SECONDARY STRUCTURE ASSIGNMENT
The Task. When looking at how chains of amino acids in proteins are ordered, we notice regular macro elements in the 3D structure of practically all known structures: helices and strands (see Chapter 2). These structures were coined protein secondary structure by Linderstrøm-Lang (1952) in the context of a protein’s primary, tertiary, and quaternary structural definitions. There is no unique inherent physical characteristic to systematically assign secondary structure from 3D coordinates. Instead there are many different assignment schemes, each constructed to reflect one or more aspects of protein structure. Here we will address these aspects, the assignment schemes, and how they have been used to study proteins.
Aspects Reflected in Secondary Structure Assignments. When protein secondary structure is assigned, the complexity of the all atom 3D structure is reduced dramatically. This level of abstraction is obtained by choosing as determinants for the assignment such aspects as physical interaction energies (e.g. H-bonds and van der Waals), geometrical idealization (e.g. idealized cylinder or Cα-distance masks) and/or other structural descriptions optimized to reflect appealing characteristics (e.g. expert assignment, invariance upon thermal fluctuations or predictability). Another generic aspect of all methods is that they assign secondary structure based on residue independent aspects.
Notation. When treating ...