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. 2018 Apr 3;8(1):5487.
doi: 10.1038/s41598-018-22905-6.

Glucose-regulated protein 78 substrate-binding domain alters its conformation upon EGCG inhibitor binding to nucleotide-binding domain: Molecular dynamics studies

K R D Sagara N S Gurusinghe  1 , Aanchal Mishra  2   3 , Seema Mishra  4
Affiliations

Glucose-regulated protein 78 substrate-binding domain alters its conformation upon EGCG inhibitor binding to nucleotide-binding domain: Molecular dynamics studies

K R D Sagara N S Gurusinghe et al. Sci Rep. .

Abstract

Glucose-regulated protein 78 (GRP78), is overexpressed in glioblastoma, other tumors and during viral and bacterial infections, and so, it is postulated to be a key drug target. EGCG, an ATP-competitive natural inhibitor, inhibits GRP78 effect in glioblastoma. Structural basis of its action on GRP78 nucleotide-binding domain and selectivity has been investigated. We were interested in exploring the large-scale conformational movements travelling to substrate-binding domain via linker region. Conformational effects of EGCG inhibitor as well as ATP on full length GRP78 protein were studied using powerful MD simulations. Binding of EGCG decreases mobility of residues in SBDα lid region as compared to ATP-bound state and similar to apo state. The decreased mobility may prevent its opening and closing over SBDβ. This hindrance to SBDα subdomain movement, in turn, may reduce the binding of substrate peptide to SBDβ. EGCG binding folds the protein stably as opposed to ATP binding. Several results from EGCG binding simulations are similar to that of the apo state. Key insights from these results reveal that after EGCG binding upon competitive inhibition with ATP, GRP78 conformation may revert to that of inactive, apo state. Further, SBD may adopt a semi-open conformation unable to facilitate association of substrates.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
EGCG is shown docked into NBD (ATPase) domain of full length GRP78 using AutoDock Vina. The interacting residues are labelled and shown as light purple sticks while EGCG is shown in yellow ball and stick representation. Interactions are highlighted as follows: hydrogen bonds (green dashed lines), electrostatic (orange dashed lines) and hydrophobic (pink dashed lines) interactions.
Figure 2
Figure 2
Superimposed crystal structures of NBD from two different PDB files, ID: 3LDL (in purple color) and 5E84 (in green colour).
Figure 3
Figure 3
Root mean-square deviation (RMSD) vs. MD simulation time plot of the Cα backbone atoms of apo GRP78 protein (black), ATP-bound system (red) and EGCG-bound system (green).
Figure 4
Figure 4
Root mean-square fluctuation (RMSF) plot for apo GRP78 protein (black), ATP-bound system (red) and EGCG-bound system (green).
Figure 5
Figure 5
Radius of gyration (Rg) vs. MD simulation time plot for apo GRP78 protein (black), ATP-bound system (red) and EGCG-bound system (green).
Figure 6
Figure 6
Number of hydrogen bonds vs. MD simulation time for ATP-bound system (red) and EGCG-bound system (green).
Figure 7
Figure 7
Graph representing Calpha-Calpha distances between Lys587 residue and Ala486 residues at each point of time. Apo state plot is shown in blue, ATP-bound state in orange and EGCG-bound state in grey.
Figure 8
Figure 8
Comparison of differences in conformations measured using distances at 1st ns and 28th ns for ATP-bound and 1st and 31st ns for EGCG-bound system. Initial conformation is depicted in red and maximum deviation from the initial conformation is depicted in green color in all the three instances. (a) Deviation of ATP-bound protein. (b) Deviation of EGCG-bound protein. (c) Deviation of apo state of protein.
Figure 9
Figure 9
Graph representing Calpha-Calpha-Calpha atom angles between Lys587 residue, Arg528 and Ala486 residues at each point of time. Apo state plot is shown in blue, ATP-bound state in orange and EGCG-bound state in grey.
Figure 10
Figure 10
Comparison of differences in conformations measured using angles at 1st ns and 28th ns for ATP-bound and 1st and 31st ns for EGCG-bound system. Initial conformation is depicted in red and maximum deviation from the initial conformation is depicted in green color in both instances. (a) Deviation of ATP-bound protein. (b) Deviation of EGCG-bound protein.
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References

    1. Bleeker FE, Molenaar RJ, Leenstra S. Recent advances in the molecular understanding of glioblastoma. J. Neuro-Oncology. 2012;108(1):11–27. doi: 10.1007/s11060-011-0793-0. - DOI - PMC - PubMed
    1. Goodenberger ML, et al. Genetics of adult glioma. Cancer Genet. 2012;205(12):613–621. doi: 10.1016/j.cancergen.2012.10.009. - DOI - PubMed
    1. Young RM, Jamshidi A, Davis G, Sherman JH. Current trends in the surgical management and treatment of adult glioblastoma. Annals of Translational Medicine. 2015;3(9):121. - PMC - PubMed
    1. Ellor, S. V., Pagano-Young, T. A. & Averopoulos, N. G. Glioblastoma: Background, Standard Treatment Paradigms, and Supportive Care Considerations. J. Law, Medicine and Ethics 171–182 (2014). - PubMed
    1. Ostrum QT, et al. The epidemiology of glioma in adults: a “A state of the science” review. Neuro Oncol. 2014;16(7):896–913. doi: 10.1093/neuonc/nou087. - DOI - PMC - PubMed

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