Secondary structure elements are elementary structural patterns that are present in most, if they are not all, known proteins. These are highly patterned sub-structures alpha helix and beta sheet consisting of loops between elements or segments of polypeptide chain that assume no stable shape. Secondary structure elements, when mapped on the sequence and depicted in the relative position they have in respect to each other, define the topology of the protein.
There are also local structures that do not belong to regular secondary structures (α-helices and β-strands). The irregular structures are coils or loops. The loops are often characterized by sharp turns or hairpin-like structures. If the connecting regions are completely irregular, they belong to random coils. Residues in the loop or coil regions tend to be charged and polar and located on the surface of the protein structure. They are often the evolutionarily variable regions where mutations, deletions, and insertions frequently occur. They can be functionally significant because these locations are often the active sites of proteins. Coiled Coils Coiled coils are a special type of super secondary structure characterized by a bundle of two or more α-helices wrapping around each other. The helices forming coiled coils have a unique pattern of hydrophobicity, which repeats every seven residues (five hydrophobic and two hydrophilic).
Hydrogen bonding between residues of proteins is the cause for secondary structure features; secondary structure is usually described to beginning biochemists as entirely independent of residue side-chain interactions.
The protein coils is a novel category of non-regular secondary structure, is a segment of contiguous polypeptide chain that traces a “loop-shaped” path in three-dimensional space; the main chain of an idealized loop resembles a Greek omega (omega). A systematic study was made of 67 proteins of known structure revealing 270 omega loops. Although such loops are typically regarded as “random coil,” they are, in fact, highly compact substructures and may also be independent folding units. Loops are almost invariably present at the protein surface where they are poised to assume important roles in molecular function and biological recognition. They are often observed to be modules of evolutionary exchange and are also natural candidates for bioengineering studies.
Secondary-structure prediction methods were evaluated by the Critical Assessment of protein Structure Prediction (CASP) experiments and continuously benchmarked, e.g. by EVA (benchmark). Based on these tests, the most accurate methods were;
The chief area for improvement appears to be the prediction of β-strands; residues confidently predicted as β-strand are likely to be so, but the methods are apt to overlook some β-strand segments (false negatives). There is likely an upper limit of nearly to 90% prediction accuracy overall, due to the idiosyncrasies of the standard method (DSSP) for assigning secondary-structure classes (helix/strand/coil) to PDB structures, against which the predictions are benchmarked.