Next Article in Journal
Nanoformulation and Evaluation of Oral Berberine-Loaded Liposomes
Next Article in Special Issue
Enzyme Models—From Catalysis to Prodrugs
Previous Article in Journal
Antiviral Properties of the NSAID Drug Naproxen Targeting the Nucleoprotein of SARS-CoV-2 Coronavirus
Previous Article in Special Issue
Effects of Polydispersity on the Phase Behavior of Additive Hard Spheres in Solution
Review

Computational Approaches: An Underutilized Tool in the Quest to Elucidate Radical SAM Dynamics

Department of Chemistry, Emory University, 1515 Dickey Dr, Atlanta, GA 30322, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Rafik Karaman
Molecules 2021, 26(9), 2590; https://doi.org/10.3390/molecules26092590
Received: 30 March 2021 / Revised: 22 April 2021 / Accepted: 26 April 2021 / Published: 29 April 2021
Enzymes are biological catalysts whose dynamics enable their reactivity. Visualizing conformational changes, in particular, is technically challenging, and little is known about these crucial atomic motions. This is especially problematic for understanding the functional diversity associated with the radical S-adenosyl-L-methionine (SAM) superfamily whose members share a common radical mechanism but ultimately catalyze a broad range of challenging reactions. Computational chemistry approaches provide a readily accessible alternative to exploring the time-resolved behavior of these enzymes that is not limited by experimental logistics. Here, we review the application of molecular docking, molecular dynamics, and density functional theory, as well as hybrid quantum mechanics/molecular mechanics methods to the study of these enzymes, with a focus on understanding the mechanistic dynamics associated with turnover. View Full-Text
Keywords: radical SAM enzymes; dynamics; computational; DFT; MD; docking; QM/MM radical SAM enzymes; dynamics; computational; DFT; MD; docking; QM/MM
Show Figures

Figure 1

MDPI and ACS Style

Blue, T.C.; Davis, K.M. Computational Approaches: An Underutilized Tool in the Quest to Elucidate Radical SAM Dynamics. Molecules 2021, 26, 2590. https://doi.org/10.3390/molecules26092590

AMA Style

Blue TC, Davis KM. Computational Approaches: An Underutilized Tool in the Quest to Elucidate Radical SAM Dynamics. Molecules. 2021; 26(9):2590. https://doi.org/10.3390/molecules26092590

Chicago/Turabian Style

Blue, Tamra C., and Katherine M. Davis. 2021. "Computational Approaches: An Underutilized Tool in the Quest to Elucidate Radical SAM Dynamics" Molecules 26, no. 9: 2590. https://doi.org/10.3390/molecules26092590

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop