Multicanonical molecular dynamics simulations of the N-terminal domain of protein L9

¹ Department of Physics Engineering, Hacettepe University - Ankara, 06800, Turkey
² Department of Chemistry and Biochemistry, University of Oklahoma - Norman, OK 73019-5251, USA

^(a) fatih@hacettepe.edu.tr
^(b) pingj@ou.edu
^(c) uhansmann@ou.edu

Received: 7 January 2014
Accepted: 3 February 2014

Abstract

We describe multicanonical molecular dynamic simulations of the N-terminal domain of the protein L9. Analyzing free energy landscapes and thermal ordering, we propose a possible folding mechanism for the protein. By comparing our results with that of molecular dynamics runs of the protein at constant temperature, we find that multicanonical molecular dynamics leads to orders of magnitude higher sampling of folding transitions.