Biology & Inorganic Chemistry of ET

Class 18-19 Advanced Inorganic Chemistry

Biology and Inorganic Chemistry of Electron Transfer
Principles of Bioinorganic Chemistry Stephen J. Lippard and Jeremy M. Berg, 1994.

Inorganic Chemistry

Yunho Lee, Ph.D. 04/24-05/01/2012

Department of Chemistry Korea Advanced Institute of Science and Technology
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Biology & Inorganic Chemistry of ET

Outer-sphere Reactions

Inorganic Chemistry

Oxidant with bridging ligands undergoes inner-sphere mechanism. [CoII(CN)5]3- + [CoIII(NH3)5X]2+ [CoIII(CN)5X]3- + [CoII(NH3)5]2+
Substitution 2. ET

Must be outersphere

Biology & Inorganic Chemistry of ET

Outer-sphere Reactions
Tunneling ET

Inorganic Chemistry

1. ET

2. Nuclear reorganization

According to FranckCondon principle Electronic transitions are so fast taking place in a stationary nuclear framework.

Product Reactant
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Biology & Inorganic Chemistry of ET

Outer-sphere Reactions
Tunneling ET

Inorganic Chemistry

Transition state; Two states are in the same energy! According to Marcus theory The movement of atoms is much slower than that of electrons, so the nuclei Reactant must move before, not during, the electron transfer. Product

Biology & Inorganic Chemistry of ET

Outer-sphere Reactions
ET

Inorganic Chemistry

Td

TBP or SP

Entatic state where Cu(I) geometry is imposed on the Cu (II) site by the protein! Little geometric change on oxidation and a low FranckCondon barrier to ET!

Biology & Inorganic Chemistry of ET

Electron Transfer Proteins

Inorganic Chemistry

1 electron transfer processes are generally preferred. Coupling of proton and electron transfer redox potential control Iron or copper metal ions are typically utilized Electron travels long distances > 10 Structural reorganization Oxidation states Electron transfer rate

Acid-Base; Proton transfer

OxidationReduction; Electron transfer

2. Blue Copper Proteins

Biology & Inorganic Chemistry of ET

1. Iron-Sulfur Proteins

Inorganic Chemistry

Although ultimate proof of the existence of the nFe-nS clusters came from protein XRD data, values for the high-resolution metrical parameters of the clusters and, especially, their overall charge have often relied heavily on the data of the replicative model systems.
Protein Rubredoxin Ferredoxin Ferredoxin Ferredoxin Cluster 1Fe-0S 2Fe-2S 3Fe-4S 4Fe-4S OS Fe3+ Fe2+ Fe3+/3+ Fe2+/3+ Fe3+/3+/3+ Fe2+/3+/3+ Fe2+/3+/3+/3+ Fe2+/2+/3+/3+ Fe2+/2+/2+/3+ EPR
4.3, 9 1.89, 1.95, 2.05 1.97, 2.00, 2.02 2.04, 2.04, 2.12 1.88, 1.92, 2.06

Mssbauer (mm/sec)
0.25 0.65 0.26 0.25, 0.55 0.27 0.30, 0.46 0.31 0.42 0.57

max (nm)
390, 490 310, 335 325, 420, 465 Abs declines 50% 305, 415, 455 425 325, 385, 450 305, 390 Unfeatured 7

Biology & Inorganic Chemistry of ET

1-a. Rubredoxin (Rb) [1Fe-0S]

Inorganic Chemistry

The protein C. pasteurianum rubredoxin (Rb) A single iron atom Tetrahedral geometry with four sulfur (Cys) atoms; Cys(6)-X-XCys(9)-Gly and Cys(39)-X-X-Cys(42)-Gly HS ferric by EPR and Mssbauer data Oxi form: red color, LMCT band at 490 nm. Redox potentials in the -50 ~ + 50 mV range at pH 7.

PDB 1FHH, 1FHM

Oxi form Fe-S 2.28 Good agreement with synthetic analog bis(oxylyldithiolato)iron(III); Fe-S 2.267 Reduced form Fe-S 2.26~2.32 Good agreement with synthetic analog bis(oxylyldithiolato)iron(II); Fe-S 2.36 The iron center does not change much upon 8 reduction! No CN and Spin state.

