What is the hierarchy of protein structure?
Primary → Secondary → Motif (Supersecondary) → Tertiary → Quaternary → Supramolecular complexes.
What defines primary structure?
Linear sequence of amino acids (N-terminal → C-terminal); determines all higher-order folding.
What stabilizes secondary structures?
Hydrogen bonds between backbone atoms (N–H → C=O).
Key features of α-helices?
Spiral with 3.6 residues/turn; N–H of residue n → C=O of residue n+4; side chains point outward; proline disrupts helix.
Key features of β-strands and β-sheets?
β-strands: short, extended. β-sheets: 2+ strands hydrogen-bonded, parallel or antiparallel; side chains alternate above/below plane.
What is a motif?
Combination of 2+ secondary structures forming a recurring 3D pattern in multiple proteins, often linked to function.
Examples of motifs and their functions?
EF-hand: helix–loop–helix, binds calcium; Zinc-finger: α-helix + 2 β-strands + zinc ion, binds DNA/RNA; β–α–β loop, hairpin (β–β), helix–turn–helix, Greek key; Coiled-coil: 2–4 α-helices coiled, hydrophobic residues stabilize interface; found in structural proteins and TFs.
Definition & stabilizing forces of tertiary structure?
Overall 3D fold of a polypeptide; stabilized by hydrophobic effect, van der Waals, hydrogen bonds, ionic interactions, disulfide bonds.
What is the oil-drop model?
Hydrophobic residues cluster in the core, hydrophilic residues exposed; folding driven by entropy increase (water release).
What are domains?
Independent folding units with distinct structure/function; can often function when isolated; modular.
Example of tertiary structure in GFP?
β-barrel of 11 β-sheets around central α-helix; chromophore forms via post-translational modification; α-helices at ends stabilize.
Definition of quaternary structure?
Assembly of multiple polypeptide chains (subunits) into a functional complex; subunits held by noncovalent interactions.
Example: Influenza Hemagglutinin?
Trimer of HA1 + HA2 subunits; each subunit from HA0 cleavage; noncovalent interactions + disulfide bonds stabilize complex.
What are supramolecular complexes?
Large molecular machines made of multiple proteins (each possibly multimeric), e.g., transcription initiation complex.
X-ray crystallography principle & limitations?
Crystallized proteins exposed to X-rays → diffraction → electron density map → atomic model. Limitations: crystallization needed, time-consuming, some proteins difficult to crystallize.
Cryo-EM principle & advantages?
Flash-frozen proteins imaged with electrons; no crystallization; good for large complexes.
AI-based prediction advantages & limitations?
Rapid prediction from sequence; predicts interactions; not 100% reliable; complements experimental methods.
How do you “zoom in” from quaternary to primary structure?
Quaternary → subunit → tertiary fold → domains → motifs → secondary structures → primary amino acid sequence.
Analogy for hierarchy?
Primary = shoelace; Secondary = curls/zigzags; Motif = assembled curls; Tertiary = 3D folded shoelace; Quaternary = multiple folded shoelaces forming functional complex.
