Protein Structure

Structure Dictates Function

• Protein in DNA replication HERE
• Insect protein assembly HERE
• Flexibility and function HERE

Amino Acids in Proteins

• D/L isomers HERE
• L structure in protein amino acids HERE
• Ionization and pH HERE
• Simple - Glycine/Alanine depictions HERE
• Aliphatics - Valine/Leucine/Isoleucine/Methionine depictions HERE
• Cyclic - Proline HERE
• Aromatics - Phenylalanine / Tyrosine / Tryptophan HERE / Absorption spectra HERE
• Aliphatic hydroxyl - Serine / Threonine HERE
• Sulfhydryl - Cysteine HERE
• Basic - Lysine / Arginine / Histidine HERE
  • Guanidinium/Imidazole HERE
  • Histidine ionization HERE
• Carboxylates & Carboxamides - Aspartate/ Glutamate /Asparagine / Glutamine HERE
• pKa Table HERE
• Abbreviations HERE
• Reactivity and structure HERE

Ionization

• Titration of acetic acid HERE
• pKa's of some amino acids HERE
• Ionization scheme of amino acids HERE

Primary Structure

• Peptide bond formation HERE
• Sequence and orientation HERE / Schematic HERE
• Disulfide bonds HERE
• Bovine insulin sequence HERE
• Peptide bond resonance HERE
• Planar nature of peptide bonds HERE / Bond lengths HERE
• Trans and cis peptide bonds HERE / around Proline HERE
• Rotation around bonds in polypeptides HERE
• Ramachandran plot HERE

Secondary Structure

• Alpha helix structures HERE / HERE / HERE
  • Hydrogen bonding in alpha helix HERE
  • Ramachandran plot relative to helices HERE
  • Ferritin structure HERE
  • Coiled coil HERE
• Beta sheets
  • Beta strands - Ramachandran HERE / Structure HERE
  • Antiparallel beta sheets HERE / Parallel beta sheets HERE / Mixed beta sheets HERE
  • Views of a twisted beta sheet HERE
  • Fatty acid binding protein HERE
  • Reverse turn HERE
  • Loop structures HERE

Tertiary Structure

• Myoglobin
  • Ball and Stick HERE
  • Schematic view HERE
  • Amino acid distribution HERE
• Porin structure HERE
• CD4 structure HERE

Quaternary Structure

• Cro protein HERE
• Human hemoglobin HERE
• Rhinovirus HERE and HERE

Sequence and Structure

• Bovine ribonuclease HERE
• Reduction of disulfide bonds HERE
• Structure disrupters
  • Urea HERE
  • Guanidinium chloride HERE
  • Beta-mercaptoethanol HERE
• Reduction and denaturation of ribonuclease HERE
• Reducation and renaturation of ribonuclease HERE
• Amino acids and secondary structure tendency HERE
• Alternative conformations of a peptide sequence HERE
• Folding/unfoding transition HERE and HERE
• Typing monkeys HERE
• Modified side chains in proteins HERE
• Chemical rearrangement in GFP HERE / GFP localization HERE