Assignment 1. Protein structure analysis.

1) Select four proteins with known structures which belong to the same family and have pairwise sequence identity of no more than 75%. The length of each protein should be less than 180 residues and structure resolution better than 1.8Å.

2) Build a multiple sequence alignment and all possible pairwise structure alignments for these proteins. Plot the values of structure similarity against sequence similarity for all pairs. Evaluate and discuss correlation between sequence and structure similarity.

3) Locate at least one fragment of high sequence similarity and one fragment of low sequence similarity in these proteins. Investigate correlations between structure and sequence similarity for these fragments. Describe a possible role of the secondary structure content in these correlations.

4) Identify functionally important site(s) in these proteins and their relationship to the structure conservation.

The report should be submitted by email as a Word or PDF file with the filename "b731_24_hw1_Your_Name.doc or .pdf". The string "b731_24_hw1_Your_Name" should be also included in the message subject line.

Due November 4, 2024.

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Assignment 2. Protein modeling.

a) Select a sequence of a prokaryotic enzyme from one of the protein sequence databases that has a homologous experimentally determined X-ray structure with at least 30%, but not more than 60% of sequence identity. (Recommended length of the selected sequence is 150-250 residues).

b) Predict the three-dimensional structure for the selected sequence using at least two methods, e.g., fold recognition and homology modeling (Phyre2, I-TASSER, RaptorX, SwissModel, Modweb, etc.).

c) Analyze the quality of your homology model using one of the structure validation or verification tools.

d) Compare the structure of your model with the model structures of the same protein from AlphaFold Protein Structure Database and ESM Metagenomic Atlas. Describe the results of this comparison. (If models of your protein are not available in one or both databases, use the models of protein closest to yours).

e) Visualize the results of comparison from Part d, highlighting the differences between the structures (if any). If there are no differences, highlight any other interesting feature of the structures.

The report should be submitted by email as a Word or PDF file with the filename "b731_24_hw2_Your_Name.doc or .pdf". The string "b731_24_hw2_Your_Name" should be also included in the message subject line.

Due December 3, 2024.