Chapter 4: The Three-Dimensional Structure of Proteins

Vocabulary flashcards covering key terms and concepts from the lecture notes on protein structure.

Native Fold

The specific three-dimensional conformation adopted by protein molecules; has a large number of favorable interactions within the protein.

Hydrophobic Effect

The aggregation of hydrophobic groups to hide their surface from water, creating a structured solvation layer around the molecule.

van der Waals/London Dispersion

Attractive force due to induced dipoles in all atoms; important to the stability in the interior of the protein.

Hydrogen Bonds

Interaction of N-H and C=O of the peptide bond leading to local regular structures such as a-helices and b-sheets; maximized in protein structure.

Ionic Interactions

Long-range strong interactions between permanently charged groups; salt-bridges, especially buried in the hydrophobic environment, strongly stabilize the protein.

Disulfide Bridge

Covalent bond between two sulfur atoms, usually on cysteine residues. Generally not found in reducing environment of cell, mostly in secreted proteins.

Peptide Bond

The chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid. Structure of the protein is partially dictated by the peptide bond, which is a partial double bond.

Phi Angle (Φ)

Angle around the a-carbon:amide nitrogen bond.

Psi Angle (Ψ)

Angle around the a-carbon:carbonyl carbon bond.

Secondary Structure

Local spatial arrangement of the polypeptide backbone. Two regular arrangements are common: the a helix and the b sheet.

Alpha Helix

Helical backbone is held together by hydrogen bonds between the backbone amides of an n and n+4 amino acids, maximizes bonds. Right-handed helix with 3.6 residues (5.4 Å) per turn.

Beta Sheet

Sheet-like arrangement of backbone is held together by hydrogen bonds between the backbone amides in different strands. Side chains protrude from the sheet alternating in up and down direction.

Beta Turns

Occur frequently whenever strands in b sheets change the direction. The 180° turn is accomplished over four amino acids.

Tertiary Structure

Overall spatial arrangement of atoms in a protein (as opposed to just nearby atoms). Stabilized by numerous weak and strong interactions between amino acid side chains, often far apart in primary sequence.

Fibrous Proteins

Proteins with long and narrow shape, structural role, (generally) insoluble in water, repetitive amino acid sequence.

Globular Proteins

Proteins with rounded/spherical shape, functional role, (generally) soluble in water, irregular amino acid sequence.

Collagen

Part of extracellular matrix (ECM), stronger than steel. Unique left-handed secondary structure of three chains twisted about each other in a superhelical right-handed triple helix.

Silk Fibroin

Main protein in silk, antiparallel b sheet structure. Small side chains (Ala and Gly) allow the close packing of sheets. Structure is stabilized by hydrogen bonding within sheets and London dispersion interactions between sheets.

Myoglobin

Globular protein. Single chain of 153 aa (16.7 kDa). Stores oxygen, allows consistent diffusion by contracting muscle, allows mammals to dive for long periods

Quaternary Structure

Formed by the assembly of individual polypeptides (subunits) into a larger functional cluster. Multimer, oligomer

Protein Denaturation

Loss of structural integrity with accompanying loss of activity.

Chaperones

Proteins that assist in protein folding and prevent misfolding.

Amyloidosis

Deposition of fibrils throughout the body (80+). Results from protein misfolding.

Prions

Misfolded proteins that can transmit their misfolded shape to normal variants of the same protein.