalnia, H. R., Bahrami, A. & 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.
132. Wang, L., Eghbalnia, H. R. & Markley, J. L. (2006) Probabilistic Approach to Determining Unbiased Random-coil Carbon-13 Chemical Shift Values from the Protein Chemical Shift Database, J Biomol NMR. 35, 155-165.
133. Wang, L., Eghbalnia, H. R. & Markley, J. L. (2007) Nearest-neighbor effects on backbone alpha and beta carbon chemical shifts in proteins, J Biomol NMR 39, 247-57.
134. Yao, H. & 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.
135. Yao, H., McCullough, C. R., Costache, A. D., Pullela, P. K. & Sem, D. S. (2007) Structural evidence for a functionally relevant second camphor binding site in P450cam: model for substrate entry into a P450 active site, Proteins. 69, 125-38.
136. Yatzeck, M. M., Lavis, L. D., Chao, T. Y., Chandran, S. S. & Raines, R. T. (2008) A highly sensitive fluorogenic probe for cytochrome P450 activity in live cells, Bioorg Med Chem Lett. 18, 5864-6. [PMCID: PMC2586036]
137. Zhang, X. Y. & Elfarra, A. A. (2005) Reaction of 1,2,3,4-diepoxybutane with 2′-deoxyguanosine: initial products and their stabilities and decomposition patterns under physiological conditions, Chem Res Toxicol. 18, 1316-23. [PMCID: PMC2556896\
138. Zhang, N., Liu, L., Liu, F., Wagner, C. R., Hanna, P. E. & Walters, K. J. (2006) NMR-based model reveals the structural determinants of mammalian arylamine N-acetyltransferase substrate specificity, J Mol Biol. 363, 188-200.
139. Zhang, X. Y. & Elfarra, A. A. (2006) Characterization of 1,2,3,4-diepoxybutane-2'-deoxyguanosine cross-linking products formed at physiological and nonphysiological conditions, Chem Res Toxicol. 19, 547-55. [PMCID: PMC2568978]
140. Zhao, Q., Song, J., Jin, Z., Danilova, V., Hellekant, G. & Markley, J. L. (2005) Probing the sweet determinants of brazzein: wild-type brazzein and a tasteless variant, brazzein-ins(R18a-I18b), exhibit different pH-dependent NMR chemical shifts, Biochem Biophys Res Commun. 335, 256-63.
141. Zornetzer, G. A., Fox, B. G. & Markley, J. L. (2006) Solution structures of spinach acyl carrier protein with decanoate and stearate, Biochemistry. 45, 5217-27. [PMCID: PMC2533275]
142. Zornetzer, G. A., White, R. D., Markley, J. L. & Fox, B. G. (2006) Preparation of isotopically labeled spinach acyl-acyl carrier protein for NMR structural studies, Protein Expr Purif. 46, 446-55.
143. Yelle, D. J., Ralph, J. & Frihart, C. R. (2008) Characterization of nonderivatized plant cell walls using high-resolution solution-state NMR spectroscopy, Magn Reson Chem. 46, 508-17.
Publications from 2005-2007 that utilized NMRFAM but did not cite the facility:
1. Bakke, C. K., Jungbauer, L. M. & Cavagnero, S. (2006) In vitro expression and characterization of native apomyoglobin under low molecular crowding conditions, Protein Expr Purif. 45, 381-92.
2. Barshteyn, N. & Elfarra, A. A. (2007) Formation of three N-acetyl-L-cysteine monoadducts and one diadduct by the reaction of S-(1,2-dichlorovinyl)-L-cysteine sulfoxide with N-acetyl-L-cysteine at physiological conditions: chemical mechanisms and toxicological implications, Chem Res Toxicol. 20, 1563-9.
3. Bunzel, M., Ralph, J. & Steinhart, H. (2005) Association of non-starch polysaccharides and ferulic acid in grain amaranth (Amaranthus caudatus L.) dietary fiber, Mol Nutr Food Res. 49, 551-9.
4. Bunzel, M., Ralph, J., Bruning, P. & Steinhart, H. (2006) Structural identification of dehydrotriferulic and dehydrotetraferulic acids isolated from insoluble maize bran fiber, J Agric Food Chem. 54, 6409-18.
5. Butcher, S. E. & Brow, D. A. (2005) Towards understanding the catalytic core structure of the spliceosome, Biochem Soc Trans. 33, 447-9.
