Role of amino acid properties to determine backbone tau(N-Calpha-C') stretching angle in peptides and proteins.
ABSTRACT The analysis of the basic geometry of amino acid residues of protein structures has demonstrated the invariability of all the bond lengths and bond angles except for tau, the backbone N-Calpha-C' angle. This angle can be widened or contracted significantly from the tetrahedral geometry to accommodate various other strains in the structure. In order to accurately determine the cause for this deviation, a survey is made for the tau angles using the peptide structures and the ultrahigh resolution protein structures. The average deviation of N-Calpha-C' angles from tetrahedral geometry for each amino acid in all the categories were calculated and then correlated with forty-eight physiochemical, energetic and conformational properties of amino acids. Linear and multiple regression analysis were carried out between the amino acid deviation and the 48 properties. This study confirms the deviation of tau angles in both the peptide and protein structures but similar forces do not influence them. The peptide structures are influenced by physical properties whereas as expected the conformational properties influence the protein structures. And it is not any single property that dominates the deviation but the combination of different factors contributes to the tau angle deviation.
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ABSTRACT: The pioneering work of Ramachandran and colleagues emphasized the dominance of steric constraints in specifying the structure of polypeptides. The ubiquitous Ramachandran plot of backbone dihedral angles (ϕ and ψ) defined the allowed regions of conformational space. These predictions were subsequently confirmed in proteins of known structure. Ramachandran and colleagues also investigated the influence of the backbone angle τ on the distribution of allowed ϕ/ψ combinations. The "bridge region" (ϕ ≤ 0° and -20° ≤ ψ ≤ 40°) was predicted to be particularly sensitive to the value of τ. Here we present an analysis of the distribution of ϕ/ψ angles in 850 non-homologous proteins whose structures are known to a resolution of 1.7 Å or less and sidechain B-factor less than 30 Å². We show that the distribution of ϕ/ψ angles for all 87,000 residues in these proteins shows the same dependence on τ as predicted by Ramachandran and colleagues. Our results are important because they make clear that steric constraints alone are sufficient to explain the backbone dihedral angle distributions observed in proteins. Contrary to recent suggestions, no additional energetic contributions, such as hydrogen bonding, need be invoked.Protein Science 07/2011; 20(7):1166-71. · 2.80 Impact Factor