Module 3 Protein Structure Database/Structure Analysis Learning objectives Understand how information is stored in PDB Learn how to read a PDB flat file Become familiar with comparative protein modelling theories Learn how to search the PDB for information. Learn how to download a structure Learn how to display a structure on the screen Learn how to compare two structures on the screen.

Primary, secondary, supersecondary, and tertiary structure Primary Secondary Supersecondary Tertiary ACFTYPL … ACFTYPL sssccss

ATOM 1 N ARG A N ATOM 2 CA ARG A C ATOM 3 C ARG A C ATOM 4 O ARG A O ATOM 5 CB ARG A C ATOM 6 CG ARG A C ATOM 7 CD ARG A C ATOM 8 NE ARG A N ATOM 9 CZ ARG A C ATOM 10 NH1 ARG A N ATOM 11 NH2 ARG A N Part of a record from the PDB X Y Z

What is PDB? Protein structure database Annotated records that represent three dimensional coordinates of atoms of biological molecules Generated from direct submissions of coordinates from the authors. In the old days, this was called the Brookhaven National Database.

3D structure data The largest 3D structure database is the Protein Database It contains over 15,000 records Each record contains 3D coordinates for macromolecules 80% of the records were obtained from X-ray diffraction studies, 16% from NMR and the rest from other methods and theoretical calculations

Protein structure viewers RasMol Deep View Cn3D WebLabViewer

Steps to tertiary structure prediction Comparative protein modeling Extrapolates new structure based on related family members Steps 1. Identification of modeling templates 2. Alignment 3. Model building

Identification of modeling templates One chooses a cutoff value from FastA or BLAST search Up to ten templates can be used but the one with the highest sequence similarity is the reference template C  atoms are selected for superimposition

Alignment Optimization of superimposition of templates “Common core” and conserved loops of target sequence is threaded onto the template structure

Building the model Framework construction Average the position of each atom in target, based on the corresponding atoms in template. Areas that do not match the template are constructed by using a “spare part” algorithm Completing the backbone-a library of PDB entries is consulted Side chains are added Model refinement-minimization of energy

Framework construction

Alpha Helix

show all the groups within 8 A of N of NAG202

Comparing similar polypeptides One of the first structures solved was that of hemoglobin. It is composed of 2 alpha and 2 beta chains. The alpha and beta chains have similar structure. With Deep View you can superimpose the chains and locate the amino acids that are near one another in the two chains. We will also print out an alignment of the two polypeptides.

Superimposition of two polypeptides

Workshop for module 3: Download hen lysozyme structure file from PDB. Show the Ramachandran plot associated with this structure. Find out the residues that surround the active site of the enzyme. Download the human hemoglobin structure from PDB. Separate the alpha chain and beta chain into two separate files. Compare the structures. Print out the overlapped structures and print out the aligned primary sequences.