Abstract
Many of the most important functions in the cell are carried out by proteins organized in large molecular machines. Cryo-electron microscopy (cryo-EM) is increasingly being used to obtain low resolution density maps of these large assemblies. A new method, ATTRACT-EM, for the computational assembly of molecular assemblies from their components has been developed. Based on concepts from the protein-protein docking field, it utilizes cryo-EM density maps to assemble molecular subunits at near atomic detail, starting from millions of initial subunit configurations. The search efficiency was further enhanced by recombining partial solutions, the inclusion of symmetry information, and refinement using a molecular force field. The approach was tested on the GroES-GroEL system, using an experimental cryo-EM map at 23.5 Å resolution, and on several smaller complexes. Inclusion of experimental information on the symmetry of the systems and the application of a new gradient vector matching algorithm allowed the efficient identification of docked assemblies in close agreement with experiment. Application to the GroES-GroEL complex resulted in a top ranked model with a deviation of 4.6 Å (and a 2.8 Å model within the top 10) from the GroES-GroEL crystal structure, a significant improvement over existing methods.
Highlights
Proteins are the clockwork of the complex molecular machinery that underlies human life [1]
Our aim is to develop a cryo-electron microscopy (cryo-EM) fitting function that can be added as an energy term to ATTRACT, acting in synergy with the existing intermolecular energies
It is not our aim to develop a global cryo-EM fitting method, which attempts to maximize the overlap with the electron density; rather, the fitting function should restrict the conformational space that is available to the ATTRACT docking program
Summary
Proteins are the clockwork of the complex molecular machinery that underlies human life [1]. Many of the most important functions in the cell are carried out by proteins organized in molecular machines: large, dynamic, macromolecular assemblies such as the ribosome, the proteasome, the spliceosome and the nuclear pore complex [2,3,4,5]. Atomic-resolution techniques such as X-ray crystallography and Nuclear Magnetic Resonance (NMR) are often difficult to apply to large and dynamic macromolecular assemblies, implicating that other techniques are necessary. Insight at the atomic level can be obtained if the molecular machine can be assembled computationally from preexisting atomic structures using the cryo-EM map [9,10,11]. Many different algorithms have been developed for sequential, rigid fitting of single components into cryo-EM maps [6,17,18,19,20,21,22,23,24,25,26,27,28]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
