Computational modeling of protein-RNA complex structures

Methods

Volumn 65, Issue 3, 2014, Pages 310-319

  Tuszynska, Irina ^a   Matelska, Dorota ^a   Magnus, Marcin ^a   Chojnowski, Grzegorz ^a   Kasprzak, Joanna M ^b   Kozlowski, Lukasz P ^a   Dunin Horkawicz, Stanislaw ^a   Bujnicki, Janusz M ^a,b  

^a INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Poland)

^b ADAM MICKIEWICZ UNIVERSITY   (Poland)

Author keywords

Computational docking; Macromolecular complex; Protein; Protein RNA binding; RNA; RNP; Structural bioinformatics

Indexed keywords

COMPUTATIONAL DOCKING; MACROMOLECULAR COMPLEX; PROTEIN; PROTEIN-RNA BINDING; RNA; RNP; STRUCTURAL BIOINFORMATICS;

BACILLUS SUBTILIS; BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MOLECULAR CONFORMATION; MOLECULAR DOCKING SIMULATION; PROTEIN BINDING; RIBOSWITCH; RNA, RIBOSOMAL, 16S; RNA-BINDING PROTEINS; SOFTWARE; THERMOANAEROBACTER;

EID: 84894241805     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2013.09.014     Document Type: Article

References (84)

