A Bioinformatics Analysis of Plant Aspartic Protease Nepenthesin I

Stephan Girard, “A Bioinformatics Analysis of Plant Aspartic Protease Nepenthesin I”
Mentor: Madhusudan Dey, Biological Science

The carnivorous pitcher plant Nepenthes alata produces digestive enzymes including proteases which degrade proteins in captured insect prey. Nepenthesin I (NEP1) is an aspartic protease similar to pepsin that is found in human stomachs. Nepenthesin is unique in that it cleaves on either side of an aspartate residue and is extremely stable in an acidic pH. This protein is important because the plant depends on prey digestion to get vital nutrients such as nitrogen. The National Center for Biotechnology Information (NCBI) database shows that the nep1 gene is mapped at gene locus AB266803 on the nuclear genome. This gene contains one exon, and codes for a protein of 437 amino acids (46.33 kDa). Using the NCBI BLAST tool, I retrieved the gene/protein sequences of 8 paralogs, homologs, and orthologs. I chose these similar genes based on the percent similarity to nep1 with a < 30% cutoff. Using the sequence of those genes, I used the program Molecular Evolutionary Genetic Analysis (MEGA) to perform a multiple sequence alignment. This showed which nitrogenous bases are critical to creating the proper amino acid and which might be substituted without having an impact on function. The multiple sequence alignment also showed sequence homology between nep1 and these homologs Using the same program and the gene alighnment, I constructed a phylogenetic tree to visualize gene sequence relatedness.A published 3-dimentional structure of this protein is not available on RCSB Protein Data Base. A SWISS-MODEL was made of Nepenthesin 1 and a homology model of Nepenthesin 2 both using the 3vla.1.A model. Aligning these 2 proteins in PyMOL gives a root mean squared deviation (RMSD) of 2.228 Å. This is the average distance between the atoms of the two superimposed proteins.

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  1. This project seems to have some importance, but the goals of the project were unclear.

    The writing was understandable, but without the intent of the project it was difficult to determine whether the work progressed as was hoped or was even aligned with the intent.

    Commonly, headings such as Long-term Goals, Objectives, and Methods are helpful for a reviewer to understand the context, the direction, the success of a project, and learning that occurred along the way.

    This reviewer anyway, missed this context. That said, I was eager to read about how the work was based in what seemed to be important goals!

  2. The purpose, goal, intent was not clear for me. As I continue to read about presentation for clarification, I did not received purpose for presentation.

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