Engineering metal-binding sites in proteins

Current Opinion in Structural Biology

Volumn 7, Issue 4, 1997, Pages 495-500

  Lu, Yi ^a   Valentine, Joan S ^b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

METALLOPROTEIN; PROTEIN;

BINDING SITE; GENETIC ENGINEERING; METAL BINDING; PRIORITY JOURNAL; PROTEIN STRUCTURE; REVIEW; STRUCTURE ACTIVITY RELATION;

EID: 0030801175     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(97)80112-1     Document Type: Article

References (61)

1. Hellinga HW. Design of metalloproteins. of special interest Cleland JL, Craik CS. Protein Engineering: Principles and practice. 1996;369-398 Wiley-Liss, New York, See annotation [2].
2. Hellinga HW. Metalloprotein design. of special interest Curr Opin Biotechnol. 7:1996;437-441 Two recently published reviews [1,2] of the field.
3. Fattorusso R, Morelli G, Lombardi A, Nastri F, Maglio O, D'Auria G, Pedone C, Pavone V. Design of metal ion binding peptides. Biopolymers. 37:1995;401-410.
4. Regan L. Protein design: novel metal-binding sites. Trends Biochem Sci. 20:1995;280-285.
5. Berg JM, Shi Y. The galvanization of biology: a growing appreciation for the roles of zinc. of outstanding interest Science. 271:1996;1081-1085 Approaches to the rational design of site-specific zinc finger DNA-binding proteins are described.
6. Kim CA, Berg JM. A 2.2 Å resolution crystal structure of a designed zinc finger protein bound to DNA. of special interest Nat Struct Biol. 3:1996;940-945 This paper reports the crystal structure of a complex formed between an oligonucleotide and a rationally designed zinc finger protein which yields valuable information concerning the nature of the intra- and intermolecular interactions involved in the binding.
7. Rebar EJ, Greisman HA, Pabo CO. Phage display methods for selecting zinc finger proteins with novel DNA-binding specificities. Methods Enzymol. 267:1996;129-149.
8. Greisman HA, Pabo CO. A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites. of outstanding interest Science. 275:1997;657-661 This paper describes a selection method to optimize the binding of zinc finger motifs to a specific DNA sequence starting first with one finger motif and then extending the protein one finger at a time. The results suggest that the interactions of individual fingers with DNA are not independent but are influenced by the nature of the neighboring fingers, in other words, the binding of each finger is 'context dependent'.
9. Struthers MD, Cheng RP, Imperiali B. Design of a monomeric 23-residue polypeptide with defined tertiary structure. Science. 271:1996;342-345.
10. Struthers MD, Cheng RP, Imperiali B. Economy in protein design - evolution of a metal-independent ββα motif based on the zinc finger domains. of outstanding interest J Am Chem Soc. 118:1996;3073-3081 This paper reports the use of different types of β turns as structural nucleation elements that can compensate for the stabilizing effect of cross-links provided by disulfides or metal chelation. A process of iterative design is followed starting with the ββα motifs found in zinc finger proteins.
11. Cheng RP, Fisher SL, Imperiali B. Metallopeptide design - tuning the metal cation affinities with unnatural amino acids and peptide secondary structure. of special interest J Am Chem Soc. 118:1996;11349-11356 This paper evaluates several strategies for increasing the metal-binding affinities of designed peptides: first, the use of unnatural amino acids with sidechains terminating in multidentate metal-binding ligands; second, positioning two or more amino acid sidechains close enough to bind simultaneously to a metal ion in the folded peptide; and third, introducing structural elements into the peptide to cause the metal-binding sites to preassemble prior to metal ion binding.
12. Walkup GK, Imperiali B. Fluorescent chemosensors for divalent zinc based on zinc finger domains. Enhanced oxidative stability, metal binding affinity, and structural and functional characterization. J Am Chem Soc. 119:1997;3443-3450.
13. 2+ complexation, respectively.
