Biocomplexes
Metal binding ability of
biomolecules
Donor atoms in biological systems
hetero atoms with electron pairs: O, N, S, (Se)
- oxygen donor ligands:
alcohols: R-OH, (e.g. carbohydrates)
ethers: R-O-R (e.g. carbohydrates)
carbonyl compounds: -CO- (e.g. proteins)
phenols: Ar-OH (e.g. polyphenols)
carboxyilic comounds: -COOH (e.g. carboxylic acids, amino acids)
O-heterocycles: (furane, ..)
- nitrogen donor ligands:
amines: R-NH2 (e.g. amino acids)
amides: -CONH- (e.g. peptide bond)
N-heterocycles: (pyrrole, pyridine, imidazole,...)
- sulphur donor ligands:
thiol compounds/disulphides: RSH/R-S-S-R (e.g. cysteine-cystine)
thioethers: R-S-R (pl. methionine)
sulphur containing heterocycles: (pl. tiophene,..)
Main groups of bioligands and their complex forming
properties
- Coordination chemistry of amino acids:
O
H2N
CH C
OH
a/ amino acids without other functional group:
Gly, Ala, Phe,....
5-membered chelate ring (NH2,COO-)-coordination
CH3
O
H2 N
CH C
CH2
O
OH
H2 N
CH C
CH2
SH
N
NH
His
Cys
OH
b/ amino acids with 3 functional groups:
formation of 2 chelate rings
alcoholic-OH: Ser, Thr
carboxylate: Asp, Glu,
amide: Asn, Gln,
amine: Lys, Orn,
thio: Cys, Met,
imidazole-N: His
- Coordination chemistry of peptides
R1
CH
H 2N
C
O
NH
CH
C
R2
O
NH
CH
C
R3
O
NH
CH
COOH
R4
1. ML, ML2,..................MLn
(NH2, CO)- or COO— coordination, the latter is less favoured
2. ML 
MLH-1 
(NH2,CO)
(NH2,N-,CO)
MLH-2 
(NH2,N-,N-,CO)
MLH-3
(NH2,N-,N-,N-)
Metal ion promoted amide deprotonation and coordination
Cu(II), Ni(II), Pd(II), ……...
Formation of joint chelate systems is preferred
O
R2
CH C
O
C
CH
R1
N-
N-
M2+
NH2 N-
R3
CH
CH
MH-3L
R4
C
O
COO-
1. Coordination of the Peptide skeletone in 4N complexes
(joint, five membered chelates)
2. Site specific role of R1, R2,.. Side chains (His, Cys)
- coordination chemistry of proteins:
(the ligands have predetermined structure)
Chelate formation has only secondary importance
Independent coordination of the side-chain donor atoms
e.g. structure of carboanhydrase:
His 96
H 2O
Zn2+
His 119
His 94
Carboanhydrase
Thr 199
His 64
Glu 106
His 96
H2O
Zn2+
His 119
His 94
Gln 92
Glu 117
Carboanhydrase
- coordination chemistry of proteins:
the proteins significantly change their structure due to
metal ion coordination
e.g. development of the zinc-finger structure:
- Coordination chemistry of nucleic acids and their building blocks
NH2
AMP
N
N
N
O
-
O
P
O
H
N
H
H
H
OH
purine (adenine/guanine)
pirimidine (cytosine/uracil)
- sugar: ribose or
deoxy-ribose
O
O-
Potential binding sites:
- nucleic bases:
- phosphate
H
Characteristics: no chelate formation →
macrochelate or loop formation is possible
Metal ion selectivity:
Nucleo bases: „soft” metal ions: e.g. Pt biological role
Phosphate: „hard” metal ions: e.g. Ca, Mg, Al,...
