David D. Weis

Academic Degrees

• B.A., 1993, Earlham College
• Ph.D., 1998, Indiana University, Bloomington
• Research Assistant Professor, 2004-2006, University of New Mexico, Albuquerque
  

Areas of Specialization

Protein mass spectrometry

Research Interests

Bioanalytical and biophysical chemistry, protein conformation and dynamics, protein-protein and protein-nucleic acid interactions, transcription factors, mass spectrometry, H/D exchange, cross-linking, data analysis software

The interaction between protein and ligand underlies nearly every biological process.  Our group explores how the ligand alters the conformation and dynamics of the protein.  Our primary tool for identifying these conformational and dynamic changes is mass spectrometry.

We seek a better understanding of the intermolecular interactions involved in the activation of gene transcription by proteins called transcription factors.  This is the first step in a process that ultimately leads to the expression of a protein.  Our motivation is that many disease states arise from the aberrant expression of proteins; therapeutically targeting transcription factors requires mechanistic understanding of their behavior.  Transcription factors are proteins that bind to specific sequences in the promoter regions of specific genes in response to cellular signaling.  Once they have bound to the promoter, they recruit the transcriptional machinery and associated cofactors.  Our research focuses on the mechanisms that lead to activation of the transcription factors and on how DNA binding leads to activation of the transcription process.

We use mass spectrometry combined with hydrogen/deuterium (H/D) exchange and covalent cross-linking to explore the conformation and dynamics of proteins of interest.  These techniques enable us to probe mixtures of large proteins in solution using only picomole to nanomole quantities.

In H/D exchange, the amide hydrogen atoms of proteins exchange with deuterium atoms at a rate that depends on hydrogen bonding and solvent accessibility.  Following exchange, the deuterium-labeled protein is subjected to enzymatic digestion and the masses of the peptides are determined by mass spectrometry.  By following the kinetics of deuterium uptake, details about the protein conformation and dynamics are revealed.

Covalent cross-linking is useful for determining the protein-ligand binding site.  A protein-protein or protein-nucleic acid complex is covalently cross-linked using any one of a variety of small molecule chemistries.  Enzymatic digestion followed by mass spectrometry is then used to locate the sites of interaction.

Selected publications

Weis, D. D., Engen, J. R., & Kass, I. J.  (2006).  Semi-automated analysis of hydrogen exchange mass spectra using HX-Express.  J. Am. Soc. Mass Spectrom. 17, 1700-1703.

Weis, D. D., Kjellen, P., Sefton, B. M., & Engen, J. R. (2006).  Altered dynamics in Lck SH3 upon binding to the LBD1 domain of Herpesvirus saimiri Tip.  Protein Science 15, 2411-2422.

Weis, D. D., Wales, T. E., Engen, J. R., Hotchko, M., & Ten Eyck, L. F. (2006).   Identification and characterization of EX1 kinetics in H/D exchange mass spectrometry by peak width analysis.  J. Am. Soc. Mass Spectrom. 17, 1498-1509.