Computational prediction of atomic structures of helical membrane proteins aided by EM maps.

ABSTRACT: Integral membrane proteins pose a major challenge for protein-structure prediction because only approximately 100 high-resolution structures are available currently, thereby impeding the development of rules or empirical potentials to predict the packing of transmembrane alpha-helices. However, when an intermediate-resolution electron microscopy (EM) map is available, it can be used to provide restraints which, in combination with a suitable computational protocol, make structure prediction feasible. In this work we present such a protocol, which proceeds in three stages: 1), generation of an ensemble of alpha-helices by flexible fitting into each of the density rods in the low-resolution EM map, spanning a range of rotational angles around the main helical axes and translational shifts al

SUBMITTER: Kovacs JA 

PROVIDER: S-EPMC1959528 | biostudies-literature | 2007 Sep

REPOSITORIES: biostudies-literature