1. Tertiary protein structure modelling May 31, 2005 Graded papers will handed back Thursday Quiz#4 today Learning objectives- Continue to learn how to manipulate protein structures in Deep View. Learn the steps to protein structure modeling with Deep View. Workshop-Manipulation of the hen lysozyme, hemoglobin and modeling of Fas antigen ligand protein structure with Deep View.

2. 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

3. Identification of modeling templates One chooses a cutoff value from FastA or BLAST search (10 -5 ) Up to ten templates can be used but the one with the highest sequence similarity to the target sequence (lowest E-value) is the reference template C  atoms of the templates are selected for superimposition. This generates a structurally corrected multiple sequence alignment

4. Alignment “Common core” and conserved loops of target sequence are threaded onto the template structure using only alpha carbons

5. Framework construction

6. Building the model Framework construction Average the position of each atom in target, based on the corresponding atoms in template. Portions of the target sequence that do not match the template are constructed from a “spare part” algorithm. Each loop is defined by its length and C  atom coordinates of the four amino acids preceding and following the loop.

7. Building the model Completing the backbone-a library of PDB entries is consulted to add carbonyl groups and amino groups. The 3-D coordinates come from a separate library of pentapeptide backbone fragments. These backbone fragments are fitted onto the target C alpha carbons. The central tri- peptide is averaged from each backbone atom (N,C,C(O)). Side chains are added from a table of most probable rotamers that depend on backbone conformation. Model refinement-minimization of energy

8. Protein Modeling Workshop Continue to work through the first 11 chapters of the tutorial you began in the previous class. ( http://www.usm.maine.edu/~rhodes/SPVTut/text/SPdbVTut.html ) http://www.usm.maine.edu/~rhodes/SPVTut/text/SPdbVTut.html Perform the protein modeling exercise described at: http://us.expasy.org/spdbv/text/modeling.htm http://us.expasy.org/spdbv/text/modeling.htm