Abstract
In this chapter, two algorithms are developed: Algorithm 1 and Algorithm 2. Algorithm 1 was developed in order to search for the interaction of a polypeptide chain of a full-length protein with short active region. Algorithm 2 was developed to determine the most active sites of interaction between full-length proteins when dimers are formed in the direction from the N-terminus to C-terminus. Numerical calculations were made using proteins Mdm2, Nap1, P53.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
System Computer Biology. Monograph. Novosibirsk: Publishing House of the SB RAS (2008), 769 p
M.J. Betts, M.J. Sternberg, An analysis of conformational changes on proteinprotein association: implications for predictive docking. Protein Eng. 12, 271–283 (1999)
T.V. Pyrkov, I.V. Ozerov, E.D. Balitskaya, R.G. Efremov, Molecular docking: the role of non-valence interactions in the formation of protein complexes with nucleotides and peptides. Bioorganic Chem. 36(4), 482–492 (2010)
The Universal Protein Resource http://www.uniprot.org/
D. Lane, A. Levine, P53 Research: the past thirty years and the next thirty years Cold. Spring. Harb. Perspect. Biol. 2(12) (2010)
S. Nag, J. Qin, K.S. Srivenugopal, M. Wang, R. Zhanga, The MDM2-p53 pathway revisited. J. Biomed. Res. 27(4), 254–271 (2013)
D.P. Lane, L.V. Crawford, T antigen is bound to a host protein in SV40-transformed cells. Nature 278, 261–263 (1979)
C.J. Sherr, F. McCormick, The RB and p53 pathways in cancer. Cancer Cell 2(2), 103–112 (2002)
T. Ozaki, A. Nakagawara, Role of p53 in cell death and human cancers. Cancers(Basel) 3(1), 994–1013 (2011)
J.T. Zilfou, S.W. Lowe, Tumor Suppressive Functions of p53 Cold. Spring. Harb. Perspect. Biol. 1(5) (2009)
Y. Qian, X. Chen, Senescence regulation by the p53 protein family. Methods Mol. Biol. 965, 37–61 (2013)
Y. Liu, M. Kulesz-Martin, p53 protein at the hub of cellular DNA damage response pathways through sequence-specific and non-sequence-specific DNA binding. Carcinogenesis 22(6), 851–860 (2001)
M. Hassan, H. Watari, A. AbuAlmaaty, Y. Ohba, N. Sakuragi, Apoptosis and molecular targeting therapy in cancer. Biomed. Res. Int. 2014 (2014)
J. Loughery, M. Cox, L.M. Smith, D.W. Meek, Critical role for p53-serine 15 phosphorylation in stimulating transactivation at p53-responsive promoters. Nucleic. Acids. Res. 42(12), 7666–7680 (2014)
P.A. Lazo, Reverting p53 activation after recovery of cellular stress to resume with cell cycle progression. Cell Signal 33, 49–58 (2017)
G.P. Zambetti (ed.), The p53 Tumor Suppressor Pathway and Cancer (Springer, Berlin, 2005)
M.A. McCoy, J.J. Gesell, M.M. Senior, D.F. Wyss, Flexible lid to the p53-binding domain of human Mdm2: implications for p53 regulation. Proc. Natl. Acad. Sci. U. S. A. 100(4), 1645–1648 (2003)
H. Liang, H. Atkins, et al., Genomic organisation of the human MDM2 oncogene and relationship to its alternatively spliced mRNAs. Gene 338(2), 217–223
T. Hamzehloie, M. Mojarrad, M. Hasanzadeh-Nazarabadi, S. Shekouhi, The role of tumor protein 53 mutations in common human cancers and targeting the murine double minute 2P53 interaction for cancer therapy. Iran. J. Med. Sci. 37(1), 3–8 (2012)
Y. Zhao, H. Yu, W. Hu, The regulation of MDM2 oncogene and its impact on human cancers. Acta Biochim. Biophys. Sin. (Shanghai) 46(3), 180–189 (2014)
P. Chene, Inhibition of the p53-MDM2 Interaction: targeting a protein-protein interface. Mol. Cancer. Res. 2(1), 20–28 (2004)
U.M. Mol, O. Petrenko, Molecular dynamic simulation insights into the normal state and restoration of p53 function. Mol. Cancer. Res. 1(14), 1001–1008 (2003)
P.H. Kussie, S. Gorina, V. Marechal, B. Elenbaas, J. Moreau, A.J. Levine, N.P. Pavletich, Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science 274(5289), 948–953 (1996)
P.L. Leslie, H. Ke, Y. Zhang, The MDM2 RING domain and central acidic domain play distinct roles in MDM2 protein homodimerization and MDM2-MDMX protein heterodimerization. J. Biol. Chem. 290(20), 12941–12950 (2015)
Y.J. Park, K. Luger, The structure of nucleosome assembly protein 1. Proc. Natl. Acad. Sci. USA 103(5), 1248–1253 (2006)
S.J. McBryant, Y.J. Park, S.M. Abernathy, P.J. Laybourn, J.K. Nyborg, K. Luger, Preferential binding of the histone (H3-H4)\(_2\) tetramer by NAP1 is mediated by the amino-terminal histone tails. J. Biol. Chem. 278(45), 44574–44583 (2003)
J. Zlatanova, C. Seebart, M. Tomschik, Nap1: taking a closer look at a juggler protein of extraordinary skills. FASEB J. 21(7), 1294–1310 (2007)
L.L. Patrick, H. Ke, Z. Yanping, The MDM2 RING domain and central acidic domain play distinct roles in MDM2 protein homodimerization and MDM2-MDMX protein heterodimerization. J. Biol. Chem. 290(20), 12941–12950 (2015)
S. Uldrijan, W.J. Pannekoek, K.H. Vousden, An essential function of the extreme C-terminus of MDM2 can be provided by MDMX. EMBO J. 26, 102–112 (2007)
M.V. Poyurovsky, C. Priest, A. Kentsis, K.L. Borden, Z.Q. Pan, N. Pavletich, C. Prives, The Mdm2 RING domain C-terminus is required for supramolecular assembly and ubiquitin ligase activity. EMBO J. 26, 90–101 (2007)
Y. Zhao, A. Aguilar, D. Bernard, S. Wang, Small molecule inhibitors of MDM2-p53 and MDMX-p53 interactions as new cancer therapeutics. J. Med. Chem. 58(3), 1038–1052 (2015)
J. Chen, V. Marechal, A.J. Levine, Mapping of the p53 and mdm-2 interaction domains. Mol. Cell. Biol. 13, 4107–4114 (1993)
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
Copyright information
© 2018 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Koshlan, T., Kulikov, K. (2018). Mathematical Modeling Identification of Active Sites Interaction of Protein Molecules. In: Mathematical Modeling of Protein Complexes. Biological and Medical Physics, Biomedical Engineering. Springer, Cham. https://doi.org/10.1007/978-3-319-98304-2_5
Download citation
DOI: https://doi.org/10.1007/978-3-319-98304-2_5
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-98303-5
Online ISBN: 978-3-319-98304-2
eBook Packages: Physics and AstronomyPhysics and Astronomy (R0)