Identification of Secondary Structure of Extracellular Signal Regulated Kinase (ERK) Interacting Proteins and Their Domain: An in Silico Study

Kurrey Khuleshwari,Paramanik Vijay

doi:10.4236/wjns.2021.111007

Abstract

ERK is involved in multiple cell signaling pathways through its interacting proteins. By in silico analysis, earlier we have identified 22 putative ERK interacting proteins namely; ephrin type-B receptor 2 isoform 2 precursor (EPHB2), mitogen-activated protein kinase 1 (MAPK1), interleukin-17 receptor D precursor (IL17RD), WD repeat domain containing 83 (WDR83), tescalcin (Tesc), mitogen-activated protein kinase kinase kinase 4 (MAPP3K4), kinase suppressor of Ras2 (KSR2), mitogen-activated protein kinase kinase 6 (MAP3K6), UL16 binding protein 2 (ULBP2), UL16 binding protein 1 (ULBP1), dual specificity phosphatase 14 (DUSP14), dual specificity phosphatase 6 (DUSP6), hyaluronan-mediated motility receptor (RHAMM), kinase D interacting substrate of 220 kDa (KININS220), membrane-associated guanylate kinase (MAGI3), phosphoprotein enriched in astrocytes 15 (PEA15), typtophenyl-tRNA synthetase, cytoplasmic (WARS), dual specificity phosphatase 9 (DUSP9), mitogen-activated protein kinase kinase kinase 1 (MAP3K1), UL16 binding protein 3 (ULBP3), SLAM family member 7 isoform a precursor (SLAMMF7) and mitogen activated protein kinase kinase kinase 11 (MAP3K11) (Table 1). However, prediction of secondary structure and domain/motif present in aforementioned ERK interacting proteins is not studied. In this paper, in silico prediction of secondary structure of ERK interacting proteins was done by SOPMA and motif/domain identification using motif search. Briefly, SOPMA predicted higher random coil and alpha helix percentage in these proteins (Table 2) and motif scan predicted serine/threonine kinases active site signature and protein kinase ATP binding region in majority of ERK interacting proteins. Moreover, few have commonly dual specificity protein phosphatase family and tyrosine specific protein phosphatase domains (Table 3). Such study may be helpful to design engineered molecules for regulating ERK dependent pathways in disease condition.

Highlights

Prediction of protein function is one of the key tasks of bioinformatics
Thereafter, secondary structure of these protein were done by Self-Optimized Prediction Method with Alignment (SOPMA) using aa sequence of protein in FASTA format (Figure 1)
The highest number of prosite patterns (ProPat) was found in ephrin type-B receptor 2 isoform 2 precursor (EPHB2)

Summary

Background

Prediction of protein function is one of the key tasks of bioinformatics. The prediction of protein function is dependent on secondary structure and their amino acid sequence. Domain/motif of a protein serves as actual site of interaction for the manifestation of a specific biological function. Cytoplasmic (WARS), dual specificity phosphatase 9 (DUSP9), mitogen-activated protein kinase kinase kinase 1 (MAP3K1), UL16 binding protein 3 (ULBP3), SLAM family member 7 isoform a precursor (SLAMMF7) and mitogen activated protein kinase kinase kinase 11 (MAP3K11) Majority of these are kinase and interact with ERK. It promotes us to identify secondary structure and prediction of domain/motif of ERK interacting proteins using in silico. Such studies are useful to understand ERK dependent pathways and helpful to design engineered molecules for regulating them in disease situation

Materials and Methods

Results and Discussion

15. Membrane-associated guanylate kinase

21. SLAM family member 7 isoform a precursor

22. Mitogen-activated protein kinase kinasekinase 11

Conclusion