Protein Structure and Function

Overview

Proteins are essential biomolecules that perform a vast array of functions in living organisms. Their function is intimately related to their structure, which is organized into four hierarchical levels: primary, secondary, tertiary, and quaternary structure. Understanding these levels is fundamental to biochemistry.

Primary Structure of Proteins

Definition and Importance

• Primary structure refers to the linear sequence of amino acids in a polypeptide chain, read from the N-terminal (amino) end to the C-terminal (carboxyl) end.

• This sequence is unique for each protein and determines its three-dimensional conformation and biological function.

• Even a single amino acid change can significantly alter protein function, as seen in diseases like sickle-cell anemia (mutation in hemoglobin).

• Primary structure is routinely determined in biochemical research.

Example: The one-letter notation is often used to represent amino acid sequences for simplicity.

Secondary Structure of Proteins

Definition and Types

• Secondary structure refers to the local three-dimensional arrangements of the polypeptide backbone, stabilized mainly by hydrogen bonds.

• The two most common types are the α-helix and the β-pleated sheet.

α-Helix

• The α-helix is a right-handed coil where each backbone N-H group forms a hydrogen bond with the C=O group of the amino acid four residues earlier.

• There are 3.6 amino acids per turn, and the pitch (distance per turn) is 5.4 Å.

• Side chains project outward from the helix, minimizing steric hindrance.

• The peptide bond is planar and usually in the trans configuration.

Example: The α-helix is abundant in fibrous proteins like keratin.

Factors Disrupting the α-Helix

• Proline introduces a bend due to its cyclic structure and lack of an N-H group for hydrogen bonding.

• Electrostatic repulsion between like-charged side chains (e.g., Lys and Arg, Glu and Asp) can destabilize the helix.

• Steric crowding from bulky side chains (e.g., Val, Ile) can also disrupt the helix.

• Glycine provides high conformational flexibility, which can destabilize the helix.

β-Pleated Sheet

• Composed of β-strands lying adjacent to each other, forming a sheet-like structure.

• Strands can be parallel or antiparallel.

• Hydrogen bonds form between backbone atoms of adjacent strands, perpendicular to the direction of the strands.

• Side chains alternate above and below the plane of the sheet.

Example: Silk fibroin is rich in β-sheets.

Turns and Loops

• Turns (especially β-turns) and loops connect secondary structure elements and allow the polypeptide chain to reverse direction.

• Often stabilized by hydrogen bonds; glycine and proline are commonly found in turns.

Tertiary Structure of Proteins

Definition and Stabilizing Interactions

• Tertiary structure is the overall three-dimensional arrangement of all atoms in a single polypeptide chain.

• Stabilized by various interactions:

  • Hydrogen bonds between polar side chains (e.g., Ser, Thr).

  • Hydrophobic interactions among nonpolar side chains (e.g., Val, Ile).

  • Electrostatic attractions between oppositely charged side chains (e.g., Lys and Glu).

  • Electrostatic repulsions between like-charged side chains.

  • Covalent disulfide bonds between cysteine residues.

• Proteins can be classified as fibrous (elongated, structural roles) or globular (compact, functional roles).

Example: Myoglobin is a globular protein with a compact tertiary structure.

Quaternary Structure of Proteins

Definition and Examples

• Quaternary structure refers to the association of multiple polypeptide chains (subunits) into a functional protein complex.

• Stabilized by the same types of interactions as tertiary structure.

• Examples include hemoglobin (α2β2 tetramer) and collagen (triple helix).

Ligand Binding and Cooperativity

Protein-Ligand Interactions

• Proteins often bind small molecules (ligands) reversibly and specifically at binding sites.

• The fraction of bound protein is given by:

• Where is the concentration of protein-ligand complex, is free protein.

• The dissociation constant is defined as:

• At , half of the protein binding sites are occupied ().

Cooperativity

• Some proteins with multiple binding sites exhibit cooperativity, where binding of one ligand affects the affinity for subsequent ligands.

• Positive cooperativity: binding increases affinity at other sites (e.g., hemoglobin and O2).

• Negative cooperativity: binding decreases affinity at other sites.

• No cooperativity: binding sites act independently (e.g., myoglobin).

• The Hill equation describes cooperative binding:

• Where is the Hill coefficient (degree of cooperativity).

Examples: Myoglobin and Hemoglobin

• Myoglobin: Single polypeptide, binds O2 non-cooperatively, hyperbolic binding curve.

• Hemoglobin: Tetrameric, binds O2 cooperatively, sigmoidal binding curve.

• Hemoglobin's function is regulated by pH (Bohr effect), CO2, and 2,3-bisphosphoglycerate (BPG).

Summary Table: Levels of Protein Structure

Additional info:

• Protein folding is a spontaneous process driven by the hydrophobic effect, where nonpolar residues are buried in the core and polar residues are exposed to the aqueous environment.

• Chaperone proteins assist in the correct folding of other proteins.

• Denaturation is the loss of structural order and biological activity, caused by changes in pH, detergents, or chemicals like urea.