APPLICATIONS

By J. William Bell and Barbara Jewett, NCSA -- Researchers use NCSA's Tungsten to investigate the protein lymphotactin, the gating pathways of mechanosensitive channels, and an allosteric signaling protein. A team of researchers from the University of Wisconsin at Madison are using NCSA's Tungsten supercomputing system to investigate lymphotactin, a protein manufactured by progenitor T-cells in the human body. Lymphotactin has been linked to autoimmune diseases and to the rejection of transplanted organs. Led by Qiang Cui, an assistant professor in the chemistry department, they are simulating the impact that temperature and salt concentration have on lymphotactin's structure. Protein structure can be influenced by such factors in the surrounding solvent, and it heavily influences protein function. Lymphotactin, for example, is thought to stimulate the immune system by binding to specific protein-coupled receptors on immune-system cells. It can only do that if it has taken on specific shapes. Contemporary experimental studies of the protein using nuclear magnetic resonance imaging tend to change temperature and salt concentration of lymphotactin's environment at the same time. In a paper published in the Journal of the American Chemical Society in July 2006, the Wisconsin team's molecular dynamics simulations treated these variables separately. They found that chloride from the salt in the solvent is more attracted to most sections of the protein at higher temperatures. In what is known as the "C-terminal helical region," however, both chloride and sodium distributions are higher at lower temperatures. The team also found that the C-terminal helix partially melts at higher temperatures, regardless of the amount of salt, whereas another region begins to form a helical structure at higher salt concentrations. "These explicit solvent simulations on the order of 70 nanoseconds would not be possible without the generous support of computational resources from NCSA. The user-friendly infrastructure of NCSA has not only provided the facility for carrying out the molecular simulations required by our projects but also stimulated us to pursue more challenging problems in the biophysical and biomedical area," says Cui. For example, the Cui group has also been using the NCSA resources to analyze the energetics associated with the conformational transitions in the molecular motor myosin. Specifically, free energy simulations are used to probe the energetic coupling between the conformation of the lever arm and the active site. Although these structural motifs are separated by more than 40 Å their motions have to be tightly coupled for myosin to avoid futile ATP hydrolysis and maintain a high working efficiency. Considering the large size of the system (about 800 amino acids), quantitative free energy simulations are impossible without the NCSA resources. These simulations will lay out a solid foundation for the development of coarse-grained models that capture the long-time behavior of myosin. Though these simulations only reveal the initial stages of lymphotactin's structural change, they demonstrate the significant impact that environmental variables can have. The team is now in the process of performing more extensive simulations for lymphotactin's other structural form, also under different salt concentrations and temperatures. "Nearly every single backbone hydrogen bond has to be broken in the structural conversion process," says Cui. "It's truly remarkable that these striking changes -- along with the tendency to dimerize, or bond two identical copies of the protein to one another -- are facilitated by something as simple as temperature and salt." Although it is unrealistic to expect to observe the entire structural transitions during the molecular dynamics simulations, hundreds of nanosecond simulations are expected to be very instructive regarding how environmental conditions stabilize different structural forms. The team also recently published NCSA-based simulations of the gating pathways of mechanosensitive channels of large conductance in two bacteria using a finite element method, as well as simulations showing the activation mechanism of a small signaling protein that exhibits allosteric characteristics, in the June 2006 issue of Proteins and the August 2006 issue of Biophysical Journal. Large-scale conformational transitions are crucial to the function of many proteins, yet the underlying mechanism remains elusive for most cases. This is because these transitions typically span a broad range of time and spatial scales, and therefore are difficult to characterize for both experiments and computations. The resources at NCSA are crucial to the development and application of novel computational techniques that can make a major contribution in this important area of biophysics. For example, the reported study of the mechanosensitive channel illustrated the great potential of continuum mechanics in describing functional transitions in proteins in response to the external perturbations like membrane deformation. At the same time, it also highlighted that a key challenge is to develop strategies to smoothly connect atomistic simulations with continuum mechanics models, which is an active area of research in the Cui group as well as his collaborators. In fact, says Cui, the work in this area done by Xi Chen and colleagues in the Civil Engineering and Engineering Mechanics Department at Columbia University was crucial to the mechanosensitive channel simulation. Three dimensional ion distribution averaged over the entire course of the explicit solvent-ion simulations of lymphotactin, pictured with the final snapshot for each simulation condition. ("n" and "s" indicate no salt and 200 mM salt, respectively; "10" and "45" indicate temperatures of 10 and 45 C, respectively.)n10n45s10s45 This research is supported by the National Institutes of Health, the National Science Foundation (CMS-0407743), the Research Corporation, and the Alfred P. Sloan Foundation. Team Members: University of Wisconsin at Madison Quang Cui Mark Formaneck Liang Ma Yang Yang Jejoong Yoo Haibo Yu Columbia University Xi Chen