ArticleProtein engineering, design & selection : PEDS2014
Nature versus design: the conformational propensities of D-amino acids and the importance of side chain chirality.
Article in Protein engineering, design & selection : PEDS, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
20 citing papers in PubMed, 38 citations in OpenAlex.
- Marine Antimicrobial Peptides: From Ocean Biodiversity to Genome Mining, Multi-Omics Discovery, and Biotechnological Innovation in the Battle Against Antimicrobial Resistance.Probiotics and antimicrobial proteins · 2026Review
- Mimicking Nonribosomal Peptides from the Marine ActinomyceteACS infectious diseases · 2024Article
- The role of α-sheet structure in amyloidogenesis: characterization and implications.Open biology · 2022Review
- Switching the N-Capping Region from all-L to all-D Amino Acids in a VEGF Mimetic Helical Peptide.Molecules (Basel, Switzerland) · 2022Article
- Racemization in Post-Translational Modifications Relevance to Protein Aging, Aggregation and Neurodegeneration: Tip of the Iceberg.Symmetry · 2021Article
- Computational study on the polymerization reaction of d-aminopeptidase for the synthesis of d-peptides.RSC advances · 2020Article
- Three dimensional structures of putative, primitive proteins to investigate the origin of homochirality.Scientific reports · 2019Article
- Chiral Inversion of Amino Acids in Antiparallel β-Sheets at Interfaces Probed by Vibrational Sum Frequency Generation Spectroscopy.The journal of physical chemistry. B · 2019Article
- Self-assembly dynamics and antimicrobial activity of all l- and d-amino acid enantiomers of a designer peptide.Nanoscale · 2018Article
- Comparison of Peptide Ion Conformers Arising from Non-Helical and Helical Peptides Using Ion Mobility Spectrometry and Gas-Phase Hydrogen/Deuterium Exchange.Journal of the American Society for Mass Spectrometry · 2018Article
- The Role of α-sheet in Amyloid Oligomer Aggregation and Toxicity.The Yale journal of biology and medicine · 2018Review
- Molecular dynamics-derived rotamer libraries for d-amino acids within homochiral and heterochiral polypeptides.Protein engineering, design & selection : PEDS · 2018Article
- 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
- Antimicrobial Peptides: Mechanisms of Action and Resistance.Journal of dental research · 2017Review
- 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
- The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design.Protein engineering, design & selection : PEDS · 2016Article
- Peptides Composed of Alternating L- and D-Amino Acids Inhibit Amyloidogenesis in Three Distinct Amyloid Systems Independent of Sequence.Journal of molecular biology · 2016Article
- Insights into Unfolded Proteins from the Intrinsic ϕ/ψ Propensities of the AAXAA Host-Guest Series.Biophysical journal · 2016Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
D-amino acids are useful building blocks for de novo peptide design and they play a role in aging-related diseases associated with gradual protein racemization. For amino acids with achiral side chains, one should be able to presume that the conformational propensities of L- and D-amino acids are a reflection of one another due to the straightforward geometric inversion at the Cα atom. However, this presumption does not account for the directionality of the backbone dipole and the inverted propensities have never been definitively confirmed in this context. Furthermore, there is little known of how alternative side chain chirality affects the backbone conformations of isoleucine and threonine. Using a GGXGG host-guest pentapeptide system, we have completed exhaustive sampling of the conformational propensities of the D-amino acids, including D-allo-isoleucine and D-allo-threonine, using atomistic molecular dynamics simulations. Comparison of these simulations with the same systems hosting the cognate L-amino acids verifies that the intrinsic backbone conformational propensities of the D-amino acids are the inverse of their cognate L-enantiomers. Where amino acids have a chiral center in their side chain (Thr, Ile) the β-configuration affects the backbone sampling, which in turn can confer different biological properties.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.