6. Chen, Y., Fender, J., Legassie, J. D., Jarstfer, M. B., Bryan, T. M. & Varani, G. (2006) Structure of stem-loop IV of Tetrahymena telomerase RNA, Embo J. 25, 3156-66. [PMCID: PMC1500990]
7. Chen, Z., Kurt, N., Rajagopalan, S. & Cavagnero, S. (2006) Secondary structure mapping of DnaK-bound protein fragments: chain helicity and local helix unwinding at the binding site, Biochemistry. 45, 12325-33.
8. Chevelkov, V., Zhuravleva, A. V., Xue, Y., Reif, B. & Skrynnikov, N. R. (2007) Combined analysis of (15)N relaxation data from solid- and solution-state NMR spectroscopy, J Am Chem Soc. 129, 12594-5.
9. 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, 2836-41. [PMCID: PMC2242445]
10. Dmitriev, O. Y., Tsivkovskii, R., Abildgaard, F. & Lutsenko, S. (2006) NMR assignment of the Wilson disease associated protein N-domain, J Biomol NMR. 36 Suppl 1, 61.
11. Dobson, N., Dantas, G. & Varani, G. (2005) 1H, 13C and 15N resonance assignments of URNdesign, a computationally redesigned RRM protein, J Biomol NMR. 33, 135.
12. Doreleijers, J. F., Nederveen, A. J., Vranken, W., Lin, J., Bonvin, A. M., Kaptein, R., Markley, J. L. & Ulrich, E. L. (2005) BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures, J Biomol NMR. 32, 1-12.
13. Funk, C., Ralph, J., Steinhart, H. & Bunzel, M. (2005) Isolation and structural characterisation of 8-O-4/8-O-4- and 8-8/8-O-4-coupled dehydrotriferulic acids from maize bran, Phytochemistry. 66, 363-71.
14. Gelis, I., Bonvin, A. M., Keramisanou, D., Koukaki, M., Gouridis, G., Karamanou, S., Economou, A. & Kalodimos, C. G. (2007) Structural basis for signal-sequence recognition by the translocase motor SecA as determined by NMR, Cell. 131, 756-69. [PMCID: PMC2170882]
15. Guo, L. W., Assadi-Porter, F. M., Grant, J. E., Wu, H., Markley, J. L. & Ruoho, A. E. (2007) One-step purification of bacterially expressed recombinant transducin alpha-subunit and isotopically labeled PDE6 gamma-subunit for NMR analysis, Protein Expr Purif. 51, 187-97.
16. Hodges, J. A. & Raines, R. T. (2006) Energetics of an n –> pi interaction that impacts protein structure, Org Lett. 8, 4695-7. [PMCID: PMC2625295]
17. Jenkins, C. L., Vasbinder, M. M., Miller, S. J. & Raines, R. T. (2005) Peptide bond isosteres: ester or (E)-alkene in the backbone of the collagen triple helix, Org Lett. 7, 2619-22.
18. Keramisanou, D., Biris, N., Gelis, I., Sianidis, G., Karamanou, S., Economou, A. & Kalodimos, C. G. (2006) Disorder-order folding transitions underlie catalysis in the helicase motor of SecA, Nat Struct Mol Biol. 13, 594-602.
19. Kotch, F. W. & Raines, R. T. (2006) Self-assembly of synthetic collagen triple helices, Proc Natl Acad Sci U S A. 103, 3028-33. [PMCID: PMC1413887]
20. Krause, R. J., Glocke, S. C., Sicuri, A. R., Ripp, S. L. & Elfarra, A. A. (2006) Oxidative metabolism of seleno-L-methionine to L-methionine selenoxide by flavin-containing monooxygenases, Chem Res Toxicol. 19, 1643-9. [PMCID: PMC2533529]
21. Kurt, N., Rajagopalan, S. & Cavagnero, S. (2006) Effect of hsp70 chaperone on the folding and misfolding of polypeptides modeling an elongating protein chain, J Mol Biol. 355, 809-20. [PMCID: PMC1570398]
22. Markley, J. L. (2005) Protein solution structure in three days or less?, Scientist. 19, 36-37.
23. Markley, J. L., Anderson, M. E., Cui, Q., Eghbalnia, H. R., Lewis, I. A., Hegeman, A. D., Li, J., Schulte, C. F., Sussman, M. R., Westler, W. M., Ulrich, E. L. & Zolnai, Z. (2007) New bioinformatics resources for metabolomics, Pac Symp Biocomput, 157-68.
