On the meaning of α–helical conformations found in proteins

Boris Haimov, Russell Berrie Nanotechnology Institute, Technion, Haifa, Israel
Simcha Srebnik, Chemical Engineering, Technion, Haifa, Israel

Proteins are the most popular biomolecules found within every living organism and participate in almost every biological process. Examples include processes of biological sensory systems such as the sense of smell and sense of vision, processes of energy transformation such as extracting the energy from glucose molecules and storing them in the form of ATP molecules, polymer synthesis processes like the process of DNA synthesis, and molecular transport processes such as carrying oxygen and carbon dioxide molecules. Because of their popularity and function, proteins are found under intense scientific research. α–helices are the most abundant structures found within proteins and play an important role in the determination of the global structure of proteins and their function. It is common to describe conformation of α–helical backbone by Ramachandran (φ,ψ) dihedrals. Observations performed on α–helical conformations found in the Protein Data Bank (PDB) demonstrate unique (φ,ψ) locations for the different amino acid transitions. To understand the observed (φ,ψ) tendencies an alternative coordinates system was developed that describes the helical conformation in terms of residues per turn (ρ) and the angle (ϑ) between backbone carbonyls relative to the helix direction through an approximate linear transformation between the two coordinates system (φ,ψ and ρ,ϑ). In this way, valuable information on the helical structure becomes directly available. Representation of the helical conformation found in PDB on the (ρ,ϑ) space allowed to understand the conformational differences between the observed α–helices.