CH 105

CH 105
Inorganic & Organic Chemistry
Module IV: Bioinorganic Chemistry

Chemistry Department
IIT Bombay

Figures prepared by using Pymol

CH 105
Outline

Relevance of
Bioinorganic Chemistry

O2 a key player in
Bioinorganic Chemistry

Hemoglobin &
reversible O2 binding

Trivia
CH 105
Outline

Relevance of
Bioinorganic Chemistry

O2 a key player in
Bioinorganic Chemistry

Hemoglobin &
reversible O2 binding

Trivia
CH 105 Why do we learn Bioinorganic Chemistry ?

Ø A close relation between biology & chemistry

Ø Various elements affects the biochemistry,

physiology, micro-biology, toxicology, pharmacology

W. Kaim, B. Schwederski, Bioinorganic Chemistry:

Inorganic Elements in Chemistry of Life, Wiley, 2013

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CH 105 Why do we learn Bioinorganic Chemistry ?

Ø A close relation between biology & chemistry

Ø Various elements affects the biochemistry,

physiology, micro-biology, toxicology, pharmacology

Ø Essential & non-essential elements

Metallomics, 2012, 4, 1017-1019

Der Pharma Chemica 4(5):1962-1968 2

CH 105 Why do we learn Bioinorganic Chemistry ?

Ø A close relation between biology & chemistry

Ø Various elements affects the biochemistry,

physiology, micro-biology, toxicology, pharmacology

Ø Essential & non-essential elements

Metallomics, 2012, 4, 1017-1019

Ø Bulk & trace elements all abundant elements

including S,Cl and P

R. J. P. Williams and R. Rickaby, “A chemical account of

evolution”, Chem. World, 2012, 6 3
CH 105 Bioinorganic Chemistry influenced evolution?
Comparing planetary environments

Venus Earth Mars

doi:10.1126/science.aad1784

CO2 96% 0.04% 95%

N2 3% 78% 3%
O2 0% 21% 0.2%

In the beginning earth atmosphere was similar to Venus or Mars

Emergence of O2 occurred at a later stage

Significant contribution from bioinorganic chemistry

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CH 105 Bioinorganic Chemistry influenced evolution?

In the beginning earth atmosphere was

anoxygenic (no O2 )

Emergence of O2 during the great

oxygenation event (GOE)
B. Biddanda et al., Nature Education Knowledge, 2012, 3(10):13

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CH 105 Bioinorganic Chemistry influenced evolution?

In the beginning earth atmosphere was

anoxygenic (no O2 )

Emergence of O2 during the great

B. Biddanda et al., Nature Education Knowledge, 2012, 3(10):13
oxygenation event (GOE)

Triggered by photosynthesis
CO2 + H2O C6H12O6+O2

H2O is the source of electron and O2 is

by-product

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CH 105 Bioinorganic Chemistry influenced evolution?

In the beginning earth atmosphere was

anoxygenic (no O2 )

Emergence of O2 during the great

B. Biddanda et al., Nature Education Knowledge, 2012, 3(10):13
oxygenation event (GOE)

Triggered by photosynthesis
CO2 + H2O C6H12O6+O2

H2O is the source of electron and O2 is

by-product

H2O oxidation is catalyzed by

Mn4O4Ca Oxygen Evolving Cluster
(OEC)
Suga et al., Nature, 2015, 517, 99–103 7
CH 105 Bioinorganic Chemistry influenced evolution?

Photosynthetic O2 evolution altered the

scenario

B. Biddanda et al., Nature Education Knowledge, 2012, 3(10):13 O2 is a strong oxidizing agent

Change in the course of evolution

1. Extinction

2. Exiled to anoxic niches

3. Adapt to oxygenic environment

Suga et al., Nature, 2015, 517, 99–103 8

CH 105
Take Home Messages

O2 binding
to Hemoglobin Ø Inorganic elements are crucial for Biology

Ø Essential/non-essential & bulk/trace elements

Ø Bioinorganic chemistry of photosynthesis

Ø Photosynthetic O2 production is a game-changer

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CH 105
Outline

Relevance of
Bioinorganic Chemistry

O2 a key player in
Bioinorganic Chemistry

Hemoglobin &
reversible O2 binding

Trivia
CH 105 Handling O2 in cellular environments
Generation of ROS in cells can cause
oxidative damage (DNA, protein, lipid)

