RT Journal Article
T1 Multiscale Workflow for Modeling Ligand Complexes of Zinc Metalloproteins
A1 Yang, Zongfan
A1 Twidale, Rebecca
A1 Gervasoni, Silvia
A1 Suardíaz Delrío, Reynier
A1 Colenso, Charlotte
A1 Lang, Eric
A1 Spencer, James
A1 Mulholland, Adrian
AB Zinc metalloproteins are ubiquitous, with protein zinc centers of structural and functional importance, involved in interactions with ligands and substrates and often of pharmacological interest. Biomolecular simulations are increasingly prominent in investigations of protein structure, dynamics, ligand interactions, and catalysis, but zinc poses a particular challenge, in part because of its versatile, flexible coordination. A computational workflow generating reliable models of ligand complexes of biological zinc centers would find broad application. Here, we evaluate the ability of alternative treatments, using (nonbonded) molecular mechanics (MM) and quantum mechanics/molecular mechanics (QM/MM) at semiempirical (DFTB3) and density functional theory (DFT) levels of theory, to describe the zinc centers of ligand complexes of six metalloenzyme systems differing in coordination geometries, zinc stoichiometries (mono- and dinuclear), and the nature of interacting groups (specifically the presence of zinc–sulfur interactions). MM molecular dynamics (MD) simulations can overfavor octahedral geometries, introducing additional water molecules to the zinc coordination shell, but this can be rectified by subsequent semiempirical (DFTB3) QM/MM MD simulations. B3LYP/MM geometry optimization further improved the accuracy of the description of coordination distances, with the overall effectiveness of the approach depending upon factors, including the presence of zinc–sulfur interactions that are less well described by semiempirical methods. We describe a workflow comprising QM/MM MD using DFTB3 followed by QM/MM geometry optimization using DFT (e.g., B3LYP) that well describes our set of zinc metalloenzyme complexes and is likely to be suitable for creating accurate models of zinc protein complexes when structural information is more limited.
PB American Chemical Society
SN 1549-9596
YR 2021
FD 2021
LK https://hdl.handle.net/20.500.14352/92416
UL https://hdl.handle.net/20.500.14352/92416
LA eng
NO Yang, Zongfan, et al. «Multiscale Workflow for Modeling Ligand Complexes of Zinc Metalloproteins». Journal of Chemical Information and Modeling, vol. 61, n.o 11, noviembre de 2021, pp. 5658-72. https://doi.org/10.1021/acs.jcim.1c01109.
NO Engineering and Physical Sciences Research Council (Reino Unido)
NO Biotechnology and BiologicalSciences Research Council (Reino Unido)
NO Ministerio de Ciencia e Innovación (España)
NO  National Institutes of Health
NO China Scholarship Council
NO Royal Society of Chemistry
DS Docta Complutense
RD 6 abr 2025