For this assignment, DNA sequence 2 was researched to determine its different properties. This sequence of DNA sequence was analyzed using several different online tools. The DNA sequence was initially inserted into the GenBank database using the Basic Local Alignment Search Tool (BLAST). This aligned the provided sequence with fifteen other similar sequences. The DNA sequence’s query score was examined and found to be a direct match with Homo Sapiens proliferating cell nuclear antigen.
The protein selected for this assignment was found to be Homo Sapiens (humans) proliferating cell nuclear antigen, transcript variant 1 and 2 (PCNA). Both transcript variants are found in the same protein-coding gene and share identical properties. PCNA is an auxiliary protein of DNA polymerase found in the cell nucleus. The structure of this protein is a homotrimer, meaning it contains three identical units of polypeptides. The amino acid length of the protein in variant one is 1,355 amino acids, while transcript variant two contains 1,319 amino acids. It functions in the replication of DNA by increasing the processing level of polymerase (mRNA) during replication. It is also strategically placed at the replication fork to carry out its duty of fixing possible mutations in newly synthesized genes. Furthermore, PCNA promotes post-damage repair and replication of genetic material.
Proliferating cell nuclear antigen is found in eukaryotic cells, in both humans and animals. In the clinical aspect, antibodies against proliferating cell nuclear antigen are found in the serum of patients with Lupus Erythematosus. This protein is found in various tissues in the human body and are most prevalent in the bone marrow and lymph nodes.
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The queried DNA provided information into the length of each protein, the alignment score, its amino acids and accession number. The accession number of the provided protein was NM_182649.1. The highest matches had the accession numbers NM_002592.2 (PNCA transcript variate 1) , and NC_000020.11 (Homo Sapiens chromosome 20).
In order to determine the putative homologs of the protein in other species, HomoloGene was used. The accession ID code of PNCA was inserted into HomoloGene. This provided information into which other organisms had the highest matching protein to PNCA in Homo Sapiens. The protein was further aligned using the “Pairwise Alignment Generated using BLAST”. This accession code for the protein was then compared to the highest correlating protein for PCNA; Pan troglodytes with accession number XP_001165515,
(the common chimpanzee), M. mulatta with the accession number XP_001115746.1 (rhesus monkey), and C. Lupus with the accession number XP_534355.3 (wolves). This alignment compared information such as identity and length of each protein.
The next step of this process was the translation of the DNA sequence. ExPasy Translate was used to translate the sequence of DNA into 3-codon amino acids. The DNA sequence was translated into six reading frames, three frames for each DNA strand. The 5’ to 3’ were analyzed. Reading frame two was determined to be the best interpretation and was selected for further analysis.
Next, the database called ExPasy ProtoParam was used to determine different features of the amino acid sequence. Using this tool, the number of amino acids, molecular weight, and instability index of the protein was shown. Proliferating cell nuclear antigen contained 33 amino acids and had a molecular index of 3585.19. The instability index of the protein was computed to be 66.36, classifying it as unstable. Additional factors such as lifespan and total number of atoms were also computed.
One primary research article relating to proliferating cell nuclear antigen discusses the possible effects of a specific mutation on PCNA’s binding characteristics. The article explains that a certain mutation in PCNA called S228I may cause large deformations in the binding pockets of wild-type PCNA, hindering its ability to replicate DNA and repair mutations. This article is relevant, timely, and authoritative. Although the results do not indicate that this mutation is harmful to the PCNA, it introduces new concepts that need to be researched further.
In conclusion, proliferating cell nuclear antigen is a critical protein in eukaryotes and is instrumental in preventing mutations that could lead to potentially harmful medical consequences. Furthermore, it plays an important role at the biological level by increasing the rate DNA replication.
Works Cited
- Duffy, C. M., Hilbert, B. J., & Kelch, B. A. (2016). A Disease-Causing Variant in PCNA Disrupts a Promiscuous Protein Binding Site. Journal of Molecular Biology, 428(6), 1023–1040. Retrieved from https://www.sciencedirect.com/science/article/pii/S0022283615006944?via%3Dihub
- UniProt. (2018, September 12). UniProtKB – P12004 (PCNA _HUMAN). Retrieved from https://www.uniprot.org/uniprot/P12004
