Lab Report C

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Seneca College *

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573

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Biology

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Apr 3, 2024

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Purpose: The purpose of the labs was to study evolutionary biology and protein structure prediction. Lab 6 focused on developing a phylogenetic tree manually using representatives from the three domains of living organisms and a molecular clock to measure evolutionary distance. Lab 7 focused on building a phylogenetic tree using the UPGMA clustering method and visualizing the tree. The protein sequences were obtained from NCBI, saved in FASTA format in a file, and the distance matrix was calculated. Lab 8 focuses on using homology modeling to predict the 3D structure of a drug-resistant mutant HIV protease and comparing it to the native HIV protease, using programs such as RCSB Protein Data Bank, FirstGlance, SWISS-MODEL, and RCSB Pairwise Structure Alignment. These exercises aim to teach important concepts and techniques related to evolutionary biology and protein structure prediction, which have applications in various fields, including medicine and drug design. Method: This method employs homology modeling to forecast the 3D configuration of a drug-resistant mutant HIV protease. The resulting predicted 3D structure is compared with the structure of the native HIV protease to investigate structure-function relationships. To accomplish this, various programs linked to protein structure prediction are employed: RCSB Protein Data Bank (PDB): PDB contains the information about the 3D structures of proteins, nucleic acids, and complex assemblies (i.e., macromolecules).  Go to PDB website by clicking the following link or typed in PDB database on google. https://www.rcsb.org/  Search for PDB ID: 1KJF and 1ODW and Download the PDB formatted files.

FirstGlance: FirstGlance shows the Visualization of macromolecules.  Go to FirstGlance website by clicking the following link: l https://www.bioinformatics.org/firstglance/fgij/  Navigate to FirstGlance and enter PDB ID: 1KJF to view its 3D structure. Swiss-Model: Homology modeling is one of the computational structure prediction methods that are used to determine protein 3D structure from its amino acid sequence.  Download the FASTA-formatted amino acid sequence of the mutant HIV protease.  Go to SWISS-MODEL website by clicking the following link or search Swiss-Model on google and Start Modelling. https://swissmodel.expasy.org/  Using User Template input mode, upload the mutant HIV protease amino acid sequence file as the target sequence and upload the 1ODW PDB file as the template file.  Click Build Model. Download the resulting model’s PDB file.

RCSB PAIRWISE STRUCTURE ALIGNMENT Pairwise Sequence Alignment is used to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences

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(protein or nucleic acid). Using RCSB Pairwise Structure Alignment, compare the 3D structure of the mutant HIV protease to 1KJF.  Go to RCSB website by clicking the following link or search PDB alignment on google. https://www.rcsb.org/alignment  For one structure, enter PDB ID 1KJF.  For Chain ID, select either A or B; this protein is a homodimer so both chains have the same sequence.  For the other structure, upload the homology model PDB file from Step 8. Type in the same letter used above (A or B) for the Chain ID Entry ID Chain ID Compare different alignments by changing the parameters.

Phylogenetic Analysis of Immunodeficiency Virus Proteases: Result: RCSB Protein Data Bank (PDB): Result page shows the summary of desired protein structure.

Download the 1KJF file in PDB format. The file contains the information about the protein structure. FirstGlance: After searching the desired protein structure (e.g., 1KJF), the website gives the 3D structure of protein. Also, it provides tools to change the view of the protein to study its structure. Swiss-Model: The result of the mutant HIV protease amino acid sequence file as the target sequence and the 1ODW PDB file as the template file. Swiss-Model predicts the following structure using homology modelling.

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RCSB PAIRWISE STRUCTURE ALIGNMENT

RCSB Pairwise Structure Alignment does the comparison and 3D alignment of protein structures to analyze structure-function relationships.

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