They can vary widely in length, from as few as three to five residues in short helices and sheets, to over fifty residues in some coiled‐coil helices (see Frequently Observed Secondary Structure Assemblies or Structural Motifs). Regular secondary structures (also referred to as secondary structure elements) common to many proteins include α‐helices, β‐sheets, and turns (see below). Secondary structure is defined as the local spatial conformation of the polypeptide backbone excluding the side chains. Hence, although structural uniqueness associated with a protein sequence is a powerful principle, it can sometimes depend on the local environment and is not rigidly followed in every case. Furthermore, a few proteins have been found to have intrinsically unstructured regions (Wright and Dyson, 1999 Tompa, 2002). For example, interactions with ligands, substrates, or other proteins can bring about controlled conformational changes producing potentially profound effects. It is noteworthy, however, that changes in the local biological environment of a protein molecule can sometimes perturb its three‐dimensional structure. In 1973, Chris Anfinsen demonstrated that the primary amino sequence of a protein uniquely determines the higher orders of structure for a protein and is thus of fundamental importance (Anfinsen, 1973). In fact, the term protein sequence is often used interchangeably with primary structure. Primary structure is defined as the linear amino acid sequence of a protein's polypeptide chain. The unit is organized into sections based on both structural and functional relations. Likewise, the PDB‐entry tables given in this unit provide some examples of various folds, but are not comprehensive lists. The scope of this unit is not to enumerate all the existing folds and tertiary structures determined to date, but rather to provide a comprehensive overview of some commonly observed protein fold families and commonly observed structural motifs which have functional significance. Several groups have already attempted to classify protein structures into fold families and superfamiles without focusing on function (Orengo et al., 1993 Murzin et al., 1995). The identification of the fold of a protein has therefore become an invaluable tool since it can potentially provide a direct extrapolation to function, and may allow one to map functionally important regions in the amino acid sequence. As a consequence, structural conservation at the tertiary level is perhaps more profound than it is at the primary. Not only do functionally related proteins generally have similar tertiary structures (see below), but even proteins with very different functions are often found to share the same tertiary folds. The complete structure of a protein can be described at four different levels of complexity: primary, secondary, tertiary, and quaternary structure.Īs a multitude of protein structures are rapidly being determined by X‐ray crystallography and by nuclear magnetic resonance (NMR), it is becoming clear that the number of unique folds is far less than the total number of protein structures. Proteins fold into stable three‐dimensional shapes, or conformations, that are determined by their amino acid sequence.
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