Biology & Inorganic Chemistry of ET

1-b. Ferredoxin (Fd) [2Fe-2S]

Inorganic Chemistry

[2Fe-2S] ferredoxin from S. platensis {Fe2S2(S-Cys)4}2- cluster with two sulfide ligands FeIII-FeIII 2.70 (FeIIFeIII 2.76 EXAFS); <Fe-S-Fe 75 FeIIFeII and FeIIFeIII (mixed-valence form) and FeIIIFeIII Latter two forms exist in the proteins HS in both oxi and reduced forms Antiferromagnetic exchange coupling through two bridging sulfur atoms FeIIFeIII (paramagnetic) and FeIIIFeIII (Diamagnetic) Redox potentials: -280 ~ -490 mV

PDB 1A70

Synthetic model complexes had been prepared and structurally and spectroscopically characterized prior to the protein

Biology & Inorganic Chemistry of ET

1-c. Ferredoxin (Fd) [3Fe-4S]

Inorganic Chemistry

[3Fe-4S] ferredoxin from A. vinelandii Originally the structure was known as 7-iron ferredoxin; [4Fe-4S] and [3Fe-3S] due to the wrong space group in XRD data. Latter found [3Fe-4S] cluster Fe4S4 cube missing one corner The same cluster was found from Fd from Desulfovibrio gigas and an inactive form of aconitase Redox potentials: -400 mV
Fe-Fe 2.7 , HS FeIIIFeIIIFeIII overall spin 1/2. HS Fe2.5Fe2.5FeIII overall spin 2.

JBC 1988, 263, 9256

Redox potentials: -110 mV

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Biology & Inorganic Chemistry of ET

1-d. Ferredoxin (Fd) [4Fe-4S]

The most ubiquitous iron-sulfur clusters in biology A distorted cube Distorted tetrahedral four iron atoms with four sulfide atoms Fe-Fe 2.75 ; S-S 3.55 It can exist in three oxidation states.

Inorganic Chemistry

P. aerogenes Fd [4Fe-4S]2+: FeIIFeIIFeIIIFeIII " 4Fe2.5 fully delocalized Reduced form [4Fe-4S]+: FeIIFeIIFeIIFeIII " fully delocalized as well High-potential iron protein (HiPIP, Chromatium Fd) oxidized form[4Fe-4S]3+: FeIIFeIIIFeIIIFeIII

PDB 1IRO, 1IUA

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Biology & Inorganic Chemistry of ET

1-d. Ferredoxin (Fd) [4Fe-4S]

Inorganic Chemistry

The most ubiquitous iron-sulfur clusters in biology A distorted cube Distorted tetrahedral four iron atoms with four sulfide atoms Fe-Fe 2.75 ; S-S 3.55 Model complexes
It can exist in three oxidation states.

P. aerogenes Fd [4Fe-4S]2+: FeIIFeIIFeIIIFeIII " 4Fe2.5 fully delocalized Reduced form [4Fe-4S]+: FeIIFeIIFeIIFeIII " fully delocalized as well High-potential iron protein (HiPIP, Chromatium Fd) oxidized form[4Fe-4S]3+: FeIIFeIIIFeIIIFeIII

2.28
2.31
2.25

Very wide redox potential range: for [4Fe-4S]2+/+ -650 ~ -280 mV for [4Fe-4S]3+/2+ + 350 mV

ET rate constant: 103 104 M-1 s-1 Minimal cluster reorganizational energy

The structural changes at each iron atom are very small. Only 1.3 % changes per added electron!

Biology & Inorganic Chemistry of ET

Biological N2 Reduction; FeMo-Nitrogenase

Inorganic Chemistry

Biological nitrogen reduction by Mo-containing Nitrogenases is the rst identied and well-studied. Fe protein - [4Fe-4S] cluster - MgATP binding site - Dissociated from MoFe Protein after delivering e MoFe protein - 232 K protein with an 22 subunit - P cluster; [8Fe-7S] cluster - FeMo-cofactor: N2 binding

Mackay, B. A., et al. Chem. Rev. 2004, 104, 385; Einsle, O., et al. Science 2002, 297, 1696; Schindelin H., et al. Nature 1997, 387, 370, Rees, D. C. et al. Science 1992, 257, 1653.

