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Characterization of Protein–Protein Interfaces

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Abstract

We analyze the characteristics of protein–protein interfaces using the largest datasets available from the Protein Data Bank (PDB). We start with a comparison of interfaces with protein cores and non-interface surfaces. The results show that interfaces differ from protein cores and non-interface surfaces in residue composition, sequence entropy, and secondary structure. Since interfaces, protein cores, and non-interface surfaces have different solvent accessibilities, it is important to investigate whether the observed differences are due to the differences in solvent accessibility or differences in functionality. We separate out the effect of solvent accessibility by comparing interfaces with a set of residues having the same solvent accessibility as the interfaces. This strategy reveals residue distribution propensities that are not observable by comparing interfaces with protein cores and non-interface surfaces. Our conclusions are that there are larger numbers of hydrophobic residues, particularly aromatic residues, in interfaces, and the interactions apparently favored in interfaces include the opposite charge pairs and hydrophobic pairs. Surprisingly, Pro-Trp pairs are over represented in interfaces, presumably because of favorable geometries. The analysis is repeated using three datasets having different constraints on sequence similarity and structure quality. Consistent results are obtained across these datasets. We have also investigated separately the characteristics of heteromeric interfaces and homomeric interfaces.

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Abbreviations

PDB:

Protein Data Bank

PQS:

Protein Quaternary Structure

ΔASA:

Changes in solvent accessible surface area

rASA:

Relative solvent accessibility

RIP:

Raw interface propensity

NIP:

Normalized interface propensity

References

  1. Chothia C, Janin J (1975) Nature 256:705–708

    Article  CAS  Google Scholar 

  2. Wodak SJ, Janin J (2002) Adv Protein Chem 61:9–73

    Article  Google Scholar 

  3. Deremble C, Lavery R (2005) Curr Opin Struct Biol 15:171–175

    Article  CAS  Google Scholar 

  4. Ponstingl H, Kabir T, Gorse D, Thornton JM (2005) Progr Biophys Mol Biol 89:9–35

    Article  CAS  Google Scholar 

  5. Reichmann D, Rahat O, Cohen M, Neuvirth H, Schreiber G (2007) Curr Opin Struct Biol 17:67–76

    Article  CAS  Google Scholar 

  6. Sheinerman FB, Norel R, Honig B (2000) Curr Opin Struct Biol 10:153–159

    Article  CAS  Google Scholar 

  7. Heifetz A, Katchalski-Katzir E, Eisenstein M (2002) Protein Sci 11:571–587

    Article  CAS  Google Scholar 

  8. Vizcarra CL, Mayo SL (2005) Curr Opin Chem Biol 9:622–626

    CAS  Google Scholar 

  9. Glaser F, Steinberg DM, Vakser IA, Ben-Tal N (2001) Proteins 43:89–102

    Article  CAS  Google Scholar 

  10. Ofran Y, Rost B (2003) J Mol Biol 325:377–387

    Article  CAS  Google Scholar 

  11. Miyazawa S, Jernigan RL (1985) Macromolecules 18:534–552

    Article  CAS  Google Scholar 

  12. Keskin O, Bahar I, Badretinov AY, Ptitsyn OB, Jernigan RL (1998) Protein Sci 7:2578–2586

    Article  CAS  Google Scholar 

  13. Young L, Jernigan RL, Covell DG (1994) Protein Sci 3:717–729

    Article  CAS  Google Scholar 

  14. Berchanski A, Shapira B, Eisenstein M (2004) Proteins 56:130–142

    Article  CAS  Google Scholar 

  15. Ben-Naima A (2006) J Chem Phys 125:24901

    Article  CAS  Google Scholar 

  16. Keskin O, Mab B, Nussinov R (2005) J Mol Biol 345:1281–1294

    Article  CAS  Google Scholar 

  17. Jones S, Thornton JM (1996) Proc Natl Acad Sci USA 93:13–20

    Article  CAS  Google Scholar 

  18. Peter Block JP, Hülermeier E, Sanschagrin P, Sotriffer CA, Klebe G (2006) Proteins 65:607–622

    Article  CAS  Google Scholar 

  19. Chakrabarti P, Janin J (2002) Proteins 47:334–343

    Article  CAS  Google Scholar 

  20. Kyu-il Cho KL, Lee KH, Kim D, Lee D (2006) Proteins 65:593–606

    Article  CAS  Google Scholar 

  21. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) Nucl Acids Res 28:235–242

