Bacterial communities within the human body greatly influence human health and play a significant role in diseas e predisposition, pathogenic, physical fitness, and dietary responsiveness. Importantly, bacteria utilize highly co operative macromolecular machines to accomplish many cellular functions. Here we seek to understand, with molecular and atomistic fidelity, two such machines: the cellulosome and the chemosensory array, which underlie the phenomen a of bacterial plant fiber degradation and chemotaxis respectively.
Biofuels: Bacteria can make a living off a very wide range of food sources. This agnosticism enables them to, among other things, serve as essential symbionts in animal digestive tracts where they assist their hosts in d egrading cellulose fibers into metabolizable compounds. In particular, bacteria in the rumen of the cow face an esp ecially tough job (see Tight Job in the Gut), digesting the hardy cellulose fibers of grasses. Key to their task are molecular tentacles on the cell s urface of certain gut bacteria, so-called cellulosomes (pictured right), which develop a tight grasp on cellulose a nd then effectively cleave the molecules. In general, human gut bacteria (and their role in the broader human micro biome) are one of the most intensely researched topics in medicine.
Bacterial Chemotaxis: Bacteria monitor their environments and respond by way of a fundamental sensory cap ability known as chemotaxis---one of the best studied behavioral systems in biology. Chemotactic responses in bacte ria involve large complexes of sensory proteins, known as chemosensory arrays, that process the information obtaine d from the bacteria's habitat to determine its swimming pattern. In this sense, the chemosensory array functions as a bacterial brain, transforming sensory input into motile output. Despite great strides in the understanding of ho w the chemosensory array's constituent proteins fit and work together, a high-resolution description has, until rec ently, remained elusive (see Computing the Bacterial Brain). Here we are combining computational and experimental techniques to explore in detail the molecular mechanisms underlying sensory signal transduction and amplification within this amazing biological appar atus.
Spotlight: Bacterium's Sweet Tooth (Dec 2006)
made with VMD
Escherichia coli are bacteria living in the intestines of mammals as part of their healthy gut flora, but also causing disease outside of the gut. The bacteria import from their environment nutriments, for example molecules of lactose, a sugar. For this purpose Escherichia coli employs in its cell membrane a protein channel, lactose permease, that translocates the sugar outside-in. This is the bacterium's "sweet tooth". To establish the unidirectional sugar transport, the bacterium utilizes an electrical potential maintained in the form of a trans-membrane proton gradient (more protons on the outer cellular than on the inner cellular side of the membrane). Protons, very small ions, that enter the channel from the outside one at a time, open the outer channel entrance. This permits access of lactose that gets bound inside the channel. Release of the proton to the cell interior closes the outer channel entrance and opens the inner channel entrance, such that the bound lactose can enter the cell. Despite extensive and elegant biochemical studies, the physical mechanism that couples unidirectional proton and sugar translocation is not yet known in detail. A crystallographic structure of lactose permease permitted now investigations into this mechanism by means of molecular dynamics simulations using NAMD. The simulations, reported in a recent publication, showed one step of the proton - sugar translocation, namely how binding and unbinding of the proton activates a spring-like bond, a so-called salt bridge, that closes and opens the inner channel exit. More information on the lactose permease project can be found here.