Evaluating conformational changes in protein structures binding RNA

Proteins: Structure, Function and Genetics

Volumn 70, Issue 4, 2008, Pages 1518-1526

  Ellis, Jonathan J ^a   Jones, Susan ^a  

^a UNIVERSITY OF SUSSEX   (United Kingdom)

Author keywords

Binding proteins; Conformational changes; Protein structure; RNA

Indexed keywords

RNA; RNA BINDING PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; EVALUATION; MOLECULAR RECOGNITION; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN RNA BINDING; QUANTITATIVE ANALYSIS; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

COMPUTATIONAL BIOLOGY; PROTEIN BINDING; PROTEIN CONFORMATION; RNA; RNA-BINDING PROTEINS;

EID: 39749121395     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21647     Document Type: Article

References (66)

1. Brennan RG, Roderick SL, Takeda Y, Matthews BW. Protein-DNA conformational changes in the crystal structure of a lambda Cro-operator complex. Proc Natl Acad Sci USA 1990;87:8165-8169.
2. Brodolin KL, Studitsky VM, Mirzabekov AD. Conformational changes in E. coli RNA polymerase during promoter recognition. Nucleic Acids Res 1993;21:5748-5753.
3. Crellin P, Chalmers R. Protein-DNA contacts and conformational changes in the Tn10 transpososome during assembly and activation for cleavage. EMBO J 2001;20:3882-3891.
4. Weljie AM, Yamniuk AP, Yoshino H, Izumi Y, Vogel HJ. Protein conformational changes studied by diffusion NMR spectroscopy: application to helix-loop-helix calcium binding proteins. Protein Sci 2003;12:228-236.
5. Yoon SI, Logsdon NJ, Sheikh F, Donnelly RP, Walter MR. Conformational changes mediate interleukin-10 receptor 2 (IL-10R2) binding to IL-10 and assembly of the signaling complex. J Biol Chem 2006;281:35088-35096.
6. Betts MJ, Sternberg MJ. An analysis of conformational changes on protein-protein association: implications for predictive docking. Protein Eng 1999;12:271-283.
7. Conte LL, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol 1999;285:2177-2198.
8. Goh CS, Milburn D, Gerstein M. Conformational changes associated with protein-protein interactions. Curr Opin Struct Biol 2004;14:104-109.
9. Rees B, Cavarelli J, Moras D. Conformational flexibility of tRNA: structural changes in yeast tRNA(Asp) upon binding to aspartyl-tRNA synthetase. Biochimie 1996;78:624-631.
10. Reyes CM, Kollman PA. Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change. J Mol Biol 2000;297:1145-1158.
11. Yikilmaz E, Rouault TA, Schuck P. Self-association and ligand-induced conformational changes of iron regulatory proteins 1 and 2. Biochemistry 2005;44:8470-8478.
12. Williamson J. Induced fit in RNA-protein recognition. Nat Struct Biol 2000;7:834-837.
13. Leulliot N, Varani G. Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture. Biochemistry 2001;40:7947-7956.
14. Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H, Shindyalov I, Bourne P. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
15. Kabsch W. Discussion of solution for best rotation to relate 2 sets of vectors. Acta Crystallogr A 1978;34:827-828.
16. Jones T, Zou J, Cowan S, Kjeldgaard M. Improved methods for building protein models in electron-density maps and the location of errors in these models. Acta Crystallogr A 1991;47:110-119.
17. Kleywegt GJ. Use of non-crystallographic symmetry in protein structure refinement. Acta Crystallogr D Biol Crystallogr 1996;52:842-857.
18. Nishikawa K, Ooi T. Comparison of homologous tertiary structures of proteins. J Theor Biol 1974;43:351-374.
19. Maiorov VN, Crippen GM. Size-independent comparison of protein three-dimensional structures. Proteins 1995;22:273-283.
20. Betancourt MR, Skolnick J. Universal similarity measure for comparing protein structures. Biopolymers 2001;59:305-309.
21. Carugo O, Pongor S. A normalized root-mean-square distance for comparing protein three-dimensional structures. Protein Sci 2001;10:1470-1473.
22. Carugo O. How root-mean-square distance (r.m.s.d.) values depend on the resolution of protein structures that are compared. J Appl Cryst 2003;36:125-128.
23. Cruickshank DW. Remarks about protein structure precision. Acta Crystallogr D Biol Crystallogr 1999;55:583-601.
24. Schneider TR. Objective comparison of protein structures: error-scaled difference distance matrices. Acta Crystallogr D Biol Crystallogr 2000;56:714-721.
25. Schneider TR. A genetic algorithm for the identification of conformationally invariant regions in protein molecules. Acta Crystallogr D Biol Crystallogr 2002;58:195-208.
26. Schneider TR. Domain identification by iterative analysis of error-scaled difference distance matrices. Acta Crystallogr D Biol Crystallogr 2004;60:2269-2275.
27. Ellis JJ, Broom M, Jones S. Protein-RNA interactions: structural analysis and functional classes. Proteins 2007;66:903-911.
28. Kim OTP, Yura K, Go N. Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction. Nucleic Acids Res 2006;34:6450-6460.
29. Morozova N, Allers J, Myers J, Shamoo Y. Protein-RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures. Bioinformatics 2006;22:2746-2752.
30. Chothia C, Janin J. Principles of protein-protein recognition. Nature 1975;256:705-708.
31. Ofran Y, Rost B. Analysing six types of protein-protein interfaces. J Mol Biol 2003;325:377-387.
