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Research Article

Deep analysis of N-cadherin/ADH-1 interaction: a computational survey

, , , , , , & show all
Pages 210-228 | Received 15 Sep 2017, Accepted 08 Dec 2017, Published online: 19 Jan 2018

References

  • Abraham, M.J., van der Spoel, D., Lindahl, E., Hess, B., & the G. development team. (2015). GROMACS user manual version 5.0.7. www.gromacs.org
  • Agiostratidou, G., Hulit, J., Phillips, G. R., & Hazan, R. B. (2007). Differential cadherin expression: Potential markers for epithelial to mesenchymal transformation during tumor progression. Journal of Mammary Gland Biology and Neoplasia, 12, 127–133. doi: 10.1007/s10911-007-9044-6
  • Anand, P., Nagarajan, D., Mukherjee, S., & Chandra, N. (2014). ABS – Scan: In silico alanine scanning mutagenesis for binding site residues in protein – ligand complex [ version 1; referees: 1 approved with reservations, 1 not approved ] referee status. F1000Research, 3(214), 1–15. http://doi.org/10.12688/f1000research.5165.1
  • Anet, F. A. L. (1990). Inflection points and chaotic behavior in searching the conformational space of cyclononane. Journal of the American Chemical Society, 112, 7172–7178.10.1021/ja00176a015
  • Bagheri Novir, S. & Hashemianzadeh, S. M. (2015a). Computational study of new azo dyes with different anchoring groups for dye-sensitised solar cells. Molecular Physics, 114(November), 650–662. doi:10.1080/00268976.2015.1110629.
  • Bagheri Novir, S. & Hashemianzadeh, S. M. (2015b). Density functional theory study of new azo dyes with different p -spacers for dyesensitized solar cells. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 143, 20–34. doi:10.1016/j.saa.2015.02.026.
  • Bagherzadeh, K., Shirgahi Talari, F., Sharifi, A., Ganjali, M. R., Saboury, A. A., & Amanlou, M. (2015). A new insight into mushroom tyrosinase inhibitors: Docking, pharmacophore-based virtual screening, and molecular modeling studies. Journal of Biomolecular Structure & Dynamics, 33(3), 487–501. doi:10.1080/07391102.2014.893203
  • Bajda, M., Więckowska, A., Hebda, M., Guzior, N., Sotriffer, C.A., & Malawska, B. (2013). Structure-based search for new inhibitors of cholinesterases. International Journal of Molecular Sciences, 14(3), 5608–5632. doi:10.3390/ijms14035608
  • Baker, N. A., Sept, D., Joseph, S., Holst, M. J., Andrew, J., Mccammon, J. A., … Michael, J. H. (2001). Electrostatics of nanosystem: Application to microtubules and the riboson ne. Proceedings of the National Academy of Sciences, 98(18), 10037–10041.10.1073/pnas.181342398
  • Barone, V., Cossi, M., Chimica, D., Uni, V., Ii, F., Mezzocannone, V., & Napoli, I. (1998). Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. The Journal of Physical Chemistry A, 102, 1995–2001.10.1021/jp9716997
  • Becker, O. M. (1998). Principal coordinate maps of molecular potential potential energy surfaces. Journal of Computational Chemistry, 19(11), 1255–1267.10.1002/(ISSN)1096-987X
  • Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., … Schwede, T. (2014). SWISS-MODEL: Modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research, 42(W1), 252–258. doi:10.1093/nar/gku340
  • Blaschuk, O. W. (2015). N-cadherin antagonists as oncology therapeutics. Philosophical Transactions B, 1661, 370–373.
  • Blaschuk, O. W., & Devemy, E. (2009). Cadherins as novel targets for anti-cancer therapy. European Journal of Pharmacology, 625(1–3), 195–198. doi:10.1016/j.ejphar.2009.05.033
  • Boehr, D. D., Nussinov, R., & Wright, P. E. (2009). The role of dynamic conformational ensembles in biomolecular recognition. Nature Chemical Biology, 5(11), 789–796. doi:10.1038/nchembio.232
  • Bradbrook, G. M., Gleichmann, T., Harrop, S. J., Habash, J., Raftery, J., Gilboa, K., … Helliwell, J. R. (1998). X-ray and molecular dynamics studies of concanavalin-A glucoside and mannoside complexes relating structure to thermodynamics of binding. Journal of the Chemical Society, 94(X), 1603–1611.
