Proteins can be composed of one or more polypeptides, each of which may be subject to post-translational modification. Interactions between a protein and either of the following may substantially alter the conformation of that protein:
• A co-factor, such as a divalent cation (like Ca2+, Fe2+, Cu2+, and Zn2+), or a small molecule required for functional enzyme activity, for example NAD+);
• A ligand (any molecule that a protein binds specifically).
Four different levels of structural organization in proteins have been distinguished and defined (Table 1).
Table1. LEVELS OF PROTEIN STRUCTURE
Even within a single polypeptide there is ample scope for hydrogen bonding between different amino acid residues. This stabilizes the partial polar charges along the back bone of the polypeptide and has profound effects on that protein’s overall shape. With regard to a protein’s conformation, the most significant hydrogen bonds are those that occur between the oxygen of one peptide bond’s carbonyl (CO) group and the hydrogen of the amino (NH) group of another peptide bond. Several fundamental structural patterns (motifs) stabilized by hydrogen bonding within a single polypeptide have been identified, the most fundamental of which are described below.
The α-helix
This is a rigid cylinder that is stabilized by hydrogen bonding between the carbonyl oxy gen of a peptide bond and the hydrogen atom of the amino nitrogen of a peptide bond located four amino acids away (Figure 1). α-Helices often occur in proteins that perform key cellular functions (such as transcription factors, where they are usually represented in the DNA-binding domains). Identical α-helices with a repeating arrangement of nonpolar side chains can coil round each other to form a particularly stable coiled coil. Coiled coils occur in many fibrous proteins, such as collagen of the extracellular matrix, the muscle protein tropomyosin, α-keratin in hair, and fibrinogen in blood clots.
Fig1. The structure of a standard α-helix and an amphipathic α-helix. (A) The structure of an α-helix is stabilized by hydrogen bonding between the oxygen of the carbonyl group (C=O) of each peptide bond and the hydrogen on the peptide bond amide group (NH) of the fourth amino acid away, making the helix have 3.6 amino acids per turn. The side chains of each amino acid are located on the outside of the helix; there is almost no free space within the helix. Note: only the backbone of the polypeptide is shown and some bonds have been omitted for clarity. (B) An amphipathic α-helix has tighter packing and has charged amino acids and hydrophobic amino acids located on different surfaces.
The β-sheet
β-Sheets (also called β-pleated sheets) are also stabilized by hydrogen bonding but, in this case, the bonds occur between opposed peptide bonds in parallel or antiparallel segments of the same polypeptide chain (Figure 2A). β-Sheets occur, often together with α-helices, at the core of most globular proteins, and can form complex structures such as the β-barrel (Figure 2B).
Fig2. The structure of β-sheets and β-barrels. (A) In a β-sheet (also called a β-pleated sheet), hydrogen bonding occurs between the carbonyl oxygens and amide hydrogens on adjacent segments of a sheet that may be composed either of parallel segments of the polypeptide chain or, as shown here, of antiparallel segments (arrows mark the direction of travel from N-terminus to C-terminus). (B) A β-barrel is a large β-sheet that forms a closed structure in which the first β-strand is hydrogen bonded to the last (the β-strands are typically arranged in an antiparallel arrangement). The barrel structure provides an insulating internal environment and is often found in proteins that span the hydrophobic cell membrane (allowing passage of small molecules that are charged or polar), and in proteins that bind hydrophobic ligands (in the center of the barrel). This example shows a side view of a single monomer of a sucrose porin protein from Salmonella typhimurium that facilitates transfer of the polar sucrose molecule (which cannot simply diffuse through the hydrophobic cell membrane). (Created from PDB 1D 1A0S using PyMol by Opabinia regalis and reproduced under the Creative Commons BY 3.0 license.)
The β-turn
Hydrogen bonding can occur between amino acids that are even nearer to each other within a polypeptide. When this arises between the peptide bond CO group of one amino acid residue and the peptide bond NH group of an amino acid residue three places farther along, this results in a hairpin β-turn. Abrupt changes in the direction of a polypeptide enable compact globular shapes to be achieved. These β-turns can connect parallel or antiparallel strands in β-pleated sheets.
Higher-order structures
Many more complex structural motifs, consisting of combinations of the above structural modules, form protein domains. Such domains are often crucial to a protein’s overall shape and stability and often represent functional units involved in binding other molecules. Another important determinant of the structure (and function) of a protein are disulfide bridges. They can form between the sulfur atoms of sulfhydryl (–SH) groups on two amino acids that may reside on a single polypeptide chain or on two polypeptide chains (Figure 3).
Fig3. Intrachain and interchain disulfide bridges in human insulin. When the insulin A and B chains are first formed by cleavage the cysteine residues have a free sulfhydryl group (–SH), but because the chains have been held in close proximity, disulfide bridges (–S–S–) can form by a condensation reaction between the sulfhydryl groups. One disulfide bridge forms between residues 6 and 11 of the A chain. Two disulfide bridges hold the A and B chains physically together (connecting Cys-7 of the A chain to Cys-7 of the B chain, and Cys-20 of the A chain to Cys-19 of the B chain).
In general, the primary structure of a protein determines the set of secondary structures that, together, generates the protein’s tertiary structure. Secondary structural motifs can be predicted from analysis of the primary structure, but the overall tertiary structure cannot easily be accurately predicted. Finally, some proteins form complex aggregates of polypeptide subunits, giving an arrangement known as the quaternary structure.
