Skip to main content

Incorporation of second coordination sphere d-amino acids alters Cd(II) geometries in designed thiolate-rich proteins

Abstract

We use a de Novo protein design strategy to demonstrate that the second coordination sphere of a metal site plays a key role in controlling coordination geometries of Cd(II)-tris-thiolate complexes. Specifically, we show that alteration of chirality within the core hydrophobic packing region of a three-stranded coiled coil (3SCC) can control the coordination number of Cd(II) by limiting steric encumbrance to the metal center. Within a specific class of 3SCCs [Ac-G-(LKALEEK) n -G-NH2], where n = 4 is TRI and n = 5 is GRAND, one l-Leu may be substituted by l-Cys to generate a planar tris-thiolate array capable of metal binding. In the native peptide containing only the l-configuration of leucine, the three-Cys ligand site leads to a mixture of 3- and 4-coordinate Cd(II). When the l-Leu above (toward the N-terminus) the tris-Cys site is substituted with d-Leu, solely a 3-coordinate structure [Cd(II)S3] was obtained. When d-Leu is located below (toward the C-terminus), a mixture of two coordination geometries, presumably Cd(II)S3O and Cd(II)S3O2, is observed, while substitution with d-Leu both above and below the tris-Cys plane yields a higher percentage of 4-coordinate Cd(II)S3O species. Thus, the use of d-amino acids around a metal’s coordination sphere provides a powerful tool for controlling the properties of future designed metalloproteins.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

References

  1. Hu C, Wang J (2016) Method for enzyme design with genetically encoded unnatural amino acids. In: Pecoraro VL (ed) Methods in enzymology, vol 580 “peptide, protein and enzyme design”, vol 580. Elsevier, United States, pp 109–134

    Google Scholar 

  2. Guo JT, Wang JY, Lee JS, Schultz PG (2008) Angew Chem 47:6399–6401

    CAS  Article  Google Scholar 

  3. Liu CC, Schultz PG (2010) Ann Rev Biochem 79:413–444

    CAS  Article  PubMed  Google Scholar 

  4. Peacock AFA, Hemmingsen L, Pecoraro VL (2008) Proc Natl Acad Sci USA 105(43):16566–16571

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  5. Peacock AFA, Stuckey JA, Pecoraro VL (2009) Angew Chem Int Ed Engl 48(40):7371–7374

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  6. Lee K-H, Cabello C, Hemmingsen L, Marsh ENG, Pecoraro VL (2006) Angew Chem Int Ed Engl 45(18):2864–2868

    CAS  Article  PubMed  Google Scholar 

  7. Petros AK, Shaner SE, Costello AL, Tierney DL, Gibney BR (2004) Inorg Chem 43(16):4793–4795

    CAS  Article  PubMed  Google Scholar 

  8. Lu Y (2005) Curr Opin Chem Biol 9(2):118–126

    CAS  Article  PubMed  Google Scholar 

  9. Kumar A, Ramakrishnan V (2010) ACS Synth Biol 4(4):221–247

    Google Scholar 

  10. Baures PW, Ojala WH, Gleason WB, Johnson RL (1997) J Pept Res 50(1):1–13

    CAS  Article  PubMed  Google Scholar 

  11. Wang A, Nairn NW, Marelli M, Grabstein K (2012) In: Kaumaya PP (ed) Protein engineering. In Tech, Croatia, pp 253–290

    Google Scholar 

  12. Privett HK, Reedy CJ, Kennedy ML, Gibney BR (2002) J Am Chem Soc 124(24):6828–6829

    CAS  Article  PubMed  Google Scholar 

  13. Zastrow ML, Peacock AFA, Stuckey JA, Pecoraro VL (2012) Nat Chem 4:118–123

    CAS  Article  Google Scholar 

  14. Balaram P (1999) J Pept Res 54(3):195–199

    CAS  Article  PubMed  Google Scholar 

  15. Mahalakshmi R, Balaram P (2006) A new frontier in amino acid and protein research. Nova Science Publishers Inc, New York, pp 416–430

    Google Scholar 

  16. Dhanasekaran M, Fabiola F, Pattabhi V, Durani S (1999) J Am Chem Soc 121:5575–5576

    CAS  Article  Google Scholar 

  17. Rana S, Kundu B, Durani S (2004) Chem Commun (Camb) 21:2462–2463

    Article  Google Scholar 

  18. Rana S, Kundu B, Durani S (2005) Chem Commun (Camb) 2:207–209

    Article  Google Scholar 

  19. Rana S, Kundu B, Durani S (2007) Bioorg Med Chem 15(11):3874–3882

    CAS  Article  PubMed  Google Scholar 

  20. Rana S, Kundu B, Durani S (2007) Biopolymer 87(4):231–243

    CAS  Article  Google Scholar 

  21. Petal K, Srivastava KR, Durani S (2010) Bioinorg Med Chem 18:8270–8276

    Article  Google Scholar 

  22. Ramachandran GN, Chandrasekaran R (1972) Indian J Biochem Biophys 9:1–11

  23. Ghadiri MR, Granja JR, Buehler LK (1994) Nature 369(6478):301–304

    CAS  Article  PubMed  Google Scholar 

  24. Fernandez-Lopez S, Kim HS, Choi EC, Delgado M, Granja JR, Khasanov A, Kraehenbuehl K, Long G, Weinberger DA, Wilcoxen KM, Ghadiri MR (2001) Nature 412:452–456

