Analysis of the Structure of SaHPF Staphylococcus aureus Protein

R.Kh. Ayupov*, N.I. Akberova**

Kazan Federal University, Kazan, 420008 Russia

E-mail: *aurusta@mail.ru, **nakberova@mail.ru

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Abstract

SaHPF (Staphylococcus aureus hibernation promoting factor) is the ribosome inactivating protein of the bacterium Staphylococcus aureus. The structure of this protein has been predicted using bioinformatics methods and represented by two domains and a hinge between them. The comparison of the primary sequence of SaHPF protein with the sequences of known structures of proteins determined by NMR and X-ray has revealed homology only for the first domain. At the same time, regions of homology to SaHPF protein entire sequence have been detected when it was compared to the Uniprot sequences. The search for homology for each individual domain has revealed 10 proteins homologous to the first domain and 3 homologs for the second domain; none of these homologous proteins have a hinge in their structure. The structural comparison of these homologues proteins with both domains of SaHPF has shown that the SaHPF first and second domain structures are accurately superimposed in the similar structural regions of homologous proteins. At least five of the identified proteins homologous to SaHPF are structurally related to the ribosome, which is an indirect indication of the quality of the SaHPF domain structure prediction and a sufficient background for the simulation of its behavior by equilibrium molecular dynamics. The analysis of SaHPF protein MD trajectories using principle components and normal modes methods has identified the characteristic collective motions of residues in the hinges regions between the β-sheet in both domains as well as in the hinge between the domains, which can be functionally important for SaHPF protein interaction with the ribosome.

Keywords: SaHPF, protein structure prediction, sequence homology, homology of structures,   molecular dynamics

Acknowledgments. This study was funded by the subsidy allocated to Kazan Federal University as part of the state program for increasing its competitiveness among the world's leading centers of science and education.

The work was supported by the Russian Foundation for Basic Research (project no. 16-34-60001_mol_a_dk).

Figure Captions

Fig. 1. Sequence alignment of SaHPF protein domains with sequences of 1IMU and 3LYV proteins: I – for the first domain, II – for the second domain.

Fig. 2. Superposition of SaHPF protein on homologous protein structures: I – for the first domain, II – the second domain. Different colors identify different proteins.

Fig. 3. RMSD (a) and RMSF (b) plots of SaHPF protein; the most moving sections of the polypeptide chain are highlighted.

Fig. 4. Proteins structure visualization: left – the predicted model of SaHPF protein, indicating the distance between the domains; right – the model of HPF and RMF protein in the ribosome structure [3], with an indication of the distance between them.

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For citation: Ayupov R.Kh., Akberova N.I. Analysis of the structure of SaHPF Staphylococcus aureus protein. Uchenye Zapiski Kazanskogo Universiteta. Seriya Estestvennye Nauki, 2016, vol. 158, no. 3, pp. 327–337. (In Russian)

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