Rattus norvegicus hypothetical protein LOC685762 classification with in silico bioinformatics computational tools

Abstract

Computer software capable of protein analysis, such as bioinformatics tools, were used to help gain preferential, thorough, and accessible significant classifying information on a hypothetical protein of interest. The tools used in this study classified the protein of choice, hypothetical protein LOC685762, found in Rattus norvegicus, a multi-pass/polytopic transmembrane protein. Tools such as SMART and Protter were able to characterize the hypothetical protein as a polytopic integral transmembrane protein, which extends through the semi-permeable lipid bilayer several times. Spermatogenesis associated multi-pass transmembrane protein 3, was discovered to be a homologous protein by using the online bioinformatics tools, Protein BLAST and Needle. Homology can be a vital aspect when determining the function of a protein. The amino acid sequence in a protein determines the structure and thus the structure defines the relative function of the protein. With this rational and conceptualization, it is implied that homology can be used to help compare the functionality of the protein of interest in this study. A homologous protein is not identical to the protein, it is simply similar. Spermatogenesis associated multi-pass transmembrane protein 3, was found to be ̴74% similar to LOC685762 and ̴ 61% identical. With this knowledge, mutational analysis can also be used to determine the stability of the protein under different conditions, such as a single amino acid variation. Mutational evaluation was performed by the tool I-mutant. At position 51 in the amino acid sequence, a lysine (K) residue was found to be more stable than a threonine (T) residue. Not only is the primary structure of a protein essential to fully understand a protein, but its secondary structure is just as significant, specifically when there are alpha helices and beta sheets present. LOC685762 maximizes its hydrogen bonding within these complex secondary structures. Phyre 2 was used to specify the specific secondary structures and domains present in the hypothetical protein and the homologous protein. With further in silico analysis scientists were able to gain a better conceptualization of what the potential function and role of LOC685762 is in the Rattus norvegicus.