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

¹ The Scripps Research Institute

^* To whom correspondence should be addressed. E-mail: jkovacs{at}scripps.edu.

Submitted on November 28, 2006
Revised on January 16, 2007
Accepted on 27 April 2007

	Abstract

Integral membrane proteins pose a major challenge for protein-structure prediction because only 100 high-resolution structures are available currently, thereby impeding the development of rules or empirical potentials to predict the packing of transmembrane -helices. However, when a low-resolution 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 -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 along the density rods; (2) fast optimization of side chains and scoring of the resulting conformations; and (3) refinement of the lowest-scoring conformations with Internal Coordinate Mechanics, by optimizing the van der Waals, electrostatics, hydrogen bonding, torsional and solvation energy contributions. In addition, our method implements a penalty term through a so-called "tethering map," derived from the EM map, which restrains the positions of the -helices. The protocol was validated on three test cases: GpA, KcsA, and MscL.

Key Words: conformational search, electron-microscopy map, energy minimization, membrane proteins, protein structure prediction, tethering map