14. Arnold PA, Shelton WR, Benson DR. Peptide helix induction in a self-assembling hemoprotein model. of special interest J Am Chem Soc. 119:1997;3181-3182 This paper describes the design of a small cysteine-linked dipeptide for which the complexation of one equivalent of a Co(III) porphyrin to form a six-coordinate low-spin Co(III) complex is accompanied by the induction of high helix content.
15. III mimochrome I δ and λ isomers. of special interest Chem Eur J. 3:1997;350-362 The NMR structural determination and spectroscopic characterization of a covalent helix-heme-helix sandwich containing the Co(III)-deuterohemin bound via two propionyl groups to two identical end-protected helical nonapeptides. Each helix has a histidine residue in the central position which is a potential ligand to the metal ion.
16. Gibney BR, Mulholland SE, Rabanal F, Dutton PL. Ferredoxin and ferredoxin - heme maquettes. of outstanding interest Proc Natl Acad Sci USA. 93:1996;15041-15046 This paper reports the design of a hexapeptide sequence that causes self-assembly and incorporation of a 4Fe4S cluster, either on its own or when incorporated into heme-binding tetra-α-helix bundles. The hexapeptide, which is designed on the basis of naturally occurring iron-sulfur proteins and inorganic model systems, is found to fold as the 4Fe4S cluster self-assembles.
17. Gibney BR, Rabanal F, Skalicky JJ, Wand AJ, Dutton PL. Design of a unique protein scaffold for maquettes. of special interest J Am Chem Soc. 119:1997;2323-2324 This paper describes substantial improvements in stability and evidence for more native-like structures for the authors' heme-binding four α-helix maquettes which are achieved by modifying the design to increase the specificity of the packing arrangement of the sidechains that make up the hydrophobic cores of these maquettes.
18. Rabanal F, Gibney BR, DeGrado WF, Moser CC, Dutton PL. Engineering photosynthesis - synthetic redox proteins. Inorg Chim Acta. 243:1996;213-218.
19. Rabanal F, DeGrado WF, Dutton PL. Toward the synthesis of a photosynthetic reaction center maquette - a cofacial porphyrin pair assembled between two subunits of a synthetic four-helix bundle multiheme protein. of special interest J Am Chem Soc. 118:1996;473-474 This paper describes the synthesis of four-helix bundle maquettes that when assembled contain cofacial porphyrin pairs.
20. 2+ to the construct significantly reduces the permeability, presumably because the presence of the metal ion induces folding of the construct such that it can no longer span the membrane.
21. 2+ with dissociation constants of 100-200 nM.
22. 2+-actuated switch that reversibly permeabilizes the plasma membrane of fibroblasts to small molecules.
23. Schmidt AM, Muller HN, Skerra A. A Zn(II)-binding site engineered into retinol-binding protein exhibits metal-ion specificity and allows highly efficient affinity purification with a newly designed metal ligand. Chem Biol. 3:1996;645-653.
24. Sheikh SP, Zvyaga TA, Lichtarge O, Sakmar TP, Bourne HR. Rhodopsin activation blocked by metal-ion-binding sites linking transmembrane helices C and F. Nature. 383:1996;347-350.
25. Elling CE, Schwartz TW. Connectivity and orientation of the seven helical bundle in the tachykinin NK-1 receptor probed by zinc site engineering. EMBO J. 15:1996;6213-6219.
26. Thirstrup K, Elling CE, Hjorth SA, Schwartz TW. Construction of a high affinity zinc switch in the kappa-opioid receptor. J Biol Chem. 271:1996;7875-7878.
27. Bonagura CA, Sundaramoorthy M, Pappa HS, Patterson WR, Poulos TL. An engineered cation site in cytochrome c peroxidase alters the reactivity of the redox active tryptophan. of special interest Biochemistry. 35:1996;6107-6115 Site-directed mutagenesis is used to introduce into cytochrome c peroxidase the ascorbate peroxidase cation-binding site - a site believed to be a reason for why ascorbate peroxidase does not form a tryptophan radical. EPR spectroscopy shows that the cation-containing mutant no longer forms a stable tryptophan radical. The activity of the cation mutants, using ferrocytochrome c as a substrate, is <1% of wild-type levels, whereas the activity toward a small molecule substrate, guaiacol, increases. These results demonstrate that long-range electrostatic effects can control the reactivity of a redox active amino acid sidechain and that the redox-reactivity of the proximal tryptophan is important in the oxidation of ferrocytochrome c.