    Article  CAS  Google Scholar 

  22. Henrick K, Thornton JM (1998) Trends Biochem Sci 23:358–361

    Article  CAS  Google Scholar 

  23. Hubbard SJ (1993) NACCESS, department of biochemistry and molecular biology. University College, London

    Google Scholar 

  24. Gutteridge A, Bartlett GJ, Thornton JM (2003) J Mol Biol 330:719–734

    Article  CAS  Google Scholar 

  25. Kyte J, Doolittle RF (1982) J Mol Biol 157:105–132

    Article  CAS  Google Scholar 

  26. Nooren IMA, Thornton JM (2003) J Mol Biol 325:991–1016

    Article  CAS  Google Scholar 

  27. Kabsch W, Sander C (1983) Biopolymers 22:2577–2637

    Article  CAS  Google Scholar 

  28. McCoy AJ, Chandana Epa V, Colman PM (1997) J Mol Biol 268:570–584

    Article  CAS  Google Scholar 

  29. Lo Conte L, Chothia C, Janin J (1999) J Mol Biol 285:2177–2198

    Article  CAS  Google Scholar 

  30. Bahadur RP, Chakrabarti P, Rodier F, Janin J (2003) Proteins 53:708–719

    Article  CAS  Google Scholar 

  31. Jones S, Thornton JM (1997) J Mol Biol 272:121–132

    Article  CAS  Google Scholar 

  32. Prasad Bahadur R, Chakrabarti P, Rodier F, Janin J (2004) J Mol Biol 336:943–955

    Article  CAS  Google Scholar 

  33. Raih MF, Ahmad S, Zheng R, Mohamed R (2005) Biophys Chem 114:63–69

    Article  CAS  Google Scholar 

  34. Creighton T (1997) Protein structures and molecular properties. WH Freeman, New York

    Google Scholar 

  35. Bahar I, Jernigan RL (1997) J Mol Biol 266:195–244

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This Research was supported in part by a grant from the National Institutes of Health (GM 066387) to VH, DD, and RLJ.

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Authors and Affiliations

  1. Department of Computer Science, Utah State University, 4205 Old Main Hill, Logan, UT, 84341, USA

    Changhui Yan

  2. Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA, 50010, USA

    Feihong Wu, Robert L. Jernigan, Drena Dobbs & Vasant Honavar

  3. Center for Computational Intelligence, Learning, and Discovery, Iowa State University, Ames, IA, 50010, USA

    Feihong Wu, Robert L. Jernigan, Drena Dobbs & Vasant Honavar

  4. Artificial Intelligence Research Laboratory, Department of Computer Science, Iowa State University, Ames, IA, 50010, USA

    Feihong Wu & Vasant Honavar

  5. Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50010, USA

    Robert L. Jernigan

  6. Laurence H Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA, 50010, USA

    Robert L. Jernigan, Drena Dobbs & Vasant Honavar

  7. Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50010, USA

    Drena Dobbs

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  1. Changhui Yan
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  2. Feihong Wu
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  3. Robert L. Jernigan
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  5. Vasant Honavar
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Correspondence to Changhui Yan.

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Yan, C., Wu, F., Jernigan, R.L. et al. Characterization of Protein–Protein Interfaces. Protein J 27, 59–70 (2008). https://doi.org/10.1007/s10930-007-9108-x

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  • DOI: https://doi.org/10.1007/s10930-007-9108-x

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