Protein structures

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Protein structures

• Haixu Tang
• School of Inforamtics

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A covalent peptide bond
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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

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Protein folding lowest energy conformation
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Protein denaturalization
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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/

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Protein secondary structure
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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)

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Coiled coil
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Protein Domains

• Independent structural unit
• Independent function
• Independent folding
• Independent evolve

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Protein families
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Protein structural classification(SCOP
http//scop.mrc-lmb.cam.ac.uk/scop/)

• Class
• Folds
• Super-families
• Families

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Sulfur-sulfur (disulfur) bonds
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Assembly of Large Structures
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Experimental determination of protein structures

• X-ray crystallography
• NMR (Nuclear Magnetic Resonance) Spectroscopy

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X-ray crystallography
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NMR spectrum