GORGON

Baylor College Of Medicine, Houston TX

Investigators

Linked publications, trials & patents

Abstract

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. As cryo-EM pushes towards atomic resolution, more complete and accurate annotation of the density map becomes possible. At subnanometer resolutions, secondary structure elements become visible;alpha helices ap-pear as cylinders and beta sheets appear as thin, flat planes. These features can be represented as simple geometric objects, having no relationship to the primary sequence. Moving to slightly higher resolutions, con-nectivity between the secondary structure elements can be seen, from which simple cartoon structural models can be derived, as in the 6.8 [unreadable] resolution structure of RDV (Zhou et al., 2001). Once 4.5 [unreadable] resolution has been reached, the pitch of the alpha helices, as well as separation of the strands in beta sheets become visible. At this resolution (4.5-4.2 [unreadable]), it has been possible to construct C-alpha backbone models for GroEL and epsilon15 phage (Jiang et al., 2008;Ludtke et al., 2008). In addition, some bulky amino acid sidechains can be seen, although their shapes generally remain ambiguous. Presently, Mat Baker and co-workers are developing a graphical tool, called Gorgon, which helps to automate and simplify these cryo-EM modeling steps. Current model generation is largely a manual process that can take weeks to months. Gorgon will allow for rapid and accurate model generation, which will be necessary as we move to other maps. This de novo cryo-EM modeling approach will help to bridge the gap between cryo-EM and X-ray crystallography.