process, requires an appropriate scaffolding to produce long-range
effects. Studying the connections between folding and functional
cooperation is therefore a crucial step that must be faced to unravel
the many mysteries of the world of allosteric enzymes [1]. A very
common feature of these proteins is their high propensity to form
oligomers, and in particular dimers and tetramers. Indeed, despite a
quaternary structure is not mandatory [2], most of the enzymes
and proteins that play a crucial role in the regulation of metabolic
pathways, signaling, and metabolites transportation are allosteric
oligomers.
But which is the basic link between allostery and folding? Since
the so-called “induced-fit” hypothesis was introduced [3], it was
clear that the balance between conformational stability and flexibility is critical for all enzymes and many proteins, too. Obviously, in
the case of oligomers the free energy of folding/unfolding also
depends on the presence of the subunits interface, whose quaternary interactions are, in several cases, the main driving force for
folding and stabilization of these complex proteins.
In oligomeric enzymes characterized by allosteric properties
the inter-subunits interactions accomplish another fundamental
task: they transmit the mechanical stress produced by ligand binding in one subunit to distal sites belonging to another subunit.
Studying what happens at such interfaces is therefore important to
characterize how the propagation of signals occurs, from regulatory
to active sites. Since the simplest oligomers are those obtained by
two identical subunits, discussing the topology of homodimeric
interfaces is paradigmatic for more complex kinds of subunits association. Indeed, in a previous of paper [4] we suggested that
correlations between the size, the sequence, and the quaternary
structure of homodimers might be easily found taking into account
a few structural parameters that can be obtained directly from the
PDB files deposited in the protein data banks. A further topological
analysis through protein contact networks [5] allowed to find a
direct correspondence between the experimental folding energy of
dimers and the roughness of the subunits interface. It was demonstrated that the topological analysis has two advantages: (1) it
drastically reduces the number of descriptors of oligomer stability;
(2) it allows predictions on the role played by the interface, independently on the kind of amino acid involved in quaternary
interactions.
Here we describe an easy procedure that can be usefully applied
to classify any homodimeric structure on the basis of its topological
features. In particular, analyzing more than 50 crystallographic
structures (Table 1), we have identified six groups of homodimers
(Table 2), whose characteristics include the stabilization energy
obtained in equilibrium unfolding measurements and the
tri-dimensional features of the two chains at the interface (such as
the “roughness” of the contact area due to the presence of
78
Giampiero Mei et al.
effects. Studying the connections between folding and functional
cooperation is therefore a crucial step that must be faced to unravel
the many mysteries of the world of allosteric enzymes [1]. A very
common feature of these proteins is their high propensity to form
oligomers, and in particular dimers and tetramers. Indeed, despite a
quaternary structure is not mandatory [2], most of the enzymes
and proteins that play a crucial role in the regulation of metabolic
pathways, signaling, and metabolites transportation are allosteric
oligomers.
But which is the basic link between allostery and folding? Since
the so-called “induced-fit” hypothesis was introduced [3], it was
clear that the balance between conformational stability and flexibility is critical for all enzymes and many proteins, too. Obviously, in
the case of oligomers the free energy of folding/unfolding also
depends on the presence of the subunits interface, whose quaternary interactions are, in several cases, the main driving force for
folding and stabilization of these complex proteins.
In oligomeric enzymes characterized by allosteric properties
the inter-subunits interactions accomplish another fundamental
task: they transmit the mechanical stress produced by ligand binding in one subunit to distal sites belonging to another subunit.
Studying what happens at such interfaces is therefore important to
characterize how the propagation of signals occurs, from regulatory
to active sites. Since the simplest oligomers are those obtained by
two identical subunits, discussing the topology of homodimeric
interfaces is paradigmatic for more complex kinds of subunits association. Indeed, in a previous of paper [4] we suggested that
correlations between the size, the sequence, and the quaternary
structure of homodimers might be easily found taking into account
a few structural parameters that can be obtained directly from the
PDB files deposited in the protein data banks. A further topological
analysis through protein contact networks [5] allowed to find a
direct correspondence between the experimental folding energy of
dimers and the roughness of the subunits interface. It was demonstrated that the topological analysis has two advantages: (1) it
drastically reduces the number of descriptors of oligomer stability;
(2) it allows predictions on the role played by the interface, independently on the kind of amino acid involved in quaternary
interactions.
Here we describe an easy procedure that can be usefully applied
to classify any homodimeric structure on the basis of its topological
features. In particular, analyzing more than 50 crystallographic
structures (Table 1), we have identified six groups of homodimers
(Table 2), whose characteristics include the stabilization energy
obtained in equilibrium unfolding measurements and the
tri-dimensional features of the two chains at the interface (such as
the “roughness” of the contact area due to the presence of
78
Giampiero Mei et al.