ArticleBiopolymers2008
Structural insights for designed alanine-rich helices: comparing NMR helicity measures and conformational ensembles from molecular dynamics simulation.
Article in Biopolymers, 2008. 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.
- CHARMM-GUI Enhanced Sampler for various collective variables and enhanced sampling methods.Protein science : a publication of the Protein Society · 2022Article
- Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity.Journal of chemical theory and computation · 2021Article
- ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution.Journal of chemical theory and computation · 2020Article
- Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.Journal of computer-aided molecular design · 2019Review
- Links between the charge model and bonded parameter force constants in biomolecular force fields.The Journal of chemical physics · 2017Article
- Inhibitory mechanism of peptides with a repeating hydrophobic and hydrophilic residue pattern on interleukin-10.Human vaccines & immunotherapeutics · 2017Article
- Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model.Journal of chemical theory and computation · 2016Article
- Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics.Proteins · 2015Article
- ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.Journal of chemical theory and computation · 2015Article
- ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins.Journal of chemical theory and computation · 2014Article
- Improved Generalized Born Solvent Model Parameters for Protein Simulations.Journal of chemical theory and computation · 2013Article
- Optimal salt bridge for Trp-cage stabilization.Biochemistry · 2011Article
- β-Sheet 13C structuring shifts appear only at the H-bonded sites of hairpins.Journal of the American Chemical Society · 2011Article
- Lysine and arginine residues do not increase the helicity of alanine-rich peptide helices.Chemical communications (Cambridge, England) · 2008Article
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Authors and funding
5 authors.
Funding
Abstract
The temperature dependence of helical propensities for the peptides Ac-ZGG-(KAAAA)(3)X-NH(2) (Z = Y or G, X = A, K, and D-Arg) were studied both experimentally and by MD simulations. Good agreement is observed in both the absolute helical propensities as well as relative helical content along the sequence; the global minimum on the calculated free energy landscape corresponds to a single alpha-helical conformation running from K4 to A18 with some terminal fraying, particularly at the C-terminus. Energy component analysis shows that the single helix state has favorable intramolecular electrostatic energy due to hydrogen bonds, and that less-favorable two-helix globular states have favorable solvation energy. The central lysine residues do not appear to increase helicity; however, both experimental and simulation studies show increasing helicity in the series X = Ala --> Lys --> D-Arg. This C-capping preference was also experimentally confirmed in Ac-(KAAAA)(3)X-GY-NH(2) and (KAAAA)(3)X-GY-NH(2) sequences. The roles of the C-capping groups, and of lysines throughout the sequence, in the MD-derived ensembles are analyzed in detail.
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