1. Chen Y., Varani G. FEBS J. 2005, 272:2088-2097.
2. Glisovic T., Bachorik J.L., Yong J., Dreyfuss G. FEBS Lett. 2008, 582:1977-1986.
3. Cheng J., Kapranov P., Drenkow J., Dike S., Brubaker S., Patel S., Long J., Stern D., Tammana H., Helt G., Sementchenko V., Piccolboni A., Bekiranov S., Bailey D.K., Ganesh M., Ghosh S., Bell I., Gerhard D.S., Gingeras T.R. Science 2005, 308:1149-1154.
4. Lasa I., Toledo-Arana A., Dobin A., Villanueva M., De los Mozos I.R., Vergara-Irigaray M., Segura V., Fagegaltier D., Penades J.R., Valle J., Solano C., Gingeras T.R. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:20172-20177.
5. Lukong K.E., Chang K.W., Khandjian E.W., Richard S. Trends Genet. 2008, 24:416-425.
6. Cooper T.A., Wan L., Dreyfuss G. Cell 2009, 136:777-793.
7. Cammer S., Carter C.W. Bioinformatics 2010, 26:709-714.
8. Ban N., Nissen P., Hansen J., Moore P.B., Steitz T.A. Science 2000, 289:905-920.
9. Ke A., Doudna J.A. Methods 2004, 34:408-414.
10. Scott L.G., Hennig M. Methods Mol. Biol. 2008, 452:29-61.
11. Steen H., Jensen O.N. Mass Spectrom. Rev. 2002, 21:163-182.
12. Wichadakul D., McDermott J., Samudrala R. Methods Mol. Biol. 2009, 541:101-143.
13. Moreira I.S., Fernandes P.A., Ramos M.J. J. Comput. Chem. 2010, 31:317-342.
14. Bujnicki J.M. Prediction of Protein Structures, Functions and Interactions 2008, Wiley & Sons.
15. Laing C., Schlick T. J. Phys.: Condens. Matter 2010, 22:283101.
16. Rother K., Rother M., Boniecki M., Puton T., Bujnicki J.M. J. Mol. Model. 2011, 17:2325-2336.
17. Kryshtafovych A., Fidelis K., Moult J. Proteins 2011, 79(Suppl. 10):196-207.
18. Chothia C., Lesk A.M. EMBO J. 1986, 5:823-826.
19. Soding J., Remmert M. Curr. Opin. Struct. Biol. 2011, 21:404-411.
20. Chothia C., Gerstein M. Nature 1997, 385(579):581.
21. Kumar S., Ma B., Tsai C.J., Sinha N., Nussinov R. Protein Sci. 2000, 9:10-19.
22. Kurowski M.A., Bujnicki J.M. Nucleic Acids Res. 2003, 31:3305-3307.
23. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Nucleic Acids Res. 1997, 25:3389-3402.
24. Rother M., Milanowska K., Puton T., Jeleniewicz J., Rother K., Bujnicki J.M. Bioinformatics 2011, 27:2441-2442.
25. Rognes T. Nucleic Acids Res. 2001, 29:1647-1652.
26. Freyhult E.K., Bollback J.P., Gardner P.P. Genome Res. 2007, 17:117-125.
27. Nawrocki E.P., Kolbe D.L., Eddy S.R. Bioinformatics 2009, 25:1335-1337.
28. Eggenhofer F., Hofacker I.L., Honer Zu Siederdissen C. Nucleic Acids Res. 2013, 41:W499-503.
29. Cruz J.A., Westhof E. Nat. Methods 2011, 8:513-521.
30. Kladwang W., Chou F.C., Das R. J. Am. Chem. Soc. 2012, 134:1404-1407.
31. Sali A., Blundell T.L. J. Mol. Biol. 1993, 234:779-815.
32. Peitsch M.C. Bio/Technology 1995, 13:658-660.
33. Flores S.C., Wan Y., Russell R., Altman R.B. Pac. Symp. Biocomput. 2010, 216-227.
34. Rother M., Rother K., Puton T., Bujnicki J.M. Nucleic Acids Res. 2011, 39:4007-4022.
35. Das R., Baker D. Annu. Rev. Biochem. 2008, 77:363-382.
36. Roy A., Kucukural A., Zhang Y. Nat. Protoc. 2010, 5:725-738.
37. Das R., Baker D. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:14664-14669.
38. Popenda M., Szachniuk M., Antczak M., Purzycka K.J., Lukasiak P., Bartol N., Blazewicz J., Adamiak R.W. Nucleic Acids Res. 2012, 40:e112.
39. Parisien M., Major F. Nature 2008, 452:51-55.
40. Flores S.C., Altman R.B. RNA 2010, 16:1769-1778.
41. Jossinet F., Westhof E. Bioinformatics 2005, 21:3320-3321.
42. Jossinet F., Ludwig T.E., Westhof E. Bioinformatics 2010, 26:2057-2059.
43. Martinez H.M., Maizel J.V., Shapiro B.A. J. Biomol. Struct. Dyn. 2008, 25:669-683.
44. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., Ferrin T.E. J. Comput. Chem. 2004, 25:1605-1612.
45. Humphrey W., Dalke A., Schulten K. J. Mol. Graph. 1996, 14(33-38):27-38.
