Protein3D: Enabling analysis and extraction of metal‐containing sites from the Protein Data Bank with molSimplify

Edholm, Freya; Nandy, Aditya; Reinhardt, Clorice R.; Kastner, David W.; Kulik, Heather J.

doi:10.1002/jcc.27242

Title: Protein3D: Enabling analysis and extraction of metal‐containing sites from the Protein Data Bank with molSimplify

Journal Article · 23 October 2023 · Journal of Computational Chemistry

DOI: https://doi.org/10.1002/jcc.27242 · OSTI ID:2203481

Edholm, Freya ^[1];

^[2]; Reinhardt, Clorice R. ^[1]; Kastner, David W. ^[3];

^[2]

Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA, Department of Chemistry Massachusetts Institute of Technology Cambridge Massachusetts USA
Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA, Department of Biological Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA

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.

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Sponsoring Organization:: USDOE

OSTI ID:: 2203481

Alternate ID(s):: OSTI ID: 2281446

Journal Information:: Journal of Computational Chemistry, Journal Name: Journal of Computational Chemistry Journal Issue: 6 Vol. 45; ISSN 0192-8651

Publisher:: Wiley Blackwell (John Wiley & Sons)Copyright Statement

Country of Publication:: United States

Language:: English

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