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  1. E. T. Yu, A. E. Hawkins, J. Eaton, D. Fabris. "MS3D structural elucidation of the HIV-1 packaging signal" (manuscript under review)
     
  2. M. Lubben, R. Portmann, G. Kock, R. Stoll, M. M. Young, M. Solioz. "Structural model of the CopA copper ATPase of Enterococcus hirae based on chemical cross-linking" (submitted to Biochem. J.)
     
  3. X. Guo, P. Bandyopadhyay, B. Schilling, M. M. Young, N. Fujii, T. Aynechi, R. K. Guy, I. D. Kuntz, B. W. Gibson "Partial Acetylation of Lysine Residues Improves Intraprotein Cross-Linking" Anal. Chem. 80(4):951-60. (2008).
     
  4. X. Guo, P. Bandyopadhyay, B. Schilling, M. M. Young, N. Fujii, T. Aynechi, R. K. Guy, I. D. Kuntz, B. W. Gibson. "Supplementary Material for Partial Acetylation of Lysine Residues Improves Intraprotein Cross-Linking" Anal. Chem. (2008) 10.1021/ac701636w.
     
  5. Q. Zhang, E. Crosland, D. Fabris. "Nested Arg-specific bifunctional crosslinkers for MS-based structural analysis of proteins and protein assemblies" Anal. Chim. Acta (2008) in press.
     
  6. A. El-Shafey, N. Tolic, M. Young, K. Sale, R. D. Smith, V. Kery. ""Zero-length" cross-linking in solid state as an approach for analysis of protein -protein interactions" Protein Science 15(3):429-440. (2006).
     
  7. S. P. Gaucher, M. Z. Hadi, M. M. Young. "Investigation of Gas Phase Dissociation Pathways of Lys-Lys Crosslinked Peptides: Influence of Crosslinker Identity and Position" J. Am. Soc. Mass Spectrom. 17:395-405. (2006).
     
  8. R. B. Jacobsen, K. L. Sale, M. J. Ayson, P. Novak, J. Hong, P. Lane, N. L. Wood, G. H. Kruppa, M. M. Young, J. S. Schoeniger. "Structure and dynamics of dark-state bovine rhodopsin revealed by chemical cross-linking and high-resolution mass spectrometry" Protein Science 15(6):1303-17. (2006).
     
  9. Q. Zhang, E. T. Yu, K. A. Kellersberger, E. Crosland, D. Fabris. "Toward building a database of bifunctional probes for the MS3D investigation of nucleic acids structures" invited contribution to J. Am. Soc. Mass Spectrom. 17:1570-1581 (2006).
     
  10. O. Akinsiku, E. T. Yu, D. Fabris. "Mass spectrometric investigation of protein alkylation by the RNA footprinting probe kethoxal" J. Mass Spectrom. 40:1372-1381 (2005).
     
  11. J. D. Myers, T. C. Allison, S. Bittner, B. Didier, M. Frenklach, W. H. Green, Jr., Y-L. Ho, J. Hewson, W. Koegler, C. Lansing, D. Leahy, M. Lee, R. McCoy, M. Minkoff, S. Nijsure, G. von Laszewski, D. Montoya, C. Pancerella, R. Pinzon, W. Pitz, L.A. Rahn, B. Ruscic, K. Schuchardt, E. Stephan, A. Wagner, T. Windus, C. Yang. "A Collaborative Informatics Infrastructure for Multi-Scale Science" Cluster Computing 8(4):243-253. (2005).
     
  12. P. Novak, W. E. Haskins, M. J. Ayson, R. B. Jacobsen, J. S. Schoeniger, M. D. Leavell, M. M. Young, G. H. Kruppa. "Unambiguous Assignment of Intra-Molecular Chemical Cross-Links in Modified Mammalian Membrane Proteins by Fourier Transform-Tandem Mass Spectrometry" Anal. Chem. 77:5101-5106. (2005).
     
  13. E. T. Yu, Q. Zhang, D. Fabris. "Untying the FIV Frameshifting Pseudoknot Structure by MS3D" J. Mol. Biol. 345:69-80 (2005).
     
