1. Tertiary protein structure viewing and prediction July 5, 2006 Learning objectives- Learn how to manipulate protein structures with Deep View software. Learn the steps to protein structure modeling with Deep View. Workshop-Manipulation of the lysozyme and hemoglobin.

2. Protein structure viewers RasMol Deep View Cn3D WebLabViewer Chimera

3. Steps to tertiary structure prediction Comparative protein modeling Extrapolates a new structure based on solved structures that are related by sequence. Steps for SWISS-ModelSWISS-Model 1. Identification of modeling templates. 2. Alignment between target and templates. 3. Model building. 4. Evaluation.

4. Step 1: Identification of modeling templates One chooses a cutoff value from FastA or BLAST search ( E<10 -5 ) and perform BLAST search of Protein Data Bank. Up to ten structure templates can be used but the one with the highest sequence similarity to the target sequence (lowest E-value) is designated as the reference template. Its structure is given the most weight. C  atoms of the templates are selected for superimposition. This generates a structurally corrected multiple sequence alignment

5. Step 2: Alignment Up to 5 template structures are superimposed. Incompatible templates are removed. Pairwise alignment is created between target and main template structures.

6. Step 3: Building the model Framework construction Average the position of each atom in target sequence, based on the corresponding atoms in template (start with C  atoms) Each loop is defined by the length of the loop and C  atom coordinates of the four residues preceding and following the loop. Constraint space programming is used. Portions of the target sequence that do not match the template are constructed from a “spare part” algorithm.

7. Framework construction

8. Step 3: 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 atoms are averaged from each backbone atom (N,C,C(O)). Side chains are added from a table of most probable rotamers given a certain backbone conformation. Model refinement-minimization of energy (GROMOS96 force field)

9. First approach mode Step Program/ Method Database Action 1BLASTP2 ExNRL -3D Will find all similarities of target sequence with sequences of known structure. 2SIM- Will select all templates with sequence identities above 25% and projected model size larger than 20 residues. Furthermore, this step will detect domains which can be modeled based on unrelated templates 3-- Generate ProModII input files 4ProModIIExPDB Generate all models 5Gromos96- Energy minimization of all models