Role of the lipid environment in the dimerization of transmembrane domains of glycophorin A

Acta Naturae

Volumn 7, Issue 4, 2015, Pages 122-127

  Kuznetsov, A S ^a   Volynsky, P E ^a   Efremov, R G ^a,b,c  

^a SHEMYAKIN OVCHINNIKOV INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

^b NATIONAL RESEARCH UNIVERSITY HIGHER SCHOOL OF ECONOMICS   (Russian Federation)

^c RUSSIAN ACADEMY OF SCIENCES   (Russian Federation)

Author keywords

Free energy of intermolecular interactions; Glycophorin A; Molecular dynamics; Protein protein interactions; Role of the lipid membrane; Transmembrane domain

Indexed keywords

EID: 84951985271     PISSN: 20758251     EISSN: None     Source Type: Journal    
DOI: 10.32607/20758251-2015-7-4-122-127     Document Type: Article

References (51)

1. Moreau A., Gosselin-Badaroudine P., Chahine M. // Q. Rev. Biophys. 2014. V. 47. No 4. P. 364-388
2. Raja M. // Arch. Biochem. Biophys. 2011. V. 510, No 1. P. 1-10
3. Williamson I.M., Alvis S.J., East J.M., Lee A.G. // Cell. Mol. Life Sci. 2003. V. 60. No 8. P. 1581-1590
4. Prasanna X., Chattopadhyay A., Sengupta A. // Biophys. J. 2014. V. 106. No 6. P. 1290-1300
5. Bocharov E.V., Mineev K.S., Goncharuk M.V., Arseniev A.S. // Biochim. Biophys. Acta-Biomembr. 2012. V. 1818. No 9. P. 2158-2170
6. Bocharov E.V., Lesovoy D.M., Goncharuk S.A., Goncharuk M.V., Hristova K., Arseniev A.S. // Structure. 2013. V. 21. No 11, P. 2087-2093
7. Jura N., Endres N.F., Engel K., Deindl S., Das R., Lamers M.H., Wemmer D.E., Zhang X., Kuriyan J. // Cell. 2009.V. 137. No 7. P. 1293-1307
8. Endres N.F., Das R., Smith A.W., Arkhipov A., Kovacs E., Huang Y., Pelton J.G., Shan Y., Shaw D.E., Wemmer D.E., et al. // Cell. 2013. V. 152. No 3. P. 543-556
9. Bocharov E.V., Mayzel M.L., Volynsky P.E., Mineev K.S., Tkach E.N., Ermolyuk Y.S., Schulga A.A., Efremov R.G., Arseniev A.S. // Biophys. J. 2010. V. 98. No 5. P. 881-889
10. Fleming K.G., Engelman D.M. // Proc. Natl. Acad. Sci. U. S. A. 2001. V. 98. No 25. P. 14340-14344
11. Efremov R.G., Vereshaga Y.A., Volynsky P.E., Nolde D.E., Arseniev A.S. // J. Comput. Aided Mol. Des. 2006. V. 20. No 1, P. 27-45
12. Polyansky A.A., Volynsky P.E., Efremov R.G. // J. Am. Chem. Soc. 2012. V. 134. No 35. P. 14390-14400
13. Volynsky P.E., Polyansky A.A., Fakhrutdinova G.N., Bocharov E.V., Efremov R.G. // J. Am. Chem. Soc. 2013. V. 135. No 22. P. 8105-8108
14. Roskoski R. // Pharmacol. Res. Off. J. Ital. Pharmacol. Soc. 2014. V. 79. P. 34-74
15. Li E., Hristova K. // Biochemistry. 2006. V. 45. No 20. P. 6241-6251
16. Hubert P., Sawma P., Duneau J.-P., Khao J., Hénin J., Bagnard D., Sturgis J. // Cell Adhes. Migr. 2010. V. 4. No 2. P. 313-324
17. Najumudeen A.K. // Sci. Signal. 2010. V. 3. No 138. P. jc6
18. Bennasroune A., Fickova M., Gardin A., Dirrig-Grosch S., Aunis D., Crémel G., Hubert P. // Mol. Biol. Cell. 2004. V. 15. No 7. P. 3464-3474
19. Arpel A., Sawma P., Spenlé C., Fritz J., Meyer L., Garnier N., Velázquez-Quesada I., Hussenet T., Aci-Sèche S., Baumlin N., et al. // Cell Rep. 2014. V. 8. No 6. P. 1714-1721
20. Yin H., Slusky J.S., Berger B.W., Walters R.S., Vilaire G., Litvinov R.I., Lear J.D., Caputo G.A., Bennett J.S., DeGrado W.F. // Science. 2007. V. 315. No 5820. P. 1817-1822
21. Yano Y., Kondo K., Kitani R., Yamamoto A., Matsuzaki K. // Biochemistry. 2015. V. 54. No 6. P. 1371-1379
22. Russ W.P., Engelman D.M. // Proc. Natl. Acad. Sci. U. S. A., 1999, V. 96. No 3. P. 863-868