Difference in DNA/: cis-OH groups → (chelate formation)
- Metalloporphyrins and related compounds
Composition/Structure:
N-donor containing, natural macrocycles
complex forming:
porphine, chlorin-, corrin-, corphin-ring containing
compounds
4 pyrrole (or indole) rings in joint conjugated or partly
conjugated system (most important: tetrapyrrole compounds)
Stability of their metal complexes:
Differs from the usual stabilty sequences
Ratio of the inner hole and the size of the metal ion has
primary importance.
Metallation is a catalytic process.
Metalloporfirinek
- Metalloporphyrins
M2+ + H2P
N
N
M
MP + 2H+
N
N
Stability
Stabilitásitrend
sor:
Mg(II) < Zn(II) < Cu(II) < Fe(II) < Ni(II) < Pd(II) < Pt(II)
All coordination
siteshely
are saturated
N = 4 (Ni(II), Pt(II), Pd(II)) - minden
koordinációs
foglalt
Axial binding
sites
N= 6 (Fe(II), Co(II), Mg(II), Zn(II) - axiális
kötõhely
Complexation with other bioligands
- carbohydrates: numerous –OH groups
in acidic/neutral milieau weak metal ion binders
might be suitable for administration of metal ions
(medicinal application)
-derivatives: aldolic acids amino sugars,
- lipids, oils: contain few functional groups
very weak complexation
Summary:
Strongest metal ion binders: proteins and macrocyclic ligands
→ enzymes, coenzymes, prosthetic groups
Further interactions:
redox and acid-base interactions with vitamines,
hormones and many other biomolecules
Ellenőrző kérdések
1.
2.
3.
4.
5.
6.
Mi az alapvető különbség az aminosavak és az
oligopeptidek fémionkötő képessége között?
Mi a jellemző a fehérjék fémion koordinációjára?
Mely oldallánc donorcsoportok játszanak meghatározó
szerepet a fémionok megkötésében a fémtartalmú
fehérjékben? Adjon példákat!
Jellemezze a nukleinsavak és nukleotidok fémion
koordinációját!
Miért gyenge a szénhidrátok fémion megkötő
képessége? Hogyan fokozható ez?
Milyen biomolekulákban fordul elő a tetrapirrol váz?
Röviden jellemezze ezeket!
Basic coordination chemistry
1. Basic terms: (see advanced inorganic chemistry)
formation: Lewis acid-base reaction
ligand: base
metal ion: acid
equilibrium:stepwise (successive)
kinetics:
labile and inert complexes
coordination number: 2 – (10)
with essential elements: (2), 4, 6
coordination geometry:
4 – tetrahedral/square planar,
6 – octahedral
effects of complex formation:
colour and magnetic feature
(crystal field theory)
changes in the redox potential:
(Fe3+/Fe2+ and Cu2+/Cu+ systems)
2. Complex formation in biological systems
(multi)component systems
pM + sH + qA + rB
MpAqBrHs
Types of complexes:
biner (parent): MA, ........... MAn
polynuclear: MnA (A – bridging ligand)
protonated:
MHA (multifunctional ligand)
MH-1A (coordinated H2O – hydroxocomplex or
„A”-ligand metal ion induced deprotonation
terner (mixed ligand/metal complexes): MAB
Reactions of complexes:
acid-base: liberation/uptake of protons
redox: redox reactions of the metal ion or coordinated ligands
other reactions of coordinated ligands: templates,
changes in conformation, etc.
Hard-soft classification of the biologically important metal ions and ligands
The preferential coordination of metal ions to bioligands/biodonors generally
can be well explained by the hard-soft acid-base theory.
The basic features of hard and soft acids and bases
Acids
Hard
Low
Low
Higher
Small
Ionic bond
Soft
Polarizability
Electronegativety
Positive charge
Size
Chemical interactions
High
High
Lower
Large
Covalent or p-bound
Bases
Hard
Low
High
Higher
Small
Ionic bond
Soft
Polarizability
Electronegativety
Negative charge
Size
Chemical interactions
High
Low
Lower
Large
Covalent or p-bound
The general rule is that hard acids makes strong interactions with hard
bases and soft acids with soft bases. Accordingly, hard acids, like Ca2+, Fe3+, Al3+
prefer the oxygen-, fluorine- and partly N donor atoms, while the soft acids, like
Cu+, Pt2+, Hg2+ and Cd2+ prefer the sulphur, phosphorous, and iodine donors in
forming coordination compounds.