  • Brasch, J., Harrison, O. J., Honig, B., & Shapiro, L. (2012). Thinking outside the cell: How cadherins drive adhesion. Trends in Cell Biology, 22(6), 299–310. doi:10.1016/j.tcb.2012.03.004
  • Bryan, R. T., Atherfold, P. A., Yeo, Y., Jones, L. J., Harrison, R. F., Wallace, D. M. A., & Jankowski, J. A. (2008). Cadherin switching dictates the biology of transitional cell carcinoma of the bladder: Ex vivo and in vitro studies. The Journal of pathology, 215, 184–194. doi: 10.1002/path
  • Cai-Rong, Z., Zi-Jiang, L., Yu-Hong, C., Hong-Shan, C., You-Zhi, W., & Li-Hua, Y. (2009). Journal of molecular structure : Theochem DFT and TDDFT study on organic dye sensitizers D5, DST and DSS for solar cells. Journal of Molecular Structure: Theochem, 899(1–3), 86–93. doi:10.1016/j.theochem.2008.12.015
  • Carlson, H. A., & Mccammon, J. A. (2000). Accommodating protein flexibility in computational drug design. Molecular Pharmacology, 57, 213–218. . Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/10648630
  • Chen, Y. (2014). Beware of docking!. Trends in Pharmacological Sciences, 1–18. doi:10.1016/j.tips.2014.12.001
  • Comeau, S. R., Gatchell, D. W., Vajda, S., & Camacho, C. J. (2004). ClusPro : A fully automated algorithm for protein–protein docking. Nucleic Acids Research, 32, 96–99. doi:10.1093/nar/gkh354
  • Cossi, M., Barone, V., Cammi, R., & Tomasi, J. (1996). Ab initio study of solvated molecules: A new implementation of the polarizable continuum model. Chemical Physics Letters, 255 (June), 327–335.10.1016/0009-2614(96)00349-1
  • Cossi, M., Rega, N., Scalmani, G., Barone, V., Chimica, D., Ii, F., & Angelo, C. M. S. (2003). Molecules in solution with the C-PCM solvation model. Journal of Computational Chemistry, 24(6), 669–681.10.1002/jcc.10189
  • Cress, A. E., & Heimark, R. L. (1999). N-Cadherin expression in human prostate carcinoma cell lines. The American Journal of Pathology, 155(3), 787–798. doi:10.1016/S0002-9440(10)65177-2
  • Da Silva, A. W. S. & Vranken, W. F. (2012). ACPYPE - antechamber PYthon parser interface. BMC Research Notes, 5, 1–8.
  • David, S., Blaschuk, O. W., & Victoria, R. (1990). Identification of a cadherin cell adhesion. Developmental Biology, 229, 90–92.
  • Dolinsky, T. J., Nielsen, J. E., Mccammon, J. A., & Baker, N. A. (2004). PDB2PQR: An automated pipeline for the setup of Poisson – Boltzmann electrostatics calculations. Nucleic Acids Research, 32, 665–667. doi:10.1093/nar/gkh381
  • Doro, F., Colombo, C., Alberti, C., Arosio, D., Belvisi, L., Piarulli, U., … Figini, M. (2015). Biomolecular chemistry inhibitors of cadherin homophilic interactions. Organic & Biomolecular Chemistry, 13, 2570–2573. doi:10.1039/c4ob02538e
  • Durrant, J. D., & McCammon, J. A. (2011). Molecular dynamics simulations and drug discovery. BMC Biology, 9, 71–80. doi:10.1186/1741-7007-9-71
  • Eslami, M., Hashemianzadeh, S. M., & Bagherzadeh, K. (2016). Molecular perception of interactions between bis (7) tacrine and cystamine-tacrine dimer with cholinesterases as the promising proposed agents for the treatment of Alzheimer’s disease. Journal of Biomolecular Structure and Dynamics ISSN, 1102(April), 855–869. doi:10.1080/07391102.2015.1057526
  • Eslami, M., Hashemianzadeh, S. M., Bagherzadeh, K., & Seyed Sajadi, S. A. (2015). Molecular perception of interactions between bis (7) tacrine and cystamine-tacrine dimer with cholinesterases as the promising proposed agents for the treatment of Alzheimer’s disease. Journal of Biomolecular Structure and Dynamics, 1102(June), 1–15. doi:10.1080/07391102.2015.1057526
  • Friedl, P., & Gilmour, D. (2009). Collective cell migration in morphogenesis, regeneration and cancer. Molecular Cell Biology, 10(july), 445–457. doi:10.1038/nrm2720
  • Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, R. J., ... Burant, J. C. (2004). GAUSSIAN 03, Revision D.01. Wallingford, CT: Gaussian,.
