Amino Acids, Peptides, and Proteins: Structure and Folding

Amino Acids, Peptides, and Proteins: Structure and Folding

Introduction to Protein Structure

Proteins are complex macromolecules composed of amino acids linked by peptide bonds. Their structure is hierarchical, progressing from the linear sequence of amino acids (primary structure) to complex folded forms (secondary, tertiary, and quaternary structures) that determine their biological function.

• Primary Structure: The linear sequence of amino acids in a polypeptide chain.

• Secondary Structure: Local folding patterns such as alpha helices and beta sheets.

• Tertiary Structure: The overall three-dimensional shape of a single polypeptide chain.

• Quaternary Structure: The assembly of multiple polypeptide chains into a functional protein complex.

• Analogy: Like a piece of wire (unfolded, non-functional) becoming a paperclip (folded, functional), a polypeptide chain must fold correctly to become a functional protein.

Polypeptide Backbone and Peptide Bonds

Formation and Identification of the Peptide Backbone

The peptide backbone is the repeating sequence of atoms that forms the core of a polypeptide chain, connecting amino acids from the N-terminus to the C-terminus.

• Peptide Bond Formation: Amino acids join via condensation reactions, forming peptide bonds and releasing water.

• Backbone Structure: The backbone consists of repeating units: N (amide nitrogen) – Cα (alpha carbon) – C (carbonyl carbon).

• Directionality: Polypeptides are always written from the N-terminus (amino end) to the C-terminus (carboxyl end).

• Example: $\text{Amino Acid}_1 + \text{Amino Acid}_2 \rightarrow \text{Dipeptide} + \text{H}_2\text{O}$

Torsion (Dihedral) Angles in Polypeptides

Types of Bonds and Associated Angles

Three types of bonds repeat in a polypeptide, each associated with a specific torsion angle:

• Amide Nitrogen (NH) to Alpha-Carbon (Cα): Phi (Φ) angle

• Alpha-Carbon (Cα) to Carbonyl Carbon (C=O): Psi (Ψ) angle

• Carbonyl Carbon (C=O) to Amide Nitrogen (NH): Omega (Ω) angle (peptide bond)

Phi (Φ) and Psi (Ψ) Angles

These angles describe the rotation around single bonds in the backbone and are crucial for protein folding.

• Phi (Φ): Rotation around the bond between the amide nitrogen and the alpha-carbon. Single bonds allow 360° rotation.

• Psi (Ψ): Rotation around the bond between the alpha-carbon and the carbonyl carbon. Also allows 360° rotation.

• Newman Projections: Used to visualize the stereochemistry and steric interactions for Phi and Psi angles.

• Example: $\text{Phi (Φ): N–C_\alpha}$ $\text{Psi (Ψ): C_\alpha–C}$

Omega (Ω) Angle and Peptide Bond Planarity

The omega angle describes rotation around the peptide bond, which is restricted due to resonance.

• Peptide Bond Resonance: The peptide bond is a resonance hybrid, giving it partial double bond character and making it planar.

• Limited Rotation: Omega angle is typically found in either cis or trans configurations, with trans being more common.

• Example: $\text{Resonance:} \quad \ce{R-C(=O)-NH-R' \leftrightarrow R-C(-O^-)=NH^+-R'}$

Ramachandran Plot and Steric Constraints

Ramachandran Experiment and Plot

The Ramachandran plot visualizes the allowed and disallowed combinations of Phi and Psi angles in polypeptides, based on steric hindrance.

• Degrees of Freedom: Each residue theoretically has 360° of rotation for both Phi and Psi, but steric clashes restrict these angles.

• Ramachandran Plot: Shows regions of high, medium, and low frequency for angle combinations. Most combinations are rarely observed due to steric hindrance.

• Bulky Side Chains: Large amino acid side chains further restrict allowed angles.

Frequency	Region on Plot
High	Alpha helix, Beta sheet regions
Medium	Some coil regions
Low	Clashing/sterically forbidden regions

Secondary Protein Structures

Types of Secondary Structures

Polypeptides commonly fold into three types of secondary structures: alpha helices, beta sheets, and random coils.

• Alpha (α) Helix: A coiled structure stabilized by hydrogen bonds between every fourth amino acid. Side chains point outward.

• Beta (β) Sheet: Extended strands connected by hydrogen bonds. Can be parallel or antiparallel.

• Random Coil: Irregular, non-repetitive structure.

Beta Sheets: Parallel and Antiparallel

Beta sheets are stabilized by hydrogen bonds between backbone atoms of adjacent strands.

Type	Phi (Φ)	Psi (Ψ)
Parallel	-119	113
Antiparallel	-139	135

• Hydrogen Bonding: Beta strands are held together by hydrogen bonds, which stabilize the sheet structure.

• Example: $\ce{C=O \cdots H-N}$ hydrogen bonds between strands.

Alpha Helices

• Structure: Right-handed coil with ~3.6 residues per turn.

• Hydrogen Bonding: Each amino acid forms a hydrogen bond with the one four residues ahead.

• Side Chains: Project outward from the helix, minimizing steric clashes.

Role of Proline in Protein Structure

Proline is a unique amino acid that introduces kinks into polypeptide chains due to its cyclic structure.

• Structure: Proline's side chain forms a ring with the backbone nitrogen, restricting rotation around the Phi angle.

• Impact: Proline disrupts alpha helices and cannot participate in backbone hydrogen bonding, often introducing bends or kinks.

• Example: Proline-induced kinks in alpha helices.

Protein Folding: Tertiary and Quaternary Structure

Tertiary Structure

The tertiary structure is the overall three-dimensional shape of a single polypeptide chain, stabilized by various interactions.

• Stabilizing Forces: Hydrogen bonds, ionic bonds, disulfide bonds, hydrophobic interactions, and van der Waals forces.

• Example: Folding of a polypeptide into a globular protein.

Quaternary Structure

Quaternary structure arises when multiple polypeptide chains (subunits) assemble into a functional protein complex.

• Complex Formation: Subunits may be identical or different, and can include inorganic or organic cofactors.

• Example: Hemoglobin, an active enzyme complex with iron ions as cofactors.

Quaternary Structure Component	Example
Inorganic Cofactor	Iron ion in hemoglobin
Organic Cofactor	NAD in polymerases

Summary of Key Concepts

• Peptide bonds are planar due to resonance, restricting rotation (omega angle).

• Phi and Psi angles allow rotation but are limited by steric hindrance, as shown in the Ramachandran plot.

• Secondary structures (alpha helices and beta sheets) are stabilized by backbone hydrogen bonding and specific torsion angles.

• Proline introduces kinks and disrupts regular secondary structures.

• Tertiary and quaternary structures result from cumulative interactions, leading to functional proteins.

Additional info: The notes include references to molecular visualization tools (Molvis) and highlight the importance of steric effects and hydrogen bonding in protein folding.