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
Abstract
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.
References
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.Suche in Google Scholar
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: 325-334.10.1016/j.surg.2010.05.005Suche in Google Scholar
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: 4906-4910.10.1074/jbc.M110078200Suche in Google Scholar
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: 1-17.10.1371/journal.pone.0067961Suche in Google Scholar
Aparoy P., Kuntal B.K. & Reddanna P. 2010. EasyModeller: a graphical interface to MODELLER. BMC Res. Notes 3: 226.10.1186/1756-0500-3-226Suche in Google Scholar
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: 408-415.10.1016/S0006-291X(03)00974-4Suche in Google Scholar
Berendsen H.J.C., Groenhof G., Hess B., Lindahl E., Mark A.E. & van Der Spoel D. 2005. GROMACS: fast, flexible, and free. J. Comput. Chem. 26: 1701-1718.Suche in Google Scholar
Bertelsena E.B., Chang L., Gestwickib J.E. & Zuiderwega E.R.P. 2009. Solution conformation of wild-typeE. coli Hsp70 (DnaK) chaperone complexed with ADP and substrate. Proc. Natl. Acad. Sci. USA 106: 8471-8476.10.1073/pnas.0903503106Suche in Google Scholar
Brandl M., Hilgenfeld R., Pal D., S¨uhnel J. & Weiss M.S. 2001. More hydrogen bonds for the (structural) biologist. Trends Biochem. Sci. 26: 521-523.10.1016/S0968-0004(01)01935-1Suche in Google Scholar
Bukau B. & Horwich A.L. 1998. The Hsp70 and Hsp60 chaperone machines. Cell 92: 351-366.10.1016/S0092-8674(00)80928-9Suche in Google Scholar
Bukau B., Mayer M.P. & Vogel M. 2006. Allosteric regulation of Hsp70 chaperones involves a conserved interdomain linker. J. Biol. Chem. 281: 38705-38711.10.1074/jbc.M609020200Suche in Google Scholar PubMed
Burgoyne N.J. & Jackson R.M. 2006. Predicting protein interaction sites: binding hot-spots in protein-protein and proteinligand interfaces. Bioinformatics 22: 1335-1342.10.1093/bioinformatics/btl079Suche in Google Scholar PubMed
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: 1099-1113.10.1016/j.jmb.2011.07.001Suche in Google Scholar
Colovos C. & Yeates T.O. 1993. Verification of protein structures: patterns of non-bonded atomic interactions. Protein Sci. 2: 1511-1519.10.1002/pro.5560020916Suche in Google Scholar
Costantini S., Colonna G. & Facchiano A.M. 2008. ESBRI: a web server for evaluating salt bridges in proteins. Bioinformation 3: 137-138.10.6026/97320630003137Suche in Google Scholar
Craig E.A. & Stone D.E. 1990. Self-regulation of 70 kilodalton heat shock proteins in Saccharomyces cerevisiae. Mol. Cell. Biol. 10: 1622-1632.10.1128/MCB.10.4.1622Suche in Google Scholar
Dinler 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: 27-39.10.1016/j.molcel.2007.02.020Suche in Google Scholar
Eisenberg D., Luthy R. & Bowie J.U. 1997. VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol. 277: 396-404.10.1016/S0076-6879(97)77022-8Suche in Google Scholar
Elengoe A., Hamdan S. & Naser M.A. 2014. Modeling and docking studies on novel mutants (K71L and T204V) of the ATPase domain of human heat shock 70 kDa protein 1. Int. J. Mol. Sci. 15: 6797-6814.10.3390/ijms15046797Suche in Google Scholar
Fiser A. & Sali A. 2003. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol. 374: 461-491.10.1016/S0076-6879(03)74020-8Suche in Google Scholar
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: 403-414.10.1016/S0969-2126(97)00197-4Suche in Google Scholar
Freeman B.C. & Yamamoto K.R. 2002. Disassembly of transcriptional regulatory complexes by molecular chaperones. Science 296: 2232-2235.10.1126/science.1073051Suche in Google Scholar PubMed
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.10.1385/1-59259-890-0:571Suche in Google Scholar
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: 1-11.10.1371/journal.pone.0031677Suche in Google Scholar PubMed PubMed Central
Gething M.J. & Sambrook J. 1992. Protein folding in the cell. Nature 355: 33-45.10.1038/355033a0Suche in Google Scholar PubMed
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: 276-290.10.1006/jmbi.1997.1237Suche in Google Scholar PubMed