  • Hajighahramani, N., Nezafat, N., Eslami, M., Negahdaripour, M., Rahmatabadi, S. S., & Ghasemi, Y. (2017). Immunoinformatics analysis and in silico designing of a novel multi-epitope peptide vaccine against Staphylococcus aureus. Infection, Genetics and Evolution, 48, 83–94. doi:10.1016/j.meegid.2016.12.010
  • Hansson, T., Oostenbrink, C., & van Gunsteren, W. (2002). Molecular dynamics simulations. Current Opinion in Structural Biology, 12(2), 190–196. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/1195949610.1016/S0959-440X(02)00308-1
  • Harris, T. J. C., & Tepass, U. (2010). Adherens junctions : From molecules to morphogenesis. Molecular Cell Biology, 11(July), 502–514. doi:10.1038/nrm2927
  • Harrison, O. J., Corps, E. M., & Kilshaw, P. J. (2005). Cadherin adhesion depends on a salt bridge at the N-terminus. Journal of Cell Science, 118 (August), 4123–4130. http://doi.org/10.1242/jcs.0253910.1242/jcs.02539
  • Harrison, O. J., Jin, X., Hong, S., Bahna, F., Ahlsen, G., Brasch, J., … Honig, B. (2011). Article the extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins. Structure/Folding and Design, 19(2), 244–256. doi:10.1016/j.str.2010.11.016
  • Jacksonville, M. H., & Jacksonville, M. C. (2006). The role of cadherins and catenins in gliomagenesis. Neurosurgical Focus, 21(4), 21–24.
  • Karimi, Z., Nezafat, N., Negahdaripour, M., Hemmati, S., & Ghasemi, Y. (2015). The effect of rare codons following the ATG start codon on expression of human granulocyte-colony stimulating factor in Escherichia coli. Protein Expression and Purification, 114, 108–114. doi:10.1016/j.pep.2015.05.017
  • Karplus, M., & Kuriyan, J. (2005). Molecular dynamics and protein function. Proceedings of the National academy of Sciences of the United States of America, 102(19), 6679–6685. doi:10.1073/pnas.0408930102
  • Kolega, J. (2004). Phototoxicity and photoinactivation of blebbistatin in UV and visible light. Biochemical and Biophysical Research Communications, 320, 1020–1025. doi:10.1016/j.bbrc.2004.06.045
  • Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., … Cheatham, T. E. (2000). Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts of Chemical Research, 33(12), 889–897. doi:10.1021/ar000033j
  • Kolossvary, I., & Guida, W. C. (1993). Comprehensive conformational analysis of the four- to twelve-membered ring cycloalkanes: Identification of the complete set of interconversion pathways on the MM2 potential energy hypersurface. Journal of the American Chemical Society, 115(8), 2107–2119.10.1021/ja00059a003
  • Kumar, P. S., Vasudevan, K., Prakasam, A., Geetha, M., & Anbarasan, P. M. (2010). Quantum chemistry calculations of 3-phenoxyphthalonitrile dye sensitizer for solar cells. Spectrochimica Acta Part A, 77, 45–50. doi:10.1016/j.saa.2010.04.021
  • Lee, E., Ewald, M. L., Sedarous, M., Kim, T., Weyers, B. W., Truong, R. H., & Yamada, S. (2016). Deletion of the cytoplasmic domain of N-cadherin reduces, but does not eliminate, traction force-transmission. Biochemical and Biophysical Research Communications, 478, 1640–1646. doi:10.1016/j.bbrc.2016.08.173
  • Lee, Y. S., Yi, J., Lim, H. R., Kim, T. S., Ahn, I. Y., Ko, K., … Lee, J. K. (2017). Phototoxicity evaluation of pharmaceutical substances with a reactive oxygen species assay using ultraviolet A. Toxicological Research, 33(1), 43–48.10.5487/TR.2017.33.1.043
  • Lindorff-larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J. L., Dror, R. O., & Shaw, D. E. (2010). Improved side-chain torsion potentials for the Amber ff99SB protein. Proteins, 78, 1950–1958. doi:10.1002/prot.22711
  • Massova, I., & Kollman, P. A. (1999). Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies. Journal of the American Chemical Society, 121(36), 8133–8143. doi:10.1021/ja990935j
  • McQuarrie, D. A. (1976). Statistical mechanics. New York, NY: Harper & Row.
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2010). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. doi:10.1002/jcc.21256.AutoDock4
  • Nakajima, S., Doi, R., Toyoda, E., Tsuji, S., Wada, M., Koizumi, M., … Mori, T. (2004). N-cadherin expression and epithelial-mesenchymal transition in pancreatic carcinoma. Clinical Cancer Research, 10, 4125–4133.
