Investigation of C-Cadherin mechanical properties by Molecular Dynamics

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List of references:

  1. А. В. Глякина, Н. К. Балабаев, О. В. Галзитская. Сравнение переходных состояний иммуноглобулинсвязывающих доменов белков L и G, полученных при моделировании разворачивания под действием внешних сил и в экспериментах под действием денатуранта // Биохимия. — 2009. — Т. 74. — С. 389–403.
  2. А. В. Глякина, О. В. Галзитская, Н. К. Балабаев. Исследование механических свойств иммуноглобулинсвязывающих доменов белков L и G методом молекулярной динамики // Компьютерные исследования и моделирование. — 2010. — Т. 2, № 1. — С. 73–81. — DOI: 10.20537/2076-7633-2010-2-1-73-81
  3. И. В. Лихачев, Н. К. Балабаев. Анализатор траекторий молекулярной динамики // Математическая биология и биоинформатика. — 2007. — Т. 2, № 1. — С. 120–129.
  4. И. В. Лихачев, Н. К. Балабаев. Построение расширенных динамических контактных карт по данным молекулярно-динамических расчетов // Математическая биология и биоинформатика. — 2009. — Т. 4, № 1. — С. 36–45.
  5. M. P. Allen, D. J. Tildesley. Computer simulation of liquids. — Clarendon Press, 1989.
  6. J. Aqvist. Ion-water interaction potentials derived from free energy perturbation simulations // J. Phys Chem. — 1990. — V. 94. — P. 8021–8024. — DOI: 10.1021/j100384a009.
  7. J. Chen, H. Ruan, S. M. Ng, C. Gao, H. M. Soo, W. Wu, Z. Zhang, Z. Wen, D. P. Lane, J. Peng. Loss of function of def selectively up-regulates Delta 113p53 expression to arrest expansion growth of digestive organs in zebrafish // Genes Dev. — 2005. — V. 19, no. 23. — P. 2900–2911. — DOI: 10.1101/gad.1366405.
  8. T. J. Boggon, J. Murray, S. Chappuis-Flament, E. Wong, B. M. Gumbiner, L. Shapiro. C-cadherin ectodomain structure and implications for cell adhesion mechanisms // Science. — 2002. — V. 296. — P. 1308–1313. — DOI: 10.1126/science.1071559. — ads: 2002Sci...296.1308B.
  9. Y. S. Choi, R. Sehgal, P. McCrea, B. M. Gumbiner. A cadherin-like protein in eggs and cleaving embryos of Xenopus laevis is expressed in oocytes in response to progesterone // J. Cell Biol. — 1990. — V. 110. — P. 1575–1582. — DOI: 10.1083/jcb.110.5.1575.
  10. R. A. Foty, M. S. Steinberg. The differential adhesion hypothesis: a direct evaluation // Dev Biol. — 2005. — V. 278, no. 1. — P. 255–263. — DOI: 10.1016/j.ydbio.2004.11.012.
  11. D. Ginsberg, D. DeSimone, B. Geiger. Expression of a novel cadherin (EP-cadherin) in unfertilized eggs and early Xenopus embryos // Development. — 1991. — V. 111. — P. 315–325.
  12. A. V. Glyakina, N. K. Balabaev, O. V. Galzitskaya. Mechanical unfolding of proteins L and G with constant force: similarities and differences // J. Chem. Phys. — 2009. — V. 131, no. 4. — P. 045102. — DOI: 10.1063/1.3183974. — ads: 2009JChPh.131d5102G.
  13. A. V. Glyakina, N. K. Balabaev, O. V. Galzitskaya. Multiple unfolding intermediates obtained by molecular dynamics simulations under stretching for immunoglobulin-binding domain of protein G // The Open Biochem. J. — 2009. — V. 3. — P. 66–77. — DOI: 10.2174/1874091X00903010066.
  14. A. V. Glyakina, N. K. Balabaev, O. V. Galzitskaya. Two-, Three-, and Four-State Events Occur in the Mechanical Unfolding of Small Protein L Using Molecular Dynamics Simulations // Protein and Peptide Letters. — 2010. — V. 17, no. 1. — P. 92–103. — DOI: 10.2174/092986610789909449.
