Molecular dynamics simulations comprise one of the most important tools in the armamentarium of chemists and biologists. Initially a curiosity for theoretical scientists, MD is now an explanatory and predictive tool in chemistry, biology, materials science, engineering and even weather prediction. In the field of biology, some masters such as Martin Karplus have honed this tool to the status of an art. While great leaps have been made in the context of methods, hardware, software and applications in this field, much remains to be still done. One of the reasons is that even now, running microsecond MD is computationally quite expensive. But many important biological events involving biomacromolecules take place on this time scale, thus making the achievement of efficient microsecond MD simulations important.
Writing in Science, scientists from D. E. Shaw company, Columbia and the Hebrew University of Jerusalem have a lovely paper documenting the application of the new and innovative MD program Desmond to the dynamics of a bacterial ion channel that transports Na+ ions using the electromotive force generated by proton transport. Desmond is supposed to enable efficient microsecond MD. It is going to be interfaced with the Maestro interface developed by Schrodinger and is due to be released this year I believe. Currently the fastest MD program on a single processor is GROMACS. While head to head comparisons of GROMACS and Desmond have not been reported to my knowledge, Desmond is supposed to be very fast on multiple processors, a facility that many can now afford to have.
In the Science paper, the researchers apply Desmond to understand the transport mechanism of the Na+/H+ antiport ion channel in E. Coli. This protein is crucial for E. Coli to survive harsh conditions of pH, alkalinity, and ionic lithium environments. The authors basically focus on the protonation state of certain key aspartates and find something pretty interesting- two crucial aspartates essentially act as switches that decide whether Na+ ions would be transported to the cytoplasm or to the periplasm. Using many long MD simulations involving different protonation states, the authors discovered that one of the carboxylates always has to be protonated. This acts like a "master aspartate" switch. Once this switch's state is set, it's the state of the other switch that decides the direction of transport- protonated leads to expulsion of the Na+ into the periplasm, while deprotonated leads to expulsion into the cytoplasm.
The observation reminded me of a high-school "staircase lighting" electricity experiment. A master switch had to be always on for the assembly to work. The On/Off state of another switch would then govern whether current flowed or not.
Using this discovery as the basis for exploring further conformational changes related to it, the authors come up with an elegant stepwise mechanism for the transport of Na+ and H+ ions that accounts for the observed stoichiometry of one Na+ ion for every two H+ transported. Using free energy perturbation binding affinity calculations, the authors also rationalize the channel's observed selectivity for Na+ over K+, and slightly for Li+ over Na+.
There is also a a very intriguing explanation for the pH sensitivity of this ion channel. The crystal structure of the channel is solved at pH 4, and it is inactive at this pH. How does the channel get activated at higher pH? To explore this, the authors do something simple but quite clever. They first identify all the key aspartates lining the channel and determine their pKa values. Perhaps not surprisingly, the pKa values of these are abnormally high- not an uncommon observation for amino acids in the unusual environments in protein interiors. They then selectively deprotonate one aspartate keeping all others protonated and do MD on the resulting structures. If there is a key "pH sensing" aspartate, its protonation state will likely govern a conformational change from inactive-active. Indeed, one aspartate, D133, turns out to modulate a conformational change involving two helices when it is deprotonated. Crucially, this results in the "master aspartate" noted above to move away from the Na+ entry/exit pathways. Thus it can no longer bind the ion, resulting in an inactive channel. Mutagenesis studies also support the observations.
A neat conclusion from a beautiful set of experiments. A fascinating example of how nature essentially and surprisingly uses high-school chemistry to modulate movements in complex proteins. And a highly successful and inspiring example of how efficient, long MD simulations can shed light on these crucial processes.
Arkin, I.T., Xu, H., Jensen, M.O., Arbely, E., Bennett, E.R., Bowers, K.J., Chow, E., Dror, R.O., Eastwood, M.P., Flitman-Tene, R., Gregersen, B.A., Klepeis, J.L., Kolossvary, I., Shan, Y., Shaw, D.E. (2007). Mechanism of Na+/H+ Antiporting. Science, 317(5839), 799-803. DOI: 10.1126/science.1142824