A novel approach for large-scale polypeptide folding based on elastic networks using continuous optimization

作者：Rakshit Sourav^*; Ananthasuresh G K

来源：Journal of Theoretical Biology, 2010, 262(3): 488-497.

DOI：10.1016/j.jtbi.2009.10.010

• MJ potential
• Native state
• Energy modeling
• Folding funnel
• Protein folding
• Rigid body

We present a new computationally efficient method for large-scale polypeptide folding using coarse-grained elastic networks and gradient-based continuous optimization techniques. The folding is governed by minimization of energy based on Miyazawa-Jernigan contact potentials. Using this method we are able to substantially reduce the computation time on ordinary desktop computers for simulation of polypeptide folding starting from a fully unfolded state. We compare our results with available native state structures from Protein Data Bank (PDB) for a few de-novo proteins and two natural proteins, Ubiquitin and Lysozyme. Based on our simulations we are able to draw the energy landscape for a small de-novo protein. Chignolin. We also use two well known protein structure prediction software, MODELLER and GROMACS to compare our results. In the end, we show how a modification of normal elastic network model can lead to higher accuracy and lower time required for simulation.

• 出版日期2010-2-7