Contribution to the Understanding of Protein–Protein Interface and Ligand Binding Site Based on Hydrophobicity Distribution—Application to Ferredoxin I and II Cases

Abstract

Ferredoxin I and II are proteins carrying a specific ligand—an iron-sulfur cluster—which allows transport of electrons. These two classes of ferredoxin in their monomeric and dimeric forms are the object of this work. Characteristic of hydrophobic core in both molecules is analyzed via fuzzy oil drop model (FOD) to show the specificity of their structure enabling the binding of a relatively large ligand and formation of the complex. Structures of FdI and FdII are a promising example for the discussion of influence of hydrophobicity on biological activity but also for an explanation how FOD model can be used as an initial stage adviser (or a scoring function) in the search for locations of ligand binding pockets and protein–protein interaction areas. It is shown that observation of peculiarities in the hydrophobicity distribution present in the molecule (in this case—of a ferredoxin) may provide a promising starting location for computer simulations aimed at the prediction of quaternary structure of proteins.