Splitting of d-orbitals in different fields
Because of the different „shape” of the d orbitals the energy degeneracy of
the orbitals is lifted. Orbitals in a given geometry directed towards the ligands
(electron pairs) will have higher energy and will be able to form  bonds, while
those not directed to ligand lone electron pairs will occupy lower energy and will be
able to form p bonds.
Distribution of electrons on the d-orbitals
When the electrons will be redistributed among the d orbitals the
sequence will be determined by the relation between the crystal field splitting
energy () and the spin pairing energy (P). The figure shows the possible electron
configurations in the case of octahedral geometry.
Common geometries for 2-6 coordinate metal ions
Cation
Na+
K+
Mg2+
Ca2+
Mn2+
(d5)
Coord number
6
6-8
6
6-8
6
Geometry
Octahedral
Flexible
Octahedral
Flexible
Octahedral
6
4
6
Tetrahedral
Tetrahedral
Octahedral
4
6
Tetrahedral
Octahedral
4
Square planar
6
Octahedral
4
Square planar
Ni2+ (d8)
6
4
Octahedral
Tetrahedral
Cu1+
(d10)
4
Tetrahedral
Mn3+
(d4)
Fe2+ (d6)
Fe3+ (d5)
Ca2+ (d7)
Suqare planar
Cu2+ (d9)
Zn2+
(d10)
6
Octahedral
4
Tetrahedral
5
Square
pyramidal
Biologic ligands
O, ether, hydroxyl, carboxylate
O, ether, hydroxyl, carboxylate
O, carboxylate, phosphate
O, carboxylate, carbonyl (phosphate)
O, carboxylate, phosphate
N, imidazole N
O, carboxylate, phosphate, hydroxyde
S, thiolate
O, carboxylate, alkoxide, oxide, phenolate,
N, imidazole N, porphyrin
S, thiolate
O, carboxylate, alkoxide, oxide, phenolate,
N, imidazole N, porphyrin
S, thiolate
N, imidazole N
O, carboxylate
N, imidazole N
S, thiolate
N, imidazole N, polypirrol (F-430)
Rare
S, thiolate, thioether
N, imidazole N
S, thiolate, thioether
N, imidazole N
O, carboxylate
N, imidazole N
O, carboxylate
N, imidazole N
O, carboxylate, carbonyl
S, thiolate
N, imidazole N
O, carboxylate, carbonyl
N, imidazole N
Standard redox potential of several iron complexes
The following basic conclusions can be drawn from the data in the above
Table: (i) a decrease in the redox potential means stabilisation of the FeIII state as
compared to FeII. That is, in the presence of hydroxide, cyanide, or oxalate ions
FeII can be oxidised to FeIII or FeIII can hardly be reduced to FeII. In basic solution
weak oxidising agents, like molecular oxygen, can oxidise FeII to FeIII. (ii) an
increase in the redox potential means that the FeII state is stabilised as compared
to the FeIII. In the presence of 2,2’-dipyridyl or 1,10-phenantrolin FeII can be
oxidised to FeIIIonly by very strong oxidising agents.
