Understanding the interactability of chikungunya virus proteins via molecular recognition feature analysis

Abstract

The chikungunya virus (CHIKV) is an alphavirus that has an enveloped icosahedral capsid and is transmitted by Aedes sp. mosquitos. It contains four non-structural proteins, namely nsP1, nsP2, nsP3, and nsP4, encoded at the 5' end of the genome, and five structural proteins encoded at the 3' end of the genome, including three glycosylated proteins, namely E1, E2, E3, a small 64 amino-acids glycoprotein 6K, and one non-glycosylated nucleocapsid protein C. The surface of this positive-stranded RNA alphavirus is covered with 80 trimeric glycoprotein spikes, which facilitate viral access into the host cell, with each consisting of three copies of E1-E2 heterodimers. The proper folding of p62, which is the precursor of E2, and formation of the E1-p62 heterodimers are controlled by E3, which is therefore essential for producing mature spikes on the alphavirus surface. Finally, 6K, a small 64 amino-acids glycoprotein, assists in the translocation of structural polyproteins to the endoplasmic reticulum and in the cleavage of p62 into mature structural proteins E2. The CHIKV proteins have been shown to contain variable levels of intrinsic disorder, often containing intrinsically disordered protein regions (IDPRs). IDPRs can interact with many unrelated partners, and these interactions are frequently accompanied by a transition from a disordered to ordered state. The corresponding sub-regions of IDPRs are acknowledged as molecular recognition features (MoRFs). Although the existence of IDPRs in CHIKV proteome has been analyzed, the prevalence of disorder-based protein-protein interactions (i.e. MoRF) in this virus have not been evaluated as of yet. To fill this gap, in our study, we utilized several computational methods to identify the MoRFs regions in CHIKV proteins. These computational tools included ANCHOR, DISOPRED3, MoRFpred and MoRFchibi_web server. These analyses revealed the presence of numerous MoRF regions in all the CHIKV proteins. In future, the results of this study could be used to identify the nature of chikungunya virus pathogenesis and might be helpful in designing drugs against this virus.

Fig. 1. Schematic depiction of all the structural and non-structural proteins within the CHIKV polyprotein (UniProt ID: Q8JUX6 and Q8JUX5). CHIKV RNA 11811 bases (top bar, blue colour), translates into non-structural and structural precursor polyproteins of 2474 and 1244 residues, respectively, and after maturation by protease cleavage, it gives 4 non-structural proteins (left bar, yellow colour) and 5 structural proteins (right bar, green colour).

Fig. 2. Evaluation of disorder-based interactivity of the CHIKV non-structural proteins nsP1 (A), nsP3 (B) and nsP4 (C). The presence of MoRF regions was evaluated by ANCHOR (blue lines) and MoRFchibi (red lines). The threshold for MoRF predictions by ANCHOR and MoRFchibi are 0.5 and 0.725. These thresholds are shown as dashed red and blue lines, respectively. Positions of MoRFs predicted by ANCHOR and MoRFchibi are shown by cyan and light pink bars, respectively. Note that for the nsP1 protein, positions of the C-terminal MoRF predicted by ANCHOR and MoRFchibi mostly overlap.

Fig. 3. Evaluation of the disorder-based interactivity of the CHIKV structural proteins CP (A) and E2 (B). The presence of MoRF regions was evaluated by ANCHOR (blue lines) and MoRFchibi (red lines). The threshold for MoRF predictions by ANCHOR and MoRFchibi are 0.5 and 0.725. These thresholds are shown as dashed red and blue lines, respectively. Positions of MoRFs predicted by ANCHOR and MoRFchibi are shown by cyan and light pink bars, respectively. Note that for the CP, the positions of the N-terminal MoRFs predicted by ANCHOR and MoRFchibi mostly overlap.

Fig. 4. Evaluation of disorder predisposition (A) and disorder-based interactivity (B) of the CHIKV TF protein. Intrinsic disorder propensity was evaluated by four predictors of the PONDR family: PONDR® VLXT (black line), PONDR® VL3 (red line), PONDR® VSL2B (green line) and PONDR FIT (pink line). Light pink shadow around PONDR FIT curve shows the error distribution. Blue dashed line represents the mean disorder propensity calculated by averaging the outputs of individual predictors. The presence of MoRF regions was evaluated by ANCHOR (blue line) and MoRFchibi (red line). The threshold for MoRF predictions by ANCHOR and MoRFchibi are 0.5 and 0.725. These thresholds are shown as dashed red and blue lines, respectively. Positions of MoRFs predicted by ANCHOR and MoRFchibi are shown by cyan and light pink bars, respectively.