Skip to main content
SpringerLink
Log in

Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

  • Published:
Journal of Structural and Functional Genomics

Abstract

Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. Liolios K, Tavernarakis N, Hugenholtz P, Kyrpides NC (2006) Nucleic Acids Res 34:D332–4

    Article  PubMed  CAS  Google Scholar 

  2. Kim SH, Shin DH, Choi IG, Schulze-Gahmen U, Chen S, Kim R (2003) J Struct Funct Genomics 4:129–135

    Article  PubMed  CAS  Google Scholar 

  3. Chandonia JM, Kim SH (2006) BMC Struct Biol 6:7

    Article  PubMed  Google Scholar 

  4. Huang L, Hung L, Odell M, Yokota H, Kim R, Kim SH (2002) J Struct Funct Genomics 2:121–127

    Article  PubMed  CAS  Google Scholar 

  5. Chen S, Yakunin AF, Kuznetsova E, Busso D, Pufan R, Proudfoot M, Kim R, Kim SH (2004) J Biol Chem 279:31854–31862

    Article  PubMed  CAS  Google Scholar 

  6. Liu J, Yokota H, Kim R, Kim SH (2004) Proteins 55:1082–1086

    Article  PubMed  CAS  Google Scholar 

  7. Oganesyan V, Pufan R, DeGiovanni A, Yokota H, Kim R, Kim SH (2004) Acta Crystallogr D Biol Crystallogr 60:1266–1271

    Article  PubMed  Google Scholar 

  8. Schulze-Gahmen U, Aono S, Chen S, Yokota H, Kim R, Kim SH (2005) Acta Crystallogr D Biol Crystallogr 61:1343–1347

    Article  PubMed  Google Scholar 

  9. Kim JS, Shin DH, Pufan R, Huang C, Yokota H, Kim R, Kim SH (2006) Proteins 62:322–328

    Article  PubMed  CAS  Google Scholar 

  10. Oganesyan V, Busso D, Brandsen J, Chen S, Jancarik J, Kim R, Kim SH (2003) Acta Crystallogr D Biol Crystallogr 59:1219–1223

    Article  PubMed  Google Scholar 

  11. Liu J, Lou Y, Yokota H, Adams PD, Kim R, Kim SH (2005) J Biol Chem 280:15960–15966

    Article  PubMed  CAS  Google Scholar 

  12. Shin DH, Oganesyan N, Jancarik J, Yokota H, Kim R, Kim SH (2005) J Biol Chem 280:18326–18335

    Article  PubMed  CAS  Google Scholar 

  13. Shin DH, Roberts A, Jancarik J, Yokota H, Kim R, Wemmer DE, Kim SH (2003) Protein Sci 12:1464–1472

    Article  PubMed  CAS  Google Scholar 

  14. Roberts A, Lee SY, McCullagh E, Silversmith RE, Wemmer DE (2005) Proteins 58:790–801

    Article  PubMed  CAS  Google Scholar 

  15. Zarembinski TI, Hung LW, Mueller-Dieckmann HJ, Kim KK, Yokota H, Kim R, Kim SH (1998) Proc Natl Acad Sci USA 95:15189–15193

    Article  PubMed  CAS  Google Scholar 

  16. Schulze-Gahmen U, Pelaschier J, Yokota H, Kim R, Kim SH (2003) Proteins 50:526–530

    Article  PubMed  CAS  Google Scholar 

  17. Shin DH, Lou Y, Jancarik J, Yokota H, Kim R, Kim SH (2004) Proc Natl Acad Sci USA 101:13198–13203

    Article  PubMed  CAS  Google Scholar 

  18. Liu J, Lou Y, Yokota H, Adams PD, Kim R, Kim SH (2005) J Mol Biol 354:289–303

    Article  PubMed  CAS  Google Scholar 

  19. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR (2004) Nucleic Acids Res 32:D138–141

    Article  PubMed  CAS  Google Scholar 

  20. Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV (2001) Nucleic Acids Res 29:22–28

