Protein Structure and Peptide Bonds

Protein Structure

• Proteins are composed of amino acids linked by peptide bonds.
• Proteins have four levels of structure: primary, secondary, tertiary, and quaternary.

Primary Structure

• The sequence of amino acids in a protein is called the primary structure.
• Amino acids are joined by peptide bonds, which are amide linkages.
• Peptide bonds are strong and not easily broken by heat or urea concentrations.
• Peptide bonds are hydrolyzed by prolonged exposure to strong acids, bases, or high temperatures.

Naming Peptides

• A peptide is two or more amino acids linked by a peptide bond.
• The free amino end is the N-terminal, and the free carboxyl end is the C-terminal.
• Amino acid sequences are read from the N-terminal to the C-terminal.
• Each amino acid in a polypeptide chain is called a residue.

Characteristics of Peptide Bonds

• Peptide bonds have a partial double bond character, making them shorter and rigid than single bonds.
• They are planar, with no free rotation around the carbonyl carbon and amide nitrogen.
• They are typically in the trans-configuration due to steric interference between the R-groups of amino acids.

Polarity of Peptide Bonds

• The -C=O and -NH groups of the amide linkage are uncharged and do not accept or release protons.
• These groups are polar and can participate in hydrogen bonds.
• The only charged groups on a polypeptide are the N-terminal α-amino group, the C-terminal α-carboxyl group, and ionized groups in the side chains of amino acids.

Secondary Structure

• The polypeptide chain forms regular arrangements of amino acids located near each other.
• Three major secondary structures include the α-helix, β-sheet, and β-bend.

The α-Helix

• The α-helix is a spiral structure with a coiled polypeptide backbone.
• Amino acid side chains extend outward from the central axis to avoid steric interference.
• The α-helix is stabilized by hydrogen bonding between peptide-bond carbonyl oxygens and amide hydrogens.
• These hydrogen bonds are parallel to the helix, extending from the carbonyl oxygen of one peptide bond to the -NH group of the peptide bond four residues ahead.
• Each turn of the α-helix contains 3.6 amino acids.
• Certain amino acids can disrupt the α-helix, including proline (due to its secondary amino group), charged amino acids, and bulky or branched side chains.

The β-Sheet

• In the β-sheet, all peptide bond components are involved in hydrogen bonding.
• The surface of the β-sheet is pleated.
• Two or more polypeptide chains are arranged in an almost fully extended form.
• Hydrogen bonds form between the carbonyl oxygen and amide hydrogen of two adjacent polypeptides.
• β-sheets can be parallel or antiparallel, depending on the arrangement of the N- and C-termini of the polypeptide chains.

β-Bends (Reverse Turns)

• β-bends reverse the direction of the polypeptide chain.
• They are commonly found on the surface of proteins and often connect successive strands of parallel β-sheets.
• β-bends usually consist of four amino acids, with proline and glycine frequently found.

Nonrepetitive Secondary Structures

• Approximately half of proteins are organized into repetitive structures like α-helices and β-sheets.
• The remaining polypeptide chain has a loop or coil conformation called a "nonrepetitive secondary structure."
• Coils and loops are not random but have less repetitive structure than helices and sheets.

Supersecondary Structures (Motifs)

• Supersecondary structures are formed from the combination of different secondary structures (α-helices, β-sheets, and nonrepetitive sequences).
• These structures are connected by β-bends and are stabilized by interactions between side chains from adjacent secondary structures.
• Supersecondary structures that occur consistently in different proteins are called motifs.

Tertiary Structure

• Tertiary structure refers to the folding of domains and the final arrangement of domains.
• Globular proteins are compact with a high-density core.
• Hydrophobic side chains are buried in the interior of the protein, while hydrophilic groups are on the surface.

Tertiary Structure Domains

• Domains are functional units of polypeptides.
• Polypeptide chains longer than 200 amino acids consist of two or more domains.
• Each domain is structurally independent from other domains on the polypeptide chain.

Interactions Stabilizing Tertiary Structure

• Four types of interactions stabilize tertiary structure: disulfide bonds, hydrophobic interactions, hydrogen bonds, and ionic interactions.
• Disulfide bonds: Covalent bonds formed by the oxidation of -SH groups from two cysteine residues, creating cystine.
• Hydrophobic interactions: Interactions between amino acids with non-polar side chains, driving them to the interior of the protein.
• Hydrogen bonds: Formed between amino acid side chains with oxygen- or nitrogen-bound hydrogen and electron-rich atoms.
• Ionic interactions: Interactions between negatively charged groups (Asp or Glu) and positively charged groups (Lys).

Protein Folding

• Interactions between side chains of amino acids determine how a polypeptide chain folds into a three-dimensional shape.
• Proteins fold to attain a low-energy state, facilitated by attractions between opposite charges, aggregation of hydrophobic side chains, and hydrogen bonds.
• Protein folding often begins as the polypeptide chain is being synthesized to prevent misfolding.

Role of Chaperones in Protein Folding

• Chaperones (heat-shock proteins) are involved in the correct folding of proteins.
• They interact with the polypeptide at different stages of the folding process.
• Functions of chaperones include:
  • Keeping the protein unfolded until synthesis is finished.
  • Acting as catalysts to increase the rate of protein folding.
  • Protecting unfolded portions of the protein as they fold, preventing misfolding.

Quaternary Structure

• Monomeric proteins consist of a single polypeptide folded into secondary and tertiary structure.
• Quaternary structure describes proteins with two or more polypeptides, called subunits.
• Subunits are held together by non-covalent interactions like hydrogen bonds, ionic bonds, and hydrophobic interactions.
• Subunits can function cooperatively or independently.

Isoforms

• Isoforms are proteins that have the same function but are encoded by different genes and have different primary structures.

Protein Denaturation

• Denaturation is the unfolding of protein secondary and tertiary structure without hydrolysis of peptide bonds.
• Denaturing agents include heat, organic solvents, detergents, acids, bases, and heavy metals.
• Denatured proteins are usually permanently disordered and insoluble.

Protein Misfolding

• Improperly folded proteins are usually degraded in the cell.
• Accumulation of misfolded proteins can lead to disease.
• Amyloidoses are a group of diseases caused by the aggregation of amyloids, which are fibrillar proteins composed of β-sheets.
• Amyloid accumulation is implicated in diseases like Alzheimer's disease.