Protein3D: Enabling analysis and extraction of metal‐containing sites from the Protein Data Bank with molSimplify
Name
J Comput Chem - 2023 - Edholm - Protein3D Enabling analysis and extraction of metal‐containing sites from the Protein Data.pdf
Description
Published version
Size
1.72 MB
Format
Adobe PDF
Checksum (MD5)
dae4f8406e997025fcadcc562d276d4f
Author(s)
Edholm, Freya
Nandy, Aditya
Reinhardt, Clorice R
Kastner, David W
Kulik, Heather J
Date Issued
March 5, 2024
Journal
Journal of Computational Chemistry
Publisher
Wiley
Citation
F. Edholm, A. Nandy, C. R. Reinhardt, D. W. Kastner, H. J. Kulik, J. Comput. Chem. 2024, 45(6), 352.
Version
Final published version
Abstract
Metalloenzymes catalyze a wide range of chemical transformations, with the active site residues playing a key role in modulating chemical reactivity and selectivity. Unlike smaller synthetic catalysts, a metalloenzyme active site is embedded in a larger protein, which makes interrogation of electronic properties and geometric features with quantum mechanical calculations challenging. Here we implement the ability to fetch crystallographic structures from the Protein Data Bank and analyze the metal binding sites in the program molSimplify. We show the usefulness of the newly created protein3D class to extract the local environment around non‐heme iron enzymes containing a two histidine motif and prepare 372 structures for quantum mechanical calculations. Our implementation of protein3D serves to expand the range of systems molSimplify can be used to analyze and will enable high‐throughput study of metal‐containing active sites in proteins.
MIT Department
Massachusetts Institute of Technology. Department of Chemical Engineering
Massachusetts Institute of Technology. Department of Chemistry
Massachusetts Institute of Technology. Department of Biological Engineering
Terms of Use
Creative Commons Attribution-Noncommercial
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1002/jcc.27242
