Dynamics and function of proteins: the search for general concepts

For an understanding of the phenomena, the first condition is the introduction of adequate concepts; only with the help of the correct concepts can we really know what has been observed. When we enter a new field, very often new concepts are needed, and these new concepts usually come up in a rather unclear and undeveloped form. Later they are modified, sometimes they are almost completely abandoned and are replaced by better concepts which then, finally, are clear and well defined. Werner Heisenberg (1) Proteins execute and control essentially all functions in living organisms, and they do it elegantly and efficiently, with designs honed by billions of years of evolution. For each protein, we can ask how it performs its specific function. Because there are at least 100,000 different proteins, all important for life, the task to study, characterize, and understand all proteins will take a very long time. There may, however, be a complementary approach to the problem, namely to find general concepts, properties, and laws that characterize proteins and other biomolecules and that may lead to shortcuts in understanding newly discovered systems. The work of Reat and collaborators in this issue of the Proceedings (2) adds new information that bears on both aspects, the detailed function of a particular protein and insight into general concepts. Reat and coworkers study the dynamics of bacteriorhodopsin (BR) with neutron scattering and hydrogen-deuterium exchange. BR is a protein that converts light into energy by pumping protons across a membrane (3). It consists of seven closely packed, essentially parallel, α helices that tightly enclose a retinal. Light is absorbed by the retinal and, through conformational changes, transports a proton (p) from the cytosolic to the extracellular side of the membrane. This process cannot be static; the proton transport requires motions of the …