Elucidation of GB1 Protein Unfolding Mechanism via a Long-timescale Molecular Dynamics Simulation

Sumaryada, Tony; Hati, Jellyta; Wahyudi, Setyanto Tri; Malau, Nya Daniaty; Sawitri, Kania Nur

doi:10.1088/1755-1315/31/1/012008

Cited by 3 publications

(1 citation statement)

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“…It was found that the RMSD of the 3LIP ( B. cepacia lipase) and 3TGL ( R. miehei lipase) was 0.77 ± 0.26 Å and 0.84 ± 0.26 Å at 313 K, and 0.84 ± 0.24 Å and 0.92 ± 0.31 Å at 343 K, respectively. Considering that the RMSD change below 2.5 Å is an indicator of no significant conformational changes in protein structure [ 75 ], and a low RMSD indicates that the protein is stable during the simulation time [ 76 ], the RMSD results for both lipases showed that increasing the temperature to 343 K did not cause great structural differences.…”

Section: Resultsmentioning

confidence: 99%

Kinetic Modeling, Thermodynamic Approach and Molecular Dynamics Simulation of Thermal Inactivation of Lipases from Burkholderia cepacia and Rhizomucor miehei

Ortega

Sáez

Palacios

et al. 2022

IJMS

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The behavior against temperature and thermal stability of enzymes is a topic of importance for industrial biocatalysis. This study focuses on the kinetics and thermodynamics of the thermal inactivation of Lipase PS from B. cepacia and Palatase from R. miehei. Thermal inactivation was investigated using eight inactivation models at a temperature range of 40–70 °C. Kinetic modeling showed that the first-order model and Weibull distribution were the best equations to describe the residual activity of Lipase PS and Palatase, respectively. The results obtained from the kinetic parameters, decimal reduction time (D and tR), and temperature required (z and z’) indicated a higher thermal stability of Lipase PS compared to Palatase. The activation energy values (Ea) also indicated that higher energy was required to denature bacterial (34.8 kJ mol−1) than fungal (23.3 kJ mol−1) lipase. The thermodynamic inactivation parameters, Gibbs free energy (DG#), entropy (DS#), and enthalpy (DH#) were also determined. The results showed a DG# for Palatase (86.0–92.1 kJ mol−1) lower than for Lipase PS (98.6–104.9 kJ mol−1), and a negative entropic and positive enthalpic contribution for both lipases. A comparative molecular dynamics simulation and structural analysis at 40 °C and 70 °C were also performed.

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Section: Resultsmentioning

confidence: 99%