Glotzer J.B., Saltik M., Chiocca S., Michou A.I., Moseley P. & Cotton M. 2000. Activation of heat-shock response by an adenovirus is essential for virus replication. Nature 407: 207-211.10.1038/35025102Suche in Google Scholar PubMed
Golas E.I., Czaplewski C., Scheraga H.A. & Liwo A. 2015. Common functionally important motions of the nucleotidebinding domain of Hsp70. Proteins 83: 282-299.10.1002/prot.24731Suche in Google Scholar PubMed PubMed Central
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. 10.1021/ct200680gSuche in Google Scholar PubMed PubMed Central
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 E1A-like activity. Mol. Cell. Biol. 4: 867-874.10.1128/mcb.4.5.867-874.1984Suche in Google Scholar PubMed PubMed Central
Hatebour G., Gennissen A., Ramos Y.F., Kerkhoven R.M., Sonntag-Buck V., Stunnenberg H.G. & Bernards R. 1995. BS69, a novel adenovirus E1A-associated protein that inhibits E1A transactivation. EMBO J. 14: 3159-3169.Suche in Google Scholar
Hendrickson W.A. & Liu Q. 2007. Insights into Hsp70 chaperone activity from a crystal structure of the yeast Hsp110 Sse1. Cell 131: 106-120.10.1016/j.cell.2007.08.039Suche in Google Scholar PubMed PubMed Central
Hightower L.E. 1991. Heat shock, stress proteins, chaperones, and proteotoxicity. Cell 66: 191-197.Suche in Google Scholar
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: 137-162.10.1146/annurev.bb.25.060196.001033Suche in Google Scholar PubMed
Jackson R.M. & Laurie A.T. 2005. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 21: 1908-1916.10.1093/bioinformatics/bti315Suche in Google Scholar
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: 10823-10830.10.1021/bi990816gSuche in Google Scholar
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: 105-111.10.1007/s12192-008-0068-7Suche in Google Scholar
Kampinga H.H & Craig E.A. 2010. The Hsp70 chaperone machinery: J-proteins as drivers of functional specificity. Nat. Rev. Mol. Cell Biol. 11: 579-592.10.1038/nrm2941Suche in Google Scholar
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: 863-874.10.1016/j.molcel.2012.09.023Suche in Google Scholar
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. 10.1006/jmbi.2000.4301Suche in Google Scholar
Laufen T., Mayer M.P., Paal K., R¨udiger S. & Schröder H. 2000. Multistep mechanism of substrate binding determines chaperone activity of Hsp70. Nat. Struct. Biol. 7: 586-593.10.1038/76819Suche in Google Scholar
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: 283-291.10.1107/S0021889892009944Suche in Google Scholar
Masselink H. & Bernards R. 2000. The adenovirus E1A binding protein BS69 is a corepressor of transcription through recruitment of N-CoR. Oncogene 19: 1538-1546.10.1038/sj.onc.1203421Suche in Google Scholar
Mayer M.P., Brehmer D., Gassler C.S. & Bukau B. 2001. Hsp70 chaperone machines. Adv. Protein Chem. 59: 1-44.10.1016/S0065-3233(01)59001-4Suche in Google Scholar
Netzer W.J. & Hartl, F.U. 1998. Protein folding in the cytosol: chaperonin-dependent and -independent mechanisms. Trends Biochem. Sci. 23: 68-73.10.1016/S0968-0004(97)01171-7Suche in Google Scholar
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.Suche in Google Scholar
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: 15874-15878.10.1074/jbc.271.27.15874Suche in Google Scholar
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: 664-666.10.1038/365664a0Suche in Google Scholar
Ritossa F. 1962. A new puffing pattern induced by heat shock and DNP in Drosophila. Experientia 18: 571-573.10.1007/BF02172188Suche in Google Scholar
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: 315-319.10.6026/97320630006315Suche in Google Scholar
Rupley J.A. & Shrake A. 1997. Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J. Mol. Biol. 79: 351-371.10.1016/0022-2836(73)90011-9Suche in Google Scholar
Sanner M.F. 1999. Python: a programming language for software integration and development. J. Mol. Graph. Model. 17: 57-61.Suche in Google Scholar
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: 1355-1363.10.1107/S0907444904011679Suche in Google Scholar PubMed
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.Suche in Google Scholar
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: 15392-15399.10.1021/bi981510xSuche in Google Scholar PubMed
