In my group we work with Molecular Dynamics to model several different proteins and protein systems. We submit our modelled molecules to changes in temperature, changes in solvent composition and even external pulling forces. To analyze our simulation results we have so far used visual inspection and statistical analysis of the resulting molecular trajectories (as everybody else!). However, recently I started assigning a particular sound frequency to each amino acid in the protein, and by setting the amplitude of each frequency according to the movement amplitude we can "hear" whenever two aminoacids are moving in synchrony, and in which direction they are moving along an axis (thanks to left-right stereo!). I am working on a small program "Protones" to do this frequency/amplitude assignment task more systematically, and to also use several other combinations of features to produce the harmonies... One example of soundfile was obtained from using Steered Molecular Dynamics for stretching the neck region of the scallop myosin molecule (in rigor, PDB-id: 1SR6), in such a way as to cause a rotation of the myosin head. Myosin is the molecule responsible for producing the force during muscle contraction. These are early days, and it still remains to be proven that this method has any advantage over other methods, but at least it is fun to do and the harmonies produced invoke an eerie sounding futuristic landscape...
|Place of Publication||UK|
|Publication status||Published - 2008|