  14. G. A. Gray, T. G. Kolda, K. L. Sale, M. M. Young. "Optimizing an Empirical Scoring Function for Transmembrane Protein Structure Determination," INFORMS Journal on Computing, Special Computational Biology Issue 4(16):406-418. (2004).
     
  15. K. A. Kellersberger, E. Yu, G. H. Kruppa, M. M. Young, D. Fabris. "Top-Down Characterization of Nucleic Acids Modified by Structural Probes Using High-Resolution Tandem Mass Spectrometry and Automated Data Interpretation" Anal. Chem. 76:(9)2438-2445 (2004).
     
  16. P. Novak, W. E. Haskins, M. D. Leavell, M. J. Ayson, R. B. Jacobsen, J. S. Schoeniger, M. M. Young, G. H. Kruppa. "Cross-Links in Modified Mammalian Membrane Proteins by Fourier Transform-Tandem Mass Spectrometry" (in preparation).
     
  17. P. Novak, G. H. Kruppa, M. M. Young, J. S. Schoeniger. "A top down method for the determination of residue specific solvent accessibility in proteins" J. Mass Spectrom. 39:322-328. (2004).
     
  18. J. J. Peterson, M. M. Young, L. J. Takemoto. "Probing Alpha Crystallin Structure Using Chemical Cross-linkers and Mass Spectrometry" Mol. Vis. 10:857-66. (2004).
     
  19. K. L. Sale, J. L. Faulon, G. A. Gray, J. S. Schoeniger, M. M. Young. "Optimal bundling of the transmembrane helices of integral membrane proteins using sparse distance constraints" Protein Science 13(10):2613-27. (2004).
     
  20. E. T. Yu, D. Fabris. "Toward multiplexing the application of solvent accessibility probes for the investigation of RNA three-dimensional structures by electrospray ionization-Fourier transform ion cyclotron mass spectrometry" Anal. Biochem. 344:356-366 (2004).
     
  21. C. Collins, B. Schilling, M. M. Young, G. Dollinger, R. K. Guy. "Isotopically labeled crosslinking reagents: Resolution of mass degeneracy in the identification of crosslinked peptides" Bioorg. Med. Chem. Lett. 13(22):4023-6. (2003).
     
  22. J. L. Faulon, K. L. Sale, M. M. Young. "Exploring the conformational space of membrane protein folds matching distance constraints" Protein Science. 12(8):1750-61. (2003).
     
  23. G. Kruppa, J. S. Schoeniger, M. M. Young. "A top down approach to protein structural studies using chemical cross-linking and Fourier transform mass spectrometry" Rapid Commun. Mass Spectrom. 17(2):155-162. (2003).
     
  24. P. Novak, M. M. Young, J. S. Schoeniger, G. H. Kruppa. "A Top Down Approach to Protein Structure Studies Using Chemical Crosslinking and Fourier Transform Mass Spectrometry" Eur. J. Mass Spectrom. 9:623-31. (2003).
     
  25. B. Schilling, M. M. Young, R. H. Row, B. W. Gibson. "MS2Assign, Automated Assignment and Nomenclature of Tandem MS Spectra of Chemically Crosslinked Peptides" J. Am. Soc. Mass Spectrom. 14(8):834-850. (2003).
     
  26. E. Yu, D. Fabris. "Direct Probing of RNA Structures and RNA-Protein Interactions in the HIV-1 Packaging Signal by Chemical Modification and Electrospray Fourier Transform Mass Spectrometry" J. Mol. Biol. 330:211-223 (2003).
     
  27. J. L. Faulon, M. D. Rintoul, M. M. Young. "Constrained walks and self-avoiding walks: implications for protein structure determination" J. Phys. A. 35:1-19. (2002).
     
  28. M. M. Young, N. Tang, J. C. Hempel, C. M. Oshiro, E. W. Taylor, I. D. Kuntz, B. W. Gibson, G. Dollinger. "High-throughput Protein Fold Identification Using Experimental Constraints Derived from Intramolecular Cross-linking and Mass Spectrometry" Proc. Natl. Acad. Sci. 97(11):5802-6. (2000).
     

 
       
 
 

Last Modified 06/17/08