The primary goal of our group continues to be development of structural models for the transmembrane portions of membrane proteins. Our most noted work has been on potassium channels and proteins, such as sodium and calcium channels and some active potassium transporters, that evolved from them. The recent determination of a crystal structure of a bacterial potassium channel, KcsA, allows us to better evaluate our methods and results, and lets us move on to a more precise level of molecular modeling that may be useful for structure-based drug design. Much of our work during this period was devoted to analyzing the evolutionary relationship between potassium channels and proteins that transport potassium across the membrane against its electrochemical gradient. We utilized statictical methods to demonstrate that the primary transporting subunit of four families of symporters (TrkH and KtrB in bacteria, Trk1,2 in fungi, and Hkt1 in plants) and one family of ATP-driven transporter (KdpA in bacteria)evolved from potassium channels. These proteins appear to have a transmembrane topology in which the M1-P-M2 transmembrane motif of the four identical subunits of a potassium channel has been duplicated four times within the single transporting subunit of the transporters. We also developed three dimensional computer models of one TrkH, one KtrB, and one Trk1,2 subunit; and have developed hypothesis for the molecular mechanisms by which potassium ions are transported. These models are supported by results from numerous mutagenesis experiments, some of which were performed in the laboratories of our collaborators. We are also using our modeling methods to predict how some channels open and close. Beginning with the crystal structure of the KcsA potassium channel, which is in a closed conformation, we have developed three dimensional models of human inwardly rectifying potassium channels in both open and closed conformations. Likewise, beginning with the crystal structure of a closed mechanosensitive channel, mscL, we have developed models for an open conformation and numerous conformations that are intermediate between the closed and open conformations. Z01 BC 08363-17 - computational chemistry, ion channels, membrane proteins, molecular models, protein structure, transport proteins,