28. Yeung BKS, Wang X, Sigman JA, Petillo PA, Lu Y. Construction and characterization of a manganese-binding site in cytochrome c peroxidase: toward a novel manganese peroxidase. of special interest Chem Biol. 4:1997;215-222 On the basis of an X-ray crystal structural comparison of cytochrome c peroxidase (CcP) and manganese peroxidase (MnP), a site-directed triple mutant near the putative Mn-binding site in CcP is prepared in an effort to mimic MnP and to elucidate factors responsible for Mn(II) oxidation - a key step in the biodegradation of lignin, a complex phenylpropanoid polymer, as well as of many aromatic pollutants. Both UV-visible and paramagnetic NMR show that a Mn-binding site similar to that in MnP is created in CcP and that it promotes Mn(II) oxidation more efficiently than native CcP.
29. Fancy DA, Melcher K, Johnston SA, Kodadek T. New chemistry for the study of multiprotein complexes: the six-histidine tag as a receptor for a protein crosslinking reagent. Chem Biol. 3:1996;551-559.
30. Crowder MW, Stewart JD, Roberts VA, Bender CJ, Tevelrakh E, Peisach J, Getzoff ED, Gaffney BJ, Benkovic SJ. Spectroscopic studies on the designed metal-binding sites of the 43C9 single chain antibody. J Am Chem Soc. 117:1995;5627-5634.
31. Roberts VA, Getzoff ED. Metalloantibody design. FASEB J. 9:1995;94-100.
32. Ghosh P, Shabat D, Kumar S, Sinha SC, Grynszpan F, Li J, Noodleman L, Keinan E. Using antibodies to perturb the coordination sphere of a transition metal complex. Nature. 382:1996;339-341.
33. 2+-specific site. Eur J Biochem. 242:1996;249-255.
34. 2+ specificity is an intrinsic property of the site. Eur J Biochem. 242:1996;256-263.
35. Persechini A, Stemmer PM, Ohashi I. Localization of unique functional determinants in the calmodulin lobes to individual EF hands. J Biol Chem. 271:1996;32217-32225.
36. Jeltsch A, Wenz C, Wende W, Selent U, Pingoud A. Engineering novel restriction endonucleases: principles and applications. Trends Biotechnol. 14:1996;235-238.
37. 2+. This structural perturbation is a specific consequence of the IIe→Leu mutation because IIe→Val and IIe→Ala do not change the metal ion requirement.
38. A variant of amicyanin. Biochemistry. 36:1997;3262-3269.
39. A-containing mutant allows the two classes of copper centers to be compared in the same protein framework.
40. Hay MT, Milberg RM, Lu Y. Preparation and characterization of mercury and silver derivatives of an engineered purple copper center in azurin. J Am Chem Soc. 118:1996;11976-11977.
41. A - a novel mixed-valence dinuclear copper electron-transfer center. J Am Chem Soc. 118:1996;11501-11514.
42. Dennison C, Vijgenboom E, Hagen WR, Canters GW. Loop-directed mutagenesis converts amicyanin from Thiobacillus versutus into a novel blue copper protein. of special interest J Am Chem Soc. 118:1996;7406-7407 The ligand loop in amicyanin from T. versutus is replaced with that of plastocyanin. The mutant protein results in a stable and redox-competent blue copper protein. Its spectroscopic features, however, resemble neither those of amicyanin nor those of plastocyanin, but instead show a striking similarity with those of pseudoazurin. This experiment indicates that, even though the ligand loop plays the major role in the formation of the metal-binding site, it is not the only factor. Other structural features have to be considered to mimic subtle structural features.
43. Matsui T, Nagano S, Ishimori K, Watanabe Y, Morishima I. Preparation and reactions of myoglobin mutants bearing both proximal cysteine ligand and hydrophobic distal cavity: protein models for the active site of P-450. Biochemistry. 35:1996;13118-13124.
44. Ozaki S, Matsui T, Watanabe Y. Conversion of myoglobin into a highly stereospecific peroxygenase by the L29H/H64I mutation. of outstanding interest J Am Chem Soc. 118:1996;9784-9785 A structural comparison of Mb and CcP indicates that the (distal) His64→Leu and Leu29→His mutations will create a distal crevice similar to that in CcP. As CcP has much higher peroxygenase activity than Mb, the His64→Leu29→His double mutant is made. This mutant significantly increases the rate of enantioselective oxidation of both thioanisole and styrene.
