Authors: Chae Kyung Jeon
Source: Deep Blue (University of Michigan) (article, 2023-01-01)
Field: Chemistry — Spectroscopy

Next-Generation Computational Methods for the Interpretation of Ion Mobility-Mass Spectrometry Data Proteins and their multi-component complexes are dynamic and perform myriad specific functions in cells. Understanding their functions is critical for drug development. Over the last three decades, mass spectrometry (MS) has emerged as a tool able to characterize complex biomolecules rapidly. Developments in native MS have extended such information to the structures of native proteins and complexes. Subsequently, ion mobility-mass spectrometry (IM-MS), in combination with collision induced unfolding (CIU), has further enhanced our understanding of native protein and protein complexes from detailed measurements of protein shapes, sizes, and stabilities, accessible within complex mixtures. While IM-MS generates a plethora of data, a range of computational approaches are typically required to extract information from these technologies. Current challenges include: 1) ambiguity associated with collision cross section (CCS) obtained from IM limiting our ability to accurately assign model structures; 2) increasing demands on IM-MS to provide access to high-throughput assays capable of tracking protein conformation. In this thesis, new computational methods are described that allow more accurate structural assignments based on IM-MS data and automation of CIU data analysis. In Chapter 2, we developed a steered molecular dynamics (MD) approach that integrates native IM-MS, CIU, and electron capture dissociation (ECD) data to develop a seamless methodology for CIU feature annotation. ECD produces product ions preferentially from disordered regions within protein structures. As CIU progresses, new ECD fragment ions are observed, highlighting those sequences linked to the CIU features observed. Ultimately, this approach is supported by a novel steered MD approach developed and described here, where we include observed fragmentation data into our simulation methodology to restrain regions within the protein that are not experimentally relevant for CIU allowing only the region identified through ECD as disordered, followed by CCS filtering. Our steered MD has enabled the complete structural assignment of a protein complex CIU fingerprint and has proven that CIU can capture subdomain-level unfolding in protein complexes. In Chapter 3, we utilized integrative modeling to investigate the gas-phase structural ensemble of immunoglobulin (Ig), in particular, IgG1. The therapeutic benefits of monoclonal antibodies (mAbs) are in many cases linked to their flexibility, however detailed rapid characterization of mAb dynamics, in a manner useful for therapeutic development efforts, remains challenging To study if gas-phase IM measurements can capture mAb ensembles that retain a memory of the range of structures occupied by the protein in solution, we utilized individual particle electron tomography (IPET) mAb models as a starting point for gas-phase MD simulations. Our study reveals that the structural diversity of native IgG1 persists in the gas-phase. In Chapter 4, we describe the development of CIUSuite 3, a next-generation software package for CIU data analysis, optimized to automate and expand the support of various instrument platforms. To accomplish this, we built and validated four new modules and added them to our previous-generation CIUSuite package: 1) On-board, automated CCS calibration supporting multiple IM analyzer types which increases CIU data analysis throughput by a factor of 50-100, 2) A feature skipping algorithm designed to improve our ability to cross-compare complex CIU datasets, 3) Automated peak detection which serves to increase the throughput of CIU data analysis by a factor of 20, and 4) a machine learning classification architecture that supports multi-dimensional CIU (e.g., CIU2) data types. Ion-mobility spectrometry ; Mass spectrometry ; Interpretation (philosophy) ; Computer science ; Ion-mobility spectrometry–mass spectrometry ; Chemistry ; Selected reaction monitoring ; Tandem mass spectrometry ; Chromatography Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Advanced Chemical Sensor Technologies