46. S. LLC., The PyMOL Molecular Graphics System, Version 1.5.0.4.
47. Guex N., Peitsch M.C. Electrophoresis 1997, 18:2714-2723.
48. Skwark M.J., Elofsson A. Bioinformatics 2013, 29:1817-1818.
49. McGuffin L.J., Buenavista M.T., Roche D.B. Nucleic Acids Res. 2013, 41:W368-W372.
50. Pawlowski M., Gajda M.J., Matlak R., Bujnicki J.M. BMC Bioinformatics 2008, 9:403.
51. Pawlowski M., Bogdanowicz A., Bujnicki J.M. Nucleic Acids Res. 2013, 41:W389-397.
52. Capriotti E., Norambuena T., Marti-Renom M.A., Melo F. Bioinformatics 2011, 27:1086-1093.
53. Norambuena T., Cares J.F., Capriotti E., Melo F. Bioinformatics 2013, 10.1093/bioinformatics/btt1441.
54. Bellay J., Han S., Michaut M., Kim T., Costanzo M., Andrews B.J., Boone C., Bader G.D., Myers C.L., Kim P.M. Genome Biol. 2011, 12:R14.
55. Kozlowski L.P., Bujnicki J.M. BMC Bioinformatics 2012, 13:111.
56. Puton T., Kozlowski L., Tuszynska I., Rother K., Bujnicki J.M. J. Struct. Biol. 2012, 179:261-268.
57. Walia R.R., Caragea C., Lewis B.A., Towfic F., Terribilini M., El-Manzalawy Y., Dobbs D., Honavar V. BMC Bioinformatics 2012, 13:89.
58. Terribilini M., Sander J.D., Lee J.H., Zaback P., Jernigan R.L., Honavar V., Dobbs D. Nucleic Acids Res. 2007, 35:W578-584.
59. Kim O.T., Yura K., Go N. Nucleic Acids Res. 2006, 34:6450-6460.
60. Perez-Cano L., Fernandez-Recio J. Proteins 2010, 78:25-35.
61. Zhao H., Yang Y., Zhou Y. Nucleic Acids Res. 2011, 39:3017-3025.
62. Vajda S., Hall D.R., Kozakov D. Proteins 2013, 10.1002/prot.24343.
63. Bastard K., Saladin A., Prevost C. Int. J. Mol. Sci. 2011, 12:1316-1333.
64. Lensink M.F., Wodak S.J. Proteins 2010, 78:3073-3084.
65. Zacharias M. Curr. Opin. Struct. Biol. 2010, 20:180-186.
66. Janin J. Mol. BioSyst. 2010, 6:2351-2362.
67. Huang Y., Liu S., Guo D., Li L., Xiao Y. Scientific reports 2013, 3:1887.
68. Dominguez C., Boelens R., Bonvin A.M. J. Am. Chem. Soc. 2003, 125:1731-1737.
69. Katchalski-Katzir E., Shariv I., Eisenstein M., Friesem A.A., Aflalo C., Vakser I.A. Proc. Natl. Acad. Sci. U.S.A. 1992, 89:2195-2199.
70. Ritchie D.W., Kemp G.J. Proteins 2000, 39:178-194.
71. Schneidman-Duhovny D., Inbar Y., Nussinov R., Wolfson H.J. Nucleic Acids Res. 2005, 33:W363-367.
72. Gabb H.A., Jackson R.M., Sternberg M.J. J. Mol. Biol. 1997, 272:106-120.
73. Karaca E., Melquiond A.S., de Vries S.J., Kastritis P.L., Bonvin A.M. Mol. Cell. Proteomics 2010, 9:1784-1794.
74. Gajda M.J., Tuszynska I., Kaczor M., Bakulina A.Y., Bujnicki J.M. Bioinformatics 2010, 26:2986-2987.
75. Tuszynska I., Bujnicki J.M. BMC Bioinformatics 2011, 12:348.
76. Russel D., Lasker K., Webb B., Velazquez-Muriel J., Tjioe E., Schneidman-Duhovny D., Peterson B., Sali A. PLoS Biol. 2012, 10:e1001244.
77. Cruz J.A., Blanchet M.F., Boniecki M., Bujnicki J.M., Chen S.J., Cao S., Das R., Ding F., Dokholyan N.V., Flores S.C., Huang L., Lavender C.A., Lisi V., Major F., Mikolajczak K., Patel D.J., Philips A., Puton T., Santalucia J., Sijenyi F., Hermann T., Rother K., Rother M., Serganov A., Skorupski M., Soltysinski T., Sripakdeevong P., Tuszynska I., Weeks K.M., Waldsich C., Wildauer M., Leontis N.B., Westhof E. RNA 2012, 14:610-625.
78. Eswar N., Eramian D., Webb B., Shen M.Y., Sali A. Methods Mol. Biol. 2008, 426:145-159.
79. Murzin A.G., Brenner S.E., Hubbard T., Chothia C. J. Mol. Biol. 1995, 247:536-540.
80. Agalarov S.C., Sridhar Prasad G., Funke P.M., Stout C.D., Williamson J.R. Science 2000, 288:107-113.
81. Matelska D., Purta E., Panek S., Boniecki M.J., Bujnicki J.M., Dunin-Horkawicz S. RNA 2013, 10.1261/rna.038794.038113.
82. Jurica M.S. Curr. Opin. Struct. Biol. 2008, 18:315-320.
83. Flores S.C., Bernauer J., Shin S., Zhou R., Huang X. Brief. Bioinform. 2012, 13:395-405.
84. Pietal M.J., Szostak N., Rother K.M., Bujnicki J.M. BMC Bioinformatics 2012, 13:333.