  • Negahdaripour, M., Eslami, M., Nezafat, N., Hajighahramani, N., Ghosshon, M. B., Shoolian, E., … Ghasemi, Y. (2017). A novel HPV prophylactic peptide vaccine, designed by immunoinformatics and structural vaccinology approaches. Infection, Genetics and Evolution., 54, 402–416 doi:10.1016/j.meegid.2017.08.002
  • Negahdaripour, M., Nezafat, N., & Ghasemi, Y. (2016). A panoramic review and in silico analysis of IL-11 structure and function. Cytokine and Growth Factor Reviews, 32, 41–61. doi:10.1016/j.cytogfr.2016.06.002
  • Negahdaripour, M., Nezafat, N., Hajighahramani, N., Rahmatabadi, S. S., & Ghasemi, Y. (2017). Investigating CRISPR-cas systems in Clostridium Botulinum via bioinformatics tools. Infection, Genetics and Evolution, 54, 355–373. doi:10.1016/j.meegid.2017.06.027
  • Negahdaripour, M., Nezafat, N., Hajighahramani, N., Rahmatabadi, S. S., Morowvat, M. H., & Ghasemi, Y. (2017). In silico study of different signal peptides for secretory production of interleukin-11 in Escherichia coli. Current Proteomics, 14(2), 112–121.10.2174/1570164614666170106110848
  • Nezafat, N., Eslami, M., Negahdaripour, M., Rahbar, M. R., & Ghasemi, Y. (2017). Designing an efficient multi-epitope oral vaccine against Helicobacter pylori using immunoinformatics and structural vaccinology. Molecular BioSystems, 13, 699–713. doi:10.1039/C6MB00772D
  • Nezafat, N., Ghasemi, Y., Javadi, G., & Javad, M. (2014). A novel multi-epitope peptide vaccine against cancer : An in silico approach. Journal of Theoretical Biology, 349, 121–134. doi:10.1016/j.jtbi.2014.01.018
  • Nezafat, N., Karimi, Z., Eslami, M., & Mohkam, M. (2016). Designing an efficient multi-epitope peptide vaccine against Vibrio cholerae via combined immunoinformatics and protein interaction based approaches. Computational Biology and Chemistry, 62, 82–95. doi:10.1016/j.compbiolchem.2016.04.006
  • Nishimura, T., & Takeichi, M. (2009). Remodeling of the adherens junctions during morphogenesis. Current topics in developmental biology (1st ed., Vol. 89). Chuo-ku, Kobe: Elsevier Inc. Retrieved from http://doi.org/10.1016/S0070-2153(09)89002-9
  • Ochterski, J. W. (2000). Thermochemistry in gaussian. Retrieved from http://gaussian.com/thermo/
  • Oda, H., & Takeichi, M. (2011). Structural and functional diversity of cadherin at the adherens junction. The Journal of Cell Biology, 193(7), 1137–1146. doi:10.1083/jcb.201008173
  • Paissoni, C., Spiliotopoulos, D., Musco, G., & Spitaleri, A. (2014). GMXPBSA 2.1: A GROMACS tool to perform MM/PBSA and computational alanine scanning. Computer Physics Communications, 186, 105–107. doi:10.1016/j.cpc.2014.06.019
  • Parr, R. G., & Pearson, R. G. (1983). Absolute hardness: Companion parameter to absolute electronegativity. Journal of the American Chemical Society, 105, 7512–7516.10.1021/ja00364a005
  • Pearson, R. G. (1963). Hard and soft acids and bases. Physical and Inorganic Chemistry Contribution, 85(22), 3533–3539.
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. doi:10.1002/jcc.20084
  • Politzer, P., Laurence, P. R., & Jayasuriya, K. (2014). Molecular electrostatic potentials: An effective tool for the elucidation of biochemical phenomena. Environmental Health Perspective, 61, 191–202.
