Malin Young, PhD,

Deputy Program Manager

Chemical and Biological

National Security Program

• Sandia National
• Laboratories MS 9951,
• PO Box 969 7011
• East Avenue Livermore, CA
• 94551-0969
• mmyoung@sandia.gov phone: 925-294-2949
• fax: 925-294-3422

Related Links

• Home of the
  MS3D Collaboratory
• Homeland Security
• Chem/Bio Research
• Biosystems Research

I am the Deputy Program Manager for Sandia's Chemical and Biological National Security Program , which involves building new business with the Department of Homeland Security, the Department of Defense, and the National Institutes of Health, and oversight of a portfolio of programs that span multiple departments, fields of study and geographic locations.

My research is focused on the development of a rapid, low-resolution protein structure determination technique called MS3D. MS3D was originally validated on a soluble protein, FGF-2, in collaboration with UCSF and Chiron Corporation (Young et al., 2000). Work is now ongoing at Sandia, CA to apply this technology to the structure determination of both soluble and membrane-bound proteins, protein-protein and protein-nucleic acid complexes. I am also developing approaches for modeling protein tertiary structure using sets of low-resolution experimentally-derived constraints.

I work closely with protein chemists and mass spectrometrists to develop MS3D-related experimental design and data analysis software packages. Online versions of the ASAP and MS2Assign programs were formerly at http://roswell.ca.sandia.gov/~mmyoung. Recently, our team was funded by NIH to develop an online MS3D collaboratory with new versions of these codes, Links and MS2Links. Please go to www.ms3d.org and register for an account to use these tools.

Recent Publications

D. Fabris, A. Hawkins, I.D. Kuntz, L.A. Rahn, C.M. Pancerella, K. Sale, M.M. Young, C.L. Yang, E. Yu. "The Collaboratory for MS3D: A New Cyberinfrastructure Supporting the Structural Elucidation of Biomolecules and Their Assemblies Using Mass Spectrometry and Chemical Cross-linking." (in preparation)

R. Portmann, K. Sale, O. Barre, M.M. Young, M. Solioz. "Structural Analysis of Copper ATPases on the Example of the Enterococcus hirae CopA Copper ATPase and New Insights into the Function of Copper Binding Domains in Eukaryotes." (in preparation)

X. Guo, B. Schilling, T. Aynechi, M. Young, P. Bandyopadhyay, R.K. Guy, N. Fujii, I.D. Kuntz, B.W. Gibson. "Partial Acetylation of Lysine Residues Improves Intraprotein Cross-linking". Anal Chem, 80(4):951-60. 2008.
PubMed

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.
PubMed

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.
PubMed

El-Shafey A, Tolic N, Young MM, Sale K, Smith RD, Kery V. "Zero-length" cross-linking in solid state as an approach for analysis of protein-protein interactions." Protein Sci. (2006) 15(3):429-40.
PubMed

Springer C, Adalsteinsson H, Young MM, Kegelmeyer PW, Roe DC. "PostDOCK: a structural, empirical approach to scoring protein ligand complexes." J Med Chem. (2005) 48(22):6821-31.
PubMed

Novak P, Haskins WE, Ayson MJ, Jacobsen RB, Schoeniger JS, Young MM, Kruppa GH. "Unambiguous assignment of intramolecular chemical cross-links in modified mammalian membrane proteins by fourier transform-tandem mass spectrometry." Anal Chem (2005) 77(16):5101-6.
PubMed

Zhou CLE, Zemla AT, Roe D, Young M, Lam M, Schoeniger JS, Balhorn R. "Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin." Bioinformatics, (2005) 21(14):3089-3096.
PubMed

Gray GA, Kolda TG, Sale K, Young, MM. "Optimizing an empirical scoring function for transmembrane protein structure determination." Informs Journal on Computing (2004) 16(4):406-418.

