Calculation of rigid-body conformational changes using restraint-driven Cartesian transformations

We present an approach for calculating conformational changes in membrane p roteins using limited distance information. The method, named restraint-dri ven Cartesian transformations, involves 1) the use of relative distance cha nges; 2) the systematic sampling of rigid body movements in Cartesian space ; 3) a penalty evaluation; and 4) model refinement using energy minimizatio n. As a test case, we have analyzed the structural basis of activation gati ng in the Streptomyces lividans potassium channel (KcsA). A total of 10 pai rs of distance restraints derived from site-directed spin labeling and elec tron paramagnetic resonance (SDSL-EPR) spectra were used to calculate the o pen conformation of the second transmembrane domains of KcsA (TM2). The SDS L-EPR based structure reveals a gating mechanism consistent with a scissori ng-type motion of the TM2 segments that includes a pivot point near middle of the helix. The present approach considerably reduces the amount of time and effort required to establish the overall nature of conformational chang es in membrane proteins. It is expected that this approach can be implement ed into restrained molecular dynamics protocol to calculate the structure a nd conformational changes in a variety of membrane protein systems.