  15. Harrison Oliver, Jin Xiangshu, Hong Soonjin, Bahna Fabiana, Ahlsen Goran, Brasch Julia, Wu Yinghao, Vendome Jeremie, Felsovalyi Klara, M. Hampton Cheri, B. Troyanovsky Regina, Ben-Shaul Avinoam, Frank Joachim, M. Troyanovsky Sergey, Shapiro Lawrence, Honig Barry. The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins // Structure. — 2011. — V. 19. — P. 244–256. — DOI: 10.1016/j.str.2010.11.016.
  16. D. Haussinger, T. Ahrens, T. Aberle, J. Engel, J. Stetefeld, . Proteolytic E-cadherin activation followed by solution NMR and X-ray crystallography // EMBO J. — 2004. — V. 23. — P. 1699–1708. — DOI: 10.1038/sj.emboj.7600192.
  17. J. Higo, M. Nakasako. Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: on the correlation between crystal water sites, solvent density, and solvent dipole // J Comput Chem. — 2002. — V. 23, no. 14. — P. 1323–36. — DOI: 10.1002/jcc.10100.
  18. A. S. Lemak, N. K. Balabaev. A comparison between collisional dynamics and Brownian dynamics // Mol Simul. — 1995. — V. 15. — P. 223–231. — DOI: 10.1080/08927029508022336.
  19. A. S. Lemak, N. K. Balabaev. Molecular dynamics simulation of a polymer chain in solution by collisional dynamics method // J Comp Chem. — 1996. — V. 17. — P. 1685–1695. — DOI: 10.1002/(SICI)1096-987X(19961130)17:15<1685::AID-JCC1>3.0.CO;2-L.
  20. B. Nagar, M. Overduin, M. Ikura, J. M. Rini. Structural basis of calcium-induced E-cadherin rigidification and dimerization // Nature. — 1996. — V. 380. — P. 360–364. — DOI: 10.1038/380360a0. — ads: 1996Natur.380..360N.
  21. H. Nose, G. W. Mack, X. Shi, E. R. Nadel. Role of osmolality and plasma volume during rehydration in humans // J Appl Physiol. — 1988. — V. 65, no. 1. — P. 325–331. — DOI: 10.1152/jappl.1988.65.1.325.
  22. Oroz Javier, Valbuena Alejandro, Vera Andres Manuel, Mendieta Jesus, Gomez-Puertas Paulino, Carrion-Vazquez Mariano. Nanomechanics of the Cadherin ectodomain // The journal of biological chemistry. — 2011. — V. 286. — P. 9405–9418. — DOI: 10.1074/jbc.M110.170399.
  23. C. M. Niessen, B. M. Gumbiner. Cadherin-mediated cell sorting not determined by binding or adhesion specificity // J Cell Biol. — 2002. — V. 156, no. 2. — P. 389–399. — DOI: 10.1083/jcb.200108040.
  24. Nimesh A. Patel, Salvador Curiel, Qizhou Zhang, T. K. Sridharan, Paul T. P. Ho, M. José. Torrelles Submillimeter Array Observations of 321 GHz Water Maser Emission in Cepheus A // The Astrophysical Journal. — 2007. — V. 658. — P. L55–L58. — DOI: 10.1086/513508.
  25. Pokutta Sabine, Herrenknecht Kurt, Kemler Rolf, Engel Jurgen. Conformational changes of the recombinant extracellular domain of E-cadherin upon calcium binding // Eur. J. Biochem. — 1994. — V. 223. — P. 1019–1026. — DOI: 10.1111/j.1432-1033.1994.tb19080.x.
  26. Sotomayor Marcos, Schulten Klaus. The Allosteric Role of the Ca2+ Switch in Adhesion and Elasticity of C-Cadherin // Biophysical Journal. — 2008. — V. 94. — P. 4621–4633. — DOI: 10.1529/biophysj.107.125591. — ads: 2008BpJ....94.4621S.
  27. J. Wang, P. Cieplak, P. A. Kollmann. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules // J. Comp Chem. — 2000. — V. 21. — P. 1049–1074. — DOI: 10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F.
  28. Y. Zhang, S. Sivasankar, J. Nelson, S. Chu. Resolving cadherin interactions and binding // PNAS. — 2009. — V. 106, no. 1. — P. 109–114. — DOI: 10.1073/pnas.0811350106. — ads: 2009PNAS..106..109Z.

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