, Volume 70, Issue 12, pp 1655–1671 | Cite as

Molecular dynamics simulation and docking studies on novel mutants (T11V, T12P and D364S) of the nucleotide-binding domain of human heat shock 70 kDa protein

  • Asita Elengoe
  • Mohammed Abu Naser
  • Salehhuddin HamdanEmail author
Section Cellular and Molecular Biology


The aim of investigating protein interaction between Homo sapiens adenovirus and heat shock 70 kDa protein (Hsp70) is to study a potentially synergistic interaction that would enhance the anti-apoptotic mechanisms, hence increasing the virus replication rate and improve the killing efficiency of tumour cells in cancer therapy. Currently, the protein interaction between Hsp70 and E1A 32 kDa of human adenovirus C serotype 5 (Ad5) is still unknown. Mutant models (T11V, T12P and D364S) were built, simulated and their interactions with Ad5 were studied. The E1A 32 kDa of human Ad5 motif (PNLVP) showed the lowest binding energy and intermolecular energy values with the novel T11V mutant at −8.26 kcal/mol and −11.21 kcal/mol. The protein-ligand complex models revealed that the T11V mutant had the strongest and most stable interaction with the PNLVP motif among all the four protein-ligand complex structures. This knowledge would assist future in vivo investigations of this protein-ligand complex structure in cancer treatment research.

Key words

NBD of Hsp70 adenovirus serotype 5 PNLVP motif molecular dynamics simulation docking 



