Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif

Nucleic Acids Research

Volumn 33, Issue 10, 2005, Pages 3435-3446

  Cojocaru, Vlad ^a   Klement, Reinhard ^a   Jovin, Thomas M ^a  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; GUANINE; SMALL NUCLEAR RNA; URACIL; SMALL NUCLEAR RIBONUCLEOPROTEIN; U4 SMALL NUCLEAR RNA;

ARTICLE; BASE MISPAIRING; COMPUTER SIMULATION; CORRELATION FUNCTION; CRYSTAL STRUCTURE; HUMAN; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN MOTIF; RNA CONFORMATION; RNA STRUCTURE; BASE PAIRING; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; METABOLISM;

ADENINE; BASE PAIRING; COMPUTER SIMULATION; GUANINE; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RIBONUCLEOPROTEINS, SMALL NUCLEAR; RNA, SMALL NUCLEAR;

EID: 20444464100     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gki664     Document Type: Article

References (51)

1. Nottrott,S., Hartmuth,K., Fabrizio,P., Urlaub,H., Vidovic,I., Ficner,R. and Lührmann,R. (1999) Functional interaction of a novel 15.5kD U4/U6 center dot U5 tri-snRNP protein with the 5′ stem-loop of U4 snRNA. EMBO J., 18, 6119-6133.
2. Nottrott,S., Urlaub,H. and Lührmann,R. (2002) Hierarchical, clustered protein interactions with U4/U6 snRNA: A biochemical role for U4/U6 proteins. EMBO J., 21, 5527-5538.
3. Vidovic,I., Nottrott,S., Hartmuth,K., Lührmann,R. and Ficner,R. (2000) Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment. Mol. Cell, 6, 1331-1342.
4. Klein,D.J., Schmeing,T.M., Moore,P.B. and Steitz,T.A. (2001) The kink-turn: A new RNA secondary structure motif. EMBO J., 20, 4214-4221.
5. Charron,C., Manival,X., Clery,A., Charpentier,B., Marmier-Gourrier,N., Branlant,C. and Aubry,A. (2004) The archaeal sRNA binding protein L7Ae has a 3D structure very similar to that of its eukaryal counterpart while having a broader RNA-binding specificity. J. Mol. Biol., 342, 757-773.
6. Hamma,T. and Ferre-D'Amare,A.R. (2004) Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA at 1.8 angstrom resolution. Structure, 12, 893-903.
7. Moore,T., Zhang,Y.M., Fenley,M.O. and Li,H. (2004) Molecular basis of box C/D RNA-protein interactions: Cocrystal structure of archaeal L7Ae and a box C/D RNA. Structure, 12, 807-818.
8. Kuhn,J.F., Tran,E.J. and Maxwell,E.S. (2002) Archaeal ribosomal protein L7 is a functional homolog of the eukaryotic 15.5kD/Snu13p snoRNP core protein. Nucleic Acids Res., 30, 931-941.
9. Chen,Y.W., Bycroft,M. and Wong,K.B. (2003) Crystal structure of ribosomal protein L30e from the extreme thermophile Thermococcus celer: thermal stability and RNA binding. Biochemistry, 42 2857-2865.
10. Goody,T.A., Melcher,S.E., Norman,D.G. and Lilley,D.M.J. (2004) The kink-turn motif in RNA is dimorphic, and metal ion-dependent. RNA, 10, 254-264.
11. Matsumura,S., Ikawa,Y. and Inoue,T. (2003) Biochemical characterization of the kink-turn RNA motif. Nucleic Acids Res., 31, 5544-5551.
12. Cojocaru,V., Nottrott,S., Klement,R. and Jovin,T.M. (2005) The snRNP 15.5K protein folds its cognate K-turn RNA: A combined theoretical and biochemical study. RNA, 11, 197-209.
13. Reyes,C.M. and Kollman,P.A. (2000) Investigating the binding specificity of U1A-RNA by computational mutagenesis. J. Mol. Biol., 295, 1-6.
14. Reyes,C.M., Nifosi,R., Frankel,A.D. and Kollman,P.A. (2001) Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex. Biophys. J., 80, 2833-2842.
15. Pitici,F., Beveridge,D.L. and Baranger,A.M. (2002) Molecular dynamics simulation studies of induced fit and conformational capture in U1A-RNA binding: Do molecular substates code for specificity? Biopolymers, 65, 424-435.
16. Réblová,K., Špačková,N., Koča,J., Leontis,N.B. and Šponer,J. (2004) Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex. Biophys. J. 87, 3397-3412.
17. Guo,J.X. and Gmeiner,W.H. (2001) Molecular dynamics simulation of the human U2B′ protein complex with U2 snRNA hairpin IV in aqueous solution. Biophys. J., 81, 630-642.
18. Guo,J.X., Daizadeh,I. and Gmeiner,W.H. (2000) Structure of the Sm binding site from human U4 snRNA derived from a 3 ns PME molecular dynamics simulation. J. Biomol. Struct. Dyn., 18, 335-344.
19. Li,W., Ma,B.Y. and Shapiro,B.A. (2001) Molecular dynamics simulations of the denaturation and refolding of an RNA tetraloop. J. Biomol. Struct. Dyn., 19, 381-396.
20. Réblová,K., Špačková,N., Štefl,R., Csaszar,K., Koča,J., Leontis,N.B. and Šponer,J. (2003) Non-Watson-Crick basepairing and hydration in RNA motifs: Molecular dynamics of 5S rRNA loop E. Biophys. J., 84, 3564-3582.
21. 2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations. Chem. Biol., 10, 551-561.
22. Auffinger,P., Bielecki,L. and Westhof,E. (2004) Anion binding to nucleic acids. Structure, 12, 379-388.
