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

Workshop and International Seminar on Science of Complex Natural Systems

Sumaryada, T.^1,2 ; Hati, J.^1 ; Wahyudi, S.T.^1 ; Malau, N.D.^1 ; Sawitri, K.N.^1

Computational Biophysics and Molecular Modelling Research Group (CBMoRG), Department of Physics, Bogor Agricultural University, Jalan Meranti Kampus IPB, Dramaga Bogor

16680, Indonesia^1

Biopharmaca Research Center, Bogor Agricultural University, Jalan Taman Kencana No. 3, Bogor

16128, Indonesia^2

关键词: Beta-hairpin;    Helix-to-coil transitions;    Hydrophobic core;    Molecular dynamics simulations;    Protein unfolding;    Simulation temperature;    Structural parameter;    Unfolding process;   

Others  :  https://iopscience.iop.org/article/10.1088/1755-1315/31/1/012008/pdf
DOI  :  10.1088/1755-1315/31/1/012008

来源: IOP

【 摘 要 】

This study investigates the unfolding mechanism of 1GB1 protein at various simulation temperatures using a long-timescale molecular dynamics simulation. Analysis of structural parameters of molecular dynamics simulation have indicated that the unfolding process of GB1 protein has started at 95 ns for 475 K simulation, and at 745 ps for 500 K simulation. The unfolding process in this simulation exhibit the feature of hydrophobic core collapse model, in which the beta-hairpin destruction precedes the a-helix to coil transition. The unfolding was started with the increasing flexibility of the beta-sheets and hydrophobic core region, continued with beta-hairpins destruction, and ended with a-helix to coil and turn transition. The final structures of GB1 protein after unfolding, suggest an unfinished denaturation of protein as seen from the small remains of α-helix structure.