Biology & Inorganic Chemistry of ET

Nitrate Reductase

Inorganic Chemistry

Obtained from the sulphate reducing bacterium Desulfavibrio desulfuricans ATCC 27774. A single polypeptide chain of 723 amino acid residues Folded into four domains Molybdenum-containing enzyme bis-molybdopterin guanine dinucleotide (MGD) cofactor One Cys 140 and a water/hydroxo ligand One [4Fe-4S] cluster

NO3 + 2e + 2H+ NO2 + H2O

Structure 1999, 7, 65

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Biology & Inorganic Chemistry of ET

Synthetic Analogues of the Active Sites of Fe-S Proteines

Inorganic Chemistry

Chem. Rev. 2004, 104, 527

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Biology & Inorganic Chemistry of ET

Synthetic Analogues of the Active Sites of Fe-S Proteines

Inorganic Chemistry

Protein Rubredoxin Ferredoxin Ferredoxin Ferredoxin

Cluster 1Fe-0S 2Fe-2S 3Fe-4S 4Fe-4S

OS Fe3+ Fe2+ Fe3+/3+ Fe2+/3+ Fe3+/3+/3+ Fe2+/3+/3+ Fe2+/3+/3+/3+ Fe2+/2+/3+/3+ Fe2+/2+/2+/3+

EPR
4.3, 9 1.89, 1.95, 2.05 1.97, 2.00, 2.02 2.04, 2.04, 2.12 1.88, 1.92, 2.06

Mssbauer (mm/sec)
0.25 0.65 0.26 0.25, 0.55 0.27 0.30, 0.46 0.31 0.42 0.57

max (nm)
390, 490 310, 335 325, 420, 465 Abs declines 50% 305, 415, 455 425 325, 385, 450 305, 390 Unfeatured 16

Chem. Rev. 2004, 104, 527

Biology & Inorganic Chemistry of ET

Synthetic Analogues of the Active Sites of Fe-S Proteines

Inorganic Chemistry

O-xylyldithiolato ligand

Holm, PNAS 1975, 72, 2868 PNAS 1973, 70, 2429

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Biology & Inorganic Chemistry of ET

Synthetic Analogues of the Active Sites of Fe-S Proteines

Inorganic Chemistry

Chem. Rev. 2004, 104, 527

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Biology & Inorganic Chemistry of ET

Synthetic Analogues of the Active Sites of Fe-S Proteines

Inorganic Chemistry

Linear Cluster

Cuboidal Cluster

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Holm, JACS 1982, 104, 5497

JACS 1996, 118, 1966

Biology & Inorganic Chemistry of ET

Synthetic Analogues of the Active Sites of Fe-S Proteines

Inorganic Chemistry

Cuboidal Cluster

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Holm, JACS 1982, 104, 5497

JACS 1996, 118, 1966

Biology & Inorganic Chemistry of ET

2. Blue Copper Proteins

Inorganic Chemistry

Chem. Rev. 2004, 104, 419

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Biology & Inorganic Chemistry of ET

2. Blue Copper Proteins

Inorganic Chemistry

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Biology & Inorganic Chemistry of ET

2. Blue Copper Proteins

Inorganic Chemistry

Electron Transfer Protein - Blue mono (Type 1) cupredoxins; plastocyanin (plants), Azurin (bacteria) - Two His, Met, Cys distorted Td - LMCT ~ 600 nm (>3,000 M1cm1) - Very small All value (~ 60 X104 cm1) Very short Cu-S distance ~ 2.1 with very long Met distance. - Eo = + 250 ~ 350 mV, vs. NHE
The site is near the surface of the protein

Entatic state!

SMet

Cu(II) () Cu-SCys 2.13 2.90 2.04 2.10

SCys

Cu(I) () 2.17 2.87 2.13 2.39

Cu

Cu-SMet Cu-NHis Cu-NHis

Plastocyanin PDB code: 1PLC

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Biology & Inorganic Chemistry of ET

2. Blue Copper Proteins

Inorganic Chemistry

Thus, Geometries of Cu(I) and Cu(II) are nearly identical!

