Rattus norvegicus hypothetical protein LOC685762 classification with in silico bioinformatics computational tools
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Issue Date
2023-04
Authors
Isereau, Allyson
Publisher
SUNY Brockport
Keywords
Friends of Drake Library , Rattus Norvegicus , Bioinformatics
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.