Identification of new discriminant factors based on distance between amino acids in the interaction zone between proteins

Proteins are macromolecules involved in the biological functions. Protein-protein interactions that occur between two or more proteins are called protein complexes. These complexes are of vital importance as they play a key role in most biological processes, such as biosynthesis, cellular regulation and signal translation. For this reason, the researchers try to understand these protein complexes in their three-dimensional structure, through data that are generated from methods such as X-ray crys­tallography or nuclear magnetic resonance. Because the tertiary structure is unique to each protein it is also directly responsible for its biological properties. These data are used for the prediction of protein-protein interactions. The prediction seeks by means of computational tools, to identify and to categorize the type of interaction that occurs in a given protein complex. This through the use of different features of the complex. In this study we try to determine if using only the distance between amino acids belonging to the interaction zone in protein complexes influences whether the interaction is classified as transient or permanent (duration time of interaction). For this we use a set of protein complexes already classified as transient or permanent, in addition to its three-dimensional structure. The distance measures used as a feature, are selected considering the energy produced in the interaction zone and the structure of the amino acids involved and their position. A 75% accuracy was obtained, using distance as a discriminant factor in the classification of protein complexes. This suggests that, there is a relation between the distance as a discriminating factor to classify these complexes as transient or permanent.