CH 4 (L7)

Question 1

Domain classification

Answer 1

• all-alpha contains alpha helices (all-α)
• all-beta contains beta sheets (all-β)
• alpha/beta class contains regions with both that arise from alternations in the peptide chain (α/β)
• alpha + beta class have clusters of each that arise form different regions in the peptide (α + β)

Question 2

alpha + beta (α + β)

Answer 2

example: PDB 2PIL
neisseria gonorrhea pilin protein
- one of the subunits of the pili on the surface of the bacteria
- pili can function to adhere to surfaces
contains two distinct regions: a long alpha helix and a beta sheet

Question 3

Quaternary structure

Answer 3

• forms when 2 or more polypeptides come together: multiunit proteins
• individual units being the individual peptides that came together
• subunits are normally designated by greek letters and subscript numbers for how many units exist:
  α2βγ protein

example:
PDB1TIM Chicken gallus gallus triose phosphate isomerase (DHAP G3P),formed from two identical subunits, alpha helical bundles

example:
PDB 1DIF HIV-1 aspartic protease, cleaves polyprotein (Gag, Gag-Pol), required for infectivity, composed of two subunits that bind symmetrically, target of new HIV drugs, all-beta

example:
PDB1BL8 Streptomyces potassium channel protein
non-pathogenic (save plants) soil bacteria, break down matter, secrete large amounts of proteins, important source of antibiotics, composed of 4 identical subunits, is membrane-spanning, specific for the cationic K+ ion, alpha-helical bundle

example: PDB 2MS2 bacteriophage capsid protein, trimer of identical units, alpha and beta but mostly beta sheets

example: PDB 1BZY
Human HGPRT protein, involved in purine nucleotide salvage, multisubunit protein, 4 subunits - tetrametric protein made with 2 different types of subunits

Question 4

Multiunit proteins

Answer 4

• held together by non-covalent interactions (most common are hydrophobic and electrostatic forces)
• typically come as dimers, tetramers, or more with trimers being the most rare
• dyad symmetry is very common

Question 5

Multiunit Proteins

Answer 5

1. Oligomers are more stable than their constituents by themselves
2. Active sites are formed by residues from adjacent polypeptide chains
3. The conformation changes when ligand binds
4. Using the same subunits can make different proteins with different functions
5. Multiunit proteins can form part of a chain of enzymatic events