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Computational Structural Biology Lab
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Computational Structural Biology Lab

Source: http://www.csb.iitkgp.ac.in/applications/affinity.php Parent: http://www.csb.iitkgp.ac.in/pages/research.php

Department of Bioscience and Biotechnology Indian Institute of Technology Kharagpur

Protein-RNA affinity Benchmark

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Table 1: The benchmark dataset for the protein-RNA binding affinity.
PDB IDa Complex Protein RNA Length of the RNA Kd (M) Temp (K) pH ΔGb (kcal/mol) Expc Interface Area (B) (Å2)d c-rmsde (Å) i-rmsdf(Å) Reference
Crystal Solution
A. Complexes with tRNA (5)
1asy (A:R) Aspartyl-tRNA synthetase tRNA (Asp) 75 76 3.0x10-8 310 5.5 10.66 A 4430 1.5 1.3 2.3 (1)
1qtq (A:B) Glutaminyl-tRNA synthetase tRNA (Gln) 75 76 3.6x10-7 310 5.2 9.13 D 5200 1.6 1.8 (2)
1u0b (B:A) Cysteinyl-tRNA synthetase tRNA (Cys) 74 74 2.7x10-7 298 7.5 8.95 B 4560 0.7 1.0 (3)
2drb (A:B) CCA-adding enzyme tRNA (35-mer) 35 73 6.7 x10-8 298 8.5 9.78 C 3200 1.1 1.8 (4)
2fmt (A:C) tRNA-fMettransformylase tRNA (fMet) 77 77 1.36x10-7 310 7.6 9.73 A 2940 1.2 0.9 1.7 (5)
B. Ribosomal protein (2)
1dfu (P:MN) Ribosomal protein L25 5S rRNA 19 120 6.7x10-8 298 7.6 9.78 A 1690 3.0 3.0 3.7 (6)
1sds (C:FF′) Ribosomal protein L7Ae box H/ACA sRNA 15 84 7.5x10-8 277 7.4 9.03 C 1200 0.3 0.4 (7)
C. Duplex RNA (2)
1yvpg (B:EFH) Ro autoantigen Y RNA 10 97 5.2x10-9 277 7.5 10.49 C 3500 1.4 1.3 (8)
2az0 (AB:CD) Silencing suppressor protein B2 siRNA 18 19 1.4x10-9 277 7.5 11.22 C 1970 1.3 1.0 (9)
D. Single stranded RNA (6)
1jbs (A:C) Sarcin-like cytotoxin restrictocin 29-mer SRD RNA analog 29 29 1.0x10-6 298 7.2 8.18 B 1310 0.7 0.6 1.9 (10)
1wsu (A:E) Elongation factor SelB SECIS RNA 23 23 1.0x10-6 277 5.4 7.60 C 940 0.7 0.5 0.8 (11)
2a8v (B:E) Rho transcription termination factor Cytosine-rich RNA 6 10 5.0x10-6 298 8.0 7.22 A 720 1.0 1.6 (12)
2asb (A:B) NusA antiterminator BoxC rRNA 11 13 1.15x10-7 291 7.8 9.23 E 2320 1.1 0.8 (13)
2b6g (A:B) Vts1p SRE hairpin RNA 19 15 1.7x10-8 277 7.0 9.84 B 483 0.9 0.3 0.9 (14)
2ix1 (A:B) RNase II Single-stranded RNA 13 25 5.3x10-9 277 8.0 10.48 F 4160 1.6 0.9 (15)

aFour-letter PDB code of the protein-RNA complexes used in the dataset with the chain ID(s) of the protein and the RNA molecules in the parentheses. Symmetry-related chains are primed (e.g., FF′ in 1sds).

bGibbs free energy calculated from ΔG= -RT lnKd, where R is the gas constant and T is the absolute temperature.

cExperimental methods used for the determination of Kd: (A) Filtration assay; (B) Fluorescence titration; (C) Electrophoretic mobility shift assay; (D) Binding kinetics; (E) Isothermal titration calorimetry; (F) Surface plasma resonance

dData taken from Barik et al. (16).

ec-rmsd is calculated over all the Cα atoms of a given protein chain. Data are taken from Barik et al (16).

fi-rmsd is calculated considering only the interface Cα atoms, and the values in italics include the phosphorus atoms of the interface nucleotides when the corresponding RNA structure is available in the unbound form. Data are taken from Barik et al (16).

gDissociation constant represents the duplex strand of the Y RNA involving E and F chains.