adenovirus C serotype 5


grand average of hydropathicity


helical lid subdomain


heat shock protein


heat shock 70 kDa protein


molecular dynamics


nucleotide-binding domain


root mean square deviation


root mean square fluctuation


solvent accessible surface area


substrate-binding domain


substrate-binding subdomain


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  1. Abavaya K., Morimoto R.I., Murphy S.P. & Myers M.P. 1992. The human heat shock protein Hsp70 interacts with HSF, the transcription factor that regulates heat shock gene expression. Genes Dev. 6: 1153–1164.CrossRefGoogle Scholar
  2. Adusumilli P.S., Carpenter S.G., Chan M.K., Eisenberg D.P., Fong Y., Hendershott K.J. & Yu Z. 2010. Hyperthermia potentiates oncolytic herpes viral killing of pancreatic cancer through a heat shock protein pathway. Surgery 148: 325–334.PubMedCrossRefGoogle Scholar
  3. Ansieau S. & Leutz A. 2002. The conserved Mynd domain of BS69 binds cellular and oncoviral proteins through a common PXLXP motif. J. Biol. Chem. 277: 4906–4910.PubMedCrossRefGoogle Scholar
  4. Aprile F.A., Dhulesia A., Stengel F., Roodveldt C., Benesch J.L.P., Tortora P., Robinson C.V., Salvatella X., Dobson C.M. & Cremades N. 2013. Hsp70 oligomerization is mediated by an interaction between the interdomain linker and the substrate-binding domain. PLoS One 8: 1–17.CrossRefGoogle Scholar
  5. Aparoy P., Kuntal B.K. & Reddanna P. 2010. EasyModeller: a graphical interface to MODELLER. BMC Res. Notes 3: 226.PubMedPubMedCentralCrossRefGoogle Scholar
  6. Benyo B., Benyo Z., Biro J.C., Fordos G., Micsik T., Sansom C. & Szlavecz A. 2003. A common periodic table of codons and amino acids. Biochem. Biophys. Res. Commun. 306: 408–415.PubMedCrossRefGoogle Scholar
  7. Berendsen H.J.C., Groenhof C., Hess B., Lindahl E., Mark A.E. & van Der Spoel D. 2005. GROMACS: fast, flexible, and free. J. Comput. Chem. 26: 1701–1718.PubMedCrossRefGoogle Scholar
  8. Bertelsena E.B., Chang L., Gestwickib J.E. & Zuiderwega E.R.P. 2009. Solution conformation of wild-type E. coli Hsp70 (DnaK) chaperone complexed with ADP and substrate. Proc. Natl. Acad. Sci. USA 106: 8471–8476.CrossRefGoogle Scholar
  9. Brandi M., Hilgenfeld R., Pal D., Sühnel J. & Weiss M.S. 2001. More hydrogen bonds for the (structural) biologist. Trends Biochem. Sci. 26: 521–523.Google Scholar
  10. Bukau B. & Horwich A.L. 1998. The Hsp70 and Hsp60 chaperone machines. Cell 92: 351–366.CrossRefGoogle Scholar
  11. Bukau B., Mayer M.P. & Vogel M. 2006. Allosteric regulation of Hsp70 chaperones involves a conserved interdomain linker. J. Biol. Chem. 281: 38705–38711.PubMedCrossRefGoogle Scholar
  12. Burgoyne N.J. & Jackson R.M. 2006. Predicting protein interaction sites: binding hot-spots in protein-protein and proteinligand interfaces. Bioinformatics 22: 1335–1342.PubMedCrossRefGoogle Scholar
  13. Cabra Ledesma V.C., Kumar D.P., Sarbeng E.B., Vorvis C. & Willis J.E. 2011. The four hydrophobic residues on the Hsp70 inter-domain linker have two distinct roles. J. Mol. Biol. 411: 1099–1113.PubMedPubMedCentralCrossRefGoogle Scholar
  14. Colovos C. & Yeates T.O. 1993. Verification of protein structures: patterns of non-bonded atomic interactions. Protein Sci. 2: 1511–1519.PubMedPubMedCentralCrossRefGoogle Scholar
  15. Costantini S., Colonna G. & Facchiano A.M. 2008. ESBRI: a web server for evaluating salt bridges in proteins. Bioinformation 3: 137–138.PubMedPubMedCentralCrossRefGoogle Scholar
  16. Craig E.A. & Stone D.E. 1990. Self-regulation of 70 kilodalton heat shock proteins in Saccharomyces cerevisiae. Mol. Cell. Biol. 10: 1622–1632.PubMedPubMedCentralCrossRefGoogle Scholar
  17. Dinier G., Montgomery D.L., Sivendran R., Stotz M. & Swain J.F. 2007. Hsp70 chaperone ligands control domain association via an allosteric mechanism mediated by the interdomain linker. Mol. Cell 26: 27–39.CrossRefGoogle Scholar
  18. Eisenberg D., Luthy R. & Bowie J.U. 1997. VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol. 277: 396–404.PubMedCrossRefGoogle Scholar
  19. Elengoe A., Hamdan S. & Naser M.A. 2014. Modeling and docking studies on novel mutants (K71L and T204V) of the AT-Pase domain of human heat shock 70 kDa protein 1. Int. J. Mol. Sci. 15: 6797–6814.PubMedPubMedCentralCrossRefGoogle Scholar
  20. Fiser A. & Sali A. 2003. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol. 374: 461–491.PubMedCrossRefGoogle Scholar
