Investigating the binding specificity of U1A-RNA by computational mutagenesis

Journal of Molecular Biology

Volumn 295, Issue 1, 2000, Pages 1-6

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

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Computational mutagenesis; Continuum solvent; MM PBSA; RNA protein recognition; U1A

Indexed keywords

RNA; RNA BINDING PROTEIN;

ARTICLE; BINDING AFFINITY; BINDING SITE; CONTROLLED STUDY; PRIORITY JOURNAL; PROTEIN RNA BINDING; SITE DIRECTED MUTAGENESIS; SPLICEOSOME;

MAMMALIA;

EID: 0034614387     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3319     Document Type: Article

References (34)

1. Allain F. H. T., Gubser C. C., Howe P. W. A., Nagai K., Nehaus D., Varani G. Specificity of ribonucleoprotein interaction determined by RNA folding during complex formation. Nature. 380:1996;646-650.
2. Allain F. H. T., Howe P. W. A., Neuhaus D., Varani G. Structural basis of the RNA-binding specificity of human U1A protein. EMBO J. 16:1997;5764-5774.
3. Avis J. M., Allain F. H. T., Howe P. W. A., Varani G., Nagai K., Neuhaus D. 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. 257:1996;398-411.
4. Case D. A., Pearlman D. A., Caldwell J. W., Cheatham T. E. III, Ross W. S., Simmerling C. S., Darden T. A., Merz K. M., Stanton R. V., Cheng A. L., Vincent J. J., Crowley M., Ferguson D. M., Radmer R. J., Seibel G. L. et al. AMBER 5. 1997;University of California San Francisco.
5. Cheatham T. E., Srinivasan J., Case D. A., Kollman P. A. Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. J. Biomol. Struct. Dynam. 16:1998;265-280.
6. 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., Kollman P. A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 118:1996;2309-2309.
7. Ferrin T. E., Huang C. C., Jarvis L. E., Langridge R. The MIDAS display system. J. Mol. Graph. 6:1988;13-27.
8. Froloff N., Windemuth A., Honig B. On the calculation of binding free energies using continuum methods: application to MHC class I protein-peptide interactions. Protein Sci. 6:1997;1293-1301.
9. Hall K. B. Interaction of RNA hairpins with the human U1A N-terminal RNA binding domain. Biochemistry. 33:1994;10076-10088.
10. Hall K. B., Kranz J. K. Thermodynamics and mutations in RNA-protein interactions. Methods Enzymol. 259:1995;261-281.
11. Honig B., Nicholls A. Classical electrostatics in biology and chemistry. Science. 268:1995;1144-1149.
12. Jessen T. H., Oubridge C., Teo C. H., Pritchard C., Nagai K. Identification of molecular contacts between the U1-A small nuclear ribonucleoprotein and U1 RNA. EMBO J. 10:1991;3447-3456.
13. Kenan D. J., Query C. C., Keene J. D. RNA recognition - towards identifying determinants of specificity. Trends Biochem. Sci. 16:1991;214-220.
14. Kranz J. K., Hall K. B. RNA binding mediates the local cooperativity between the beta-sheet and the C-terminal tail of the human U1A RBD1 protein. J. Mol. Biol. 275:1998;465-481.
15. Kranz J. K., Hall K. B. RNA recognition by the human U1A protein is mediated by a network of local cooperative interactions that create the optimal binding surface. J. Mol. Biol. 285:1999;215-231.
16. Kranz J. K., Lu J. R., Hail K. B. Contribution of the tyrosines to the structure and function of the human U1A N-terminal RNA binding domain. Protein Sci. 5:1996;1567-1583.
17. Laird-Offringa I. A., Belasco J. G. Analysis of Rna-binding proteins by in vitro genetic selection -identification of an amino acid residue important for locking U1A onto its RNA target. Proc. Natl Acad. Sci. USA. 92:1995;11859-11863.
18. Massova I., Kollman P. A. Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J. Am. Chem. Soc. 121:1999;8138-8143.
19. Nagai K., Oubridge C., Ito N., Avis J., Evans P. The RNP domain - a sequence-specific RNA-binding domain involved in processing and transport of RNA. Trends Biochem. Sci. 20:1995;235-240.
20. Nagai K., Oubridge C., Jessen T. H., Li J., Evans P. R. Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein-A. Nature. 348:1990;515-520.
21. Oubridge C., Ito H., Evans P. R., Teo C. H., Nagai K. Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature. 372:1994;432-438.
22. Reyes C. M., Kollman P. A. Molecular dynamics studies of U1A-RNA complexes RNA. RNA. 5:1999;235-244.
23. Sanner M. F., Olson A. J., Spehner J. C. Reduced surface - an efficient way to compute molecular surfaces. Biopolymers. 38:1996;305-320.
24. Sharp K. A., Honig B. Electrostatic interactions in macromolecules - theory and applications. Annu. Rev. Biophys. Biophys. Chem. 19:1990;301-332.
25. Shen J., Quicho F. A. Calculation of the binding energy differences for receptor-ligand systems using the Poisson-Boltzmann method. J. Comp. Chem. 16:1995;445-448.
26. Shen J., Wendoloski J. Electrostatic binding energy calculation using the finite difference solution to the linearized Poisson-Boltzmann equation: assessment of its accuracy. J. Comp. Chem. 17:1996;350-357.
27. Sitkoff D., Sharp K. A., Honig B. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98:1994;1978-1988.
28. Smith K. C., Honig B. Evaluation of the conformational free energies of loops in proteins. Protein: Struct. Funct. Genet. 18:1994;119-132.
29. Srinivasan J., Cheatham T. E., Cieplak P., Kollman P. A., Case D. A. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate - DNA helices. J. Am. Chem. Soc. 120:1998a;9401-9409.
30. Srinivasan J., Miller J., Kollman P. A., Case D. K. Continuum solvent studies of the stability of RNA hairpin loops and helices. J. Biomol. Struct. Dynam. 16:1998b;671-675, 677-682.
31. Varani G., Nagai K. RNA recognition by RNP proteins during RNA processing. Annu. Rev. Biophys. Biomol. Struct. 27:1998;407-445.
32. Williams D. J., Hall K. B. RNA hairpins with non-nucleotide-spacers bind efficiently to the human U1A protein. J. Mol. Biol. 257:1996;265-275.
33. Zeng Q. Y., Hall K. B. Contribution of the C-terminal tail of U1A RBD1 to RNA recognition and protein stability. RNA. 3:1997;303-314.
34. Zhang T., Koshland D. E. Jr. Computational method for relative binding energies of enzyme-substrate complexes. Protein Sci. 5:1996;348-356.