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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