  21. Freeman B.C., Joachimiak A., Morimoto R.I., Osipiuk J. & Sriram M. 2007. Human Hsp70 molecular chaperone binds two calcium ions within the ATPase domain. Structure 5: 403–414.Google Scholar
  22. Freeman B.C. & Yamamoto K.R. 2002. Disassembly of transcriptional regulatory complexes by molecular chaperones. Science 296: 2232–2235.PubMedCrossRefGoogle Scholar
  23. Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R. & Appel R.D. 2005. Protein identification and analysis tools on the ExPASy server, pp: 571–607. In: Walker J.M. (ed.) The Proteomics Protocols Handbook. Humana Press.CrossRefGoogle Scholar
  24. George Priya Doss C. & Nagasundaram N. 2012. Investigating the structural impacts of I64T and P311S mutations in APE1-DNA complex: a molecular dynamics approach. PLoS One 7: 1–11.CrossRefGoogle Scholar
  25. Gething M.J. & Sambrook J. 1992. Protein folding in the cell. Nature 355: 33–45.PubMedCrossRefGoogle Scholar
  26. Gilis D. & Rooman M. 1997. Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence. J. Mol. Biol. 272: 276–290.PubMedCrossRefGoogle Scholar
  27. Glotzer J.B., Saltik M., Chiocca S., Michou A.L, Moseley P. & Cotton M. 2000. Activation of heat-shock response by an adenovirus is essential for virus replication. Nature 407: 207–211.PubMedPubMedCentralCrossRefGoogle Scholar
  28. Golas E.I., Czaplewski C., Scheraga H.A. & Liwo A. 2015. Common functionally important motions of the nucleotidebinding domain of Hsp70. Proteins 83: 282–299.PubMedCrossRefGoogle Scholar
  29. Golas E., Maisuradze G.G., Senet P., Oldziej S., Czaplewski C., Scheraga H.A. & Liwo A.J. 2012. Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics. J. Chem. Theory Comput. 8: 1750–1764.PubMedPubMedCentralCrossRefGoogle Scholar
  30. Imperiale M.J, Kao H.T., Feldman L.T., Nevins J.R. & Strickland S. 1984. Common control of the heat shock gene and early adenovirus genes: evidence for a cellular ElA-like activity. Mol. Cell. Biol. 4: 867–874.PubMedPubMedCentralCrossRefGoogle Scholar
  31. Hatebour C., Gennissen A., Ramos Y.F., Kerkhoven R.M., Sonntag-Buck V, Stunnenberg H.G. & Bernards R. 1995. BS69, a novel adenovirus ElA-associated protein that inhibits E1A transactivation. EMBO J. 14: 3159–3169.CrossRefGoogle Scholar
  32. Hendrickson W.A. & Liu Q. 2007. Insights into Hsp70 chaperone activity from a crystal structure of the yeast HspllO Ssel. Cell 131: 106–120.PubMedPubMedCentralCrossRefGoogle Scholar
  33. Hightower L.E. 1991. Heat shock, stress proteins, chaperones, and proteotoxicity. Cell 66: 191–197.PubMedCrossRefGoogle Scholar
  34. Hurley J.H. 1996. The sugar kinase heat shock protein 70 actin super family: Implications of conserved structure for mechanism. Annu. Rev. Biophys. Biomol. Struct. 25: 137–162.PubMedCrossRefGoogle Scholar
  35. Jackson R.M. & Laurie A.T. 2005. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 21: 1908–1916.PubMedCrossRefGoogle Scholar
  36. Johnson E.R. & McKay D.B. 1999. Mapping the role of active site residues for transducing an ATP-induced conformational change in the bovine 70-kDa heat shock cognate protein. Biochemistry 38: 10823–10830.PubMedCrossRefGoogle Scholar
  37. Kampinga H.H., Hageman J., Vos M.J., Kubota H., Tanguay R.M., Bruford E.A., Cheetham M.E., Chen B. & Hightower, L.E. 2009. Guidelines for the nomenclature of the human heat shock proteins. Cell Stress Chaperones 14: 105–111.PubMedCrossRefGoogle Scholar
  38. Kampinga H.H & Craig E.A. 2010. The Hsp70 chaperone machinery: J-proteins as drivers of functional specificity Nat. Rev. Mol. Cell Biol. 11: 579–592.CrossRefGoogle Scholar
  39. Kityk R., Kopp J., Sinning I. & Mayer M.P. 2012. Structure and dynamics of the ATP-bound open conformation of Hsp70 chaperones. Mol. Cell 48: 863–874.PubMedCrossRefGoogle Scholar
  40. Koellner G. & Steiner T. 2001. Hydrogen bonds with p-acceptors in proteins: frequencies and role in stabilising local 3-D structures. J. Mol. Biol. 305: 535–557.PubMedCrossRefGoogle Scholar
  41. Laufen T., Mayer M.P., Paal K., Rüdiger S. & Schröder H. 2000. Multistep mechanism of substrate binding determines chaperone activity of Hsp70. Nat. Struct. Biol. 7: 586–593.PubMedCrossRefGoogle Scholar
  42. Laskowski R.A., MacArthur M.W., Moss D.S. & Thornton J.M. 1993. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26: 283–291.CrossRefGoogle Scholar
  43. Masselink H. & Bernards R. 2000. The adenovirus E1A binding protein BS69 is a corepressor of transcription through recruitment of N-CoR. Oncogene 19: 1538–1546.PubMedCrossRefGoogle Scholar
