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 language | English |
|---|---|
| Pages (from-to) | 42-49 |
| Number of pages | 8 |
| Journal | Journal of the Taiwan Institute of Chemical Engineers |
| Volume | 92 |
| DOIs | |
| Publication status | Published - 2018 Nov 1 |
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All Science Journal Classification (ASJC) codes
- Chemistry(all)
- Chemical Engineering(all)
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Fast estimation of protein conformational preference at air/water interface via molecular dynamics simulations. / Han, Meng huai; Chiu, Chi-cheng.
In: Journal of the Taiwan Institute of Chemical Engineers, Vol. 92, 01.11.2018, p. 42-49.Research output: Contribution to journal › Article
TY - JOUR
T1 - Fast estimation of protein conformational preference at air/water interface via molecular dynamics simulations
AU - Han, Meng huai
AU - Chiu, Chi-cheng
PY - 2018/11/1
Y1 - 2018/11/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85043317661&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85043317661&partnerID=8YFLogxK
U2 - 10.1016/j.jtice.2018.02.026
DO - 10.1016/j.jtice.2018.02.026
M3 - Article
AN - SCOPUS:85043317661
VL - 92
SP - 42
EP - 49
JO - Journal of the Taiwan Institute of Chemical Engineers
JF - Journal of the Taiwan Institute of Chemical Engineers
SN - 1876-1070
ER -