Unfolding Simulation
Tahere Khaghani
Institute of Biochemistry and Biophysics, University of Tehran, Iran
Introduction: Understanding the determinants of the native structure of proteins and how this
structure is gained or lost during folding and unfolding is a central objective in structural
biology. Study unfolding pathways with simulation methods can be useful in predicting protein
stability. Typical molecular dynamics simulations can examine the trajectories of proteins up to
tens of nanoseconds. A fruitful approach is to investigate protein unfolding by performing
simulations under strongly denaturing conditions (high temperature and/or pressure). Method:
In this study we focus on the simulation method. Conclusion: The analysis of trajectories
obtained from molecular dynamic simulations can determine the unfolding pathway and the
most stable protein. So unfolding can be a deterministic factor in stability of a protein which
can be analyses by simulation methods.
Keywords: Unfolding; Simulation; Stability of proteins
References:
1. Lee, Jinhyuk, and Seokmin Shin. "Understanding β-Hairpin Formation by Molecular
Dynamics Simulations of Unfolding." Biophysical journal 81.5 (2001): 2507-2516.
2. Choi, Ho Sup, June Huh, and Won Ho Jo. "Similarity of force-induced unfolding of
apomyoglobin to its chemical-induced unfolding: an atomistic molecular dynamics
simulation approach." Biophysical journal 85.3 (2003): 1492-1502.
3. Huang, Xiaoqin, and Huan-Xiang Zhou. "Similarity and difference in the unfolding of
thermophilic and mesophilic cold shock proteins studied by molecular dynamics
simulations." Biophysical journal 91.7 (2006): 2451-2463.