Protein Structure

How are the 20 amino acids organized into polypeptides consisting of peptide bonds?

● Proteins are polypeptides consisting of amino acids covalently linked together by peptide bonds. Peptide bonds are formed by a condensation reaction between the carboxylic acid group of one amino acid and the amine group of a second amino acid.

● Twenty different amino acids are commonly found in proteins. Their stereochemistry is that of L-amino acids with a Cα chiral center, except for glycine, the smallest of the 20 amino acids, which has a Cα that is not chiral.

● The chemical properties of the amino acid side chains determine the structure and function of proteins. The 20 amino acids can be divided into four chemical groups on the basis of shared properties: charged, hydrophilic, hydrophobic, and aromatic.

● The peptide bond is rigid with partial double bond characteristics and defines a flat plane containing six atoms. Rotation around the N-Cα and the Cα-C bonds is defined by the ϕ (phi) and ψ (psi) torsional angles, respectively. Rotation is limited by steric hindrance of amino acid functional groups, as shown by a Ramachandran plot.

What are the 1º, 2º, 3º and 4º hierarchical structures of proteins?

● The three-dimensional structure of a protein is defined by four hierarchical levels: primary (amino acid sequence), secondary (α helix, β sheet, β turn), tertiary (positions of all atoms within the protein), and quaternary (subunit interactions).

● α helices are stabilized by intrastrand hydrogen bonding between N-H and C=O groups along the polypeptide backbone. β sheets are stabilized by interstrand hydrogen bonding between N-H and C=O groups along the polypeptide backbone.

● Tertiary structures are stabilized by weak noncovalent interactions and describe the positions of all the atoms within the polypeptide. The arrangements of α helices, β sheets, β turns, and polypeptide loops compose the protein fold. Examples of folds include four-helix bundles, the Greek key fold, and the Rossmann fold.

● Quaternary structures consist of two or more protein subunits that can be identical or different. Quaternary structures provide increased structural integrity (as demonstrated in fibrous proteins), regulatory functions commonly found in large protein complexes, and increased enzyme efficiency provided by nearby catalytic sites.

What are the mechanisms of protein folding and what happens when proteins are misfolded?

● High-fidelity protein folding is critical to protein structure and function and is governed by three principles: (1) protein folding must follow a preferred path of energy minimization; (2) the change in free energy between the folded and unfolded states must be favorable (delta G < 0) for folding to occur; and (3) mechanisms of in vitro and in vivo folding may be different, because chaperone proteins are often required for in vivo protein folding to occur.

● Protein folding in vitro is a cooperative process based on protein-unfolding curves, which show a sharp transition between the number of molecules in the folded and unfolded states as a function of increased temperature or denaturant concentration. The transition curve midpoint, Tm, corresponds to the temperature where 50% of the molecules are folded and 50% are unfolded.

● Chaperone proteins function in vivo to assist in de novo protein folding, rescue unfolded proteins, and disrupt nonfunctional protein aggregates. The two major types of ATP-dependent chaperone proteins are the clamp type (for example, Hsp70) and the chamber type (for example, the bacterial GroEL–GroES complex).

● The prion hypothesis states that scrapie-related protein folding diseases, such as kuru, Creutzfeldt–Jakob, and mad cow disease, are the result of infectious protein particles that induce misfolding in protein molecules that contain no mutations in the amino acid sequence.