Stone D.E. & Craig E.A. 1990. Self-regulation of 70 kilodalton heat shock proteins in Saccharomyces cerevisiae. Mol. Cell. Biol. 10: 1622-1632.10.1128/MCB.10.4.1622Suche in Google Scholar
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: 2239-2247.10.1099/0022-1317-79-9-2239Suche in Google Scholar PubMed
Wallner B. & Elofsson A. 2003. Can correct protein models be identified? Protein Sci. 12: 1073-1086.10.1110/ps.0236803Suche in Google Scholar PubMed PubMed Central
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: 4153-4166.10.1128/jvi.62.11.4153-4166.1988Suche in Google Scholar
Wickner S., Skowyra D., Hoskins J. & Mckenney K. 1992. DnaJ, DNAK, and GrpE heat shock proteins are required in oriP1 DNA replication solely at the RepA monomerization step. Proc. Natl. Acad. Sci. USA 89: 10345-10349.Suche in Google Scholar
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-W410.10.1093/nar/gkm290Suche in Google Scholar PubMed PubMed Central
Yamamoto M. & Curiel, D.T. 2010. Current issues and future directions of oncolytic adenoviruses. Mol. Ther. 18: 243-250.10.1038/mt.2009.266Suche in Google Scholar PubMed PubMed Central
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: 6987-6992.10.1073/pnas.1014448108Suche in Google Scholar PubMed PubMed Central
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. 10.1016/j.jmb.2009.01.062Suche in Google Scholar PubMed PubMed Central
© 2016
Artikel in diesem Heft
- Escherichia coli expression of NDV fusion protein gene and determination of its antigenic epitopes
- Screening for fibrinolytic filamentous fungi and enzymatic properties of the most potent producer, Aspergillus brasiliensis AUMC 9735
- Biochemical, anatomical and molecular level changes in cucumber (Cucumis sativus) seedlings exposed to copper oxide nanoparticles
- Expression of bacterial glutamine synthetase gene in Arabidopsis thaliana increases the plant biomass and level of nitrogen utilization
- Comparison between natural and impacted Alpine lakes six years after hydropower exploitation has ceased
- Formation of radial symmetric needle-like rosette leaves in Arabidopsis
- Contribution to the knowledge of lohmanniid oribatid mites (Acari: Oribatida: Lohmanniidae) of Cuba
- Aquatic insects of a lowland rainforest in Papua New Guinea: assemblage structure in relation to habitat type
- Short-horned grasshopper subfamilies feed at different rates on big bluestem and switchgrass cultivars
- Nests of the harvest mouse (Micromys minutus) as habitat for invertebrates
- Comparison of the anatomical arrangement of the branches arising from the descending aorta in rabbit (Oryctolagus cuniculus f. domestica) and European hare (Lepus europaeus)
- 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
- Paraoxonase 1 activity and polymorphisms in multiple sclerosis patients
Artikel in diesem Heft
- Escherichia coli expression of NDV fusion protein gene and determination of its antigenic epitopes
- Screening for fibrinolytic filamentous fungi and enzymatic properties of the most potent producer, Aspergillus brasiliensis AUMC 9735
- Biochemical, anatomical and molecular level changes in cucumber (Cucumis sativus) seedlings exposed to copper oxide nanoparticles
- Expression of bacterial glutamine synthetase gene in Arabidopsis thaliana increases the plant biomass and level of nitrogen utilization
- Comparison between natural and impacted Alpine lakes six years after hydropower exploitation has ceased
- Formation of radial symmetric needle-like rosette leaves in Arabidopsis
- Contribution to the knowledge of lohmanniid oribatid mites (Acari: Oribatida: Lohmanniidae) of Cuba
- Aquatic insects of a lowland rainforest in Papua New Guinea: assemblage structure in relation to habitat type
- Short-horned grasshopper subfamilies feed at different rates on big bluestem and switchgrass cultivars
- Nests of the harvest mouse (Micromys minutus) as habitat for invertebrates
- Comparison of the anatomical arrangement of the branches arising from the descending aorta in rabbit (Oryctolagus cuniculus f. domestica) and European hare (Lepus europaeus)
- 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
- Paraoxonase 1 activity and polymorphisms in multiple sclerosis patients