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

Irena Roterman,Mateusz Banach,Jacques Chomilier

doi:10.3390/app11188514

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.

Highlights

IntroductionPublisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations
Sequence similarities between FdI and Ferredoxin II (FdII), their structural features and hydrophobicity profiles eventually leading to prediction of non-bonded interactions are the object of this work
We start from the sequence, move to the structure to finalize with presentation how a “seed” for the search for residues engaged in P-L and P-P interaction can be found in these two ferredoxins through hydrophobic

Summary

Introduction

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. Ferredoxins are proteinaceous electron carriers that play key physiological roles ensuring an electron flux to many essential biochemical pathways [1,2], such as—among others—steroid hormones biosynthesis in the adrenal mitochondria of vertebrates [3]. They shuttle electrons through the binding of various iron-sulfur clusters, mainly [3F4S] or [4F4S]. Other types of clusters are [3F4S] together with one [4F4S], and two [4F4S] [4,5,6,7]

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