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

Protein mass spectrometry

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.

Keppel, Theodore R.; Weis, David D., Analysis of Disordered Proteins Using a Simple Apparatus for Millisecond Quench-Flow H/D Exchange, Analytical Chemistry, May 21, 2013, 85(10):5161-5168. Rathinavelan, T., Zhang, L., Picking, W.L., Weis, D.D., De Guzman, R.N., Im, W., A repulsive electrostatic mechanism for protein export through the type III secretion apparatus, Biophysical Journal, 2010, 98(3), 452-461. Keppel TR, Jacques ME, Weis DD. The use of acetone as a substitute for acetonitrile in analysis of peptides by liquid chromatography/electrospray ionization mass spectrometry. Rapid Commun. Mass Spectrom. 2010; 24: 6. Weis DD, Kaveti S, Wu Y, Engen JR. Probing protein interactions using hydrogen-deuterium exchange mass spectrometry. In Mass Spectrometry of Protein Interactions. Edited by Downard KM: John Wiley and Sons; 2007:45-62. Mitchell JL, Trible RP, Emert-Sedlak LA, Weis DD, Lerner EC, Applen JJ, Sefton BM, Smithgall TE, Engen JR. Functional characterization and conformational analysis of the Herpesvirus saimiri Tip-C484 protein. J. Mol. Biol. 2007; 366: 1282.

Weis DD, Wales TE, Engen JR, Hotchko M, Ten Eyck LF. Identification and characterization of EX1 kinetics in H/D exchange mass spectrometry by peak width analysis. J. Amer. Soc. Mass Spectrom. 2006; 17: 1498.