Protein Assembly: Defining the Strength of Protein-Protein Interactions Coupling the Theory with Experiments

Giampiero Mei; Almerinda Di Venere; Luisa Di Paola; Alessandro Finazzi Agrò

doi:10.1007/978-1-0716-1154-8_6

Protein Assembly: Defining the Strength of Protein-Protein Interactions Coupling the Theory with Experiments

Methods Mol Biol. 2021:2253:77-88. doi: 10.1007/978-1-0716-1154-8_6.

Authors

Giampiero Mei¹, Almerinda Di Venere², Luisa Di Paola³, Alessandro Finazzi Agrò²

Affiliations

¹ Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy. mei@med.uniroma2.it.
² Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy.
³ Unit of Chemical-Physics Fundamentals in Chemical Engineering, Department of Engineering, Università Campus Bio-Medico di Rome, Rome, Italy.

PMID: 33315219
DOI: 10.1007/978-1-0716-1154-8_6

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.

Keywords: Dimeric interface; Homodimers; Protein structure; Protein topology; Protein-protein interaction.

MeSH terms

Binding Sites
Computational Biology
Crystallography, X-Ray
Databases, Protein
Models, Molecular
Protein Binding
Protein Conformation
Protein Interaction Mapping / methods*
Protein Multimerization
Proteins / chemistry*
Proteins / metabolism*

Substances

Proteins