Bioinformatic tools for protein structure prediction and for molecular docking applied to enzyme active site analysis

Authors: FANELLI, AMANDA - Oak Ridge Institute For Science And Education (ORISE); Sullivan, Michael

Submitted to: Methods in Enzymology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/28/2022
Publication Date: 11/20/2022
Citation: Fanelli, A., Sullivan, M.L. 2022. Bioinformatic tools for protein structure prediction and for molecular docking applied to enzyme active site analysis. In: Jez, Joseph, editor. Methods in Enzymology. Volume 683. Cambridge, MA: Academic Press. p.41-79.
DOI: https://doi.org/10.1016/bs.mie.2022.10.004

Interpretive Summary: Elucidating the structure of an enzyme and how substrates bind to the active site is an important step for understanding its reaction mechanism and function. Nevertheless, the methods available to obtain three-dimensional structures of proteins, such as x-ray crystallography and NMR, can be expensive and time-consuming. Considering this, an alternative is using bioinformatics tools to predict the tertiary structure of a protein from its primary sequence, followed by molecular docking of one or more substrates into the enzyme structure model. In the past few years, significant advances have been made in these computational tools, and they can give useful information about the active site and enzyme-substrate interactions before the structure can be resolved using physical methods. Here we describe methods and work flows for protein structure prediction and molecular docking that can be performed on a personal computer using only readily available open-source tools. This information will be useful to researchers seeking to relate enzyme function to enzyme structure, especially those without access to resources for determining the three-dimensional structure by physical means.

Technical Abstract: Elucidating the structure of an enzyme and how substrates bind to the active site is an important step for understanding its reaction mechanism and function. Nevertheless, the methods available to obtain three-dimensional structures of proteins, such as x-ray crystallography and NMR, can be expensive and time-consuming. Considering this, an alternative is using bioinformatics tools to predict the tertiary structure of a protein from its primary sequence, followed by molecular docking of one or more substrates into the enzyme structure model. In the past few years, significant advances have been made in these computational tools, and they can give useful information about the active site and enzyme-substrate interactions before the structure can be resolved using physical methods. Here, using bean hydroxycinnamoyl-coenzyme A:tetrahydroxyhaxanedioic acid hydroxycinnamoyl transerferase (HHHT) as an example, we describe methods and work flows for protein structure prediction and molecular docking that can be performed on a personal computer using only open-source tools.