The whole protein structure is stabilized by a large number of relatively weak
binding forces such as van der Waals interactions
14 of aliphatic chains and π-π
stacking of aromatic amino acids, which are predominantly located inside the
protein core (Scheme 1.2). In contrast, stronger hydrogen bonds and salt bridges
made up of Coulomb interactions are often close to the surface. As a consequence
of the weak binding forces inside and strong bonds at the surface, in a rough
approximation, enzymes have a soft core but a hard shell and thus represent delicate
and soft (jellyfish-like) structures.
The latter facilitates conformational movements during catalysis (such as the
‘induced fit’, see below) and is a prerequisite of the pronounced dynamic character
of enzyme catalysis. Besides the main polyamide backbone, the only covalent
bonds are –S–S– disulfide bridges. Enzymes are intrinsically unstable in solution
and can be deactivated by denaturation, caused by increased temperature, extreme
pH, or an unfavorable dielectric environment such as high salt concentrations.
The types of reaction leading to an enzyme’s deactivation are as follows [109]:
– Rearrangement of peptide chains (due to partial unfolding) starts at around
40–50
C. Most of these rearrangements are reversible and therefore relatively
harmless.
– Hydrolysis of peptide bonds in the backbone, in particular adjacent to asparagine
units, occurs at more elevated temperatures. Functional groups of amino acids
(e.g. asparagine and glutamine residues) can be hydrolytically cleaved to furnish
aspartic and glutamic acid, respectively. Both reaction mechanisms are favored
by the presence of neighboring groups, such as glycine, which enable the
formation of a cyclic intermediate. Thus, a negative charge (i.e., –COO
À ) is
H O
H
H
O H
H O
H
H
O
H H
O
H
H O
H
H O
H
H
O
O
H 2 N
H
O
H
H
O
H
H
O
H
H
O
H
H
O
H
H
O
H
NH 3
O
O
Hydrogen Bonding
π-π Stacking
Van der Waals
Salt Bridge
Scheme 1.2 Schematic representation of binding forces within a protein structure
14 Also called London forces.
12
1 Introduction and Background Information
binding forces such as van der Waals interactions
14 of aliphatic chains and π-π
stacking of aromatic amino acids, which are predominantly located inside the
protein core (Scheme 1.2). In contrast, stronger hydrogen bonds and salt bridges
made up of Coulomb interactions are often close to the surface. As a consequence
of the weak binding forces inside and strong bonds at the surface, in a rough
approximation, enzymes have a soft core but a hard shell and thus represent delicate
and soft (jellyfish-like) structures.
The latter facilitates conformational movements during catalysis (such as the
‘induced fit’, see below) and is a prerequisite of the pronounced dynamic character
of enzyme catalysis. Besides the main polyamide backbone, the only covalent
bonds are –S–S– disulfide bridges. Enzymes are intrinsically unstable in solution
and can be deactivated by denaturation, caused by increased temperature, extreme
pH, or an unfavorable dielectric environment such as high salt concentrations.
The types of reaction leading to an enzyme’s deactivation are as follows [109]:
– Rearrangement of peptide chains (due to partial unfolding) starts at around
40–50
C. Most of these rearrangements are reversible and therefore relatively
harmless.
– Hydrolysis of peptide bonds in the backbone, in particular adjacent to asparagine
units, occurs at more elevated temperatures. Functional groups of amino acids
(e.g. asparagine and glutamine residues) can be hydrolytically cleaved to furnish
aspartic and glutamic acid, respectively. Both reaction mechanisms are favored
by the presence of neighboring groups, such as glycine, which enable the
formation of a cyclic intermediate. Thus, a negative charge (i.e., –COO
À ) is
H O
H
H
O H
H O
H
H
O
H H
O
H
H O
H
H O
H
H
O
O
H 2 N
H
O
H
H
O
H
H
O
H
H
O
H
H
O
H
H
O
H
NH 3
O
O
Hydrogen Bonding
π-π Stacking
Van der Waals
Salt Bridge
Scheme 1.2 Schematic representation of binding forces within a protein structure
14 Also called London forces.
12
1 Introduction and Background Information