23. Bocharov E.V., Volynsky P.E., Pavlov K.V., Efremov R.G., Arseniev A.S. // Cell Adhes. Migr. 2010. V. 4. No 2. P. 284-298
24. Mineev K.S., Lesovoy D.M., Usmanova D.R., Goncharuk S.A., Shulepko M.A., Lyukmanova E.N., Kirpichnikov M.P., Bocharov E.V., Arseniev A.S. // Biochim. Biophys. Acta - Biomembr. 2014. V. 1838. No 1. P. 164-172
25. Smith S.O., Bormann B.J. // Proc. Natl. Acad. Sci. U. S. A., 1995, V. 92. No 2. P. 488-491
26. Pohorille A., Jarzynski C., Chipot C. // J. Phys. Chem. B., 2010, V. 114. No 32. P. 10235-10253
27. Hénin J., Pohorille A., Chipot C. // J. Am. Chem. Soc. 2005. V. 127. No 23. P. 8478-8484
28. Engelman D.M., Adair B.D., Brünger A., Flanagan J.M., Hunt J.F., Lemmon M.A., Treutlein H., Zhang J. // Soc. Gen. Physiol. Ser. 1993. V. 48. P. 11-21
29. Melnyk R.A., Kim S., Curran A.R., Engelman D.M., Bowie J.U., Deber C.M. // J. Biol. Chem. 2004. V. 279. No 16. P. 16591-16597
30. Doura A.K., Kobus F.J., Dubrovsky L., Hibbard E., Fleming K.G. J. // Mol. Biol. 2004. V. 341. No 4. P. 991-998
31. Prakash A., Janosi L., Doxastakis M. // Biophys. J. 2011. V. 101. No 8. P. 1949-1958
32. Cuthbertson J.M., Bond P.J., Sansom M.S.P. // Biochemistry. V. 45. No 48. P. 14298-14310
33. Duong M.T., Jaszewski T.M., Fleming K.G., MacKenzie K.R. // J. Mol. Biol. 2007. V. 371. No 2. P. 422-434
34. Mueller B.K., Subramaniam S., Senes A. // Proc. Natl. Acad. Sci. U. S. A. 2014. V. 111. No 10. P. E888-E895
35. Janosi L., Prakash A., Doxastakis M. // Biophys. J. 2010. V. 99. No 1. P. 284-292
36. Johnson R.M., Rath A., Melnyk R.A., Deber C.M. // Biochemistry. V. 45. No 28. P. 8507-8515
37. Mehrbod M., Mofrad M.R.K. // PLoS Comput. Biol. 2013. V. 9. No 3. P. e1002948
38. Caputo G.A. // Methods Mol. Biol. 2013. V. 1063. P. 95-116
39. Pyrkova D.V., Tarasova N.K., Pyrkov T.V., Krylov N.A., Efremov R.G. // Soft Matter. 2011. V. 7. No 6. P. 2569-2579
40. Parton D.L., Tek A., Baaden M., Sansom M.S.P. // PLoS Comput. Biol. 2013. V. 9. No 4. P. e1003034
41. Lensink M.F., Govaerts C., Ruysschaert J.-M. // J. Biol. Chem. 2010. V. 285. No 14. P. 10519-10526
42. Poveda J.A., Giudici A.M., Renart M.L., Molina M.L., Montoya E., Fernández-Carvajal A., Fernández-Ballester G., Encinar J.A., González-Ros J.M. // Biochim. Biophys. Acta-Biomembranes. 2014. V. 1838. No 6. P. 1560-1567
43. Dave P.C., Tiburu E.K., Damodaran K., Lorigan G.A. // Biophys. J. 2004. V. 86. No 3. P. 1564-1573
44. Stangl M., Schneider D. // Biochim. Biophys. Acta-Biomembr., 2015, V. 1848. No 9. P. 1886-1896
45. Kuznetsov A.S., Polyansky A.A., Fleck M., Volynsky P.E., Efremov R.G. // J. Chem. Theory Comput. 2015. V. 11. No 9. P. 4415-4426
46. Lemmon M.A., Flanagan J.M., Treutlein H.R., Zhang J., Engelman D.M. // Biochemistry. 1992. V. 31. No 51. P. 12719-12725
47. Lee J., Im W. // J. Am. Chem. Soc. 2008. V. 130. No. 20. P. 6456-6462
48. Mineev K.S., Bocharov E.V, Volynsky P.E., Goncharuk M.V., Tkach E.N., Ermolyuk Y.S., Schulga A.A., Chupin V.V., Maslennikov I.V., Efremov R.G., et al. // Acta Naturae. 2011. V. 3. No 2. P. 90-98
49. Van Der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A.E., Berendsen H.J.C. // J. Comput. Chem. 2005. V. 26. No 16, P. 1701-1718
50. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., Di-Nola A., Haak J.R. // J. Chem. Phys. 1984. V. 81. No 8. P. 3684
51. Bussi G., Donadio D., Parrinello M. // J. Chem. Phys. 2007. V. 126. No 1. P. 014101