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BY DR. KAROBI MOITRA, CFD, MSC. PHD.
FORMER ASSOCIATE PROFESSOR OF MOLECULAR BIOLOGY
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Bioinformatics Annotation Projects
Meghna Pandey, Richard Montgomery High School
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The protein that was annotated in this project was a hypothetical protein (Protein ID: KAF3843209.1), found in the organism Dissostichus mawsoni, commonly known as the Antarctic toothfish. D. mawsoni is a species native to the Southern Ocean, and lives in subzero degree water. Antarctic toothfish are especially remarkable since they have the ability to produce antifreeze proteins that prevent crystallization of blood under sub-zero conditions. Additionally, instead of a swim bladder, members of this species control their buoyancy with lipids and fats. These adaptations are what enable the survival of Antarctic toothfish in frigid temperatures. To determine the structure and function of the hypothetical protein in question, the given protein sequence was input into multiple databases, including Basic Local Alignment Search Tool (BLAST), Transmembrane Helices Hidden Markov Model (TMHMM), Protein Family (PFAM), and Protein Data Bank (PDB) among a few. Results and information about the protein were gleaned from each database, which revealed characteristics of the protein pertaining to its identity. Based on the BLAST results, the most similar protein to the protein in question was involved in multidrug resistance in eukaryotes and belonged to the ABC Transporter C Subfamily. The PFAM results suggested that there were ATP binding domains in the protein, and that the protein contained certain Walker sequences found only in ABC transporters. The results of the analysis led to the following conclusion: the predicted protein is the ATP Binding Cassette Subfamily C Member 4 (ABCC4) protein of Dissostichus mawsoni.
Aishani Das, Middleton High School
We are investigating and annotating the protein sequence of a hypothetical protein KAF3843965.1 found in Dissostichus mawsoni, also known as the Antarctic toothfish. The Antarctic toothfish is dispersed in the waters of the Southern Ocean, and is studied for its abilities to produce antifreeze proteins that keep its blood from crystallizing. The materials and methods we used include BLAST, TMHMM, PSORT II, Phobius, PFAM, PDB, Skylign, and SWISSMODEL. We found this hypothetical protein to be a putative member of the ABC transporter family through BLAST and through analysis of the conserved domain LSGGQ. More specifically, we found that it is related to the ABCC1 protein found across many species and explored a similar structure through PDB. Using TMHMM and Phobius, we found that the protein has 14 putative transmembrane alpha helices. We observed that the human ABCC1 transporter has 17 transmembrane helices, so we deem the hypothetical protein to be incomplete. By modeling this hypothetical structure with SWISSMODEL, we found the structure to share most similarities with the solved structure of ABCC1 protein in bovines. In summary, the hypothetical protein can be classified as a partial ABCC1 transporter found in the species Dissostichus mawsoni.