Download Protein structures - Informatics: Indiana University

Protein structures
Haixu Tang
School of Inforamtics
A covalent peptide bond
Protein conformation is specified by
tts Amino Acid sequence
• Steric interactions
• Weak non-covalent bonds
– hydrogen bonds
– ionic bonds
– van der Waals attractions
• Hydrophobic interaction
– distribution of its polar and nonpolar amino acids
Protein folding: lowest energy
conformation
Protein denaturalization
Visualizing protein conformations
• Protein structures in atomic level
• Protein Data Bank (PDB) http://www.rcsb.org
• Pymol: http://pymol.sourceforge.net/
• Rasmol: http://www.umass.edu/microbio/rasmol/
Protein secondary structure
Secondary structure prediction
• Prefer a-helix: Ala, Leu, Met, Phe, Glu, Gln,
His, Lys, Arg (sidechains cover and protect the
backbone H-bonds)
• Prefer b-sheet: Tyr, Trp, Phe, Ile, Val, Thr, Cys
(large bulky sidechains)
• Disrupt secondary structure: Gly, Pro, Ser, Asp,
Asn (small, restrained, or sidechain hydrogen
bonds)
Coiled coil
Protein Domains
• Independent structural unit
• Independent function
• Independent folding
• Independent evolve
Protein families
Protein structural classification
(SCOP: http://scop.mrc-lmb.cam.ac.uk/scop/)
• Class
• Folds
• Super-families
• Families
Sulfur-sulfur (disulfur) bonds
Assembly of Large Structures
Experimental determination of
protein structures
• X-ray crystallography
• NMR (Nuclear Magnetic Resonance)
Spectroscopy
X-ray crystallography
NMR spectrum