Elongated Cu-S

Strong covalent Cu-S

Both subject to Jahn-Teller distortion upon oxidation

Entatic state! 24
No J-T distortion

Biology & Inorganic Chemistry of ET

2. Blue Copper Proteins

Inorganic Chemistry

CuA: Electron Transfer Site - Purple binuclear center; also found in CcO - Two bridging Cys, two His, Met, CarbonlyTrp - 480 nm (~5000 M1cm1), 530 nm (~4000 M1cm1) - Eo = ~ + 240 mV, vs. NHE
SCys Cu Cu SMet SCys O=CTrp

Electron Transfer Protein - Blue mono (T1) cupredoxins; plastocyanin, Azurin - Two His, Met, Cys - ~ 600 nm (5000 M1cm1) - very small All value (~ 60 X104 cm1) - Eo = + 250 ~ 350 mV, vs. NHE
SMet

Cu

SCys

e
Trp N O Cu N N

CuI CuI

Cu1.5 Cu1.5
e
Plastocyanin PDB code: 1PLC

N Cu S

S
2.47

- - - -

Cu-His: ~ 2 Cu-Cys: ~ 2.3 Cu-Met: 2.47 Cu-Ocarbonyl: 2.6

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Biology & Inorganic Chemistry of ET

Nitrite Reductase; T1 Copper

Inorganic Chemistry

Homotrimer with 36 kDa monomer Three identical subunits are tightly associated around a 3-fold axis to form a trimer around a central channel of 5-6 . Each monomer contains type 1 copper (2 His, 1 Met and 1 Cys) and type 2 copper (3 His and solvent) Intense 593 nm absorption band (3,800 M-1 cm-1) due to LMCT in type 1 copper. can be classified into two group green or blue.

NO2 + e + 2H+ NO + H2O

Cu-Scys: 2.08-2.18 Cu-Smet: 2.62-2.64

12.6

Acc. Chem. Res. 2000, 33, 728-735

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Biology & Inorganic Chemistry of ET

Mono Copper Center in PHM

Inorganic Chemistry

PHM (Peptidylglycine -Hydroxylating Monooxygenase) catalyzes stereo-specific hydroxylation of a glycine -carbon in peptide amidation of many neuropeptides and peptide hormones.

Crystal structure of PHM

O

H N

O H H PHM N COOH O2 R H Ascorbate

H N O

O H OH N COOH R H

H atom abstraction
O

H N

O H N COOH R H

Prigge S. T. et al., Science, 2004, 304, 864.

Prigge S. T. et al., Science 1997, 278, 1300-1305; 27 Prigg e S. T. et al., Cell. Mol. Life Sci. 2000, 57, 1236-1259

Biology & Inorganic Chemistry of ET

Electron Transfer; CuA site

Inorganic Chemistry

Head-to-tail homodimer
SCys Cu Cu SMet SCys O=CTrp

Cu+1.5Cu+1.5 S = , 7 lines in EPR

Haltia et al., Biochem. J. 2003, 369, 77-88

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Biology & Inorganic Chemistry of ET

Modeling the Blue Copper Proteins

Tris(pyrazolyl)borate

Inorganic Chemistry

-diketiminate

Utilizing the same Triphenylmethylthiolate ligand Axial ligand exists in complex 1 but not in complex 2.

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Biology & Inorganic Chemistry of ET

3. Cytochromes

Inorganic Chemistry

The final class of ET proteins utilizing iron porphyrins Most cytochromes have two axial ligands, affording coordinately saturated octahedral complexes. Eukaryotic cytochrome c uses His and Met. In addition, the prosthetic group is bound to covalently via two thioether linkages. Two propionic acid substituents is exposed to solvent.

LS Fe(II/III)

Why?
Nonbonding T2g
Propionic acid

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Biology & Inorganic Chemistry of ET

Nitrite Reductase; Iron

Multi-heme NIR 120 kDa homodimer Each monomer contains one heme c and one heme d1. Heme c is a ET center with His51 and Met88 axial ligands. Heme d1 is a catalytic center.

Inorganic Chemistry

Structure 1997, 5, 1157

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Biology & Inorganic Chemistry of ET

Nitric Oxide Reductase

Inorganic Chemistry

TM domain: 13 helices span the transmembrane region Two heme b and b3 and one none-heme iron, FeB Globular hydrophilic domain: heme c. NOR is an evolutionary progenitor of cytochrome oxidases.
The topology of the TM region and the arrangement of the metal centers in cNOR are similar to those of cytochrome oxidases, a superfamily of enzymes that act as the terminal oxidases in aerobic respiratory transport chains.

Science 2010, 330, 1666-1670

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Biology & Inorganic Chemistry of ET

Bovine Heart Cytochrome c Oxidase Crystal Structure

H161

Inorganic Chemistry

M207 C200

CuA

CuA
C196 E198

CuA Heme a Heme a3 CuB

H61

H204

H291

CuB
H376 H378

H290 H24 0

Heme a3 Heme a!

S. Yoshikawa et al., Science 1998, 280, 1723.