BMI 731. Protein Structures and Related Database Searches. Protein. DNA (Genotype). Biology … Protein…. A single amino acid substitution in a protein causes sickle-cell disease…. What the.....!?. Why do we care about structure?.
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Protein Structures and Related Database Searches
A torsion angles is defined by 4 atoms, A, B, C and D.
When atoms A, B, C and D are mainchain atoms (ie. the carboxylic carbon, C1; the alpha carbon, C2 or C-alpha; and the amide group nitrogen, N), There are THREE repeating torsion angles along the backbone chain called phi, psi and omega.
1 - Primary structure
2 - Secondary structure
3 - Tertiary structure
4 - Quaternary structure
SCOP--Gold standard for structure classification!
Growth of PDB demands automated techniques
for classification and fold detection
NCBI Reference Sequences
PIR International Protein Sequence Database
Database similarity search
Protein family, domain, cluster analysis
Does sequence align with protein of known 3D structure?
three dimensional structure
3D comparative modeling
Relation-ship to known structure?
3D analysis in laboratory
Is there a predicted structure?
Computer generated image, showing 3-D structure of uteroglobin, a protein secreted in the uterus of mammals.
A computer image of the charge density over the molecule chymosin, an important enzyme in cheese making. Overall negative charge is depicted as red, overall positive charge is shown in blue.
Thanks to Selnur Erdal for preparing initial versions of these slides.