Identification and Physiochemical Analysis of ERK Interacting Proteins Using Bio-Computational Tools

ERK (Extracellular Signal Regulated Kinase) or MAP kinase is an intracellular signaling molecule. ERK is involved in regulation of various functions i.e. cell proliferation, cell migrations, cell survival and many more. It gets activated in response of various stimuli like growth factors, cytokines, virus, second messengers, transforming agents and carcinogens. While transferring signals from cell surface receptors to cell nucleus, ERK interacts with a numbers of proteins. Physiochemical and functional characterization of these proteins is little known. Thus, we attempted to study physiochemical and functional properties of ERK interacting proteins using bio-computational tools. ExPASy and SOSUI server suggested 22 ERK interacting proteins. Physical and chemical parameters of these ERK interacting partners indicated higher percentage of hydrophobic amino acid and leucine as major constituent. Moreover, the instability index indicated that four proteins are stable in over wide range temperature in vitro, and remaining eighteen proteins were found unstable. In addition, SOSUI server showed that fifteen proteins were soluble and six are trans-membrane in nature.


Physiochemical Characterization of Interacting Proteins
Using ExPASy ProtParam (http://web.expasy.org/protparam/) computational server, primary structure and physiochemical characters of proteins, such as amino acids number (AA), Molecular weight of protein, Theoretical pI, Amino acids compositions of protein, total number of negatively charged residues (Asp + Glu), total number of positively charged residues (Arg + Lys), extinction coefficient, instability index, aliphatic index and Grand Average Hydropathicity (GRAVY) were observed.

Physiochemical Characterization
ERK interactive protein's amino acids (AA) composition was presented in Table   2 and Table 3. Most of the ERK interacting proteins are hydrophilic in nature.
AA composition indicates that higher percentage of hydrophobic amino acid leucine. This is due to presence of all the hydrophobic proteins inside the cell membrane and hydrophilic amino acids on the outside. Sequence length of protein represents basic nature of protein [6] [7] [8].

Extinction Coefficients (EC)
The extinction coefficient of ERK interacting proteins at 280nm ranged from

The Instability Index (II)
It gives estimation of protein stability in vitro. Protein

Aliphatic Index
Aliphatic index of a protein is considered as the relative volume captured by aliphatic side chains (alanine, valine, isoleucine, and leucine). It is considered as a positive factor for the increase of thermal stability of annular proteins. Aliphatic index of ERK interactive proteins limit from 62.34 to 107.02. Both MAP3K11 and MAGI3 have lower thermal stability representing their more flexible structure as compared to other proteins ( Table 4). The high aliphatic index of other proteins indicates their stability in high range of temperature [6] [7] [8].

A GRAVY (Grand Average of Hydropathy)
GRAVY is understood as the total hydropathy values of all the amino acids of a

Functional Characterization
The SOSUI server data expressed ERK interacting proteins namely EPHB2 (

Discussion
There are several genes responsible for the long term synaptic plasticity. ERK is one of these gene involved in long term learning and memory. During this process, a cascade of regulatory immediate early genes is recruited to particular gene including ERK [11] [12]. These genes are required for long-term synaptic     Food provides energy and building blocks to the body. Its ability to prevent and protect against diseases is started to be recognized. Especially research over the past one decade has provided exciting evidence suggests the influence of dietary factors on brain functions. For example, omega-3 fatty acids rich diet is useful for cognitive processes in humans [16] and up-regulating genes that are significant for maintaining synaptic function and plasticity in rodents [17]. Further, high unsaturated fat diets are responsible for reducing molecular substrates that support cognitive processing and increases the risk of neurological dysfunctions in both humans and animals [18] [19]. The important effects of food on brain functions are cited still further research is necessary to determine underlying mechanisms of action and for therapeutic applications in humans. In this study, we found that most of the ERK interacting are rich in leucine, suggesting that their roles as transcription factor. The leucine zipper motif contains leucine residues spaced 7 amino acids apart repeating at least 3 times (L××××××L××××××L)  [20]. In the process of dimerization, parallel leucine zipper motifs interact through a coiled coil hydrophobic interface that juxtaposes 2 adjacent basic regions [21]. Further, once bound to DNA, these adjacent basic regions undergo key changes in conformation [22]. As almost ERK interacting proteins contain leucine so it may be assumed that these are involved in ERK mediated functions including learning and memory. In addition, leucine rich food could be good for cognition and healthy brain functions. Thus such findings regarding ERK interacting proteins are instrumental to understand learning and memory via ERK.
Moreover, it may be helpful to target these interacting proteins during learning and memory deficit and neurodegenerative diseases.