References

  1. Eriani, G. and Gangloff, J. (1999) Yeast aspartyl-tRNA synthetase residues interacting with tRNA(Asp) identity bases connectively contribute to tRNA(Asp) binding in the ground and transition-state complex and discriminate against non-cognate tRNAs. J Mol Biol, 291, 761-773.

  2. Uter, N.T., Gruic-Sovulj, I. and Perona, J.J. (2005) Amino acid-dependent transfer RNA affinity in a class I aminoacyl-tRNA synthetase. J Biol Chem, 280, 23966-23977.

  3. Hauenstein, S., Zhang, C.M., Hou, Y.M. and Perona, J.J. (2004) Shape-selective RNA recognition by cysteinyl-tRNA synthetase. Nat Struct Mol Biol, 11, 1134-1141.

  4. Okabe, M., Tomita, K., Ishitani, R., Ishii, R., Takeuchi, N., Arisaka, F., Nureki, O. and Yokoyama, S. (2003) Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure. EMBO J, 22, 5918-5927.

  5. Janiak, F., Dell, V.A., Abrahamson, J.K., Watson, B.S., Miller, D.L. and Johnson, A.E. (1990) Fluorescence characterization of the interaction of various transfer RNA species with elongation factor Tu.GTP: evidence for a new functional role for elongation factor Tu in protein biosynthesis. Biochemistry, 29, 4268-4277.

  6. Spierer, P., Bogdanov, A.A. and Zimmermann, R.A. (1978) Parameters for the interaction of ribosomal proteins L5, L18, and L25 with 5S RNA from Escherichia coli. Biochemistry, 17, 5394-5398.

  7. Rozhdestvensky, T.S., Tang, T.H., Tchirkova, I.V., Brosius, J., Bachellerie, J.P. and Huttenhofer, A. (2003) Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea. Nucleic Acids Res, 31, 869-877.

  8. Stein, A.J., Fuchs, G., Fu, C., Wolin, S.L. and Reinisch, K.M. (2005) Structural insights into RNA quality control: the Ro autoantigen binds misfolded RNAs via its central cavity. Cell, 121, 529-539.

  9. Chao, J.A., Lee, J.H., Chapados, B.R., Debler, E.W., Schneemann, A. and Williamson, J.R. (2005) Dual modes of RNA-silencing suppression by Flock House virus protein B2. Nat Struct Mol Biol, 12, 952-957.

  10. Yang, X., Gerczei, T., Glover, L.T. and Correll, C.C. (2001) Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping. Nat Struct Biol, 8, 968-973.

  11. Yoshizawa, S., Rasubala, L., Ose, T., Kohda, D., Fourmy, D. and Maenaka, K. (2005) Structural basis for mRNA recognition by elongation factor SelB. Nat Struct Mol Biol, 12, 198-203.

  12. Martinez, A., Opperman, T. and Richardson, J.P. (1996) Mutational analysis and secondary structure model of the RNP1-like sequence motif of transcription termination factor Rho. J Mol Biol, 257, 895-908.

  13. Beuth, B., Pennell, S., Arnvig, K.B., Martin, S.R. and Taylor, I.A. (2005) Structure of a Mycobacterium tuberculosis NusA-RNA complex. EMBO J, 24, 3576-3587.

  14. Aviv, T., Lin, Z., Lau, S., Rendl, L.M., Sicheri, F. and Smibert, C.A. (2003) The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators. Nat Struct Biol, 10, 614-621.

  15. Barbas, A., Matos, R.G., Amblar, M., Lopez-Vinas, E., Gomez-Puertas, P. and Arraiano, C.M. (2008) New insights into the mechanism of RNA degradation by ribonuclease II: identification of the residue responsible for setting the RNase II end product. J Biol Chem, 283, 13070-13076.

  16. Barik, A., Nithin, C., Manasa, P. and Bahadur, R.P. (2012) A protein-RNA docking benchmark (I): nonredundant cases. Proteins, 80, 1866-1871.