    CAS  Article  PubMed  Google Scholar 

  25. Aravinda S, Shamala N, Pramanik A, Das C, Balaram P (2000) Biochem Biophys Res Commun 273(3):933–936

    CAS  Article  PubMed  Google Scholar 

  26. Aravinda S, Shamala N, Bandyopadhyay A, Balaram P (2003) J Am Chem Soc 125(49):15065–15075

    CAS  Article  PubMed  Google Scholar 

  27. Ruckthong L, Peacock AFA, Pascoe CE, Hemmingsen L, Stuckey JA, Pecoraro VL (2017) Chemistry 23(34):8232–8243

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  28. Dieckmann GR, McRorie DK, Lear JD, Sharp KA, DeGrado WF, Pecoraro VL (1998) J Mol Biol 280(5):897–912

    CAS  Article  PubMed  Google Scholar 

  29. Dieckmann GR, Mcrorie DK, Tierney DL, Utschig LM, Singer CP, O’Halloran TV, Penner-Hahn JE, Degrado WF, Pecoraro VL (1997) J Am Chem Soc 119(4):6195–6196

    CAS  Article  Google Scholar 

  30. Ghosh D, Pecoraro VL (2004) Inorg Chem 43(25):7902–7915

    CAS  Article  PubMed  Google Scholar 

  31. Farrer BT, McClure CP, Penner-Hahn JE, Pecoraro VL (2000) Inorg Chem 39(24):5422–5423

    CAS  Article  PubMed  Google Scholar 

  32. Touw DS, Nordman CE, Stuckey JA, Pecoraro VL (2007) Proc Natl Acad Sci USA 104(29):11969–11974

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  33. Chakraborty S, Touw DS, Peacock AFA, Stuckey J, Pecoraro VL (2010) J Am Chem Soc 132(38):13240–13250

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  34. Matzapetakis M, Pecoraro VL (2005) J Am Chem Soc 127(51):18229–18233

    CAS  Article  PubMed  Google Scholar 

  35. Matzapetakis M, Farrer BT, Weng T-C, Hemmingsen L, Penner-Hahn JE, Pecoraro VL (2002) J Am Chem Soc 124(27):8042–8054

    CAS  Article  PubMed  Google Scholar 

  36. Matzapetakis M, Ghosh D, Weng T-C, Penner-Hahn JE, Pecoraro VL (2006) J Biol Inorg Chem 11(7):876–890

    CAS  Article  PubMed  Google Scholar 

  37. Lee K-H, Matzapetakis M, Mitra S, Marsh ENG, Pecoraro VL (2004) J Am Chem Soc 126(30):9178–9179

    CAS  Article  PubMed  Google Scholar 

  38. Zampella G, Neupane KP, De Gioia L, Pecoraro VL (2012) Eur J Inorg Chem 18(7):2040–2050

    CAS  Google Scholar 

  39. Neupane KP, Pecoraro VL (2010) Angew Chem Int Ed Engl 49(44):8177–8180

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  40. Iranzo O, Thulstrup PW, Ryu S-B, Hemmingsen L, Pecoraro VL (2007) Chemistry 13(33):9178–9190

    CAS  Article  PubMed  Google Scholar 

  41. Iranzo O, Jakusch T, Lee K-H, Hemmingsen L, Pecoraro VL (2009) Chemistry 15(15):3761–3772

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  42. Ruckthong L, Zastrow ML, Stuckey JA, Pecoraro VL (2016) J Am Chem Soc 138(36):11979–11988

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  43. Iranzo O, Cabello C, Pecoraro VL (2007) Angew Chem Int Ed Engl 46(35):6688–6691

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  44. Dieckmann G, Heilman S, DeGrado W, Pecoraro VL (1995) De novo design of metallopeptides. In: Kessissoglou DP, Coucouvanis D, Kanatzidas M (eds) An inorganic perspective of life. Elsevier, Amsterdam, p 275

    Google Scholar 

  45. Pecoraro VL, Peacock AFA, Iranzo O, Marek Ł (2009) Understanding the biological chemistry of mercury using a de novo protein design strategy. In: Long E et al. (eds) Bioinorganic Chemistry, ACS Symposium Series; American Chemical Society, Washington, DC, pp 183–197

