2012Spring-AIC-18-ET-Web

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Inorganic Chemistry

Biology & Inorganic Chemistry of ET

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

Department of Chemistry

Korea Advanced Institute of Science and Technology

Class 18-19Advanced Inorganic Chemistry

Biology and Inorganic Chemistry ofElectron Transfer

Principles of Bioinorganic ChemistryStephen J. Lippard and Jeremy M. Berg, 1994.

1


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Inorganic Chemistry


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

Must be outer-sphere

Substi-tution 2. ET


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Outer-sphere ReactionsTunneling

ET

According to Franck-

Condon principleElectronic transitions

are so fast taking placein a stationary nuclear

framework. Reactant

Product

1. ET 2. Nuclearreorganization


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Inorganic Chemistry


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Outer-sphere ReactionsTunneling

ET

According to Marcus theoryThe movement of atoms ismuch slower than that ofelectrons, so the nucleimust move before, notduring, the electron

transfer.

Reactant

Product

Transition state;Two states are inthe same energy!


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Inorganic Chemistry


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Outer-sphere ReactionsET

Entatic state where Cu(I)geometry is imposed on the Cu

(II) site by the protein! Little geometric change onoxidation and a low Franck-

Condon barrier to ET!

TdTBP or SP


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Electron Transfer Proteins 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

Oxidation-Reduction;Electrontransfer

2. Blue CopperProteins


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1. Iron-Sulfur Proteins 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 overallcharge have often relied heavily on the data of the replicativemodel systems.

Protein Cluster OS EPR Mssbauer

(mm/sec)

max

(nm)

Rubredoxin 1Fe-0SFe3+

Fe2+4.3, 9

-0.250.65

390, 490310, 335

Ferredoxin 2Fe-2SFe3+/3+

Fe2+/3+-

1.89, 1.95, 2.050.26

0.25, 0.55325, 420, 465

Abs declines 50%

Ferredoxin 3Fe-4S Fe3+/3+/3+Fe2+/3+/3+

1.97, 2.00, 2.02-

0.270.30, 0.46

305, 415, 455425

Ferredoxin 4Fe-4SFe2+/3+/3+/3+

Fe2+/2+/3+/3+

Fe2+/2+/2+/3+

2.04, 2.04, 2.12-

1.88, 1.92, 2.06

0.310.420.57

325, 385, 450305, 390

Unfeatured


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1-a. Rubredoxin (Rb) [1Fe-0S] The protein C. pasteurianumrubredoxin (Rb) A single iron atom Tetrahedral geometry with four sulfur (Cys) atoms; Cys(6)-X-X-Cys(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(o-

xylyldithiolato)iron(III); Fe-S 2.267 Reduced form Fe-S 2.26~2.32 Good agreement with synthetic analog bis(o-

xylyldithiolato)iron(II); Fe-S 2.36 The iron center does not change much uponreduction! No CN and Spin state.

l h f E


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1-b. Ferredoxin (Fd) [2Fe-2S] [2Fe-2S] ferredoxin from S.platensis {Fe2S2(S-Cys)4}2- cluster with two sulfide ligands FeIII-FeIII 2.70 (FeIIFeIII 2.76 EXAFS);


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

an inactive form of aconitase Fe-Fe 2.7 ,

HS FeIII

FeIII

FeIII

overall spin 1/2. HS Fe2.5Fe2.5FeIII overall spin 2.

JBC1988, 263, 9256 Redox potentials: -110 mV

Redox potentials: -400 mV

Bi l & I i Ch i f ET


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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.

PDB 1IRO, 1IUA

P. aerogenesFd [4Fe-4S]2+: FeIIFeIIFeIIIFeIII" 4Fe2.5 fully delocalized Reduced form [4Fe-4S]+: FeIIFeIIFeIIFeIII

" fully delocalized as well High-potential iron protein (HiPIP,

ChromatiumFd) oxidized form[4Fe-4S]3+:FeIIFeIIIFeIIIFeIII

Bi l & I i Ch i t f ET


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Inorganic Chemistry

Biology & Inorganic Chemistry of ET1-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. P. aerogenesFd [4Fe-4S]2+: FeIIFeIIFeIIIFeIII" 4Fe2.5 fully delocalized Reduced form [4Fe-4S]+: FeIIFeIIFeIIFeIII

" fully delocalized as well High-potential iron protein (HiPIP,

ChromatiumFd) oxidized form[4Fe-4S]3+:FeIIFeIIIFeIIIFeIII

2.31 2.28

2.25

Model complexes

The structural changes ateach iron atom are very small.

Only 1.3 % changes peradded electron!

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

ET rate constant: 10

3

104

M-1

s-1

Minimal cluster reorganizational energy



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Inorganic Chemistry

Biology & Inorganic Chemistry of ETBiological N2 Reduction; FeMo-Nitrogenase

Biological nitrogen reduction by Mo-containing Nitrogenasesis the first identified and well-studied.

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.

