Designed metal-binding sites in biomolecular and bioinorganic interactions

Current Opinion in Structural Biology

Volumn 18, Issue 4, 2008, Pages 484-490

  Matthews, Jacqueline M ^a   Loughlin, Fionna E ^a   Mackay, Joel P ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

CUPRIC ION; INORGANIC COMPOUND; METAL; METAL ION; NANOMATERIAL; ZINC;

BIOMEDICINE; BIOSENSOR; BIOTECHNOLOGY; IN VITRO STUDY; IN VIVO STUDY; METAL BINDING; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW;

BINDING SITES; METALS; MODELS, MOLECULAR; PROTEINS;

EID: 49549085951     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2008.04.009     Document Type: Review

References (51)

1. Shi W., Zhan C., Ignatov A., Manjasetty B.A., Marinkovic N., Sullivan M., Huang R., and Chance M.R. Metalloproteomics: high-throughput structural and functional annotation of proteins in structural genomics. Structure 13 (2005) 1473-1486
2. Harding M.M. Geometry of metal-ligand interactions in proteins. Acta Crystallogr D Biol Crystallogr 57 (2001) 401-411
3. Ghadiri M.R., and Choi C. Secondary structure nucleation in peptides. Transition metal ion stabilized alpha-helices. J Am Chem Soc 112 (1990) 1630-1632
4. Higaki J.N., Haymore B.L., Chen S., Fletterick R.J., and Craik C.S. Regulation of serine protease activity by an engineered metal switch. Biochemistry 29 (1990) 8582-8586
5. Merkle D.L., Schmidt M.H., and Berg J.M. Design and characterization of a ligand-binding metallopeptide. J Am Chem Soc 113 (1991) 5450-5451
6. Regan L., and Clarke N.D. A tetrahedral zinc(II)-binding site introduced into a designed protein. Biochemistry 29 (1990) 10878-10883
7. Bender G.M., Lehmann A., Zou H., Cheng H., Fry H.C., Engel D., Therien M.J., Blasie J.K., Roder H., Saven J.G., et al. De novo design of a single-chain diphenylporphyrin metalloprotein. J Am Chem Soc 129 (2007) 10732-10740. This designed four-helix bundle non-covalently self-assembles with a range of fully synthetic, non-natural porphyrin cofactors. The protein appears to bind with high specificity to a target cofactor to create a well-defined porphyrin centre.
8. Cochran F.V., Wu S.P., Wang W., Nanda V., Saven J.G., Therien M.J., and DeGrado W.F. Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor. J Am Chem Soc 127 (2005) 1346-1347
9. Huang S.S., Koder R.L., Lewis M., Wand A.J., and Dutton P.L. The HP-1 maquette: from an apoprotein structure to a structured hemoprotein designed to promote redox-coupled proton exchange. Proc Natl Acad Sci U S A 101 (2004) 5536-5541
10. Monien B.H., Drepper F., Sommerhalter M., Lubitz W., and Haehnel W. Detection of heme oxygenase activity in a library of four-helix bundle proteins: towards the de novo synthesis of functional heme proteins. J Mol Biol 371 (2007) 739-753. De novo designed heme proteins with enzymatic activity were assembled from sets of short amphipathic helices on membrane-bound templates. Five-coordinate high-spin iron and a positive reduction potential were found to promote oxygenase activity in a small set of selected proteins.
11. Nanda V., Rosenblatt M.M., Osyzka A., Kono H., Getahun Z., Dutton P.L., Saven J.G., and Degrado W.F. De novo design of a redox-active minimal rubredoxin mimic. J Am Chem Soc 127 (2005) 5804-5805
12. Wright C.M., Heins R.A., and Ostermeier M. As easy as flipping a switch?. Curr Opin Chem Biol 11 (2007) 342-346
13. Silvaggi N.R., Martin L.J., Schwalbe H., Imperiali B., and Allen K.N. Double-lanthanide-binding tags for macromolecular crystallographic structure determination. J Am Chem Soc 129 (2007) 7114-7120
14. Su X.C., McAndrew K., Huber T., and Otting G. Lanthanide-binding peptides for NMR measurements of residual dipolar couplings and paramagnetic effects from multiple angles. J Am Chem Soc 130 (2008) 1681-1687. Lanthanide-binding peptide tags containing a single cysteine residue can be attached to proteins via a disulfide bond. This class of lanthinide-binding peptides generate large pseudocontact shifts and residual dipolar couplings for use in structure determination by NMR methods.
15. Hopfner K.P., Craig L., Moncalian G., Zinkel R.A., Usui T., Owen B.A., Karcher A., Henderson B., Bodmer J.L., McMurray C.T., et al. The Rad50 zinc-hook is a structure joining Mre11 complexes in DNA recombination and repair. Nature 418 (2002) 562-566
16. Dong J., Canfield J.M., Mehta A.K., Shokes J.E., Tian B., Childers W.S., Simmons J.A., Mao Z., Scott R.A., Warncke K., et al. Engineering metal ion coordination to regulate amyloid fibril assembly and toxicity. Proc Natl Acad Sci U S A 104 (2007) 13313-13318
