The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design.
The conformational propensities of amino acids are an amalgamation of sequence effects, environmental effects and underlying intrinsic behavior. Many have attempted to investigate neighboring residue effects to aid in our understanding of protein folding and improve structure prediction efforts, especially with respect to difficult to characterize states, such as disordered or unfolded states. Host-guest peptide series are a useful tool in examining the propensities of the amino acids free from the surrounding protein structure. Here, we compare the distributions of the backbone dihedral angles (φ/ψ) of the 20 proteogenic amino acids in two different sequence contexts using the AAXAA and GGXGG host-guest pentapeptide series. We further examine their intrinsic behaviors across three environmental contexts: water at 298 K, water at 498 K, and 8 M urea at 298 K. The GGXGG systems provide the intrinsic amino acid propensities devoid of any conformational context. The alanine residues in the AAXAA series enforce backbone chirality, thereby providing a model of the intrinsic behavior of amino acids in a protein chain. Our results show modest differences in φ/ψ distributions due to the steric constraints of the Ala side chains, the magnitudes of which are dependent on the denaturing conditions. One of the strongest factors modulating φ/ψ distributions was the protonation of titratable side chains, and the largest differences observed were in the amino acid propensities for the rarely sampled αL region.
Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA.
Matthew Carter
MC
Childers
Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA.
Clare-Louise
CL
Towse
Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA daggett@u.washington.edu.
Valerie
V
Daggett
D000409:Alanine / Q000737:chemistry; D000595:Amino Acid Sequence; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013237:Stereoisomerism
D009842:Oligopeptides; D011506:Proteins; D000409:Alanine
chirality; conformational propensity; denatured state; host–guest series; intrinsic propensity; molecular dynamics simulation