Protein Structure I

Structure Dictates Function

• Primary/Secondary/Tertiary/Quaternary HERE
• Protein in DNA replication HERE
• Insect protein assembly HERE
• Flexibility and function HERE

Amino Acids in Proteins

• D/L isomers HERE
• Ionization and pH HERE
• Hydrophobics - Glycine/Alanine/Proline/Valine/Leucine depictions HERE
• Hydrophobics - Isoleucine/Methionine/Tryptophan/Phenylalanine depictions HERE
• Polar - Serine / Threonine/Tyrosine/Asparagine/Glutamine/Cysteine HERE
• Positive R-groups - Lysine / Arginine / Histidine HERE
  • Guanidinium/Imidazole HERE
  • Histidine ionization HERE
• Negative R-groups - Aspartate/ Glutamate HERE
• pKa Table HERE
• Abbreviations HERE

Amino Acid Ionization

• Ionization scheme of amino acids HERE
• Amino acid titration HERE (external site)

Primary Structure

• Peptide bond formation HERE
• Sequence and orientation HERE / Schematic HERE
• Peptide bond resonance HERE
• Planar nature of peptide bonds HERE
• Trans and cis peptide bonds HERE / around Proline HERE
• Phi/Psi bonds in polypeptides HERE
• Ramachandran plot HERE

Secondary Structure

• Alpha helix structures HERE
  • Hydrogen bonding in alpha helix HERE
  • Ramachandran plot relative to helices HERE
  • Alpha-helical protein HERE
• Beta sheets
  • Beta strands - Ramachandran HERE / Structure HERE
  • Antiparallel beta sheets HERE / Parallel beta sheets HERE
  • Fatty acid binding protein HERE
  • Reverse turn HERE
  • Loop structures HERE
• Fibrous Proteins
  • Alpha helical coiled coil (superhelix) HERE
  • Heptad repeats HERE
  • Collagen sequence HERE
  • Collagen strand conformation HERE
  • Collagen coiled structure HERE

Tertiary Structure

• Myoglobin
  • Structures HERE
  • Amino acid distribution HERE (blue = charged, yellow = hydrophobic, white = other)
• Porin's inside-out structure HERE
• Disulfide cross-link bonds HERE
• Helix-turn-helix (supersecondary structure) HERE

Quaternary Structure

• Human hemoglobin HERE
• Rhinovirus structure HERE

Sequence and Structure

• Bovine ribonuclease HERE
• Reduction of disulfide bonds HERE
• Structure disrupters HERE
  • Urea
  • Guanidinium chloride
  • Beta-mercaptoethanol
• Reduction and denaturation of ribonuclease HERE
• Renaturation of ribonuclease HERE / Steps in folding Chymotrypsin inhibitor HERE
• Amino acids and secondary structure tendency HERE
• Folding/unfoding transition HERE and HERE
• Prion recruitment HERE
• Modified side chains in proteins HERE