Protein Structure: Primary and Secondary

• Protein structure is determined by the sequence of amino acids and can be described at four levels: primary, secondary, tertiary, and quaternary.
• Proteins can be divided into functional or structural domains that are independently folding sub-regions within the protein sequence.
• Polypeptide chains often exist as highly ordered, 3D structures.
• The 3D structure of a protein determines its function.

Primary Structure

• The primary structure consists of a linear sequence of amino acid residues.
• The mRNA code determines the primary structure.
• The primary structure, combined with a protein's environment, determines secondary, tertiary, and quaternary structures.

Secondary Structure

• Secondary structure involves the folding and twisting of the peptide backbone.
• Weak hydrogen bonds between C=O (carbonyl) and N-H (amine) groups in the backbone hold it together.
• R-groups protrude from the backbone.
• Alpha helices and beta sheets are two well-known secondary structures.

Alpha Helix

• The alpha helix has a rigid cylindrical structure.
• Forms when hydrogen bonding occurs between C=O and N-H groups that are four amino acids apart on the polypeptide backbone.
• Coiling happens in a clockwise direction down the length of the chain.

Beta Sheet

• The beta sheet has a flat, sheet-like structure.
• Forms when hydrogen bonding occurs between C=O and N-H groups on adjacent polypeptide chains.
• Adjacent chains can run parallel (N-terminal to C-terminal).
• Adjacent chains can run antiparallel (in opposite directions).
• Rigid proline residues insert a "kink" in a protein's backbone and disrupt secondary structures.

Tertiary Structure

• Tertiary structure involves the 3D arrangement of secondary structures.
• It is mostly held together by noncovalent attractions between R-groups and between R-groups and the surrounding environment (i.e., aqueous or hydrophobic lipid bilayer interior).
• R-group interactions lead to the folding of secondary structures into 3D structures.
• Unstructured loops (aka random coils) link secondary structures together.
• Covalent disulfide bonds can form between cysteine residues to cross-link parts of the polypeptide backbone.

Protein Folding

• 3D folding of proteins results in structures that assume the lowest possible energy state.
• Protein stability depends on the free energy change between the folded and unfolded states (ΔG = GFOLDED - GUNFOLDED).
• Proteins become more stable as GUNFOLDED > GFOLDED
• 3D folding is not rapid for all proteins.
• Many proteins require "molecular chaperones" called chaperonins that provide an isolated chamber for folding.
• Prions are proteins alone that cause some unusual contagious neurological diseases.
• Prion proteins can adopt an alternative folded state.
• Abnormally folded proteins cause normally folded protein misfolding.

Protein Domains

• A protein "domain" is a region of the protein that folds independently of other regions.
• A protein can have single or multiple domains.
• A domain often represents a functional region of the protein, so proteins can be thought of as modular, built up from a "toolbox" of domains.
• Different domains of a protein often have different functions.
• Catalytic domain inhibits host cell protein synthesis
• Receptor binding domain attaches to cell surface.
• Hydrophobic domain inserts into membranes.
• Similar domains that occur in many related proteins are called motifs, like a DNA-binding motif.
• Two DNA-binding proteins separated by billions of years of evolution share the same DNA-binding domain structure with three alpha-helices

Quaternary Structure

• Quaternary structure is the arrangement of multiple tertiary structures.
• Quaternary structure is held together by weak bonds and some disulphide bonds
• Homomers are structures of identical subunit polypeptides
• Heteromers are structures of different subunit polypeptides
• It can be simple, like hemoglobin (two copies each of two subunits), or complex, like RNA polymerase II (17 subunits, 11 different polypeptide chains)