As the NIH Resource for Resource for Macromolecular Modeling and Bioinformatics, the group invites collaborations with biomedical and biomaterials researchers on new and challenging projects. Projects of this kind include the design of novel biomaterials and proteins, and simulations of very large scale systems (eg ribosome), chaperone proteins (eg GroEL, GroES), and molecular motors.

The group favors studies which can benefit from our expertise in large scale systems, physical analysis, molecular electronics, and Interactive Molecular Dynamics.

Gold Binding Proteins

GBP adsorbed onto Au surface Through modelling and quantum chemical studies, the group is supporting the design of novel proteins in collaboration with M. Sarikaya, U. Washington, Seattle. It is hypothesized that electrostatic interactions between the polar residues of this genetically engineered polypeptide and the gold surface allow stronger adsorbtion onto the {111} surface than to other Au crystal faces, thus influencing the crystalization of gold in the presence of this polypeptide.

Mechanosensitive Channels

Mechanosensitive channels (MscL) open a conductance pore in cell membranes in response to mechanical stress. Molecular dynamics simulations of the channel-membrane system can provide a description of the mechanical properties of this channel. We plan to simulate a MscL-POPC membrane system at constant surface tension, corresponding to the closed-to-open transition tention as determined experimentally. MscL Channel


kinesin The discovery of the crystal structure of the kinesin motor domain has made it possible to study kinesin's dynamics by computer simulations. To model pH- and nucleotide-dependent changes in the kinesin structure, we carried out conformational searches by simulated annealing. The conformational differences of the ATP-bound protein relative to the ADP-bound state can be attributed to a force-producing power stroke.