Hydrophobic, Hydrophilic, and Charged Amino Acid Networks within Protein

Abstract

The native three dimensional structure of a single protein is determined by the physico chemical nature of its constituent amino acids. The twenty different types of amino acids, depending on their physico chemical properties, can be grouped into three major classeshydrophobic, hydrophilic and charged. We have studied the anatomy of the weighted and unweighted networks of hydrophobic, hydrophilic and charged residues separately for a large number of proteins. Our results show that the average degree of the hydrophobic networks has significantly larger value than that of hydrophilic and charged networks. The average degree of the hydrophilic networks is slightly higher than that of charged networks. The average strength of the nodes of hydrophobic networks is nearly equal to that of the charged network; whereas that of hydrophilic networks has smaller value than that of hydrophobic and charged networks. The average strength for each of the three types of networks varies with its degree. The average strength of a node in charged networks increases more sharply than that of the hydrophobic and hydrophilic networks. Each of the three types of networks exhibits the 'small-world' property. Our results further indicate that the all amino acids' networks and hydrophobic networks are of assortative type. While maximum of the hydrophilic and charged networks are of assortative type, few others have the characteristics of disassortative mixing of the nodes. We have further observed that all amino acids' networks and hydrophobic networks bear the signature of hierarchy; whereas the hydrophilic and charged networks do not have any hierarchical signature.

From Network Structure to Dynamics and Back Again: Relating Dynamical Stability and Connection Topology in Biological Complex Systems

“…This small-world property of PCNs for different protein molecules have indeed been noted several times in the literature (see, e.g., Ref. [2]). This is probably not very surprising, given that it is also true for a randomly folded polymer.…”

Disordered Proteins and Network Disorder in Network Descriptions of Protein Structure, Dynamics and Function: Hypotheses and a Comprehensive Review

“…Hydrophobic hubs also show a hierarchical 'superhub' structure, which have a large number of hub-neighbors. These structures cannot be observed for the subnetworks of hydrophilic and charged amino acids consistent with the key role of hydrophobic interactions in the core-structure of proteins [Aftabuddin and Kundu, 2007]. Central amino acids do not tend to associate with each other, thus protein structure networks are not 'clumpy' ( Fig.…”

In silico analysis of Shiga toxins (Stxs) to identify new potential vaccine targets for Shiga toxin-producing Escherichia coli

“…On the other hand, although the best predicted Stx1A T-cell epitope 187-TAEALRFRQIQRGFR-201 has 93% identity with the Stx2A sequence, it has not been identified as T-cell epitope in Stx2A. The amino acid substitution of glutamic acid by glycine in Stx2A may explain the difference (Betts and Russell 2003;Aftabuddin and Kundu 2007). Glutamic acid is a polar negatively hydrophilic charged amino acid while glycine is an aliphatic neutral amino acid.…”

“…Although, methionine and valine have different sizes and hydropathy scores, they are both aliphatic hydrophobic amino acids. Therefore, the amino acid substitution in the predicted epitope may not remarkably modify the properties of the epitope to alter its universality (Betts and Russell 2003;Aftabuddin and Kundu 2007).…”