Research Overview

Inspiration

At the scale of a few nanometers, chemical interactions (from covalent bonds to hydrogen bonds and van der Waals interactions) collectively give rise to material phenomena, such as viscosity, elasticity, and phase separation, in many condensed phase systems.  Biological cells, for instance, likely exploit delicate balances of these interactions to regulate signalling, endocytosis, and many other processes, although precise characterization of the nanoscale structures that are involved can be extremely challenging.  Mass spectrometry and allied techniques have proved invaluable for studying the structure and organization of many kinds of matter, from simple molecules to megadalton-sized cytosolic and membrane protein assemblies.  Using methods capable of transferring and analyzing intact macromolecular assemblies in the gas phase while retaining much of their condensed-phase tertiary and quaternary structure, our lab learns complementary information about their shape and folding state in these same experiments using ion mobility.  Combined with computational modeling and results from other bioanalytical experiments, data obtained with these methods can be used to construct detailed models of these assemblies.  Studying the relationship between these structures and the condensed-phase environment in which they arise enables us to paint a vivid picture of how biology bridges the gap from chemical to material properties, with a view toward biochemical and pharmaceutical applications.

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Technology and Innovation

The Prell Group has a Synapt G2-Smass spectrometer equipped with an M-class UPLC, both from Waters Corporation.  Both “static” nanoelectrospray and UPLC-interfaced ion sources are used.  The instrument can achieve a resolving power > 50,000 and is fitted with a quadrupole capable of isolating ions with m/z up to 32,000.  This instrument can perform ion mobility measurements and ion separations in addition to electron transfer dissociation, making it a highly versatile tool for studying biomolecular complexes, which often comprise many different sizes and types of biomolecules. Surface-induced dissociation (SID) capabilities are also available to access fragmentation pathways not available with collision-induced dissociation (CID).  We also use a Q-TOF Premier mass spectrometer from Waters Corporation, owned by the CAMCOR Facilities at the University of Oregon and maintained by our group.  This instrument is equipped with electrospray and nanoelectrospray sources.  Resolving power of > 15,000 can be achieved, and ions with m/z up to 8,000 can be mass-selected and fragmented before mass analysis.

Beyond and in conjunction with using commercially available technology, our group also approaches challenging problems in studying nanoscale assemblies by designing, building, and using our own instrumentation.  Updates will be added here as these projects develop.

Computational Modeling

Computational models can be extremely useful to predicting and interpreting experimental results, from the appearance of a complicated mass spectrum to the bonds that hold molecules together.  Projects in our group incorporate statistical mechanics, molecular dynamics, and quantum mechanical simulations as well as ion trajectory modeling. We have written a program (Collidoscope) to calculate collisional cross sections of very large (up to a few MDa) molecules and assemblies that implements a classical “trajectory method” based on non-equilibrium statistical mechanics. We have also developed software to facilitate analysis of congested electrospray mass spectra for ions with repeated subunits (IFAMS).

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