23. 2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations. J. Mol. Biol., 335, 555-571.
24. Auffinger,P. and Westhof,E. (2000) RNA solvation: A molecular dynamics simulation perspective. Biopolymers, 56, 266-274.
25. Auffinger,P. and Westhof,E. (1998) Hydration of RNA base pairs. J. Biomol. Struct. Dyn., 16, 693-707.
26. Auffinger,P. and Westhof,E. (1997) RNA hydration: Three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin. J. Mol. Biol., 269, 326-341.
27. Auffinger,P., Louise-May,S. and Westhof,E. (1999) Molecular dynamics simulations of solvated yeast tRNA(Asp). Biophys. J., 76, 50-64.
28. Rázga,F., Špačková,N., Réblová,K., Koča,J., Leontis,N.B. and Šponer,J. (2004) Ribosomal RNA kink-turn motif - a flexible molecular hinge. J. Biomol. Struct. Dyn., 22, 183-193.
29. Rázga,F., Koča,J., Šponer,J. and Leontis,N.B. (2005 Hinge-like motions in RNA kink-turns: The role of the second A-minor motif and nominally unpaired bases. Biophys. J., 88, 3466-3485.
30. Elber,R. and Karplus,M. (1990) Enhanced sampling in molecular dynamics - use of the time-dependent hartree approximation for a simulation of carbon-monoxide diffusion through myoglobin. J. Am. Chem. Soc. 112, 9161-9175.
31. Simmerling,C. and Kollman,P. (1996) Improved simulation of flexible systems through locally enhanced sampling. Abstracts of Papers of the American Chemical Society, 212, 153.
32. Simmerling,C., Miller,J.L. and Kollman,P.A. (1998) Combined locally enhanced sampling and Particle Mesh Ewald as a strategy to locate the experimental structure of a nonhelical nucleic acid. J. Am. Chem. Soc., 120, 7149-7155.
33. Simmerling,C., Fox,T. and Kollman,P.A. (1998) Use of locally enhanced sampling in free energy calculations: Testing and application to the α β anomerization of glucose. J. Am. Chem. Soc., 120, 5771-5782.
34. Stultz,C.M. and Karplus,M. (1998) On the potential surface of the locally enhanced sampling approximation. J. Chem. Phys., 109 8809-8815.
35. Fadrná,E., Špačková,N., Štefl,R., Koča,J., Cheatham,T.E.,III and Šponer,J. (2004) Molecular dynamics simulations of guanine quadruplex loops: Advances and force field limitations. Biophys. J., 87, 227-242.
36. Cornell,W.D., Cieplak,P., Bayly,C.I., Gould,I.R., Merz,K.M., Ferguson,D.M., Spellmeyer,D.C., Fox,T., Caldwell,J.W. and Kollman,P.A. (1996) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc., 117 5179-5197.
37. Pearlman,D.A., Case,D.A., Caldwell,J.W., Ross,W.S., Cheatham,T.E., Debolt,S., Ferguson,D., Seibel,G. and Kollman,P. (1995) Amber, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun., 91, 1-41.
38. Humphrey,W., Dalke,A. and Schulten,K. (1996) VMD-Visual molecular dynamics. J. Mol. Graph., 14, 33-38.
39. Kitao,A. and Go,N. (1999) Investigating protein dynamics in collective coordinate space. Curr. Opin. Struct. Biol., 9, 164-169.
40. Doruker,P., Atilgan,A.R. and Bahar,I. (2000) Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to α-amylase inhibitor. Proteins, 40, 512-524.
41. Alakent,B., Doruker,P. and Camurdan,M.C. (2004) Application of time series analysis on molecular dynamics simulations of proteins: A study of different conformational spaces by principal component analysis. J. Chem. Phys., 121, 4759-4769.
42. Ota,N. and Agard,D.A. (2001) Enzyme specificity under dynamic control II: Principal component analysis of α-lytic protease using global and local solvent boundary conditions. Protein Sci., 10, 1403-1414.
43. Mongan,J. (2004) Interactive essential dynamics. J. Comput. Aided Mol. Des., 18, 433-436.
44. Balsera,M.A., Wriggers,W., Oono,Y. and Schulten,K. (1996) Principal component analysis and long time protein dynamics. J. Phys. Chem., 100, 2567-2572.
45. Saenger,W. (1984) Principles of Nucleic Acids Structure. Springer-Verlag, New York, NY.
46. Chen,G., Znosko,B.M., Kennedy,S.D., Krugh,T.R. and Turner,D.H. (2005) Solution structure of an RNA internal loop with three consecutive sheared GA pairs. Biochemistry, 44, 2845-2856.
47. Rhee,Y.M. and Pande,V.S. (2003) Multiplexed-replica exchange molecular dynamics method for protein folding simulation. Biophys. J., 84 775-786.
48. Sanbonmatsu,K.Y. and Garcia,A.E. (2002) Structure of Metenkephalin in explicit aqueous solution using replica exchange molecular dynamics. Proteins, 46, 225-234.
49. Zhou,R.H. (2004) Exploring the protein folding free energy landscape: coupling replica exchange method with P3ME/RESPA algorithm. J. Mol. Graph. Model., 22, 451-463.
50. Williamson,J.R. (2000) Induced fit in RNA-protein recognition. Nature Struct. Biol., 7, 834-837.
51. Leulliot,N. and Varani,G. (2001) Current topics in RNA-protein recognition: Control of specificity and biological function through induced fit and conformational capture. Biochemistry, 40, 7947-7956.