CHEM 114A: Chapter 6 - Lecture 2

Recap – Levels of Protein Structure

• 4 hierarchical levels repeatedly referenced throughout the course:
– Primary → Secondary → Tertiary → Quaternary.
• Part 2 of Chapter 6 focuses on tertiary (overall 3-D fold) and then transitions to quaternary (multi-subunit assembly).

Tertiary Structure – Definition & Governing Forces

• 3-D fold results from the way individual secondary structures (α-helices, β-sheets, turns, coils) pack against each other.
• Amino acids that are far apart in the primary sequence can be neighbors in the tertiary fold.
• “Any intermolecular force that can be made will be made” – the protein relentlessly seeks maximum stability (minimum free energy).

Catalogue of Stabilizing Interactions

• Hydrogen bonding
– Backbone C=O···H–N between β-strands.
– Backbone–backbone H-bonds within α-helices or turns.
– Side-chain···side-chain or side-chain···backbone H-bonds.
• Hydrophobic interactions (e.g. Leu–Val clustering).
• Electrostatic / salt-bridge interactions between oppositely charged side chains; modulated by local dielectric constant.
• Van-der-Waals / London dispersion contacts (close-packing stabilization).
• Disulfide bonds (covalent S–S links between Cys residues).

General Folding Tendencies That Lower Free Energy

• Non-polar (hydrophobic) residues bury inside, away from water, to avoid high-energy water–hydrophobe contacts.
• Polar / charged residues usually lie on the surface where they can H-bond or ion-dipole interact with water.
– If an isolated charge is forced into the core, an oppositely charged partner must accompany it to neutralize the electrostatic penalty (dielectric argument).
• Disulfide bonds contribute in two ways:

1. Provide strong covalent stabilization.

2. Reduce conformational freedom, constraining the fold around fixed linkages.
   • Atoms pack tightly; internal cavities are minimal.
   – Prevents bulk solvent ingress that would disrupt hydrophobe burial.

Integral Membrane Proteins – Special Case

• Must traverse a hydrophobic lipid bilayer.
– Possess a hydrophobic trans-membrane segment (shown gray in lecture fig.).
– Hydrophilic N- or C-terminal domains project into cytosol and/or extracellular fluid.
• Not all follow the rule: Porin is an “inside-out” β-barrel.
– Hydrophobic residues face the membrane lipids; hydrophilic residues line a central aqueous pore for water/ion passage.
– Demonstrates context-dependent folding logic.

Motifs (Super-Secondary Structure Patterns)

• Recurrent, recognizable arrangements of α/β elements.
• Serve as building blocks; knowing motifs aids sequence-to-structure prediction (a major goal of protein design).
• Core examples shown in lecture:
– β–α–β motif (two β-strands linked by an α-helix).
– β-hairpin (strand–turn–strand).
– α–α motif (crossing helices connected by loop).

Structural Classification by Secondary-Structure Content

• Proteins often categorized as:
– α-proteins (mostly helices).
– β-proteins (mostly sheets).
– α/β-proteins (mixed).
• Average composition across globular proteins ≈ $31\%$ α-helix, $28\%$ β-sheet, remainder irregular coils/loops.

Eight-Stranded β-Barrels – Same Sheet Count, Different Folds

• Left: classic closed barrel.
• Middle: twisted barrel variant.
• Right: TIM barrel (named for triose-phosphate isomerase).
• Connectivity + sequence dictate distinct architecture and function, despite identical β-strand count.

Coils / Loops (Irregular Secondary Structure)

• Occur when successive residues do not share similar $\phi,\psi$ angles → no uniform helix or sheet.
• Typically surface-exposed; confer flexibility and dynamic motion.

Domains – Independent Folding Units within Large Chains

• Proteins >$200$ residues usually fold segregated “modules.”
• Each domain folds autonomously; overall protein stability is a sum of domain stabilities.
• Functional hotspots (ligand binding, catalysis) often reside at domain interfaces.

Quaternary Structure – Multi-Subunit Assembly

• Formed when two or more polypeptide chains associate into one functional complex.

Nomenclature

• Homodimer / homotrimer: identical chains.
• Heterodimer (αβ), heterotetramer, etc.: different chains.
• Example: Hemoglobin – $\alpha<em>1,\alpha</em>2,\beta<em>1,\beta</em>2$ → a heterotetramer.

Advantages of Oligomerization

1. Size increase via repeating subunits is more efficient than synthesizing one gigantic chain (avoids folding frustration).

2. Individual subunits can be regulated at the gene-expression level (on/off assembly control).

3. Independent genetic drift of each chain allows differential evolutionary optimization of function.

Symmetry in Quaternary Assemblies

• Nature favors aesthetically symmetric arrangements (parallels leaves, trees, fractals).

Cyclic Symmetry (Cₙ)

• $C<em>2$ – two identical subunits; 180° rotation ( $\frac{360^{\circ}}{2}$ ) yields identical view. • $C</em>3$ – three subunits; 120° rotation.
• $C_5$ – five subunits; 72° rotation.

Dihedral Symmetry (Dₙ)

• $D<em>2$ – three perpendicular 2-fold axes. • $D</em>3, D_4$ – increasingly complex perpendicular axes sets.

Higher Symmetries

• Tetrahedral, octahedral, icosahedral (e.g., viral capsids resemble icosahedra akin to a “buckyball”).
• Biochemists rarely push symmetry analysis as far as inorganic chemists, yet these principles underpin protein assembly.

Ethical / Practical Outlook

• Understanding tertiary/quaternary rules enables rational protein engineering (drug design, synthetic enzymes, membrane channels).
• Predict-fold-from-sequence remains a central “grand challenge” – motifs, domain logic, and symmetry knowledge are stepping-stones toward fully de-novo designed proteins.