  44. Mayer M.P., Brehmer D., Gassler C.S. & Bukau B. 2001. Hsp70 chaperone machines. Adv. Protein Chem. 59: 1–44.PubMedCrossRefGoogle Scholar
  45. Netzer W.J. & Hartl, F.U. 1998. Protein folding in the cytosol: chaperonin-dependent and -independent mechanisms. Trends Biochem. Sci. 23: 68–73.PubMedCrossRefGoogle Scholar
  46. Nicolai A., Senet P., Delarue P. & Ripoll D.R. 2010. Human inducible Hsp70: structures, dynamics, and interdomain communication from all-atom molecular dynamics simulations. J. Chem. Theory Comput. 206: 2501–2519.CrossRefGoogle Scholar
  47. O’Brien M.C., Flaherty K.M. & McKay D.B. 1996. Lysine 71 of the chaperone protein Hsc70 is essential for ATP hydrolysis. J. Biol. Chem. 271: 15874–15878.PubMedCrossRefGoogle Scholar
  48. Palleros D.R., Reid K.L., Shi L., Welch W.J. & Fink A.L. 1993. ATP-induced protein Hsp70 complex dissociation requires K+ but not ATP hydrolysis. Nature 365: 664–666.PubMedCrossRefGoogle Scholar
  49. Ritossa F. 1962. A new puffing pattern induced by heat shock and DNP in Drosophila. Experientia 18: 571–573.CrossRefGoogle Scholar
  50. Roy S., Maheshwari N., Chauhan R., Sen N.K. & Sharma A. 2011. Structure prediction and functional characterization of secondary metabolite proteins of Ocimum. Bioinformation 6: 315–319.PubMedPubMedCentralCrossRefGoogle Scholar
  51. Rupley J.A. & Shrake A. 1997. Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J. Mol. Biol. 79: 351–371.Google Scholar
  52. Sanner M.F. 1999. Python: a programming language for software integration and development. J. Mol. Graph. Model. 17: 57–61.PubMedGoogle Scholar
  53. Schuttelkopf A.W. & van Aalten D.M. 2004. PRODRG — a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. D Biol. Crystallogr. 60: 1355–1363.PubMedCrossRefGoogle Scholar
  54. Simon M.C., Kitchener K., Kao H.T., Hickey E., Weber L., Voellmy R., Heintz N. & Nevins J.R. 1987. Selective induction of human heat shock gene transcription by the adenovirus E1A gene products, including the 12S E1A product. Mol. Cell. Biol. 7: 2884–2890.PubMedPubMedCentralCrossRefGoogle Scholar
  55. Sousa M.C. & McKay D.B. 1998. The hydroxyl of threonine 13 of the bovine 70-kDa heat shock cognate protein is essential for transducing the ATP-induced conformational change. Biochemistry 37: 15392–15399.PubMedCrossRefGoogle Scholar
  56. Stone D.E. & Craig E.A. 1990. Self-regulation of 70 kilodalton heat shock proteins in Saccharomyces cerevisiae. Mol. Cell. Biol. 10: 1622–1632.PubMedPubMedCentralCrossRefGoogle Scholar
  57. Vasconcelos D.Y., Cai X.H. & Oglesbee M.J. 1998. Constitutive overexpression of the major inducible 70 kDa heat shock protein mediates large plaque formation by measles virus. J. Gen. Virol. 79: 2239–2247.PubMedCrossRefGoogle Scholar
  58. Wallner B. & Elofsson A. 2003. Can correct protein models be identified? Protein Sci. 12: 1073–1086.PubMedPubMedCentralCrossRefGoogle Scholar
  59. White E., Spector D. & Welch W. 1988. Differential distribution of the adenovirus E1A proteins and colocalization of E1A with the 70-kilodalton cellular heat shock protein in infected cells. J. Virol. 62: 4153–4166.PubMedPubMedCentralGoogle Scholar
  60. Wickner S., Skowyra D., Hoskins J. & Mckenney K. 1992. DnaJ, DNAK, and GrpE heat shock proteins are required in oriPl DNA replication solely at the RepA monomerization step. Proc. Natl. Acad. Sci. USA 89: 10345–10349.PubMedCrossRefPubMedCentralGoogle Scholar
  61. Wiederstein M. & Sippl M. 2007. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res. 35: W407-W410.Google Scholar
  62. Yamamoto M. & Curiel, D.T. 2010. Current issues and future directions of oncolytic adenoviruses. Mol. Ther. 18: 243–250.PubMedCrossRefPubMedCentralGoogle Scholar
  63. Zhuravleva A. & Gierasch M. 2010. Allosteric signal transmission in the nucleotide-binding domain of 70kDa heat shock protein (Hsp70) molecular chaperones. Proc. Natl. Acad. Sci. USA 108: 6987–6992.CrossRefGoogle Scholar
  64. Zuiderwerg E.R.P., Bhattacharya A., Kurochkin A.V., Yip G.N.B., Zhang Y. & Bertelsen E.B. 2009. Allostery in Hsp70 chaperones is transduced by subdomain rotations. J. Mol. Biol. 388: 475–490.CrossRefGoogle Scholar

Copyright information

© Slovak Academy of Sciences 2015

Authors and Affiliations

  • Asita Elengoe
    • 1
  • Mohammed Abu Naser
    • 1
  • Salehhuddin Hamdan
    • 1
    Email author
  1. 1.Department of Biosciences and Health Sciences, Faculty of Biosciences and Medical EngineeringUniversiti Teknologi MalaysiaSkudaiMalaysia

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