24. Marlier, J. F., Campbell, E., Lai, C., Weber, M., Reinhardt, L. A. & Cleland, W. W. (2006) Multiple isotope effect study of the acid-catalyzed hydrolysis of formamide, J Org Chem. 71, 3829-36.
25. 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. & Bonvin, A. M. (2005) RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank, Proteins. 59, 662-72.
26. Oldfield, C. J., Ulrich, E. L., Cheng, Y., Dunker, A. K. & Markley, J. L. (2005) Addressing the intrinsic disorder bottleneck in structural proteomics, Proteins. 59, 444-53.
27. Peterson, F. C., Lytle, B. L., Sampath, S., Vinarov, D., Tyler, E., Shahan, M., Markley, J. L. & Volkman, B. F. (2005) Solution structure of thioredoxin h1 from Arabidopsis thaliana, Protein Science. 14, 2195-200. [PMCID: PMC2279331]
28. Plonska-Ocypa, K., Grzywacz, P., Sicinski, R. R., Plum, L. A. & DeLuca, H. F. (2007) Synthesis and biological evaluation of a des-C,D-analog of 2-methylene-19-nor-1alpha,25-(OH)2D3, J Steroid Biochem Mol Biol. 103, 298-304.
29. Schlieve, C. R., Tam, A., Nilsson, B. L., Lieven, C. J., Raines, R. T. & Levin, L. A. (2006) Synthesis and characterization of a novel class of reducing agents that are highly neuroprotective for retinal ganglion cells, Exp Eye Res. 83, 1252-9.
30. Shoulders, M. D., Hodges, J. A. & Raines, R. T. (2006) Reciprocity of steric and stereoelectronic effects in the collagen triple helix, J Am Chem Soc. 128, 8112-3. [PMCID: PMC2517127]
31. Soellner, M. B., Tam, A. & Raines, R. T. (2006) Staudinger ligation of peptides at non-glycyl residues, J Org Chem. 71, 9824-30. [PMCID: PMC2565276]
32. Staple, D. W. & Butcher, S. E. (2005) Pseudoknots: RNA structures with diverse functions, PLoS Biol. 3, e213. [PMCID: PMC1149493]
33. Sugimori, N., Torizawa, T., Aceti, D. J., Thao, S., Markley, J. L. & Kainosho, M. (2004) (1)H, (13)C and (15)N backbone assignment of a 32 kDa hypothetical protein from Arabidopsis thaliana, At3g16450.1, J Biomol NMR. 30, 357-8.
34. Tyler, R. C., Bitto, E., Berndsen, C. E., Bingman, C. A., Singh, S., Lee, M. S., Wesenberg, G. E., Denu, J. M., Phillips, G. N., Jr. & Markley, J. L. (2006) Structure of Arabidopsis thaliana At1g77540 protein, a minimal acetyltransferase from the COG2388 family, Biochemistry. 45, 14325-36. [PMCID: PMC2533278]
35. Vinarov, D. A. & Markley, J. L. (2005) High-throughput automated platform for nuclear magnetic resonance-based structural proteomics, Expert Rev Proteomics. 2, 49-55.
36. Vranken, W. F., Boucher, W., Stevens, T. J., Fogh, R. H., Pajon, A., Llinas, M., Ulrich, E. L., Markley, J. L., Ionides, J. & Laue, E. D. (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline, Proteins. 59, 687-96.
37. Wrobel, R. L., Bingman, C. A., Jeon, W. B., Song, J., Vinarov, D. A., Frederick, R. O., Aceti, D. J., Sreenath, H. K., Zolnai, Z., Vojtik, F. C., Bitto, E., Fox, B. G., Phillips, G. N. & Markley, J. L. (2006) Structural Proteomics, in Plant Proteomics in (C., E. F., ed) pp. 99-128, Blackwell Publishing, Oxford.
38. Zhang, L. M., Gellerstedt, G., Ralph, J. & Lu, F. C. (2006) NMR studies on the occurrence of spirodienone structures in lignins, Journal of Wood Chemistry and Technology. 26, 65-79.