O2 + e - O2•-

O2•- + e- + 2H+ H2O2

H2O2 + e- + H+ OH • + H2O

OH • + e- + H+ H2O

ROS: Reactive Oxygen Species

O2•-, H2O2, OH •

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CH 105 Handling O2 in cellular environments

Superoxide Dismutase (SOD) Generation of ROS in cells can cause

oxidative damage (DNA, protein, lipid)
'-' beside dot signify an odd e species with
an electron gained.

O2 + e - O2•-

O2•- + e- + 2H+ H2O2

H2O2 + e- + H+ OH • + H2O

PDB 1SXZ OH • + e- + H+ H2O

2O2•- + 2H+ H2O2 + O2
Dismutation reaction Anti-oxidants: Defense system of biology

Mn-, Fe-, and Ni-SOD also exist Ø Superoxide Dismutase (SOD)

H2O2 still an issue 10

CH 105 Handling O2 in cellular environments
Generation of ROS in cells can cause
Catalase oxidative damage (DNA, protein, lipid)

O2 + e - O2•-

O2•- + e- + 2H+ H2O2

H2O2 + e- + H+ OH • + H2O

PDB 1DGF OH • + e- + H+ H2O

2H2O2 2H2O + O2 Anti-oxidants: Defense system of biology

Dismutation reaction
Ø Superoxide Dismutase (SOD)
Removal of toxic H2O2
Ø Catalase 11
CH 105 Handling O2 in cellular environments
Generation of ROS in cells can cause
Peroxidase oxidative damage (DNA, protein, lipid)

O2 + e - O2•-

O2•- + e- + 2H+ H2O2

H2O2 + e- + H+ OH • + H2O

PDB 1HCH OH • + e- + H+ H2O

H2O2 + 2 Sub(red) 2H2O + 2 Sub(ox) Anti-oxidants: Defense system of biology

Controlled utilization of Ø Superoxide Dismutase (SOD)

the oxidizing power of H2O2
Ø Catalase & Peroxidase 12
CH 105 Handling O2 in cellular environments
Cytochrome P450

PDB 1JOD

O2 + Sub(red) + 2e- + 2H+ H2O + 2 Sub(ox) Poison O2 becomes lifeline

Harnessing the oxidizing power of O2

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CH 105 Handling O2 in cellular environments
Cytochrome P450

Erythromycin

PDB 1JOD

O2 + Sub(red) + 2e- + 2H+ H2O + 2 Sub(ox) Poison O2 becomes lifeline

Harnessing the oxidizing power of O2 Requires controlled O2

Critical for pharmaceutical metabolism transport in biology
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CH 105
Take Home Messages

O2 a key player in Ø Oxidizing agent O2 can produce ROS [O2 •-, H2O2 , OH •]
Bioinorganic Chemistry
Ø Transition metal containing enzymes as defense system

2O2•- 2H2O2 H2O2

Sub(red)

Sub(ox)
H2O2 + O2 2H2O + O2 2H2O
Superoxide Dismutase Catalase Peroxidase
Ø Use of H2O2 for controlled oxidation
O2
(peroxidase)
Sub(red)
Ø Further advancement: Use of O2 as an oxidant
Sub(ox)
Cytochrome P450 H2O (cytochrome P450) 15
CH 105
Outline

Relevance of
Bioinorganic Chemistry

O2 a key player in
Bioinorganic Chemistry

Hemoglobin &
reversible O2 binding

Trivia
CH 105 Hemoglobin & reversible O2 binding
B E C S
S 1.

