Usage of MD protein modeling simulations to quantify results from the novel method of absolute quantitative protein footprinting mass spectrometry
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Date
2024-03
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Abstract
There are currently a couple ways to elucidate 3D protein structures, the 2 current gold standards being nuclear magnetic resonance (NMR) and X-ray crystallography, alongside a new emerging method of cryogenic electron microscopy (Cryo-EM). However, there are many issues associated with these methods that include high overhead, poor suitability to specific groups of proteins, and various other issues.
Absolute quantitative protein footprinting mass spectrometry (aqPFMS) is a method recently developed in PI Dr. Hao Chen laboratory at NJIT, taking advantage of electrochemically active residues, surface area exposure of these residues to external solvents, and subsequent ability to covalently bind to certain tags. Our usage of MD simulations is to provide a theoretical comparison to the experimental results for verification. PDB files of Calmodulin bound and unbound from the calcium ion are acquired from a protein database, solvated in a water box, and run through NAMD for 500 ns using computers provided by the Ohio Supercomputer Center. Root-mean-square fluctuations of individual residues (RMSF), and Solvent accessible surface areas (SASA) of lysines are calculated for comparison to the results from the aqPFMS experiments. Once verified, future analysis with this novel technique may be conducted on an alternative configuration of Calmodulin, the Calmodulin-Melitten complex, the SARS-CoV-2 spike protein, and various other proteins.
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Innovations in Medicine (The Ohio State University Denman Undergraduate Research Forum)
Keywords
Molecular Dynamic Simulations, Protein Footprinting, Protein Imaging, Mass Spectrometry