  • Rahmatabadi, S. S., Nezafat, N., & Negahdaripour, M. (2016). Studying the features of 57 confirmed CRISPR loci in 29 strains of Escherichia coli. Journal of Basic Microbiology, 56, 645–653. doi:10.1002/jobm.201500707
  • Sakhteman, A., Khoddami, M., & Negahdaripour, M. (2016). Exploring 3D structure of human gonadotropin hormone receptor at antagonist state using homology modeling, molecular dynamic simulation, and cross-docking studies. Journal of Molecular Modeling, 22, 225–235. doi:10.1007/s00894-016-3091-0
  • Sheela, N. R., Muthu, S., & Sampathkrishnan, S. (2014). Molecular orbital studies (hardness, chemical potential and electrophilicity), vibrational investigation and theoretical NBO analysis abinitio and DFT methods. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 120, 237–251. doi:10.1016/j.saa.2013.10.007
  • Shih, W., Yamada, S., & Yamada, S. (2012). N-cadherin-mediated cell-cell adhesion promotes cell migration in a three- dimensional matrix. Journal of Cell Science, 125(15), 3661–3670.10.1242/jcs.103861
  • Shintani, Y., Fukumoto, Y., Chaika, N., Grandgenett, P. M., Hollingsworth, M. A., Wheelock, M. J., & Johnson, K. R. (2008). ADH-1 suppresses N-cadherin-dependent pancreatic cancer progression. International Journal of Cancer, 77 ( August 2007), 71–77. http://doi.org/10.1002/ijc.2302710.1002/(ISSN)1097-0215
  • Sinha, L., Karabacak, M., Narayan, V., Cinar, M., & Prasad, O. (2013). Molecular structure, electronic properties, NLO, NBO analysis and spectroscopic characterization of Gabapentin with experimental (FT-IR and FT-Raman) techniques and quantum chemical calculations. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 109, 298–307. doi:10.1016/j.saa.2013.02.035
  • Sliwoski, G., Kothiwale, S., Meiler, J., & Lowe, E. W. (2014). Computational methods in drug discovery. Pharmacological Reviews, 66 ( January), 334–395.
  • Tanak, H., & Toy, M. (2014). Molecular structure, spectroscopic and quantum chemical studies on 2 0 - chloro-4-dimethlamino azobenzene. Journal of Molecular Structure, 1068, 189–197. doi:10.1016/j.molstruc.2014.04.014
  • Trott, O., & Olson, A. J. (2009). Software news and update autodock vina : Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31, 455–461. doi:10.1002/jcc
  • Vendome, J., Posy, S., Jin, X., Bahna, F., Ahlsen, G., Shapiro, L., & Honig, B. (2011). Molecular design principles underlying β -strand swapping in the adhesive dimerization of cadherins. Nature Structural & Molecular Biology, 18, 693–700. doi:10.1038/nsmb.2051
  • Wang, J., Morin, P., Wang, W., Kollman, P. A. (2001). Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of Efavirenz by docking and MM-PBSA. Journal of the American Chemical Society, 123(22), 5221–5230. doi:10.1021/ja003834q
  • Weijer, C. J., Martin, P., & Sci, J. C. (2009). Collective cell migration in development. Journal of Cell Science, 122(18), 3215–3223. doi:10.1242/jcs.036517
  • Williams, E., Williams, G., Barbara, J., Blaschuk, O. W., Doherty, P., Williams, E., … Doherty, P. (2000). A novel family of cyclic peptide antagonists suggests that N-cadherin specificity is determined by amino acids that flank the HAV motif a novel family of cyclic peptide antagonists suggests that N-cadher. The Journal of Biological Chemistry, 275, 4007–4012. doi:10.1074/jbc.275.6.4007
  • Xavier, S., Periandy, S., & Ramalingam, S. (2015). NBO, conformational, NLO, HOMO – LUMO, NMR and electronic spectral study on 1-phenyl-1-propanol by quantum computational methods. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 137, 306–320. doi:10.1016/j.saa.2014.08.039
  • Yajun, J., Zizhong, L. I. U., Hongxia, L. I. U., Wenying, C. U. I., Na, W., Dongsheng, L. I. U., & Xiangwei, G. E. (2012). DFT study on nonlinear optical properties of lithium-doped corannulene. Chinese Science Bulletin, 57(34), 4448–4452. doi:10.1007/s11434-012-5437-z
  • Yarom, N., Stewart, D., Malik, R., Wells, J., Avruch, L., & Jonker, D. J. (2013). Phase I clinical trial of exherin (ADH-1) in patients with advanced solid tumors. Current Clinical Pharmacology, 8, 81–88.
  • Zhang, C., Liu, L., Liu, Z., Shen, Y., Sun, Y., Wu, Y., … Chen, H. (2012). Electronic structures and optical properties of organic dye sensitizer NKX derivatives for solar cells: A theoretical approach. Journal of Molecular Graphics and Modelling, 38, 419–429. doi:10.1016/j.jmgm.2012.09.004
  • Zoete, V., & Michielin, O. (2011). SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Research, 39(May), 270–277. doi:10.1093/nar/gkr366

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