Amino acid conformational analyses of proteins (ACAP program)

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Abstract

The secondary structure analysis of proteins is a powerful tool, efficiently supporting spectroscopic (CD, IR, NMR) and biochemical research projects. However, the precise location of the different secondary structural elements in a sequence incorporates some subjectivity. A linearized notation of a uniform and objective description of protein backbone structures was developed. This involves a three-dimensional to one-dimensional transformation (3D → 1D). The classification is based on a step-by-step comparison performed between reference conformers (also called template values) and backbone sub-conformations of the protein. The readily provided structure templates may be modified, but the procedure still remains objective and uniform. This linearized notation of protein structures provides a description of the three-dimensional backbone conformation without relying on the traditional concept of secondary structure. Previously, the sequence analysis (primary structure) of proteins resulted in the identification of the 20 natural amino acid residues. Similarly, the backbone conformation analysis of the same proteins confirmed the presence of nine basically different subconformers. This recognition and the application of the linearized notation of the 3D structure makes easier the comparison of proteins at the levels of primary to tertiary structure.

Original languageEnglish
Pages (from-to)263-273
Number of pages11
JournalJournal of Molecular Structure: THEOCHEM
Volume362
Issue number3
DOIs
Publication statusPublished - Mar 8 1996

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Keywords

  • Ab initio calculation
  • Acap program
  • Amino acid
  • Conformational analysis
  • Conformational cluster
  • Protein

ASJC Scopus subject areas

  • Biochemistry
  • Condensed Matter Physics
  • Physical and Theoretical Chemistry

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