  46. Farrer BT, Pecoraro VL (2003) Proc Natl Acad Sci USA 100(7):3760–3765

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  47. Iranzo O, Chakraborty S, Hemmingsen L, Pecoraro VL (2011) J Am Chem Soc 133(2):239–251

    CAS  Article  PubMed  Google Scholar 

  48. Coleman JE (1993) Methods Enzymol 227:16–43

    CAS  Article  PubMed  Google Scholar 

  49. Summers F (1988) Coord Chem Rev 86:43–134

    CAS  Article  Google Scholar 

  50. Oz G, Pountney DL, Armitage IM (1998) Biochem Cell Biol 76(2–3):223–234

    CAS  Article  PubMed  Google Scholar 

  51. Hemmingsen L, Olsen L, Antony J, Sauer SPA (2004) J Biol Inorg Chem 9(5):591–599

    CAS  Article  PubMed  Google Scholar 

  52. Hemmingsen L, Stachura M, Thulstrup PW, Christensen NJ, Johnston K (2010) Hyperfine Interact 197(1–3):255–267

    CAS  Article  Google Scholar 

  53. Hemmingsen L, Sas KN, Danielsen E (2004) Chem Rev 104(9):4027–4062

    CAS  Article  PubMed  Google Scholar 

  54. Farrer BT, Harris NP, Balchus KE, Pecoraro VL (2001) Biochemistry 40(48):14696–14705

    CAS  Article  PubMed  Google Scholar 

  55. Ellman GL (1959) Arch Biochem Biophys 82:70–77

    CAS  Article  PubMed  Google Scholar 

  56. Cobas C, Cruces J, Sardina FJ (2000) In: 2.3 edn. Universidad de Santiago de Compostela, Santiago de Compostela

  57. Hemmingsen L, Bauer R, Bjerrum M, Adolph H, Zeppezauer M, Cedergren-Zeppezauer E (1996) Eur J Biochem 241:546–551

    CAS  Article  PubMed  Google Scholar 

  58. McMaster WH, Del Grande NK, Mallett JH, Hubbell JH (1969) Lawrence Livermore Radiation Laboratory, Livermore

  59. Duhme AK, Strasdeit H (1999) Z Anorg Allg Chem 625:6–8

    CAS  Article  Google Scholar 

  60. Clark-Baldwin K, Tierney D, Govindaswamy N, Gruff ES, Kim C, Berg J, Koch SA, Penner-Hahn JE (1998) J Am Chem Soc 120:8401–8409

    CAS  Article  Google Scholar 

  61. Ruckthong L (2016) Dissertation, University of Michigan, Ann Arbor

  62. Chen YH, Yang JT, Chau KH (1974) Biochemistry 13:3350–3359

    CAS  Article  PubMed  Google Scholar 

  63. Dieckmann GR (1995) Dissertation, University of Michigan, Ann Arbor

  64. Shannon RD (1976) Acta Crystallogr A 32:751–767

    Article  Google Scholar 

  65. Ghosh D, Lee K-H, Demeler B, Pecoraro VL (2005) Biochemistry 44(31):10732–10740

    CAS  Article  PubMed  Google Scholar 

  66. Santos RA, Gruff ES, Koch SA, Harbison GS (1991) J Am Chem Soc 5:469–475

    Article  Google Scholar 

Download references

Acknowledgements

This manuscript is dedicated to Prof. Dr. Helmut Sigel on the occasion of his 80th birthday. Prof. Sigel’s contributions over 5 decades have been immense. His description of metal interactions with nucleotides has been groundbreaking and authoritative, while his inexhaustible energy to the community with his book series and service roles to the Society of Biological Inorganic Chemistry and the International Conference on Biological Inorganic Chemistry has helped place the discipline of bioinorganic chemistry as a major field of scientific endeavor. The authors acknowledge funding from the National Institutes of Health (L.R. and V.L.P., ES012236; A.D. and J.E.P.-H., GM 38047) for support of this research. Synchrotron measurements were made at the Stanford Synchrotron Radiation Laboratory, which is supported by the NIH Research Resource Program and the US Department of Energy.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Vincent L. Pecoraro.

Ethics declarations

Conflict of interest

The author(s) declare that they have no competing interests.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 1,067 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Ruckthong, L., Deb, A., Hemmingsen, L. et al. Incorporation of second coordination sphere d-amino acids alters Cd(II) geometries in designed thiolate-rich proteins. J Biol Inorg Chem 23, 123–135 (2018). https://doi.org/10.1007/s00775-017-1515-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00775-017-1515-7

Keywords

  • Protein engineering
  • Heavy metal
  • Metallocenter assembly
  • Metal sensor