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dc.contributor.authorMera-Adasme R.
dc.contributor.authorDomínguez M.
dc.contributor.authorDenis-Alpizar O.
dc.date.accessioned2020-09-02T22:22:57Z
dc.date.available2020-09-02T22:22:57Z
dc.date.issued2019
dc.identifier10.1007/s00894-019-4066-8
dc.identifier.citation25, 6, -
dc.identifier.issn16102940
dc.identifier.urihttps://hdl.handle.net/20.500.12728/5316
dc.descriptionThe protein superoxide dismutase 1 (SOD1) is a copper and zinc-binding protein that has been implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS). The Zn(II) binding to SOD1 is critical for the stability of the protein, and has been by itself implicated in ALS pathogenesis. Hence, the quantum mechanical (QM) study of the Zn(II)-site of SOD1 is relevant for understanding ALS. The hybrid QM-molecular mechanics (QM/MM) approach commonly employed for the QM study of proteins is highly dependent on the size of the sub-system treated quantum-mechanically. The size of the QM system also determines the computational feasibility of a given method. In the present work, we compare optimized geometries for the metal site and Zn(II) dissociation energies obtained with a QM/MM methodology employing different sizes for the QM sub-system. We find that geometries converge rapidly to RMSDs of around 0.3 Å, and fails to converge further, while a QM system of 480 atoms was required for converging the Zn(II) interaction energy of SOD1 to within 5 kcal*mol−1, and a 611-atoms QM system for a 1 kcal*mol−1 convergence with respect to our reference, 1280 QM-atoms system. [Figure not available: see fulltext.]. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.
dc.language.isoen
dc.publisherSpringer Verlag
dc.subjectQM-system size
dc.subjectQMMM
dc.subjectSOD1
dc.subjectcopper zinc superoxide dismutase
dc.subjectzinc
dc.subjectcopper
dc.subjectprotein binding
dc.subjectsuperoxide dismutase
dc.subjectArticle
dc.subjectdissociation
dc.subjectenergy
dc.subjectgeometry
dc.subjectpriority journal
dc.subjectquantum mechanics
dc.subjectchemistry
dc.subjectconformation
dc.subjectmolecular dynamics
dc.subjectquantum theory
dc.subjectCopper
dc.subjectMolecular Conformation
dc.subjectMolecular Dynamics Simulation
dc.subjectProtein Binding
dc.subjectQuantum Theory
dc.subjectSuperoxide Dismutase
dc.subjectZinc
dc.titleA benchmark for the size of the QM system required for accurate hybrid QM/MM calculations on the metal site of the protein copper, zinc superoxide dismutase
dc.typeArticle


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