MoFe protein- 232 K protein with an 22

subunit

-P cluster; [8Fe-7S] cluster- FeMo-cofactor: N2 binding

Fe protein- [4Fe-4S] cluster- MgATP binding site- Dissociated from MoFe

Protein after delivering e



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Nitrate Reductase

Structure1999, 7, 65

Obtained from the sulphate reducing bacterium DesulfavibriodesulfuricansATCC 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] clusterNO3 + 2e + 2H+ NO2 + H2O



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Synthetic Analogues of the Active Sites of Fe-S Proteines

Chem. Rev. 2004, 104, 527



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Chem. Rev. 2004, 104, 527

Protein Cluster OS EPR Mssbauer

(mm/sec)

max

(nm)

Rubredoxin 1Fe-0SFe3+

Fe2+4.3, 9

-0.250.65

390, 490310, 335

Ferredoxin 2Fe-2SFe3+/3+

Fe2+/3+-

1.89, 1.95, 2.050.26

0.25, 0.55325, 420, 465

Abs declines 50%

Ferredoxin 3Fe-4S Fe3+/3+/3+Fe2+/3+/3+

1.97, 2.00, 2.02-

0.270.30, 0.46

305, 415, 455425

Ferredoxin 4Fe-4SFe2+/3+/3+/3+

Fe2+/2+/3+/3+

Fe2+/2+/2+/3+

2.04, 2.04, 2.12-

1.88, 1.92, 2.06

0.310.420.57

325, 385, 450305, 390

Unfeatured

Bi l & In nic Ch mist f ET


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Holm, PNAS1975, 72, 2868 PNAS1973, 70, 2429

O-xylyldithiolato ligand



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Chem. Rev. 2004, 104, 527



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Holm, JACS1982, 104, 5497

Linear Cluster

Cuboidal Cluster

JACS1996, 118, 1966



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Holm, JACS1982, 104, 5497

Cuboidal Cluster

JACS1996, 118, 1966



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2. Blue Copper Proteins

Chem. Rev. 2004, 104, 419



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PlastocyaninPDB code: 1PLC

Cu

SMet

SCys

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

Cu(II) () Cu(I) ()

Cu-SCys 2.13 2.17

Cu-SMet 2.90 2.87Cu-NHis 2.04 2.13

Cu-NHis 2.10 2.39

The site is near the surfaceof the protein

Entatic state!



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Both subject to Jahn-Teller

distortion upon oxidation

Entatic state!

No J-T distortion

ElongatedCu-S

Strongcovalent Cu-S

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



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Cu

SMet

SCys

SCys

Cu

O=CTrp

2. Blue Copper ProteinsCuA: 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

PlastocyaninPDB code: 1PLC

Cu

SMet

SCys

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

N

N

SS

OS

N

N

Cu Cu

N

Trp

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

Cu-Ocarbonyl: 2.6

CuICuI Cu

1.5Cu

1.5

e

e



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Nitrite Reductase; T1 Copper 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.

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

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

NO2 + e + 2H+ NO + H2O



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PHM (Peptidylglycine -Hydroxylating Monooxygenase) catalyzesstereo-specific hydroxylation of a glycine -carbon in peptide

amidation of many neuropeptides and peptide hormones.

Mono Copper Center in PHM

Crystal structure of PHM

Prigge S. T. et al., Science1997, 278, 1300-1305; Prigge S. T. et al., Cell. Mol. Life Sci. 2000, 57, 1236-1259

N

O

H O

N

H

COOH

R

HH

N

O

H O

N

H

COOH

R

OHHPHM

O2

Ascorbate

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

N

O

H O

N

H

COOH

R

H

H atom

abstraction



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Electron Transfer; CuA site

Head-to-tail homodimer

Cu

SMet

SCys

SCys

Cu

O=CTrp

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

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



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

Tris(pyrazolyl)borate

-diketiminate

Modeling the Blue Copper Proteins



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3. Cytochromes The final class of ET proteins utilizing iron porphyrins Most cytochromes have two axial ligands, affording coordinately saturated

octahedral complexes. Eukaryotic cytochrome cuses His and Met. In addition, the prosthetic group is bound to covalently via two thioether

linkages. Two propionic acid substituents is exposed to solvent.

Propionic acid

LS Fe(II/III)

Why?

Nonbonding T2g



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Nitrite Reductase; Iron Multi-heme NIR 120 kDa homodimer Each monomer contains one heme cand oneheme d1. Heme cis a ET center with His51 and

Met88 axial ligands. Heme d1 is a catalytic center.

Structure1997, 5, 1157



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Nitric Oxide Reductase TM domain: 13 helices span the transmembrane region

Two heme band b3 and one none-heme iron, FeB Globular hydrophilic domain: heme c. NOR is an evolutionary progenitor of cytochrome oxidases.

Science2010, 330, 1666-1670

The topology of the TMregion and the arrangement ofthe metal centers in cNOR

are similar to those ofcytochrome oxidases, a

superfamily of enzymes thatact as the terminal oxidases

in aerobic respiratorytransport chains.



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Inorganic Chemistry

Biology & Inorganic Chemistry of E Bovine Heart Cytochrome cOxidase Crystal Structure

Heme a3Heme

a

CuA

CuB

CuACuA

H161

H204 E198

C196C200

M207

H61

H378

H376

H291

H290

H240

CuB

Heme a3Heme a!

2012Spring-AIC-18-ET-Web

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