Chapter 6
Protein Assembly: Defining the Strength of Protein-Protein
Interactions Coupling the Theory with Experiments
Giampiero Mei, Almerinda Di Venere, Luisa Di Paola,
and Alessandro Finazzi Agro `
Abstract
In this paper we report a procedure to analyze protein homodimer interfaces.
We approached the problem by means of a topological methodology. In particular, we analyzed the
subunits interface of about 50 homodimers and we have defined a few parameters that allow to organize
these proteins in six different classes. The main characteristics of each class of homodimers have been
discussed also taking into account their stabilization energy, as reported in the literature from the experimental measurements. A paradigmatic example for each class has been reported and a graphical representation proposed in order to better explain the meaning of the parameters chosen.
Key words Dimeric interface, Protein structure, Homodimers, Protein-protein interaction, Protein
topology
1 Introduction
The peculiarity of allosteric proteins and enzymes resides in the
mechanism of their regulation, a process that requires the propagation through long distances of a mechanical stress produced in a
limited region of the macromolecule structure. Such mechanical
stress is typically induced by the binding to the polypeptidic chain
of molecules that are generally very small in size, as compared to the
overall protein dimensions. It is therefore obvious that this
“machinery” requires a concerted movement of the protein
domains and, in fact, flexibility and cooperativity are the main
features that characterize the network of amino acids involved in
the fine, complex regulation of allosteric enzymes.
As known, what confers a protein its specific functional properties is its tri-dimensional shape, which is dictated by the sequence of
its amino acids and obtained through the so-called folding mechanism. This is even more so if a quality as allostery is needed: the
propagation of local changes, produced by the modulator binding
Luisa Di Paola and Alessandro Giuliani (eds.), Allostery: Methods and Protocols, Methods in Molecular Biology, vol. 2253,
https://doi.org/10.1007/978-1-0716-1154-8_6, © Springer Science+Business Media, LLC, part of Springer Nature 2021
77
Protein Assembly: Defining the Strength of Protein-Protein
Interactions Coupling the Theory with Experiments
Giampiero Mei, Almerinda Di Venere, Luisa Di Paola,
and Alessandro Finazzi Agro `
Abstract
In this paper we report a procedure to analyze protein homodimer interfaces.
We approached the problem by means of a topological methodology. In particular, we analyzed the
subunits interface of about 50 homodimers and we have defined a few parameters that allow to organize
these proteins in six different classes. The main characteristics of each class of homodimers have been
discussed also taking into account their stabilization energy, as reported in the literature from the experimental measurements. A paradigmatic example for each class has been reported and a graphical representation proposed in order to better explain the meaning of the parameters chosen.
Key words Dimeric interface, Protein structure, Homodimers, Protein-protein interaction, Protein
topology
1 Introduction
The peculiarity of allosteric proteins and enzymes resides in the
mechanism of their regulation, a process that requires the propagation through long distances of a mechanical stress produced in a
limited region of the macromolecule structure. Such mechanical
stress is typically induced by the binding to the polypeptidic chain
of molecules that are generally very small in size, as compared to the
overall protein dimensions. It is therefore obvious that this
“machinery” requires a concerted movement of the protein
domains and, in fact, flexibility and cooperativity are the main
features that characterize the network of amino acids involved in
the fine, complex regulation of allosteric enzymes.
As known, what confers a protein its specific functional properties is its tri-dimensional shape, which is dictated by the sequence of
its amino acids and obtained through the so-called folding mechanism. This is even more so if a quality as allostery is needed: the
propagation of local changes, produced by the modulator binding
Luisa Di Paola and Alessandro Giuliani (eds.), Allostery: Methods and Protocols, Methods in Molecular Biology, vol. 2253,
https://doi.org/10.1007/978-1-0716-1154-8_6, © Springer Science+Business Media, LLC, part of Springer Nature 2021
77