Thus, more hydrophobic residues such as trp are often surrounded by other parts of the protein, excluding water, while charged residues such as asp are more often on the surface. Much like detergent micelles, proteins are most stable when their hydrophobic parts are buried, while hydrophilic parts are on the surface, exposed to water. Polypeptide chains generally contain both hydrophobic and hydrophilic residues. Usually, the most important force is hydrophobic interaction (or hydrophobic bonds). Whereas secondary structure is stabilized by H-bonding, all four “weak” forces contribute to tertiary structure. Every protein has a particular pattern of folding and these can be quite complex. Tertiary structure results from interactions between side chains, or between side chains and the polypeptide backbone, which are often distant in sequence. This level of structure describes how regions of secondary structure fold together – that is, the 3D arrangement of a polypeptide chain, including a helices, b sheets, and any other loops and folds. This contributes to the next level of protein structure, the tertiary structure. Another major factor is the presence of other chemical groups that interact with each other. Further, there is no H on one peptide bond when proline is present, so a hydrogen bond cannot form.
Proline contains a ring that constrains bond angles so that it will not fit exactly into an a helix or b sheet. Several factors come into play: steric hindrance between nearby large side chains, charge repulsion between nearby similarly-charged side chains, and the presence of proline. What determines whether a particular part of a sequence will fold into one or the other of these structures? A major determinant is the interactions between side chains of the residues in the polypeptide. In fact, many proteins have a mixture of a helices, b sheets, and other types of folding patterns to form various overall shapes. A single polypeptide chain may have different regions that take on different secondary structures. These include various loops, helices and irregular conformations. While the a helix and b sheet are by far the most common types of structure, many others are possible. The major constituent of silk (silk fibroin) consists mainly of layers of b sheet stacked on top of each another. In this arrangement, side chains project alternately upward and downward from the sheet. Generally the primary structure folds back on itself in either a parallel or antiparallel arrangement, producing a parallel or antiparallel b sheet.
Again, the polypeptide N-H and C=O groups form hydrogen bonds to stabilize the structure, but unlike the a helix, these bonds are formed between neighbouring polypeptide (b) strands. In a b sheet, the polypeptide chain folds back on itself so that polypeptide strands like side by side, and are held together by hydrogen bonds, forming a very rigid structure.
The structure of a b sheet is very different from the structure of an a helix.
An example of a protein with many a helical structures is the keratin that makes up human hair. The side chains project outward and contact any solvent, producing a structure something like a bottle brush or a round hair brush. The alpha helix has precise dimensions: 3.6 residues per turn, 0.54 nm per turn. All C=O and N-H groups are involved in hydrogen bonds, making a fairly rigid cylinder. Each carbonyl is linked by a hydrogen bond to the N-H of a residue located 4 residues further on in the sequence within the same chain. In this conformation, the carbonyl and N-H groups are oriented parallel to the axis. An a helix, as the name implies, is a helical arrangement of a single polypeptide chain, like a coiled spring.