Peterson JJ, Young MM, Takemoto LJ. "Probing Alpha Crystallin Structure Using Chemical Cross-linkers and Mass Spectrometry" Mol Vis. (2004) 10 (103-4): 857-866.
PubMed

Sale K, Faulon JL, Gray GA, Schoeniger JS, Young MM, "Optimal bundling of transmembrane helices using sparse distance constraints." Protein Sci. (2004) 13(10):2613-27.
PubMed

Novak P, Kruppa GH, Young MM, Schoeniger J. "A top-down method for the determination of residue-specific solvent accessibility in proteins." J Mass Spectrom. (2004) 39(3):322-8.
PubMed

Kellersberger KA, Yu E, Kruppa GH, Young MM, Fabris D. "Top-down characterization of nucleic acids modified by structural probes using high-resolution tandem mass spectrometry and automated data interpretation." Anal Chem. (2004) 76(9):2438-45.
PubMed

Novak P, Young MM, Schoeniger JS, Kruppa GH. "A top-down approach to protein structure studies using chemical cross-linking and Fourier transform mass spectrometry." Eur J Mass Spectrom (Chichester, Eng). 2003;9(6):623-31.
PubMed

Gray GA, Kolda TG, Sale KA, Young MM. "Optimizing an empirical scoring function for transmembrane protein structure determination." INFORMS Fall 2004 Special Issue.

Collins CJ, Schilling B, Young M, Dollinger G, Guy RK. "Isotopically labeled crosslinking reagents: resolution of mass degeneracy in the identification of crosslinked peptides." Bioorg. Med. Chem. Lett (2003) 13(22): 4023-6.
PubMed

Faulon JL, Sale KL, Young MM. "Exploring the conformational space of membrane protein folds matching distance constraints." Protein Science (2003) 12(8): 1750-61.
PubMed

Schilling B, Row RH, Gibson BW, Guo X, Young MM. "MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides." J Am Soc Mass Spectrom. (2003) 14(8):834-50.
PubMed

Kruppa GH, Schoeniger J, Young MM. "A top down approach to protein structural studies using chemical cross-linking and Fourier transform mass spectrometry." Rapid Commun Mass Spectrom. (2003) 17(2):155-62.
PubMed

Laboissiere MCA, Young MM, Pinho RG, Todd S, Fletterick R, Kuntz ID, Craik C. "Computer assisted mutagenesis of ecotin to engineer its secondary binding site for urokinase inhibition." J Biol Chem Apr 16 2002.
PubMed

Faulon JL, Rintoul MD, Young MM. "Constrained walks and self-avoiding walks: Implication for protein structure determination." J Phys A (2002) 35:1-19.

Bracken C, Young MM, Dunker K. "Disorder and flexibility in protein structure and function." Pac Symp Biocomput 6:64-66. 2001.

Lamb ML, Burdick KW, Toba S, Arnold JR, Skillman AG, Young MM, Zou X, Kuntz ID. "Design, docking and evaluation of multiple libraries against multiple targets." Proteins (2001) 42(3):296-318.
PubMed

Young MM, Tang N, Hempel JC, Oshiro CM, Taylor EW, Kuntz ID, Gibson BW, Dollinger G. "High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry". Proc Natl Acad Sci USA, (2000) 97(11):5802-5806.
PubMed

Young MM, Kirshenbaum K, Dill KA, Highsmith S. "Predicting Conformational Switches in Proteins". Protein Science (1999) 8(9):1752-1764.
PubMed

Young MM, Kirshenbaum K, Highsmith S. "Predicting Allosteric Switches in Myosins". Protein Science (1999) 8(9):1806-1815.
PubMed

Young MM, Skillman AG, Kuntz ID. "A Rapid Method for Exploring the Protein Structure Universe." Proteins (1999) 34:317-332.

Patents:

"Structural Determination of Intact Proteins Using Mass Spectrometry." U.S. Patent 7,368,290, issued May 6, 2008.

"Napthols useful in antiviral methods." U.S. Patent 6,140,368, filed May 4, 1998.

"Method for analyzing proteins to determine their three-dimensional shape." U.S. Patent Application, filed 2000.

©2008 Sandia Corporation | Questions and Comments | Privacy and Security | Modified: April 29, 2008