Quantitative Determination of High-Order Protein Structure with Native Ion Mobility-Mass Spectrometry and Computational Chemistry - PROJECT SUMMARY/ABSTRACT Characterizing the structures and interactions of biomolecules and their complexes is of fundamental importance in human physiology, disease, and therapeutics. Many of the advances of the last century in these areas are attributed to improvements in bioanalytical techniques and controlling the processes that underlie them. For example, x-ray crystallography, nuclear magnetic resonance spectroscopy, and cryoelectron microscopy have achieved atomic-level resolution of the structure of many thousands of proteins and protein complexes, and these methods are often complemented by Molecular Dynamics studies to further understand biomolecule structure and reactivity. However, these methods can be challenging to use for very small or highly heterogeneous samples or samples that require a membrane environment. Native Ion Mobility-Mass Spectrometry (IM-MS) is a complementary technique that ionizes and transfers intact biomolecules and complexes directly from buffered, aqueous solution into the gas-phase for mass and shape/size analysis, and modern sample preparation and data analysis methods make it highly suitable for membrane proteins in lipid environments as well as heterogeneous and polydisperse samples. In commonly available IM-MS instrumentation, Collision Induced Dissociation and Unfolding are used to activate native biomolecular ions by colliding them repeatedly with neutral buffer gas until they dissociate or unfold, and recently-introduced Surface Induced Dissociation and Unfolding activate ions via a single, controlled collision with a hard surface inside the mass spectrometer. These native IM-MS methods can be extremely useful for profiling the composition, size, and shape of biomolecules and their complexes with exquisite chemical specificity, sensitivity, and speed. However, two major hurdles to the use of these methods for accurate, quantitative interpretation of biomolecule domain, surface, and interface structure are the lack of a flexible, robust method for computing and interpreting the energy required to induce the observed structural changes and a dearth of reliable benchmark values. Here, we tackle these challenges with a combined computational and experimental approach aimed at producing a “universal,” validated ion activation model that can be readily used for across many commonly used native MS and IM-MS platforms and by producing a benchmark library for prototypical local and large-scale interactions that govern protein unfolding, dissociation, and surface labeling. Expected outcomes include open-source, publicly available software for researchers world-wide to model unfolding/dissociation energetics for their own samples, heuristics for the design of effective gas-phase surface-labeling reagents, and a quantitative understanding of cataract-associated human eye lens protein heterooligomerization as a case study. The long- term goal of the project is to facilitate the acquisition and interpretation of decisive structural and dynamical information for a wide range of biomolecules and complexes relevant to human health.
