Accurate methods to probe the structure, conformation and dynamics of biopolymers, as well as their specific noncovalent interactions, are tremendously important for understanding biochemistry at the molecular level. Mass spectrometry has the advantages of high speed, ultrahigh sensitivity (attomole detection), and high specificity (mass accuracy +/- a few Da at >100,000 Da). Tandem mass spectrometry is used for identifying and locating postranslational modifications and binding sites, identifying proteins present in complex mixtures, etc. It is one aim of this proposal to improve the efficiency and extent of backbone fragmentation using electron capture dissociation, and develop this method to obtain information about biopolymer conformation. H/D exchange measurements, both in the gas and solution phase, will be combined with collisional cross section measurements, electron capture dissociation, and molecular dynamics simulations to obtain detailed information about conformation both in solution and in the gas phase. By comparing results in these two different environments, information about the role of solvent on biopolymer conformation can be directly obtained. Another aim is to understand how the structure of an ion changes during the transition from bulk solution to the isolated environment of the gas phase during the electrospray ionization process. It is hoped that by understanding this process, we can relate the structural information of biopolymers and noncovalent complexes determined from gas-phase experiments back to the structures of the ions in bulk solution. Another aim is to understand the role of specific noncovalent interactions and the influence of solvent on these interactions. Noncovalent interactions are important in enzyme-substrate reactivity, supermolecular complex formation and in many diseases, such as prion based diseases including spongiform encephalopathies and CreutzfeldJacob disease.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM064712-03
Application #
6701310
Study Section
Special Emphasis Panel (ZRG1-BECM (01))
Program Officer
Edmonds, Charles G
Project Start
2002-02-01
Project End
2006-01-31
Budget Start
2004-02-01
Budget End
2005-01-31
Support Year
3
Fiscal Year
2004
Total Cost
$217,474
Indirect Cost
Name
University of California Berkeley
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
124726725
City
Berkeley
State
CA
Country
United States
Zip Code
94704
Leib, Ryan D; Williams, Evan R (2011) Simultaneous quantitation of amino acid mixtures using clustering agents. J Am Soc Mass Spectrom 22:624-32
Kintzer, Alexander F; Sterling, Harry J; Tang, Iok I et al. (2010) Role of the protective antigen octamer in the molecular mechanism of anthrax lethal toxin stabilization in plasma. J Mol Biol 399:741-58
Flick, Tawnya G; Leib, Ryan D; Williams, Evan R (2010) Direct standard-free quantitation of Tamiflu and other pharmaceutical tablets using clustering agents with electrospray ionization mass spectrometry. Anal Chem 82:1179-82
Feld, Geoffrey K; Thoren, Katie L; Kintzer, Alexander F et al. (2010) Structural basis for the unfolding of anthrax lethal factor by protective antigen oligomers. Nat Struct Mol Biol 17:1383-90
Sterling, Harry J; Daly, Michael P; Feld, Geoffrey K et al. (2010) Effects of supercharging reagents on noncovalent complex structure in electrospray ionization from aqueous solutions. J Am Soc Mass Spectrom 21:1762-74
Kintzer, Alexander F; Sterling, Harry J; Tang, Iok I et al. (2010) Anthrax toxin receptor drives protective antigen oligomerization and stabilizes the heptameric and octameric oligomer by a similar mechanism. PLoS One 5:e13888
Sterling, Harry J; Batchelor, Joseph D; Wemmer, David E et al. (2010) Effects of buffer loading for electrospray ionization mass spectrometry of a noncovalent protein complex that requires high concentrations of essential salts. J Am Soc Mass Spectrom 21:1045-9
Sterling, Harry J; Williams, Evan R (2010) Real-time hydrogen/deuterium exchange kinetics via supercharged electrospray ionization tandem mass spectrometry. Anal Chem 82:9050-7
Batchelor, Joseph D; Sterling, Harry J; Hong, Eunmi et al. (2009) Receiver domains control the active-state stoichiometry of Aquifex aeolicus sigma54 activator NtrC4, as revealed by electrospray ionization mass spectrometry. J Mol Biol 393:634-43
Donald, William A; Leib, Ryan D; O'Brien, Jeremy T et al. (2009) Directly relating gas-phase cluster measurements to solution-phase hydrolysis, the absolute standard hydrogen electrode potential, and the absolute proton solvation energy. Chemistry 15:5926-34

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