Protein Structure: Primary and Secondary

Primary Structure

• The primary structure of a protein refers to the sequence of amino acids in a polypeptide chain, read from the N-terminal end to the C-terminal end.
• It is the linear amino acid sequence from N- to C-terminal end.

Secondary Structure

• The secondary structure of a protein refers to local conformations, maintained by extensive H-bonding that involves components of the peptide bond.
• There are two major kinds of secondary structures found in proteins: α-helices and β-sheets.
• α-helix: a helical structure formed by a regular pattern of hydrogen bonds between the amide N-H and C=O groups of amino acids that are near each other in the primary sequence.
• In an α-helix, the C=O of one amino acid is hydrogen bonded to the N-H of an amino acid that is four down the chain.
• The pattern of H-bonds pulls the polypeptide chain into a helical structure, with each turn containing 3.6 amino acids.
• The turn repeat distance is 5.4Å (1 Å = 0.1 nm).
• Factors that can disrupt an α-helix include proline, strong electrostatic repulsion, and steric crowding.
• β-pleated sheet: a sheet-like structure formed by polypeptide chains lying adjacent to one another, with hydrogen bonds forming between the backbone of sheets.
• R groups alternate, first above and then below the plane, and extend above and below the plane of the sheet.

Super-Secondary Structures

• Examples of super-secondary structures include β-α-β, α-α, β-meander, Greek key, and β-barrels.
• Two ways to represent protein structures are space-filling models and ribbon structures.

Tertiary Structure

• The tertiary structure of a protein describes the completely folded and compacted polypeptide chain.
• It is stabilized by interactions of amino acid side chains in non-neighboring regions of the polypeptide chain.
• There are several types of tertiary structures, including globular and fibrous proteins.
• Globular proteins are often approximated as spheres, tend to be water soluble, and have polar side chains on the exterior and non-polar side chains inside.
• Fibrous proteins are often strong, insoluble, and have structural roles, with examples including keratin and collagen.

Tertiary Structure Forces

• Non-covalent forces that stabilize tertiary structures include H-bonding, electrostatic interactions, and hydrophobic interactions.
• Covalent forces include disulfide bonds.

Quaternary Structure

• The quaternary structure of a protein refers to the association of multiple polypeptide chains.
• Examples include hemoglobin, which has four sub-units labeled α and β.
• Hemoglobin exhibits cooperativity, and the binding of oxygen is affected by pH and CO2 levels.

Comparison of Hemoglobin and Myoglobin

• Myoglobin is found in muscle and tissue, has no quaternary structure, and binds one oxygen molecule.
• Hemoglobin is found in blood, has a quaternary structure, and binds four oxygen molecules.

The Bohr Effect

• The Bohr effect refers to the decrease in oxygen binding affinity of hemoglobin in response to increased CO2 and H+ levels.
• In actively metabolizing tissue, hemoglobin releases oxygen and binds CO2 and H+.
• In the lungs, hemoglobin releases CO2 and H+ and binds oxygen.

Structure Determination

• Methods of protein structure determination include X-ray diffraction of protein crystals, multi-dimensional nuclear magnetic resonance of proteins in solutions and membranes, and cryo-electron microscopy.

Denaturation of Proteins

• Denaturation refers to the loss of structural order that gives a protein its biological activity.
• Causes of denaturation include pH changes, mercaptoethanol, detergent, heat, and urea/guanidine.
• Denaturation may or may not be reversible, and errors in folding can contribute to diseases.

Protein Folding

• The hydrophobic effect refers to the reduction of entropy as non-polar species in water reduce entropy.
• Globular proteins have hydrophobic residues inside, and membrane proteins have hydrophobic residues in the membrane interior.
• Protein folding chaperones are part of a quality control system that aims to ensure proper protein folding or restore proteins that have become misfolded.

Molten Globule

• A molten globule is a third phase of proteins, characterized by a native-like secondary structure content but without the tightly packed protein interior.
• It was first found in cytochrome c under low pH and high salt concentration.