Ex.1: Parsing Protein Structures

1 Parsing PDB files

1.1 Learning Goals

1. Get familiar with PDB format and quick alternatives to parse this files.
2. Understand the meaning of protein contact maps and their correlation with protein structure.

1.2 Data

You must parse the following structures from the protein data bank.

1RBP

1QRE

1DGF

1.3 Tasks

Important

Choose your favorite flavor! You are free to complete this exercise using Python or R, but do not use structural biology-specific packages, you must write your own functions.

1. Write a function that parses the files and prepares a table or report with key information from the structure, including protein name, source organism, determination method, authors, release date, resolution, and the number of peptide chains and other molecules.

Tip

You may find some amino acids that are not canonical. If so, you can either change to the canonical one or use X in the fasta sequence.

2. Parse the data to extract the protein structural information from the PDB file in tabular format, then compute the pairwise distance matrix for each PDB structure. The distance between two amino acids is usually calculated as the 3D Euclidean distance between their C-alpha (CA) atoms.

Figure 1: Euclidean distance explanation

3. Write a function for plotting the corresponding contact map for each structure, using a standard contact threshold (6-12 Å) and different colors for different contacts (intra- and interchain).

4. Try to interpret the plots. Can you identify any structure in the contact maps? If so, which ones? Determine the type of structure as well (monomer,homo- or hetero- dimer, tetramer… ).