Structure and Function: Insights into Bioinorganic Systems from Molecular Mechanics Calculations

Marques, Helder M.; Egan, Timothy J.; Villiers, Katherine A. de

doi:10.1007/978-90-481-2888-4_4

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Figure 1: Ghk Structure1

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2020

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“…Accurate quantum mechanical methods are computationally expensive, even for those methods that are relatively efficient such as density functional theory (DFT). Molecular mechanics (MM) is applicable for many problems in biochemistry for exploring conformational space [19][20][21][22][23][24] , but is not well suited for treatment of d-orbital effects in transition metals [25][26][27][28] .…”

Section: Figure 1: Ghk Structurementioning

confidence: 99%

Theoretical study of copper binding to GHK peptide

Alshammari

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2020

Computational Biology and Chemistry

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We report ligand field molecular mechanics, density functional theory and semi-empirical studies on the binding of Cu(II) to GlyHisLys (GHK) peptide. Following exhaustive conformational searching using molecular mechanics, we show that relative energy and geometry of conformations are in good agreement between GFN2-xTB semi-empirical and B3LYP-D DFT levels. Conventional molecular dynamics simulation of Cu-GHK shows the stability of the copper-peptide binding over 100ps trajectory. Four equatorial bonds in 3N1O coordination remain stable throughout simulation, while a fifth in apical position from Cterminal carboxylate is more fluxional. We also show that the automated conformer and rotamer search algorithm CREST is able to correctly predict the metal binding position from a starting point consisting of separated peptide, copper and water.

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