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Tertiary protein structure viewing and prediction - PowerPoint PPT Presentation
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Tertiary protein structure viewing and prediction. July 3, 2007 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.
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Tertiary protein structure viewing and prediction
- July 3, 2007
- 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.
Protein structure viewers
- RasMol
- Deep View
- Cn3D
- WebLabViewer
- Chimera
Steps to tertiary structure prediction
- Comparative protein modeling
- Extrapolates a new structure based on solved structures that are related by sequence.
- Steps for SWISS-Model
- Identification of modeling templates.
- Alignment between target and templates.
- Model building.
- Evaluation.
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.
- Ca atoms of the templates are selected for superimposition.
- This generates a structurally corrected multiple sequence alignment
Step 2: Alignment
- Up to 5 template structures are superimposed.
- Incompatible templates are removed.
- Pairwise alignment is created between target and main template structures.
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.
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.
Step 4: Energy Minimization
Model refinement-minimization of energy (GROMOS96 force field)