Redox potential of several copper complex
Redox system
Cu(alanine)22+ + e- → Cu(alanine)2+
Cu(glycine)22+ + e- → Cu(glycine)2+
Cu2+ + e- → Cu+
CuL22+ + e- → CuL2+
Cu(pyridine)22+ + e- → Cu(pyridine)2+
Cu(imidazole)22+ + e- → Cu(imidazole)2+
Cu(CN)2 + e- → Cu(CN)-
E0(V)
-0.130
-0.160
+0.167
+0.243
+0.270
+0.345
+1.103
(L = 2-methyl-thioethyl-amine)
In aqueous solution standard redox potential of the Cu2+ + e-  Cu+
system is +,167 V. This suggests that in the absence of any complexing agents
the Cu2+ ions are more stable. Depending on the type of the ligands either the CuII,
or the CuI state can stabilised. From the data in the above Table it can be
concluded that the lower oxidation state of copper the CuI can be stabilised in the
presence of aromatic N-compounds (pyridin, imidazol), furthermore sulphur
containing compounds, while the CuII state can be stabilised by N or O containing
ligands (e.g. amino acids, such as alanin).
Exchange rates for inner sphere water molecules
In general, it can be said that the exchange rate is higher for the less highly
charged less strongly bound metal ions, than the more highly charged metal ions.
The highly inert first row Cr3+ és Co3+ metal ions practically have no biological
importance. Similarly, the second and third row transition metal ions have less
biological importance too.
pK of various ligands in the absence and presence of biologically relevant metal ions
Ligand and reaction
Metal
ion
lg K
Methods in bioinorganic chemistry I.
1. Determination of the composition:
- solid phases: elemental analysis
- solution equilibrium studies (determination of the stability constants)
(potentiometry, other techniques → measurements of some
of the free components)
- mass spectrometry (ESI-MS)
2. Kinetics:
- slow substitution reactions (inert complexes):
classical analytical methods
→
measurements of the concentration of some of the components)
- fast substitution reactions (labile complexes):
stopped flow, T- jump and realxation methods (e.g. NMR).
Physical methods in bioinorganic chemistry II.
3. Structural investigating methods:
a/ optical spectroscopic methods:
- UV-Vis spectrophotometry
(d-d transitions, charge transfer (CT) and ligand transitions)
- circular dicroism (CD, optical active compounds)
b/ magnetic methods:
- magnetic momentum (low and high spin complexes)
- ESR (EPR) spestroscopy (e.g. Cu2+, Mn2+, VO2+,...)
- NMR spectroscopy (1H, 13C, ligand peaks)
multinuclear: 15N, 17O, 19F, 27Al, 51V, 113Cd, 195Pt,..
c/ other methods:
- Mössbauer spectroscopy: (pl. Sn, Fe...)
- X-ray diffraction
- mass spectrometry
Enzymes I.
1. Definition: Catalysts of biological systems
2. Importance:
chemical process: A
B
the catalyst accelerates the time reaching the equilibrium state,
but equilibrium concentrations [A], [B] do not change.
Biological system: stationer equilibrium (steady state)
→ A
B
C
D ............... →
E1
E2
E3
[A]stat, [B]stat, [C]stat = f(E1,E2,…En)
The concentrations measured at the stationer equilibrium state
are not the same as those in the thermodynamic equilibrium, but
depend upon the reaction rates (enzymes). → The system is in
continous change, it „goes” to the equilibrium state.
Enzymes II.
3. Naming enzymes:
process + ase
e.g.
peptidase (hydrolysis of peptides)
carboxypeptidase (from the direction of the C-terminus)
( enzyme catalogue: EC x.y.z.w.
e.g. EC 6.3.1.2. glutaminsynthetase)
4. Classification of Enzymes:
Class
oxidoreductases
transferases
hydrolases
liasese
ligases
isomerases
type pf reaction
redox reactions
transfer of atom or group of atoms
hydrolysis
non hydrolytic cleavege
linking groups together
isomeric trasformation
Enzymes III.
5. Selectivity: usually high
function specificity: catalysis of a given reaction type (e.g. carboxypeptidase)
substrate specificity: catalysis of a given range of substrates within
the function specificity (e.g. carboxypeptidase A: only with substrates with
hydrophobic side chain)
6. Composition: simple or complex proteins
simple protein: M ≥ 10.000 ( ≥ 100 amino acid)
complex protein: protein + prosthetic group or coenzyme
prosthetic group: reversible non separable
(e.g. hem, biotin, metal ions, e.g. Cu, Fe,..)
coenzyme: existing biomolecule
(e.g. NAD, ATP, Mo-co, metal ions, e.g. Ca, Mg, Zn,...)
