(Phys.org)—Protein folding is the process by which a polypeptide (a linear organic polymer chain consisting of many amino acid residues, or monomers) transforms from a random coil into the 3D conformation in which it can perform its biological function. Since different proteins fold into a range of very different shapes, the Protein Data Bank (PDB) – a database archive comprising experimentally-determined three-dimensional structures of large biological molecules, including numerous protein conformations – can be disarmingly complex. This is problematic because that space is fundamental to understanding how sequence encodes structure. Recently, however, scientists at Dartmouth College deconstructed the universe of known protein structures into reusable building blocks that they term tertiary structural motifs, or TERMs. (Structural motifs are compact blocks of a 3D protein structure.) They found that 50% of PDB protein conformations were described – at sub-Angstrom resolution – by a surprisingly small group of roughly 600 TERMs. Moreover, TERMs allowed them to discern sequence–structure relationships. The researchers state that these results can be used for protein structure prediction, protein design and other applications.
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