The GRAVY value for a protein is calculated
The GRAVY value for a protein is calculated as the sum of hydropathy values of all the amino acids, divided by the number of residues in the sequence (Kyte and Doolittle, 1982). According to Kyte and Doolittle (1982) integral membrane proteins typically have higher GRAVY scores than do globular proteins. Though the GRAVY score is a helpful piece of information, it cannot reliably predict the structure without the help of hydropathy plots. Gravy index score of proteins below are more likely globular (hydrophilic protein), while scores above are more probable membranous (hydrophobic protein). The positive GRAVY values of all P-ATPase representative protein samples designated them to be hydrophobic in nature which is confirmed by the plot in Fig. 2. The aliphatic index of a protein is defined as the relative volume occupied by aliphatic side chains (alanine, valine, isoleucine, and leucine). The aliphatic index value of proteins from thermophilic bacteria was found to be significantly higher than that of ordinary proteins and hence, it can serve as a measure of thermostability of proteins (Ikai, 1980). So, this is a positive indicator of globular protein thermostability. As it was shown in Table 4, the most aliphatic index in P-ATPase13A1 and P-ATPase13A3 D-erythro-Sphingosine (synthetic) synthesis belonged to Bt-13A1 (104.75) and Ap-13A3 (104.22), respectively; however the least was observed in Mdo-13A1 (98.27) and Hh-13A3 (96.28) in each family. Based on the obtained result, high aliphatic index in P-ATPases indicated structural stability of this protein in both families. The instability index is a measure of proteins, used to determine if it will be stable in a test tube or not. It is also known that an instability index less than 40 predicts a stable protein, whereas values higher than 40 denote a potentially unstable protein. Analysis of insect's P-ATPases showed that six of the representative insect samples including Ap-13A1, Bm-13A1, Hh-13A1, Mdo-13A1, Ap-13A3 and Bm-13A3 had the instability index more than 40 and were unstable but the rest of them were stable. The secondary structure analysis revealed that in all representative protein samples alpha helices dominated among all other elements. Stretches of approximately 25 hydrophobic residues with an occasional polar residue of integral proteins that pass across membrane are recognized as transmembrane (TM) domains. Moreover anchoring to the membrane they participate in the functions of these proteins in some unspecified way (Ramasarma et al., 2012). Although the number of transmembrane domains varies from 6 to 11, all P-ATPases have an even numbers of transmembrane domains facing the cytoplasmic side of the membrane. In current research, transmembrane domains of P-ATPase families were studied in topology prediction (Fig. 3) and the number of transmembrane domains was predicted in different insect species. According to the results, the numbers of transmembrane helices in representative insects were variable between 6 and 10. So that in P-ATPase13A1 family there were between 6 and 10 while in the other family the least number of transmembrane domains were 10 and the most were 11. The least number of transmembrane domains in all insect samples belonged to Hh-13A1 with 6 domains; however three species of P-ATPase13A3 families had the most number of transmembrane domains with 11 of them which were including: Bt-13A3, Bm-13A3 and Tc-13A3. As it is known the 3D structure is the crucial goal of protein structure prediction and it is necessary to fully understand protein function. In this study, the structural similarities and differences between B. terrestris model and the other representative insect samples in each family were analyzed and the values of TM-scores were computed. TM-score is a metric for measuring the structural similarity of two protein models. It is designed to solve two major problems in the traditional metrics such as RMSD (Root Mean Square Deviation). Firstly, TM-score measures the global fold similarity and is less sensitive to the local structural variations; secondly, magnitude of TM-score for random structure pairs is length-independent. TM-score has the value in and 1; where 1 indicates a perfect match between two structures. Following strict statistics of structures in the PDB, scores below 0.17 corresponds to randomly chosen unrelated proteins whereas with a score higher than 0.5 assume generally the same fold. Results of TM-score server in this research showed that the most similarity among Bt-13A1 and the other samples of 13A1 family belonged to Tc-13A1with TM-score 0.7304 and the least was observed in Hh-13A1 (0.1224). But in the 13A3 family the most similarity among Bt-13A3 structure and the other samples was observed in Tc-13A3 (0.4416) while the least was found in Ap-13A3 (0.1859). Also to find out the differences among these structures the superpose model showed no significant differences.