2.  Four levels of protein structure  Linear  Sub-Structure  3D Structure  Complex Structure

3.  Hydrogen Bonding  Intermolecular Forces  Dipole-Dipole  Ion-Dipole  Van der Waals

4.  Nonpolar molecules disrupt dynamic hydrogen bonds  Hydrophobic amino acids include  alanine, valine, leucine, isoleucine, phenylalanine, tryptophan and methionine

5.  Hydrophobic amino acids face the interior of the protein

6.  Hydrophobicity Scale  Physical scales based on surface tension or energy solvation  Wimley-White Scale  Peptide bonds and side chains  Experimentally determined values

7.  Refers to the total external charge, while polarity refers to the difference in charge

8.  Opposites attract, so charge can influence protein binding activity

12.  Physical structures resulting from amino acid sequences  Predictive techniques  FoldIt

13.  Binding sites  Chemical bonds from with ligands  Specific molecules and ions

14.  Critical Assessment of Protein Structure Prediction  Competition structure  Advancing predictive science  Based on structure, complex, domain, function

15.  Structural Classification of Proteins  Collaborative classification effort  Based on amino acid sequence, domain structure, and function  Classified into families and superfamilies  Sourced from Protein Data Bank (PDB)

16.  Protein data bank – PDB  Useful for low sequence similarity  Computational methods  X-Ray Crystallography  NMR Spectroscopy

17.  Distance alignment matrix based on hexapeptide contact patterns  FSSP (Families of Structurally Similar Proteins) Database  Server-based  DaliLite standalone

18.  Breaks structures into aligned fragment pairs  Originally only structural superpositions and inter-residue distances  Now includes secondary structure, solvent exposure, hydrogen- bonding patterns, and dihedral angles

19.  Sequential Structure Alignment Program  Vectors between non- contiguous residues  Optimal local alignments compiled into summary matrix  Dynamic programming

20.  Crystal  X-ray diffraction  Angles and intensities  Electron density  Atom positions and chemical bonds  Good resolution

21.  Water solution  Solid methods in development  Sample is placed in magnet  Different nuclei absorb different radio frequencies  Interaction  Determine orientation and structure