A comprehensive in silico exploration of the impacts of missense variants on two different conformations of human pirin protein

Abstract

Background: Pirin, a member of the cupin superfamily, is an iron-binding non-heme protein. It acts as a coregulator of several transcription factors, especially the members of NFκB transcription factor family. Based on the redox state of its iron cofactor, it can assume two different conformations and thereby act as a redox sensor inside the nucleus. Previous studies suggested that pirin may be associated with cancer, inflammatory diseases as well as COVID-19 severities. Hence, it is important to explore the pathogenicity of its missense variants. In this study, we used a number of in silico tools to investigate the effects of missense variants of pirin on its structure, stability, metal cofactor binding affinity and interactions with partner proteins. In addition, we used protein dynamics simulation to elucidate the effects of selected variants on its dynamics. Furthermore, we calculated the frequencies of haplotypes containing pirin missense variants across five major super-populations (African, Admixed American, East Asian, European and South Asian).

Results: Among a total of 153 missense variants of pirin, 45 were uniformly predicted to be pathogenic. Of these, seven variants can be considered for further experimental studies. Variants R59P and L116P were predicted to significantly destabilize and damage pirin structure, substantially reduce its affinity to its binding partners and alter pirin residue fluctuation profile via changing the flexibility of several key residues. Additionally, variants R59Q, F78V, G98D, V151D and L220P were found to impact pirin structure and function in multiple ways. As no haplotype was identified to be harboring more than one missense variant, further interrogation of the individual effects of these seven missense variants is highly recommended.

Conclusions: Pirin is involved in the transcriptional regulation of several genes and can play an important role in inflammatory responses. The variants predicted to be pathogenic in this study may thus contribute to a better understanding of the underlying molecular mechanisms of various inflammatory diseases. Future studies should be focused on clarifying if any of these variants can be used as disease biomarkers.

Supplementary information: The online version contains supplementary material available at 10.1186/s42269-022-00917-7.

Keywords: Cancer; Inflammation; NFκB pathway; Non-heme protein; Oxidative stress; Pathogenic variants; Pirin; Transcriptional regulation.

Fig. 1

Interactions between pirin and its binding partners. Docking was performed between Fe²⁺ conformation of pirin and three ankyrin repeat domains (ANK 5-7) of BCL3 (A), as well as, Fe³⁺ conformation of pirin and Rel homology domain (RHD) of p65 (residues 19-306) (B). The protein–protein complex structures were depicted using PyMOL (Schrodinger and Delano 2020) (Aa and Ba). Pirin is illustrated in deep teal and its partners in hot pink. Protein–protein interfaces are delineated in yellow. Inter-residue interactions are delineated with iCn3D (Wang et al. 2020) (Ab and Bb). Each gray square represents contacts/interactions within 6 (Å). Residues of pirin are displayed in the x-axis and those of its binding partners are in the y-axis

Fig. 2

Fluctuation profiles of the wild-type and two variant (R59P and L116P) structures of pirin. A comparison between the predicted residue fluctuation profiles of the wild-type and the variant structures in case of Fe²⁺ (A) and Fe³⁺ (B) conformations of pirin is graphically presented. RMSF denoting root mean square fluctuation in Å is displayed in the y-axis and pirin residues are displayed in the x-axis