17. Dong J., Shokes J.E., Scott R.A., and Lynn D.G. Modulating amyloid self-assembly and fibril morphology with Zn(II). J Am Chem Soc 128 (2006) 3540-3542
18. Chiti F., and Dobson C.M. Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 75 (2006) 333-366
19. Smith J.F., Knowles T.P., Dobson C.M., Macphee C.E., and Welland M.E. Characterization of the nanoscale properties of individual amyloid fibrils. Proc Natl Acad Sci U S A 103 (2006) 15806-15811
20. Dublin S.N., and Conticello V.P. Design of a selective metal ion switch for self-assembly of peptide-based fibrils. J Am Chem Soc (2007). An engineered variant of a trimeric isoleucine zipper folds upon specifically binding one molar equivalent of Ag(I), an interaction, that drives the formations of long aspect helical fibres. This work shows that engineered metal-binding sites can be used to modulate the assembly of nanoscale architectures.
21. Matzapetakis M., Ghosh D., Weng T.C., Penner-Hahn J.E., and Pecoraro V.L. Peptidic models for the binding of Pb(II), Bi(III) and Cd(II) to mononuclear thiolate binding sites. J Biol Inorg Chem 11 (2006) 876-890
22. Lee K.H., Matzapetakis M., Mitra S., Marsh E.N., and Pecoraro V.L. Control of metal coordination number in de novo designed peptides through subtle sequence modifications. J Am Chem Soc 126 (2004) 9178-9179
23. Touw D.S., Nordman C.E., Stuckey J.A., and Pecoraro V.L. Identifying important structural characteristics of arsenic resistance proteins by using designed three-stranded coiled coils. Proc Natl Acad Sci U S A 104 (2007) 11969-11974. Although arsenic is a common toxic contaminant of water supplies, little is known about how proteins bind the metal. This structure of an As(III)-ligated three-stranded coil-coil provides a model by which repressor proteins of the Ars-operon from As-resistant bacteria function.
24. Kharenko O.A., and Ogawa M.Y. Metal-induced folding of a designed metalloprotein. J Inorg Biochem 98 (2004) 1971-1974
25. 4 cofactor of a synthetic 4-helix bundle. J Am Chem Soc 127 (2005) 7678-7679
26. Tsurkan M.V., and Ogawa M.Y. Formation of peptide nanospheres and nanofibrils by metal coordination. Biomacromolecules 8 (2007) 3908-3913
27. Salgado E.N., Faraone-Mennella J., and Tezcan F.A. Controlling protein-protein interactions through metal coordination: assembly of a 16-helix bundle protein. J Am Chem Soc 129 (2007) 13374-13375. Designed metal-binding sites were used to mediate new protein-protein interactions in cytochrome cb562. The association state is sensitive to metal loading, and a structure at low levels of metal loading reveals a 16-helix bundle that is formed by four molecules of engineered cb562 and four zinc ions.
28. Whaley S.R., English D.S., Hu E.L., Barbara P.F., and Belcher A.M. Selection of peptides with semiconductor binding specificity for directed nanocrystal assembly. Nature 405 (2000) 665-668
29. Thai C.K., Dai H., Sastry M.S., Sarikaya M., Schwartz D.T., and Baneyx F. Identification and characterization of Cu(2)O- and ZnO-binding polypeptides by Escherichia coli cell surface display: toward an understanding of metal oxide binding. Biotechnol Bioeng 87 (2004) 129-137
30. Wang S., Humphreys E.S., Chung S.Y., Delduco D.F., Lustig S.R., Wang H., Parker K.N., Rizzo N.W., Subramoney S., Chiang Y.M., et al. Peptides with selective affinity for carbon nanotubes. Nat Mater 2 (2003) 196-200
31. Kase D., Kulp III J.L., Yudasaka M., Evans J.S., Iijima S., and Shiba K. Affinity selection of peptide phage libraries against single-wall carbon nanohorns identifies a peptide aptamer with conformational variability. Langmuir 20 (2004) 8939-8941
32. Sano K., Sasaki H., and Shiba K. Specificity and biomineralization activities of Ti-binding peptide-1 (TBP-1). Langmuir 21 (2005) 3090-3095. This report demonstrates that small peptides with the ability to bind to metal surfaces can exhibit selectivity for a small subset of metals.
33. Zuo R., Ornek D., and Wood T.K. Aluminum- and mild steel-binding peptides from phage display. Appl Microbiol Biotechnol 68 (2005) 505-509
34. Sarikaya M., Tamerler C., Jen A.K., Schulten K., and Baneyx F. Molecular biomimetics: nanotechnology through biology. Nat Mater 2 (2003) 577-585
35. Chan P., Phan T., Kao M.C., Dolan C., and Tok J.B. Generating short peptidic ligands for silver nanowires from phage display random libraries. Bioorg Med Chem Lett 16 (2006) 5261-5264
36. Naik R.R., Stringer S.J., Agarwal G., Jones S.E., and Stone M.O. Biomimetic synthesis and patterning of silver nanoparticles. Nat Mater 1 (2002) 169-172
