Journal Article

The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design

Matthew Carter Childers, Clare-Louise Towse and Valerie Daggett

in Protein Engineering, Design and Selection

Volume 29, issue 7, pages 271-280
Published in print July 2016 | ISSN: 1741-0126
Published online June 2016 | e-ISSN: 1741-0134 | DOI: https://dx.doi.org/10.1093/protein/gzw023
The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design

Show Summary Details

Preview

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.

Keywords: chirality; conformational propensity; denatured state; host–guest series; intrinsic propensity; molecular dynamics simulation

Journal Article.  7439 words.  Illustrated.

Subjects: Proteins

Full text: subscription required

How to subscribe Recommend to my Librarian

Users without a subscription are not able to see the full content. Please, subscribe or login to access all content. subscribe or login to access all content.