45. Tanaka M, Ishimori K, Morishima I. The distal glutamic acid as an acid - base catalyst in the distal site of horseradish peroxidase. Biochem Biophys Res Commun. 227:1996;393-399.
46. Kroes SJ, Hoitink CW, Andrew CR, Ai J, Sanders-Loehr J, Messerschmidt A, Hagen WR, Canters GW. The mutation Met121His creates a type-1.5 copper site in Alcaligenes denitrificans azurin. Eur J Biochem. 240:1996;342-351.
47. Lu Y, Roe JA, Bender CJ, Peisach J, Banci L, Bertini I, Gralla EB, Valentine JS. New type 2 copper-cysteinate proteins - copper site histidine-to-cysteine mutants of yeast copper-zinc superoxide dismutase. Inorg Chem. 35:1996;1692-1700.
48. Van Pouderoyen G, Andrew CR, Loehr TM, Sanders-Loehr J, Mazumdar S, Hill HA, Canters GW. Spectroscopic and mechanistic studies of type-1 and type-2 copper sites in Pseudomonas aeruginosa azurin as obtained by addition of external ligands to mutant His46Gly. Biochemistry. 35:1996;1397-1407.
49. Bonander N, Karlsson BG, Vånngård T. Environment of copper in Pseudomonas aeruginosa azurin probed by binding of exogenous ligands to Met121X (X = Gly, Ala, Val, Leu, or Asp) mutants. Biochemistry. 35:1996;2429-2436.
50. Van Pouderoyen G, den Blaauwen T, Reedijk J, Canters GW. Dimerization of a His117Gly azurin mutant by external addition of 1,omega-di(imidazol-1-yl)alkanes. Biochemistry. 35:1996;13205-13211.
51. Sun J, Fitzgerald MM, Goodin DB, Loehr TM. Solution and crystal structures of the H175G mutant of cytochrome c peroxidase: a resonance Raman study. of special interest J Am Chem Soc. 119:1997;2064-2065 The solution and crystal structure of the proximal histidine mutant of cytochrome c peroxidase His 175→Gly is studied using resonance Raman and EPR spectroscopy. The results confirm the cavity nature of the metal-binding site and reveal an interesting pH-dependent spin state change of the heme that is related to the presence of two water ligands in the cavity.
52. Newmyer SL, Sun J, Loehr TM, Ortiz de Montellano PR. Rescue of the horseradish peroxidase His170→Ala mutant activity by imidazole: importance of proximal ligand tethering. of special interest Biochemistry. 35:1996;12788-12795 Creating a cavity in the proximal histidine mutant of horesradish peroxidase (HRP) His170→Ala results in the distal histidine binding to the heme and a dramatically reduced activity. However, the addition of imidazole restores a large part of the activity. This result suggests that a primary function of the proximal histidine in HRP is to tether the iron atom to disfavor a sixth ligand binding, in particular, the coordination of the iron to the distal histidine.
53. Breaker RR. In vitro selection of catalytic polynucleotides. of outstanding interest Chem Rev. 97:1997;371-390 An excellent and comprehensive review of the in vitro selection field.
54. Breaker RR. Are engineered proteins getting competition from RNA? Curr Opin Biotechnol. 7:1996;442-448.
55. 2+ ion as a cofactor for a novel RNA-cleaving deoxyribozyme. Angew Chem Int Ed Engl. 35:1996;2837-2841.
56. Lehman N, Joyce GF. Evolution in vitro of an RNA enzyme with altered metal dependence. Nature. 361:1993;182-185.
57. Cuenoud B, Szostak JW. A DNA metalloenzyme with DNA ligase activity. Nature. 375:1995;611-614.
58. Carmi N, Shultz LA, Breaker RR. In vitro selection of self-cleaving DNAs. Chem Biol. 3:1996;1039-1046.
59. m close to the value for the metalation of mesoporphyrin with Fe(II), which is catalyzed by recombinant ferrochelatase.
60. Li Y, Sen D. A catalytic DNA for porphyrin metallation. of outstanding interest Nat Struct Biol. 3:1996;743-747 A guanine-rich, 33-base DNA that catalyzes the insertion of Cu(II) and Zn(II) into mesoporphyrin IX is selected from a random-sequence DNA library using N-methylmesoporphyrin IX as a transition-state analog.
61. Li Y, Geyer CR, Sen D. Recognition of anionic porphyrins by DNA aptamers. Biochemistry. 35:1996;6911-6922.