32. Tjong H, Zhou HX. DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Nucleic Acids Res 2007;35:1465-1477.
33. Jeong E, Chung I, Miyano S. Prediction of residues in protein-RNA interaction sites by neural networks. Genome Informatics 2003;14:506-507.
34. Wallace AC, Borkakoti N, Thornton JM. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci 1997;6:2308-2323.
35. Barker JA, Thornton JM. An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics 2003;19:1644-1649.
36. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LSL. The universal protein resource (UniProt). Nucleic Acids Res 2005;33:D154-D159.
37. Martin ACR. Mapping PDB chains to UniProtKB entries. Bioinformatics 2005;21:4297-4301.
38. Murzin A, Brenner S, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
39. Hoang C, Ferré-D'Amaré AR. Cocrystal structure of a tRNA Ψ55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme. Cell 2001;107:929-939.
40. Pan H, Agarwalla S, Moustakas DT, Finer-Moore J, Stroud RM. Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit. Proc Natl Acad Sci USA 2003;100:12648-12653.
41. Grahn E, Moss T, Helgstrand C, Fridborg K, Sundaram M, Tars K, Lago H, Stonehouse NJ, Davis DR, Stockley PG, Liljas L. Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex. RNA 2001;7:1616-1627.
42. Ni CZ, Syed R, Kodandapani R, Wickersham J, Peabody DS, Ely KR. Crystal structure of the MS2 coat protein dimer: implications for RNA binding and virus assembly. Structure 1995;3:255-263.
43. Xiong Y, Steitz TA. Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template. Nature 2004;430:640-645.
44. Xiong Y, Li F, Wang J, Weiner AM, Steitz TA. Crystal structures of an archaeal class I CCA-adding enzyme and its nucleotide complexes. Mol Cell 2003;12:1165-1172.
45. Sekine SI, Nureki O, Dubois DY, Bernier S, Chênevert R, Lapointe J, Vassylyev DG, Yokoyama S. ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding. EMBO J 2003;22:676-688.
46. Rupert PB, Massey AP, Sigurdsson ST, Ferré-D'Amaré AR. Transition state stabilization by a catalytic RNA. Science 2002;298:1421-1424.
47. Rupert PB, Xiao H, Ferré-D'Amaré AR. U1A RNA-binding domain at 1.8 Å resolution. Acta Crystallogr D Biol Crystallogr 2003;59:1521-1524.
48. Hamma T, Ferré-D'Amaré AR. Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA at 1.8 Å resolution. Structure 2004;12:893-903.
49. Suryadi J, Tran EJ, Maxwell ES, Brown BA. The crystal structure of the Methanocaldococcus jannaschii multifunctional L7Ae RNA-binding protein reveals an induced-fit interaction with the box C/D RNAs. Biochemistry 2005;44:9657-9672.
50. Wang X, McLachlan J, Zamore PD, Hall TMT. Modular recognition of RNA by a human pumilio-homology domain. Cell 2002;110:501-512.
51. Wang X, Zamore PD, Hall TM. Crystal structure of a Pumilio homology domain. Mol Cell 2001;7:855-865.
52. Bogden CE, Fass D, Bergman N, Nichols MD, Berger JM. The structural basis for terminator recognition by the Rho transcription termination factor. Mol Cell 1999;3:487-493.
53. Newberry KJ, Hou YM, Perona JJ. Structural origins of amino acid selection without editing by cysteinyl-tRNA synthetase. EMBO J 2002;21:2778-2787.
54. Hauenstein S, Zhang CM, Hou YM, Perona JJ. Shape-selective RNA recognition by cysteinyl-tRNA synthetase. Nat Struct Mol Biol 2004;11:1134-1141.
55. Yang X, Gérczei T, Glover LT, Correll CC. Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping. Nat Struct Biol 2001;8:968-973.
56. Yang X, Moffat K. Insights into specificity of cleavage and mechanism of cell entry from the crystal structure of the highly specific Aspergillus ribotoxin, restrictocin. Structure 1996;4:837-852.
57. + inhibition of an RNA-dependent RNA polymerase. Structure 2004;12:307-316.
58. Butcher SJ, Grimes JM, Makeyev EV, Bamford DH, Stuart DI. A mechanism for initiating RNA-dependent RNA polymerization. Nature 2001;410:235-240.
59. Hopcroft NH, Wendt AL, Gollnick P, Antson AA. Specificity of TRAP-RNA interactions: crystal structures of two complexes with different RNA sequences. Acta Crystallogr D Biol Crystallogr 2002;58:615-621.
60. Chen X, Antson AA, Yang M, Li P, Baumann C, Dodson EJ, Dodson GG, Gollnick P. Regulatory features of the trp operon and the crystal structure of the trp RNA-binding attenuation protein from Bacillus stearothermophilus. J Mol Biol 1999;289:1003-1016.
61. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 1994;50:760-763.
62. McDonald I, Thornton J. Statisfying hydrogen-bonding potential in proteins. J Mol Biol 1994;238:777-793. HBPLUS reference.
63. Gutgsell N, Englund N, Niu L, Kaya Y, Lane BG, Ofengand J. Deletion of the Escherichia coli pseudouridine synthase gene truB blocks formation of pseudouridine 55 in tRNA in vivo, does not affect exponential growth, but confers a strong selective disadvantage in competition with wild-type cells. RNA 2000;6:1870-1881.
64. Valegard K, Liljas L, Fridborg K, Unge T. The three-dimensional structure of the bacterial virus MS2. Nature 1990;345:36-41.
65. Deutscher MP, Ni RC. Purification of a low molecular weight form of rat liver arginyl-tRNA synthetase. J Biol Chem 1982;257:6003-6006.
66. Lutz CS, Cooke C, O'Connor JP, Kobayashi R, Alwine JC. The snRNP-free U1A (SF-A) complex(es): identification of the largest subunit as PSF, the polypyrimidine-tract binding protein-associated splicing factor. RNA 1998;4:1493-1499.