37. Su Z., Leung T., and Honek J.F. Conformational selectivity of peptides for single-walled carbon nanotubes. J Phys Chem B 110 (2006) 23623-23627. The sequence and conformational requirements of peptides selected from phage-displayed peptide libraries for high-affinity binding to single-walled carbon nanotubes (SWNTs) are described.
38. Su Z., Mui K., Daub E., Leung T., and Honek J. Single-walled carbon nanotube binding peptides: probing tryptophan's importance by unnatural amino acid substitution. J Phys Chem B 111 (2007) 14411-14417
39. Kulp J.L., Sarikaya M., and Evans J.S. Molecular characterization of a prokaryotic polypeptide sequence that catalyzes Au crystal formation. J Mater Chem 14 (2004) 2325-2332
40. Seker U.O., Wilson B., Dincer S., Kim I.W., Oren E.E., Evans J.S., Tamerler C., and Sarikaya M. Adsorption behavior of linear and cyclic genetically engineered platinum binding peptides. Langmuir 23 (2007) 7895-7900. Linear and cyclic Pt-binding peptides were analyzed by a variety of methods. The absence or presence of constraints result in very different structures and binding properties and might be used to tune the adsorption and structural features of inorganic-binding peptide sequences.
41. Oren E.E., Tamerler C., Sahin D., Hnilova M., Seker U.O., Sarikaya M., and Samudrala R. A novel knowledge-based approach to design inorganic-binding peptides. Bioinformatics 23 (2007) 2816-2822. A bioinformatic approach was developed to classify peptides that bind to quartz and the information used to design new sequences that have specific affinities for quartz. The binding properties of novel designed peptides were verified experimentally, showing a high accuracy of predictions. This appears to be a general approach that can be used to design new sequences that binds an inorganic solid target with enhanced affinity.
42. Lee S.W., Mao C., Flynn C.E., and Belcher A.M. Ordering of quantum dots using genetically engineered viruses. Science 296 (2002) 892-895
43. Mao C., Flynn C.E., Hayhurst A., Sweeney R., Qi J., Georgiou G., Iverson B., and Belcher A.M. Viral assembly of oriented quantum dot nanowires. Proc Natl Acad Sci U S A 100 (2003) 6946-6951
44. Mao C., Solis D.J., Reiss B.D., Kottmann S.T., Sweeney R.Y., Hayhurst A., Georgiou G., Iverson B., and Belcher A.M. Virus-based toolkit for the directed synthesis of magnetic and semiconducting nanowires. Science 303 (2004) 213-217
45. Sweeney R.Y., Mao C., Gao X., Burt J.L., Belcher A.M., Georgiou G., and Iverson B.L. Bacterial biosynthesis of cadmium sulfide nanocrystals. Chem Biol 11 (2004) 1553-1559
46. Souza G.R., Christianson D.R., Staquicini F.I., Ozawa M.G., Snyder E.Y., Sidman R.L., Miller J.H., Arap W., and Pasqualini R. Networks of gold nanoparticles and bacteriophage as biological sensors and cell-targeting agents. Proc Natl Acad Sci U S A 103 (2006) 1215-1220. Bacteriophage expressing peptides that target cells and gold nanoparticles were co-assembled to form biologically active molecular networks. The gold nanoparticles appear to bind non-covalently to unmodified phage. The organization of these networks can be modified by the incorporation of imidazole and the various networks used to label cells.
47. Jensen K.K., Martini L., and Schwartz T.W. Enhanced fluorescence resonance energy transfer between spectral variants of green fluorescent protein through zinc-site engineering. Biochemistry 40 (2001) 938-945
48. Evers T.H., Appelhof M.A., de Graaf-Heuvelmans P.T., Meijer E.W., and Merkx M. Ratiometric detection of Zn(II) using chelating fluorescent protein chimeras. J Mol Biol 374 (2007) 411-425. A genetically encoded Zn(II)-sensor was engineered by tethering green fluorescent protein variants. The resulting sensor has sensitivity for Zn(II) over other physiologically relevant metals, generates a high change in FRET signal and allows ratiometric fluorescent detection of Zn(II) over a concentration range from 10 nM to 1 mM.
49. van Dongen E.M., Dekkers L.M., Spijker K., Meijer E.W., Klomp L.W., and Merkx M. Ratiometric fluorescent sensor proteins with subnanomolar affinity for Zn(II) based on copper chaperone domains. J Am Chem Soc 128 (2006) 10754-10762
50. Mizuno T., Murao K., Tanabe Y., Oda M., and Tanaka T. Metal-ion-dependent GFP emission in vivo by combining a circularly permutated green fluorescent protein with an engineered metal-ion-binding coiled-coil. J Am Chem Soc 129 (2007) 11378-11383
51. Koradi R., Billeter M., and Wüthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graphics 14 (1996) 51-55