Computational Analysis of Non‐covalent Interactions in Phycocyanin Subunit Interfaces

Abstract

Protein-protein interactions are an important phenomenon in biological processes and functions. We used the manually curated non-redundant dataset of 118 phycocyanin interfaces to gain additional insight into this phenomenon using a robust inter-atomic non-covalent interaction analyzing tool PPCheck. Our observations indicate that there is a relatively high composition of hydrophobic residues at the interfaces. Most of the interface residues are clustered at the middle of the range which we call "standard-size" interfaces. Furthermore, the multiple interaction patterns founded in the present study indicate that more than half of the residues involved in these interactions participate in multiple and water-bridged hydrogen bonds. Thus, hydrogen bonds contribute maximally towards the stability of protein-protein complexes. The analysis shows that hydrogen bond energies contribute to about 88 % to the total energy and it also increases with interface size. Van der Waals (vdW) energy contributes to 9.3 % � 1.7 % on average in these complexes. Moreover, there is about 1.9 % � 1.5 % contribution by electrostatic energy. Nevertheless, the role by vdW and electrostatic energy could not be ignored in interface binding. Results show that the total binding energy is more for large phycocyanin interfaces. The normalized energy per residue was less than À 16 kJ mol À 1 , while most of them have energy in the range from À 6 to À 14 kJ mol À 1 . The non-covalent interacting residues in these proteins were found to be highly conserved. Obtained results might contribute to the understanding of structural stability of this class of evolutionary essential proteins with increased practical application and future designs of novel protein-bioactive compound interactions.

Influence of cation−π interactions to the structural stability of phycocyanin proteins: A computational study

“…No His and Trp residues were noticed. These results are in concord with an earlier report on phycocyanin proteins (Breberina et al, 2019). The contribution of Arg was 26 times that of Lys.…”

On the importance of π-π interactions in the structural stability of phycocyanins

“…Less than 1 % of the His and Trp residues in our database are in phycocyanin interfaces. 17 Considering the benzene ring in Phe and Tyr residues, the greater electro negativity of sp 2 C relative to H, produces substantial C  H + dipole. The CH dipole accounts well for ππ interaction in phenylalanine.…”

“…7,16 The presented study expands on our previous work on the non-covalent interactions and cation-π interactions of phycocyanin crystal structures by analyzing the same protein group with respect to π-π interactions to better understand their stabilizing role. 17,18 We have focused our study on the phycocyanin interfaces and therefore the π-π interactions within a protein are not considered. Obtained results might contribute to the understanding of the structural stability of this class of evolutionary essential proteins with increased practical application and future designs of novel protein-bioactive compound interactions.…”

Coassembly of Fiber Hydrogel with Antibacterial Activity for Wound Healing

“…Phycocyanin is a kind of sky-blue fluorescent protein with strong water solubility, which plays a key role in the photosynthesis of cyanobacteria and certain algae. 29 Phycocyanin can induce the expression of HO-1 and plays a variety of anti-inflammatory activities. The fluorescent properties and biological activities of phycocyanin make it popular in the nutrition and pharmaceutical industries.…”

“…Phycocyanin is a kind of sky-blue fluorescent protein with strong water solubility, which plays a key role in the photosynthesis of cyanobacteria and certain algae . Phycocyanin can induce the expression of HO-1 and plays a variety of anti-inflammatory activities.…”