Fast estimation of protein conformational preference at air/water interface via molecular dynamics simulations

Meng huai Han, Chi-cheng Chiu

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1 Citation (Scopus)

Abstract

Understanding the protein structural stability and thus its functional integrity at interface are critical for its biotechnology application development. Conventionally, it requires two extensive free energy calculations of protein in bulk and at interface to evaluate the conformational preference change during the adsorption. In this work, we derive an estimation of adsorption free energy at air/water interface for a protein in a defined conformation with the contributions of partial desolvation ΔGdesolv and surface energy ΔGa/w, which can be quickly evaluated from equilibrium MD trajectories. Via thermodynamics cycle, the free energy variation of α-helix to β-hairpin transition during the adsorption ΔΔGwat→int α→β can be obtained from the difference between the adsorption free energies of the two conformations. Applying the method, we estimate ΔΔGwat→int α→β of 6.31kJ/mol for DP5, in excellent agreement with the MD free energy data of 6.35 kJ/mol. Consistent results for four other tested proteins compared with MD free energy calculation further validate the derived adsorption model. The combination of MD simulations and thermodynamic estimations provide valuable physical insights for protein interfacial folding behaviors and serve as basis for developing prediction tools of protein conformations at interface.

Original languageEnglish
Pages (from-to)42-49
Number of pages8
JournalJournal of the Taiwan Institute of Chemical Engineers
Volume92
DOIs
Publication statusPublished - 2018 Nov 1

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Free energy
Molecular dynamics
Proteins
Water
Computer simulation
Adsorption
Air
Conformations
Thermodynamics
Biotechnology
Interfacial energy
Trajectories

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Chemical Engineering(all)

Cite this

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abstract = "Understanding the protein structural stability and thus its functional integrity at interface are critical for its biotechnology application development. Conventionally, it requires two extensive free energy calculations of protein in bulk and at interface to evaluate the conformational preference change during the adsorption. In this work, we derive an estimation of adsorption free energy at air/water interface for a protein in a defined conformation with the contributions of partial desolvation ΔGdesolv and surface energy ΔGa/w, which can be quickly evaluated from equilibrium MD trajectories. Via thermodynamics cycle, the free energy variation of α-helix to β-hairpin transition during the adsorption ΔΔGwat→int α→β can be obtained from the difference between the adsorption free energies of the two conformations. Applying the method, we estimate ΔΔGwat→int α→β of 6.31kJ/mol for DP5, in excellent agreement with the MD free energy data of 6.35 kJ/mol. Consistent results for four other tested proteins compared with MD free energy calculation further validate the derived adsorption model. The combination of MD simulations and thermodynamic estimations provide valuable physical insights for protein interfacial folding behaviors and serve as basis for developing prediction tools of protein conformations at interface.",
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