Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Area of Science:

• Biochemistry and Molecular Biology
• Structural Biology
• Biophysics

Background:

• Proteins are crucial macromolecules involved in fundamental cellular processes like DNA repair.
• Understanding protein complex dynamics is essential for deciphering cellular functions.
• Integrative structural mass spectrometry (MS) methods provide insights into protein assembly and interactions.

Purpose of the Study:

• To describe a protocol for integrating diverse MS data with molecular dynamics simulations.
• To investigate the structural and dynamical properties of a helicase-nuclease DNA repair protein complex.
• To provide a framework for studying ligand binding in protein complexes.

Main Methods:

• Native MS
• Ion mobility-mass spectrometry (IM-MS)
• Molecular dynamics simulations
• Integration of diverse MS data

Main Results:

• Characterization of large DNA binding proteins and membrane proteins using integrative structural MS.
• Detailed insights into a helicase-nuclease DNA repair protein complex structure and dynamics.
• Demonstration of a framework for studying protein complex assembly, connectivity, and ligand binding.

Conclusions:

• Integrative structural MS combined with molecular dynamics offers a powerful approach for studying complex biological systems.
• This methodology enables detailed investigations of protein complexes involved in critical cellular processes.
• The described framework facilitates the understanding of ligand interactions within protein complexes.