K Ashokan, M Pillai
computational analysis, homology modeling, mussel adhesive protein, phosphorylation site, proteomic tools, signal peptide
K Ashokan, M Pillai. Characterization of biomimetc material, Mussel adhesive protein, using computer tools and servers.. The Internet Journal of Bioengineering. 2008 Volume 4 Number 1.
In this paper six different mussel adhesion proteins (MAPs) retrieved from SwissProt database are analyzed using computer tools and servers. Primary analysis showed that all the MAPs are hydrophobic in nature due to the high content of non-polar amino acid residues. The sequence analysis showed the absence of sulphide bridges and non polar amino acid tryptophan in MAPs. Signal peptide is a common feature in MAPs. The aliphatic index computed by Expasy's Protparm infers that most of the MAPs are stable at a wide range of temperature. Secondary structure analysis showed that MAPs could results in a better interaction with water. The secondary structure analysis showed MAPs contain more β- helices and turns. The SOSUI server predicts one transmembarne region in Mytilus galprovincialis. The predicted transmembrane region was visualized and analyzed using helical wheel plots generated by EMBOSS PepWheel tool. The absence of disulphide bonds in MAPS was confirmed by SYC_REC tools and from 3 Dimensional structures created by Rasmol tool. The cystein position identified by Rasmol tool might be correct as the evaluated parameters (Rampage, CE and ProQ) are within the accepted limits for the model 3D structure. The signal peptide identified by SignalP server showed that they are secretary pathway in localization except in Mytilus edulus, where it is cytoplasmic. Based on the signal peptides reliability class the MAPs are classified into three groups. The phosphorylation sites of serine, threonoine and tyrosine are predicted by NetPhos server. Interestingly tyrosine is the most phosphorylated amino acid in the MAPs; hence it is inferred that MAPs can be purified by using antibodies.
Materials and methods
Mussel adhesive protein (MAP) sequences were retrieved from the manually curated public protein databank SwissProt (Bockman
Computational tools and servers
The amino acid composition of MAP sequences was computed using the tool CLC sequence viewer (http://www.clcbio.com). Percentage of hydrophobic and hydrophilic residues were calculated from the primary structure analysis results and tabulated. The physicochemical parameters, theoretical isoelectric point (Ip), molecular weight, total number of positive and negative residues, extinction coefficient (E.C) (Gill and Hippel 1989), half life (Bachmair
Results and Discussion
The result of the primary analysis suggests that most of the MAPs are hydrophobic in nature due to the presence of high non-polar residues (Table 2 and 3).
The primary analysis also suggests that the MAPs contain one signal peptide in
(Primary structure) and identified rasmol (using 3D structure modelled)
Obtained using BLASTP search against the protein data bank
computed by Expasy‟s ProtParam showed all the MAPs selected are stable with II greater than 30 (II>30). The aliphatic index (AI) which is defined as the relative volume of a protein occupied by aliphatic side chain (A, V, I and L) is regarded as a positive factor for increasing of thermal stability of globular proteins. The lower AI of BAA09850,
BAA09851, AAL87245 and Q25434 are indication of more flexible structure when compared to other MAPs. The very high AI of CAA38294 and ABC84184 infer these are stable at wide range of temperature .GRAVY index of MAPs are range from -0.835 to - 3.384. The very low GRAVY of all the selected MAPs infers that
these MAPs could results in a better interaction with water. The secondary structures predicted with the help of SOPMA (Data not presented) infer that the MAPs have rich lysine and tyrosine and contain mostly β- helices. In
helices predominant and shows 30 times more than other MAPs (Fig1a-1f). The server SOSUI classifies the MAPs of
The biomimetic, mussel adhesive proteins have been chosen mainly to study their physicochemical properties, primary and secondary structure, by using computational tools and servers. Primary structure analysis reveals that MAPs are hydrophobic in nature, not contain any disulphide bridges, and contain signal peptide in some MAPs. Physicochemical characterization studies give good idea about the properties of such as pI, CE, AI, GRAVY and II that are essential and vital in providing data about the proteins and their properties. Secondary structure analysis predicts that the MAPs contain more β- helices than ά- helices. The signal peptide predicted showed that the peptide sequence located in secretory pathway and the cleavage site lies invariably between 24th and 25th position of the sequence. The phosphorylation site prediction showed tyrosine is the most phosphorylated in all the MAPSs and hence MAPS can be purified by using antibodies.