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Arch Biochem Biophys. 2015 Nov 1;585:1-9. doi: 10.1016/ Epub 2015 Sep 9.

Enhanced heme accessibility in horse heart mini-myoglobin: Insights from molecular modelling and reactivity studies.

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Department of Sciences, Roma Tre University, Viale Guglielmo Marconi 446, I-00146 Roma, Italy; National Institute of Nuclear Physics, Roma Tre University Section, Via Della Vasca Navale 84, I-00146 Roma, Italy. Electronic address:
UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Science, University College Dublin, Belfield Dublin 4, Ireland.
Department of Clinical Sciences and Translational Medicine, University of Roma "Tor Vergata", Via Montpellier 1, I-00133 Roma, Italy; Interuniversity Consortium for the Research on Chemistry of Metals in Biological Systems, Via Celso Ulpiani 1, I-70125 Bari, Italy.
Biosciences and Biotechnology School, University of Camerino, Via Gentile III da Varano, I-62032 Camerino (MC), Italy.
Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Via Della Vasca Navale 79, I-00146 Roma, Italy; Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, I-80181 Napoli, Italy.


Mini-myoglobin (mini-HHMb) is a fragment of horse-heart myoglobin (HHMb) considered to be the prototype of the product encoded by the central exon of the HHMb gene. For this reason, mini-HHMb has been studied extensively showing that carbonylation and oxygenation properties of the ferrous form are similar to those of the full-length protein, while kinetics and thermodynamics of azide binding to the ferric form are significantly different from those of HHMb. To analyze the structure-function relationships in mini-HHMb and the role of conformational fluctuations in ligand accessibility, the molecular model of mini-HHMb has been built and refined by molecular dynamics simulations, and analyzed in parallel with that of full length HHMb. Moreover, imidazole binding parameters of ferric mini-HHMb and HHMb have been determined. Furthermore, structural data of ferric mini-HHMb and HHMb have been correlated with the imidazole and previously determined azide binding properties. Present results indicate that, despite the extensive trimming, the heme-α-helices E-F substructure is essentially unaltered in mini-HHMb with respect to HHMb. However, the heme-Fe atom displays an enhanced accessibility in mini-HHMb, which may affect both ligand association and dissociation kinetics.


Mini-myoglobin; Molecular modelling; Protein matrix tunnels; Reactivity properties; Structure

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