Various molecular docking software packages are available for modeling interactions between small molecules and proteins.However,there have been few reports of modeling the interactions between metal ions and metalloproteins.In this study,the AutoDock package was employed to example docking into a di-iron binding protein,bacterioferritin.Each binding site of this protein was tested for docking with iron ions.Blind docking experiments showed that all docking conformations converged into two clusters,one for internal iron binding in sites within the metalloprotein and the other for external iron binding on the protein surface.Local docking experiments showed that there were significant differences between two internal iron binding sites.Docking at one site gave a reasonable root-mean-square deviation(RMSD) distribution with relatively low binding energy.Analysis of the binding mode quality for this site revealed that more than half of the docking conformations were categorized as having good binding geometry,while no good conformations were found for the other site.Further investigations indicated that coordinating water molecules contributed to the stability of binding geometries.This study provides an empirical approach towards the study of molecular docking in metalloproteins. 相似文献
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A facile one-step approach to synthesize various phase-separated porous, raspberry-like, flower-like, core–shell and anomalous nanoparticles and nanocapsules via 1,1-diphenylethene (DPE) controlled soap-free emulsion copolymerization of styrene (S) with glycidyl methacrylate (GMA), or acrylic acid (AA) is reported. By regulating the mass ratio of S/GMA, transparent polymer solution, porous and anomalous P(S-GMA) particles could be produced. The P(S-GMA) particles turn from flower-like to raspberry-like and then to anomalous structures with smooth surface as the increase of divinylbenzene (DVB) crosslinker. Transparent polymer solution, nanocapsules and core–shell P(S-AA) particles could be obtained by altering the mole ratio of S/AA; anomalous and raspberry-like P(S-AA) particles are produced by adding DVB. The unpolymerized S resulted from the low monomer conversion in the presence of DPE aggregates to form nano-sized droplets, and migrates towards the external surfaces of the GMA-enriched P(S-GMA) particles and the internal bulk of the AA-enriched P(S-AA) particles. The nano-sized droplets function as in situ porogen, porous P(S-GMA) particles and P(S-AA) nanocapsules are produced when the porogen is removed. This novel, facile, one-step method with excellent controllability and reproducibility will inspire new strategies for creating hierarchical phase-separated polymeric particles with various structures by simply altering the species and ratio of comonomers. The drug loading and release experiments on the porous particles and nanocapsules demonstrate that the release of doxorubicin hydrochloride is very slow in weakly basic environment and quick in weakly acidic environment, which enables the porous particles and nanocapsules with promising potential in drug delivery applications.
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