Conformational search simulations of Trp-cage using genetic crossover

Abstract

We applied an effective conformational sampling method using genetic crossover to Trp-cage mini-protein. In this method, we incorporate the genetic crossover, which is one of the operations of genetic algorithm, in parallel molecular dynamics simulations. The genetic crossover can search the global conformational space by exchanging the corresponding parts between a pair of conformations of a protein. In this study, we applied this method to an -helical protein, Trp-cage mini protein, which has 20 amino-acid residues. The conformations obtained from the simulations are in good agreement with the experimental results.

Keywords::

• folding simulation
• conformational search
• genetic algorithm
• genetic crossover
• replica-exchange method

Acknowledgements

The computations were performed on the computers at the Research Center for Computational Science, Institute for Molecular Science and Information Technology Center, Nagoya University.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work was supported, in part, by the Grants-in-Aid for Scientific Research (A) [grant number 25247071], for Scientific Research on Innovative Areas (‘Dynamical Ordering & Integrated Functions’), for the Computational Materials Science Initiative, and for High Performance Computing Infrastructure from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan.