ArticleProtein engineering, design & selection : PEDS2016
The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design.
Article in Protein engineering, design & selection : PEDS, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Applications of large-scale artificial intelligence models in bioinformatics.Quantitative biology (Beijing, China) · 2026Review
- The design of functional proteins using tensorized energy calculations.Cell reports methods · 2023Article
- Impact of Non-Covalent Interactions of Chiral Linked Systems in Solution on Photoinduced Electron Transfer Efficiency.International journal of molecular sciences · 2023Article
- Sortase A transpeptidation produces seamless, unbranched biotinylated nanobodies for multivalent and multifunctional applications.Nanoscale advances · 2023Article
- Molecular Dynamics Methods for Antibody Design.Methods in molecular biology (Clifton, N.J.) · 2023Article
- The role of α-sheet structure in amyloidogenesis: characterization and implications.Open biology · 2022Review
- The hot sites of α-synuclein in amyloid fibril formation.Scientific reports · 2020Article
- Modeling pH-Dependent NMR Chemical Shift Perturbations in Peptides.Biophysical journal · 2019Article
- Molecular dynamics-derived rotamer libraries for d-amino acids within homochiral and heterochiral polypeptides.Protein engineering, design & selection : PEDS · 2018Article
- Tuning the Flexibility of Glycine-Serine Linkers To Allow Rational Design of Multidomain Proteins.Biochemistry · 2017Article
- Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective.Journal of computational chemistry · 2017Article
- Using chirality to probe the conformational dynamics and assembly of intrinsically disordered amyloid proteins.Scientific reports · 2017Article
- Insights from molecular dynamics simulations for computational protein design.Molecular systems design & engineering · 2017Article
- Designed α-sheet peptides suppress amyloid formation inNPJ biofilms and microbiomes · 2017Article
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Authors and funding
3 authors.
Funding
Abstract
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.
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