TITLE:
Identification of Secondary Structure of Extracellular Signal Regulated Kinase (ERK) Interacting Proteins and Their Domain: An in Silico Study
AUTHORS:
Kurrey Khuleshwari, Paramanik Vijay
KEYWORDS:
ERK, Secondary Structure, Motif Scan, Random Coils, Alpha Helix, Protein Kinases
JOURNAL NAME:
World Journal of Neuroscience,
Vol.11 No.1,
February
26,
2021
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.