[ribozymes: RNA based enzymes]
Enzymes IV.
7. Metalloenzymes: ~ 30 % of the enzymes
- Binding of the metal ions:
prosthetic group (e.g. hem, Fe, Cu,...)
coenzyme: (e.g. B12, Mo-co, Ca, Mg, Zn, .....)
- Role of the metal ions:
active centre: direct interactions with the substrate.
characteristics: distorted and unsaturated coordination
geometry (high energy state)
(e.g. carbonanhydrase (Zn), carboxypeptidase(Zn),
superoxide dismutase(Cu))
structure maker (stabilizer): the metal ion fixes the conformation
of the protein, usually saturated coordination geometry.
(e.g. alcohol dehydrogenase(Zn), superoxide dismutase(Zn)
Kinetics of enzyme reactions I.
1. Kinetic model: Michaelis-Menten
Thesis: The initial rate (vo) of the enzyme catalysed reactions show
saturation curve in the function of the concentration of the substrate ([S]).
vo
Vmax
Vmax/2
KM
[S]
Kinetics of enzyme reactions II.
The general equation describing the previous function:
a  S
vo 
b  S
E+S
k1
a = Vmax
b = KM
To explain this the stationary equilibrium
(steady state) has to be applied:
ES
k-1
k2
→
E+P
i.e. the product (P) is formed through an enzyme-substrate complex (ES).
If the concentration of the substrate is sufficiently high ([S] >> [Eo])
Concentration of ES is constant in time, i.e. the rate of its formation and
decomposition equals:
dES
 k1  E  S
dt

dES
 (k 1  k 2 )  ES
dt
Kinetics of enzyme reactions III.
Assuming the stationary equilibrium:
dES 
dES 

dt
dt
k1  E  S  (k 1  k 2 )  ES
Taking into account the equations expressing of total enzyme concentrations
and the rate equation of product formation:
v o  k 2  ES 
E  Eo   ES
By substituting and rearranging the above equations:
k 2  Eo   S
vo 
k 1  k 2
S
k1
The initial rate is at maximum, when [ES] = [Eo]
Vmax = k2·[Eo], i.e. in the rate equation:
a  k 2  Eo   Vmax
and
b = KM
k 1  k 2

k1
Inhibition of enzyme reactions I.
1. Reversible inhibition:
(I: inhibitor, E: enzyme,
S: substrate)
a/ competitiv inhibition:
the inhibitor and the substrate compete for the active
centres of the enzyme
I→E
but I → ES

KM increases, but Vmax ≠ f(I)
b/ non-competitiv inhibition:
the inhibitor interacts also with the enzyme-substrate
complex (a Vmax also decreases)
Inhibition of enzyme reactions II.
2. Irreversible inhibition:
Strong (covalent) interactions between the inhibitor and the
Enzyme, which can not be cleaved by the substrate.
If [I] > [E] activity of the enzyme can be completely stopped.
Heavy metal ions and chelators can be frequent inhibitors.
Mechanism of enzyme reactions (metalloenzymes)
Mechanism of the metalloenzyme catalysed reactions can be
grouped in three main types:
(L: substrate, activator or inhibitor)
1. Ligand bridged (or substrat bridged)
There is no direct interaction between the metal ion and the
enzyme,
But it is necessary for the activation of the enzyme-substrate
complex.
2. Metal bridged
a/ The substrate is in direct interaction only with the metal ion
(occurs very rarely)
b/ The substrate is in interactions with the enzyme and the metal ion
too (mpost frequent case)
3. Enzyme bridged
There is no direct interaction between the metal ion and the
substrate,
But binding of the metal ion to the protein is necessary to the
catalytic activity (structure maker)
(e.g. alcohol dehydrogenase)