26.9 Protein Structure

Protein Structure

Proteins carry out nearly every task in a living organism, and their function depends entirely on their three-dimensional shape. That shape emerges from four hierarchical levels of structure, each building on the one before it. This section covers those four levels, the specific forces that stabilize them, and what happens when that structure falls apart.

Four Levels of Protein Structure

Primary structure is the linear sequence of amino acids in a polypeptide chain, linked together by peptide bonds. This sequence is dictated by the gene encoding the protein, and even a single amino acid change can alter function dramatically (as in sickle-cell hemoglobin, where one glutamate is replaced by valine).

Secondary structure refers to local folding patterns that arise from hydrogen bonds between backbone atoms (specifically, between $\text{C=O}$ and $\text{N–H}$ groups). The two main types are alpha helices and beta-pleated sheets. These patterns form in short stretches of the chain before the protein adopts its full 3D shape.

Tertiary structure is the overall three-dimensional shape of a single polypeptide chain. It results from interactions between amino acid side chains (R groups), not just backbone atoms. This is the level that gives enzymes their active-site geometry and antibodies their binding specificity. Many proteins also contain distinct domains, which are independently folding structural or functional units within the same chain.

Quaternary structure describes how two or more folded polypeptide chains (subunits) assemble into a larger functional complex. Not every protein has quaternary structure. Hemoglobin is a classic example: it consists of four subunits (two alpha and two beta chains) that must associate correctly for proper oxygen transport. The interactions holding subunits together are the same types found in tertiary structure.

Alpha Helices vs. Beta-Pleated Sheets

These are the two dominant forms of secondary structure, and they differ in geometry, hydrogen-bonding pattern, and where you'll find them.

• Alpha helices
  • The polypeptide backbone coils into a right-handed spiral
  • Hydrogen bonds form between the $\text{C=O}$ of residue n and the $\text{N–H}$ of residue n+4, running roughly parallel to the helix axis
  • Each turn contains 3.6 amino acid residues with a rise of 1.5 Å per residue
  • Common in both globular proteins (myoglobin) and fibrous proteins (alpha-keratin in hair and nails)
• Beta-pleated sheets
  • The polypeptide chain adopts an extended, zigzag conformation with residues spaced about 3.5 Å apart
  • Hydrogen bonds form between backbone atoms of adjacent strands, running perpendicular to the chain direction
  • Strands can be parallel (all N-termini pointing the same way) or antiparallel (N- and C-termini alternating), with antiparallel sheets having slightly stronger, more linear hydrogen bonds
  • Found in silk fibroin (almost entirely beta-sheet) and in the structural core of many globular proteins like immunoglobulins

Forces That Stabilize Tertiary Structure

Tertiary structure depends on interactions between the R groups (side chains) of amino acids, often between residues that are far apart in the primary sequence but close together in 3D space. Five main types of interactions contribute:

• Hydrogen bonds form between polar side chains, or between side chains and backbone atoms
• Disulfide bridges are covalent bonds ($\text{–S–S–}$) formed by oxidation of two cysteine residues; these are the strongest stabilizing interaction in tertiary structure (e.g., the two chains of insulin are held together partly by disulfide bonds)
• Ionic interactions (salt bridges) occur between positively charged side chains (Lys, Arg) and negatively charged ones (Asp, Glu)
• Hydrophobic interactions drive nonpolar side chains into the protein interior, away from water; this is often the single largest driving force in folding
• Van der Waals forces arise from the close packing of atoms in the protein core; individually weak, but collectively significant

Denaturation

Denaturation is the loss of a protein's secondary, tertiary, and (if present) quaternary structure while the primary sequence remains intact. The peptide bonds don't break, but the noncovalent interactions and sometimes disulfide bridges are disrupted.

Common denaturing conditions:

1. Heat increases molecular motion, breaking hydrogen bonds and hydrophobic interactions (think of egg whites turning opaque when cooked)
2. Extreme pH alters the charge on ionizable side chains, disrupting salt bridges and hydrogen bonds
3. Chemical agents like urea and detergents interfere with hydrophobic interactions or hydrogen bonding

Denaturation typically destroys biological function (an enzyme loses catalytic activity, for instance). Some small proteins can refold spontaneously when denaturing conditions are removed, a process called renaturation. However, many larger proteins cannot refold on their own and require assistance.

Protein Folding and Misfolding

How a polypeptide chain finds its correct 3D shape is one of the central questions in biochemistry. The amino acid sequence contains all the information needed to fold, but the process is not always straightforward.

• Chaperone proteins (such as the GroEL/GroES system in bacteria and Hsp70 in eukaryotes) assist folding by providing a sheltered environment that prevents the polypeptide from aggregating with other molecules before it reaches its native state
• Misfolded proteins can expose hydrophobic regions that are normally buried, causing them to stick together and form insoluble aggregates
• Prions are a striking example of misfolding: a misfolded form of the prion protein ($\text{PrP}^{\text{Sc}}$) can template its abnormal conformation onto normally folded copies ($\text{PrP}^{\text{C}}$), propagating the misfolded state and leading to neurodegenerative diseases such as Creutzfeldt-Jakob disease