E S :
P
C O2 a key player in the energy
transduction process
H2 O + + O2
Respiration liberates stored
chemical energy

Regulated O2 supply in the

S 2. cells is vital

E U :
M
R
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CH 105 Hemoglobin & reversible O2 binding
Transfer of aerial
O2 to cells

http://organismalbio.biosci.gatech.edu/

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CH 105 Hemoglobin & reversible O2 binding
Transfer of aerial Need an O2 transporter
O2 to cells Hemoglobin (Hb)

and an O2-storage system

Myoglobin (Mb)

http://organismalbio.biosci.gatech.edu/

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CH 105 Hemoglobin & reversible O2 binding

Differential O2 binding ability

of Hb & Mb is crucial

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CH 105 Hemoglobin & reversible O2 binding

O2 binding curve: Notice x- and y-axes

Differential O2 binding ability
of Hb & Mb is crucial Mb follows a hyperbolic O2 binding

Binds O2 strongly even at low O2 conc.

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CH 105 Hemoglobin & reversible O2 binding

Mb follows a hyperbolic O2 binding

Differential O2 binding ability
of Hb & Mb is crucial Hb follows a sigmoidal trend

Binds O2 strongly only at higher O2 conc.

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CH 105 Hemoglobin & reversible O2 binding

In cells/tissues Mb binds O2 better than Hb

Differential O2 binding ability
of Hb & Mb is crucial Hb binds O2 better in lungs

Reasons behind such differential O2 binding?

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CH 105 Hemoglobin & reversible O2 binding

PDB 1HHB PDB 1MBN

Hemoglobin (Hb)
Myoglobin (Mb)
a2b2 hetero-tetrameric
Monomeric structure
structure

Deciphering the relationship between differential O2 binding & structure for Mb/Hb
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CH 105 Hemoglobin: structure-function relationship

Hemoglobin (Hb)
a2b2 hetero-tetrameric
structure Fe-containing
heme core

Myoglobin (Mb)
Monomeric structure
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CH 105 Hemoglobin: structure-function relationship

Hemoglobin (Hb) Catalase Peroxidase

a2b2 hetero-tetrameric
structure Fe-containing
heme core

Analogous to
catalase,
Myoglobin (Mb) peroxidase, Cytochrome P450
Monomeric structure cyt-P450
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CH 105 Hemoglobin: structure-function relationship

Porphyrins are
macrocyclic tetrapyrrole
ligands

Variation in the
Hemoglobin (Hb) substituents on
a2b2 hetero-tetrameric porphyrin tunes its
structure electronic properties
Fe-containing
heme core Creates a planar N4-
coordination for metal
Analogous to binding
catalase,
Myoglobin (Mb) peroxidase, Anchored to protein via
Monomeric structure cyt-P450 axial ligation
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CH 105 Hemoglobin: structure-function relationship

O2

Hemoglobin (Hb)
a2b2 hetero-tetrameric
structure

Heme core-originated O2-binding reactivity

Each heme core binds to one molecule of O2

Myoglobin (Mb)
Monomeric structure
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CH 105 Hemoglobin: structure-function relationship

Hemoglobin (Hb) Myoglobin (Mb)

a2b2 hetero-tetrameric Monomeric structure
structure
Hb can bind 4 O2 Mb binds only one O2
Mb (Deoxy) + O2 Mb-O2 (oxy)
Not all the O2 binds at the same time to Hb (Deoxy) + xO2 Hb-(O2)x(oxy)
four hemes at Hb
x = 1-4
Binding of O2 in one subunit of Hb affect
others: Cooperativity effect 24
CH 105 Hemoglobin: Cooperativity Effect

An insight into Hb-O2 interaction

O2
Hemoglobin (Hb)
a2b2 hetero-tetrameric
structure

O2 binding pulls the

Fe center & Deoxy-Hb Oxy-Hb
proximal histidine Fe(II) high-spin system Fe(III) low-spin system
towards the Too big to fit in the porphyrin cavity Smaller size fits better
porphyrin plane (78 pm ) (55 pm)
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CH 105 Hemoglobin: Cooperativity Effect

An insight into Hb-O2 interaction

Stabilization of
Fe-O2 bond
O2 via H-bonding
Hemoglobin (Hb)
a2b2 hetero-tetrameric
structure

O2 binding pulls the

Fe center & Deoxy-Hb Oxy-Hb
proximal histidine Fe(II) high-spin system Fe(III) low-spin system
towards the Too big to fit in the porphyrin cavity Smaller size fits better
porphyrin plane (78 pm ) (55 pm)
26
CH 105 Hemoglobin: Cooperativity Effect

