Many proteins interact with gas molecules such as oxygen to perform their functions. In most cases, the gas molecules must reach sites buried deep inside the proteins that bind the molecules, with no obvious way in. Understanding how, for example, oxygen enters the protein, and mapping out which pathways it takes has been a long-standing challenge. As reported recently, computational biologists, inspired by previous work on the hydrogenase enzyme (see the September 2005 highlight), have developed a method, called implicit ligand sampling, that maps the pathways taken by gas molecules inside proteins. The mapping is determined by monitoring fluctuations of the protein, surprisingly, in the absence of the gas molecules. The mapping method is available in the most recent version of the program VMD used for structure and sequence analysis of proteins. The researchers applied the method to myoglobin, an oxygen-storing protein present in muscle cells, and determined detailed three-dimensional maps of oxygen and carbon monoxide pathways inside the protein (for more information see our web page). While some details of these pathways were already known from experiment, the implicit ligand maps revealed a large number of new pathways and suggest that oxygen enters myoglobin using many different entrance doors.

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