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Lecture 9

Lecture 9. Redox metallo-biochemistry (continued). e - transfer proteins. Cytochromes Fe-S proteins Blue copper proteins. Kinetics of electron transfer reactions.

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Lecture 9

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  1. Lecture 9 Redox metallo-biochemistry (continued)

  2. e- transfer proteins Cytochromes Fe-S proteins Blue copper proteins

  3. Kinetics of electron transfer reactions • Electron transfer between 2 metal centers can be either inner-sphere (via a bridging ligand) or outer-sphere (no bridging ligand, coordination spheres remain the same for both metal ions) • Only outer-sphere known for metalloproteins • Reasonably fast (> 10 s-1) over large distances (up to 30 Å) • Can be rationalised by Marcus Theory • Qualitatively: e- transfer is fast if the states before and after the redox reactions are similar (reorganisation energy is small)

  4. Cytochromes • Name comes from the fact that they are coloured • Differ by axial ligands and whether covalently bound • Involved in electron transfer (a,b,c) or oxygen activation (P450) • Essential for many redox reactions

  5. UV-Vis Spectra of cytochromes • classified by a bands: • a: 580-590 nm • b: 550-560 nm • c: 548-552 nm • (there’s also d and f) • all involved in electron transfer, all CN6 • P450: 450 nm: • Oxygen activation; CN5 Absorption spectra of oxidized (Fe(III) and reduced (Fe(II)) horse cytochrome c.

  6. Cytochrome c • Small soluble proteins (ca. 12 kDa) • Near inner membrane of mitochondria • Transfers electrons between 2 membrane proteins ( for respiration) • Heme is covalently linked to protein via vinyl groups (thioether bonds with Cys) • 1 Met and 1 His ligand (axial) horse heart cytochrome c Bushnell, G.W.,  Louie, G.V.,  Brayer, G.D. J.Mol.Biol.v214pp.585-595 , 1990 • Conserved from bacteria to Man

  7. Cytochromes b • Heme has no covalent link to protein • Two axial His ligands • Shown is only soluble domain; the intact protein is bound to membrane F Arnesano, L Banci, I Bertini, IC Felli:The solution structure of oxidized rat microsomal cytochrome b5. Biochemistry (1998) 37, 173-84.

  8. Not for electron transfer:the cytochromes P450 • CN5, axial ligand is a Cys • 6th site for substrate/oxygen binding • Hydroxylates camphor P450Cam

  9. Tuning of heme function • In (deoxy)hemoglobin, Fe(II) is 5-coordinate • Must avoid oxidation to Fe(III) (Met-hemoglobin) • Neutral His ligand: His-Fe(II)-porphyrin is uncharged: Favourable • P450: Catalyses hydroxylation of hydrophobic substrates. Also 5-coordinate • 1 axial Cys thiolate ligand (negatively charged): Resting state is Fe(III), also uncharged • In cytochromes, CN=6: No binding of additional ligand, but very effective 1 e- transfer

  10. Iron-sulfur proteins

  11. Fe-S proteins • Probably amongst the first enzymes • Generally, Fe, Cys thiolate and sulfide • Main function: fast e- transfer • At least 13 Fe-S clusters in mitochondrial respiration chain • Rubredoxins: mononuclear FeCys4 site • Ferredoxins: 2,3 or 4 irons • Other functions: Aconitase: An isomerase IRE-BP: An iron sensor (see lecture 5)

  12. Rubredoxins: FeCys4 X-ray Structure of RUBREDOXIN from Desulfovibrio gigas at 1.4 A resolution. FREY, M., SIEKER, L.C., PAYAN, F.

  13. 1rfs: Spinach Fe2S2(Cys-S)4 1 awd: CHLORELLA FUSCA Fe2S2(Cys-S)2-(His-N)2: Rieske proteins Fe3S4(Cys-S)4 Fe4S4(Cys-S)4 1fda: Azotobacter vinelandii

  14. Fe-S clusters can be easily synthesised from Fe(III), sulfide and organic thiols, but are prone to rapid oxidation Self-assembly of Fe-S clusters Richard Holm

  15. Delocalisation of electrons: Mixed valence • localized Fe3+ (red) and localized Fe2+ (blue) sites, and • delocalized Fe2.5+Fe2.5+pairs (green) • Why e- transfer is fast: • Clusters can delocalize the “added” electron • minimizes bond length changes • decreases reorganization energy

  16. Fe-S proteins often contain more than one cluster: Azotobacter vinelandii: 2 clusters

  17. The five Fe-S clusters of the Fe-only hydrogenase from Clostridium pasteurianum • Activation of H2 • Active site (binuclear Fe cluster) on top • The other five Fe-S clusters provide long-range electron transfer pathways Pdb 1feh

  18. FeMoCo cofactor cluster of nitrogenase P cluster of nitrogenase

  19. Nitrogenase (Klebsiella pneumoniae) • Catalyses nitrogen fixation • N2 + 8H+ + 8e- + 16 ATP → 2NH3 + H2 + 16ADP + 16 Pi

  20. Redox potentials

  21. Tuning of redox potentials • For both heme proteins and Fe-S clusters, ligands coarsely tune redox potential • In [4Fe-4S] clusters, proteins can stabilise a particular redox couple • Further effects (a) solvent exposure of the cluster (b) specific hydrogen bonding networks especially NH-S bonds (c) the proximity and orientation of protein backbone and side chain dipoles (d) the proximity of charged residues to the cluster

  22. Tuning of redox potentials • Bacterial ferredoxins and HiPIPs: Both have Fe4S4Cys4 clusters • -400 mV vs. +350 mV • Ferredoxins: [Fe4S4Cys4]3-→ [Fe4S4Cys4]2- • HiPIPs: [Fe4S4Cys4]2- → [Fe4S4Cys4]1- • HiPIPs are more hydrophobic: Favours -1 • NH...S bonds: 8-9 in Fd, only 5 in HiPIPs • Compensate charge on cluster; -3 favoured *) HiPIP: high potential iron-sulfur proteins

  23. Copper proteins

  24. Copper proteins • Oxidases • Cytochrome oxidase(s) • Enzymes dealing with oxides of nitrogen • Blue copper proteins • Superoxide dismutase • Tyrosinase • Caeruloplasmin

  25. Principles • Cu(II) forms the strongest M(II) complexes (see Irving Williams series) • Cu(I) also forms stable complexes • The Cu(I)/Cu(II) redox couple: 0.2V-0.8V • Most Cu proteins either extracellular or membrane-bound • Many Cu proteins involved in electron transfer

  26. Preferred geometries • Cu(II): Tetrahedron • Cu(I): trigonal planar or 2-coordinate

  27. Blue copper proteins • Azurin, stellacyanin, plastocyanin • Unusual coordination geometry: Another example for how proteins tune metal properties • Consequences: • Curious absorption and EPR spectra • High redox potential (Cu(I) favoured) • No geometric rearrangement for redox reaction: Very fast

  28. Blue copper proteins: coordination geometry 2.11 Å 2.9 Å Angles also deviate strongly from ideal tetrahedron (84-136°) Amicyanin (pdb 1aac) from Paracoccus denitrificans

  29. Key points • Properties such as redox potentials are tuned by proteins • Coarse tuning by metal ligands • Charge imposed by ligand can favour particular oxidation state • Geometry can be imposed by protein: Can favour particular oxidation state, and also increase reaction rate • Fine tuning by “second shell”: hydrophobicity, hydrogen bonds, charges in vicinity

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