An insight into Hb-O2 interaction

Hemoglobin (Hb)
a2b2 hetero-tetrameric O2
structure

O2 binding pulls the

Fe center &
proximal histidine Deoxy-Hb Oxy-Hb
towards the Fe(II) high-spin system Fe(III) low-spin system
porphyrin plane O2 binding pulls the proximal histidine and the protein scaffold
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CH 105 Hemoglobin: Cooperativity Effect
Hb-O2 interaction & structural dynamics

Hemoglobin (Hb)
a2b2 hetero-tetrameric
Structure doi.org/10.1371/journal.pone.0012389

H-bonding & salt-bridge

interaction between residues Oxy-Hb
on the subunit borders
The Hb-O2 binding pulls off the protein chain and strains the sub-unit interactions 28
CH 105 Hemoglobin: Cooperativity Effect
Hb-O2 interaction & structural dynamics

Hemoglobin (Hb)
a2b2 hetero-tetrameric
Structure

https://pdb101.rcsb.org/motm/41 Oxy-Hb

The Hb-O2 binding induces fluxionality in Hb structure

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CH 105 Hemoglobin: Cooperativity Effect
Competition between Hb-O2 binding & breaking of bonding
interactions between sub-units
1. First O2:
Unfavorable (Tensed)

2. Second O2:
Unfavorable (Tensed)
https://pdb101.rcsb.org/motm/41

Hemoglobin (Hb) 3.Third O2:

a2b2 hetero-tetrameric Tilts the bar (Relaxed)
Structure
4. Fourth O2:
Favorable (Relaxed)

Binding of O2 to one-subunit effect others: Cooperativity or Allosteric Effect

Only in Hb not in Mb 30
CH 105
Take Home Messages

O2 a key player in Ø Differential O2 binding for Hb & Mb

Bioinorganic Chemistry

Ø O2-binding to heme pulls Fe-center and proximal histidine

towards porphyrin plane

Ø This movement affects the H-bonding and salt-bridge

interactions between subunits in Hb (not in monomeric Mb)

Ø Cooperativity effect observed in Hb

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CH 105
Outline

Relevance of
Bioinorganic Chemistry

O2 a key player in
Bioinorganic Chemistry

Hemoglobin &
reversible O2 binding

Trivia
CH 105
Effect of pH on Hb-O2 binding

Why such effect?

The O2-binding ability for Hb decreases at

lower conc. of O2 with increasing acidity
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CH 105
Effect of pH on Hb-O2 binding

Bohr effect

doi.org/10.1371/journal.pone.0012389

H-bonding & salt-bridge interaction

between subunits improves in acidic
conditions
Protonation of histidine (pKa ~7.5)

The O2-binding ability for Hb decreases at Needs more energy to break them
lower conc. of O2 with increasing acidity CO2 rich condition
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CH 105
Better O2 delivery in fatigued cells

Hb delivers higher amount of O2 than normal to the

cells/tissues after exercise or at higher altitude
Why?

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CH 105
Better O2 delivery in fatigued cells

2,3-Biphosphoglyceric
acid (2,3-BPG)

Cells release 2,3-BPG under stress

2,3-BPG facilitate strong interaction between 2,3-BPG is known as an

subunits allosteric effector
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CH 105
Hb structure saves us from CO poisoning?

In free heme CO binds Fe-center 25000 times strongly compared to O2

But in Hb, CO binds only 200 times strongly than O2

Why?

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CH 105
Hb structure saves us from CO poisoning?

Hb binds O2 in bent mode

1. Interaction with
distal histidine

2. Favored s - and p -
bonding interactions
between O2 p* and Fe
d-orbitals

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CH 105
Hb structure saves us from CO poisoning?

Hb binds CO in bent mode

1. Steric interaction
with distal histidine

2. Disfavored s -
bonding interactions
between CO2 s and
Fe dz2-orbital

PDB 1COH Toxic dose of CO 20-30%

Lethal dose > 60%
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