Molecular dynamics studies of U1A-RNA complexes

RNA

Volumn 5, Issue 2, 1999, Pages 235-244

  Reyes, Carolina M ^a   Kollman, Peter A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Molecular dynamics simulations; Nucleic acids; PIE RNA; RNA protein interactions

Indexed keywords

RNA; SMALL NUCLEAR RIBONUCLEOPROTEIN; WATER;

ARTICLE; BINDING AFFINITY; COMPLEX FORMATION; COMPUTER SIMULATION; CRYSTAL STRUCTURE; HYDROGEN BOND; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; POLYADENYLATION; PRIORITY JOURNAL; PROTEIN RNA BINDING;

HYDROGEN BONDING; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR CONFORMATION; NUCLEIC ACID CONFORMATION; PROTEIN STRUCTURE, SECONDARY; RIBONUCLEOPROTEIN, U1 SMALL NUCLEAR; RIBONUCLEOPROTEINS, SMALL NUCLEAR; RNA; RNA-BINDING PROTEINS;

EID: 0033057703     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838299981657     Document Type: Article

References (32)

1. Abola EE, Sussman JL, Prilusky J, Manning NO. 1997. Protein data bank archives of three-dimensional macromolecular structures. Methods Enzymol 277:556-571.
2. Allain FHT, Gubser CG, Howe PWA, Nagai K, Neuhaus D, Varani G. 1996. Specificity of ribonucleoprotein interaction determined by RNA folding during complex formation. Nature 380:646-650.
3. Allain FHT, Howe PWA, Neuhaus D, Varani G. 1997. Structural basis of the RNA-binding specificity of human U1A protein. EMBO J 16:5764-5774.
4. Auffinger P, Westhof E. 1998. Simulations of the molecular dynamics of nucleic acids. Curr Opin Struct Biol 8:227-236.
5. Avis JM, Allain FHT, Howe PWA, Varani G, Nagai K, Neuhaus D. 1996. Solution structure of the N-terminal RNP domain of U1A protein: The role of C-terminal residues in structure stability and RNA binding. J Mol Biol 257:398-411.
6. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. 1984. Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684-3690.
7. Birney E, Kumar S, Krainer AR. 1993. Analysis of the RNA-recognition motif and RS and RGG domain: Conservation in metazoan premRNA splicing factors. Nucleic Acids Res 21:5803-5816.
8. Boelens WC, Jansen EJR, van Venrooij WJ, Stripecke R, Mattaj IW, Gunderson SI. 1993. The human U1 snRNP-specific UIA protein inhibits polyadenylation of its own pre-mRNA. Cell 72:881-892.
9. Burd CG, Dreyfuss G. 1994. Conserved structures and diversity of functions of RNA-binding proteins. Science 265:615-621.
10. Case DA, Pearlman DA, Caldwell JW, Cheatham TE III, Ross WS, Simmerling CS, Darben TA, Merz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Ferguson DM, Radmer RJ, Seibel GL, Singh UC, Weiner PK, Kollman PA. 1997. AMBER 5 (software). University of California, San Francisco.
11. Cheatham TE III, Miller JL, Fox T, Darden TA, Kollman PA. 1995. Molecular dynamics simulations on solvated biomolecular systems: The Particle Mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins. J Am Chem Soc 117:4193-4194.
12. Cornell WD, Cieplak P, Bayly CI, Kollman PA. 1995. A second generation force field for the simulation of proteins and nucleic acids. J Am Chem Soc 117:5179-5197.
13. DardenT, York D, Pedersen L. 1993. Particle Mesh Ewald: An N·log(N) method for Ewald sums in large systems. J Chem Phys 98:10089-10092.
14. Eriksson MAL, Nilsson L. 1995. Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution. Biophys J 68:402-26.
15. Ferrin TE, Huang CC, Jarvis LE, Langridge R. 1988. The MIDAS display system. J Mol Graphics 6:13-27, 36-37.
16. Fox T, Kollman PA. 1996. The application of different solvation and electrostatic models in molecular dynamics simulation of ubiquitin: How well is the X-ray structure "maintained"? Proteins Struct Funct Genet 25:315-34.
17. Gubser CG, Varani G. 1996. Structure of the polyadenylation regulatory element of the human U1A pre-mRNA 3′-untranslated region and interaction with the U1A protein. Biochemistry 35:2253-2267.
18. Hall KB. 1994. Interaction of RNA hairpins with the human U1A N-terminal RNA binding domain. Biochemistry 33:10076-10088.
19. Hall KB, Kranz JK. 1995. Thermodynamics and mutations in RNA-protein interactions. Methods Enzymol 259:261-281.
20. Jessen TH, Oubridge C, Teo CH, Pritchard C, Nagai K. 1991. Identification of molecular contacts between U1A small nucleoprotein and U1 RNA. EMBO J 10:3447-3456.
21. Laird-Offinga IA, Belasco JG. 1995. Analysis of RNA-binding protein by in vitro genetic selection: Identification of an amino acid residue important for locking U1A onto its RNA target. Proc Natl Acad Sci USA 92:11859-11863.
22. Lu J, Hall KB. 1997. Tertiary structure of RBD2 and backbone dynamics of RBD1 and RBD2 of the human U1A protein determined by NMR spectroscopy. Biochemistry 36:10393-10405.
23. Miaskiewicz K, Ornstein RL 1996. DNA binding by TATA-box binding protein (TBP): A molecular dynamics computational study. J Biomol Struct Dynam 13:593-600.
24. Miller JL, Kollman PA. 1997. Theoretical studies of an exceptionally stable RNA tetraloop: Observation of convergence from an incorrect NMR structure to the correct one using unrestrained molecular dynamics. J Mol Biol 270:436-450.
25. Moras D, Poterszman A. 1995. Diverse modes of recognition. Curr Biol 5:249-251.
26. Nagai K, Oubridge C, Ito N, Avis J, Evans P. 1995. The RNP domain: A sequence-specific RNA-binding domain involved in processing and transport of RNA. Trends Biochem Sci 20:235-240.
27. Nagai K, Oubridge C, Jessen TH, Li J, Evans PR. 1990. Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein A. Nature 348:515-520.
28. Oubridge C, Ito N, Evans PR, Teo CH, Nagai K. 1994. Crystal structure at 1.92 Å resolution of the RNA-binding domain of the u1A spliceosomal protein complexed with an RNA hairpin. Nature 372:432-438.
29. Roxström G, Velàzquez I, Paulino M, Tapia O. 1998. Molecular dynamics simulation of a Zif268-DNA complex in water. Spatial patterns and fluctuations sensed form a nanosecond trajectory. J Phys Chem B 102:1828-1832.
30. Scherly D, Kambach C, Boelens W, van Venrooij WJ, Mattaj IW. 1991. Conserved amino acid residues within and outside the N-terminal ribonucleoprotein motif of U1A small nuclear ribonucleoprotein involved in u1 RNA binding. J Mol Biol 219:577-584.
31. Tang Y, Nilsson L. 1998. Interaction of human SRY protein with DNA: A molecular dynamics study. Proteins Struct Funct Genet 31:417-433.
32. Zeng Q, Hall K. 1997. Contribution of the C-terminal tail of U1A RBD1 to RNA recognition and protein stability. RNA 3:303-314.