    Article  PubMed  CAS  Google Scholar 

  21. Hwang KY, Chung JH, Kim SH, Han YS, Cho Y (1999) Nat Struct Biol 6:691–696

    Article  PubMed  CAS  Google Scholar 

  22. Numata T, Fukai S, Ikeuchi Y, Suzuki T, Nureki O (2006) Structure 14:357–366

    Article  PubMed  CAS  Google Scholar 

  23. Kim KK, Kim R, Kim SH (1998) Nature 394:595–599

    Article  PubMed  CAS  Google Scholar 

  24. Choi IG, Shin DH, Brandsen J, Jancarik J, Busso D, Yokota H, Kim R, Kim SH (2003) J Struct Funct Genomics 4:31–34

    Article  PubMed  CAS  Google Scholar 

  25. Kim JS, DeGiovanni A, Jancarik J, Adams PD, Yokota H, Kim R, Kim SH (2005) Proc Natl Acad Sci USA 102:3248–3253

    Article  PubMed  CAS  Google Scholar 

  26. Liu J, Huang C, Shin DH, Yokota H, Jancarik J, Kim JS, Adams PD, Kim R, Kim SH (2005) J Mol Biol 350:987–996

    Article  PubMed  CAS  Google Scholar 

  27. Hou J, Sims GE, Zhang C, Kim SH (2003) Proc Natl Acad Sci USA 100:2386–2390

    Article  PubMed  CAS  Google Scholar 

  28. Holm L, Sander C (1998) Nucleic Acids Res 26:316–319

    Article  PubMed  CAS  Google Scholar 

  29. Chandonia JM, Brenner SE (2006) Science 311:347–51

    Article  PubMed  CAS  Google Scholar 

  30. Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A (2006) Nucleic Acids Res 34:D247–51

    Article  PubMed  CAS  Google Scholar 

  31. Chandonia JM, Kim SH, Brenner SE (2005) Proteins 62:356–70

    Article  Google Scholar 

  32. Baker D, Sali A (2001) Science 294:93–6

    Article  PubMed  CAS  Google Scholar 

  33. Chandonia JM, Brenner SE (2005) Proteins 58:166–79

    Article  PubMed  CAS  Google Scholar 

  34. Chandonia JM, Brenner SE (2005) Proceedings of the 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference, Shanghai, China, 751–55

  35. Service R (2005) Science 307:1554–8

    Article  PubMed  CAS  Google Scholar 

  36. Hutchison CA, Peterson SN, Gill SR, Cline RT, White O, Fraser CM, Smith HO, Venter JC (1999) Science 286:2165–9

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

We thank all the component members of BSGC for their efforts towards accomplishing the BSGC objectives. We gratefully acknowledge the supports of the NIH grant GM62412 for most of the structures cited in this article, NIH (R01-GM073109) and the U.S. Department of Energy under contract DE-AC02-05CH11231.

Author information

Author notes

  1. Dong Hae Shin

    Present address: College of Pharmacy, Ewha Womans University, Seoul, 120-750, Korea

  2. In-Geol Choi

    Present address: Division of Life Sciences and Biotechnology, College of Life Sciences, Korea University, Seoul, 136-713, Korea

Authors and Affiliations

  1. Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA

    Jingtong Hou, John-Marc Chandonia, Debanu Das, Rosalind Kim & Sung-Hou Kim

  2. Department of Chemistry, University of California, Berkeley, CA, 94720, USA

    Jingtong Hou, Rosalind Kim & Sung-Hou Kim

  3. Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA

    John-Marc Chandonia & In-Geol Choi

Authors
  1. Dong Hae Shin
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jingtong Hou
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. John-Marc Chandonia
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Debanu Das
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. In-Geol Choi
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Rosalind Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Sung-Hou Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sung-Hou Kim.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Shin, D.H., Hou, J., Chandonia, JM. et al. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center. J Struct Funct Genomics 8, 99–105 (2007). https://doi.org/10.1007/s10969-007-9025-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10969-007-9025-4

Keywords

Search

Navigation