ArticleBiophysical journal2016
Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility.
Article in Biophysical journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 12 citations in OpenAlex.
- Revisiting the influence of pH onRoyal Society open science · 2023Article
- Quantitative description of a contractile macromolecular machine.Science advances · 2021Article
- Physical Chemistry of the Protein Backbone: Enabling the Mechanisms of Intrinsic Protein Disorder.The journal of physical chemistry. B · 2020Review
- Free Energy Calculations Based on Coupling Proximal Distribution Functions and Thermodynamic Cycles.Journal of chemical theory and computation · 2019Article
- Improvements to the ABSINTH Force Field for Proteins Based on Experimentally Derived Amino Acid Specific Backbone Conformational Statistics.Journal of chemical theory and computation · 2019Article
- Thermodynamics of Conformational Transitions in a Disordered Protein Backbone Model.Biophysical journal · 2018Article
- Tuning the Flexibility of Glycine-Serine Linkers To Allow Rational Design of Multidomain Proteins.Biochemistry · 2017Article
- Intramolecular Interactions Overcome Hydration to Drive the Collapse Transition of GlyThe journal of physical chemistry. B · 2017Article
- Nonpolar Solvation Free Energy from Proximal Distribution Functions.The journal of physical chemistry. B · 2017Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Oligoglycine is a backbone mimic for all proteins and is prevalent in the sequences of intrinsically disordered proteins. We have computed the absolute chemical potential of glycine oligomers at infinite dilution by simulation with the CHARMM36 and Amber ff12SB force fields. We performed a thermodynamic decomposition of the solvation free energy (ΔG(sol)) of Gly2-5 into enthalpic (ΔH(sol)) and entropic (ΔS(sol)) components as well as their van der Waals and electrostatic contributions. Gly2-5 was either constrained to a rigid/extended conformation or allowed to be completely flexible during simulations to assess the effects of flexibility on these thermodynamic quantities. For both rigid and flexible oligoglycine models, the decrease in ΔG(sol) with chain length is enthalpically driven with only weak entropic compensation. However, the apparent rates of decrease of ΔG(sol), ΔH(sol), ΔS(sol), and their elec and vdw components differ for the rigid and flexible models. Thus, we find solvation entropy does not drive aggregation for this system and may not explain the collapse of long oligoglycines. Additionally, both force fields yield very similar thermodynamic scaling relationships with respect to chain length despite both force fields generating different conformational ensembles of various oligoglycine chains.
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