Computational prediction of atomic structures of helical membrane proteins aided by EM maps.
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 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 alpha-helices. The protocol was validated on three test cases: GpA, KcsA, and MscL.
Kovacs
Julio A
JA
Department of Molecular Biology, Department of Cell Biology, The Scripps Research Institute, La Jolla, CA, USA. jkovacs@scripps.edu
Yeager
Mark
M
Abagyan
Ruben
R
D001426:Bacterial Proteins / Q000737:chemistry / Q000648:ultrastructure; D055592:Biophysical Phenomena; D001703:Biophysics; D006021:Glycophorins / Q000737:chemistry / Q000648:ultrastructure; D006801:Humans; D006860:Hydrogen Bonding; D007473:Ion Channels / Q000737:chemistry / Q000648:ultrastructure; D008565:Membrane Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D046529:Microscopy, Electron, Transmission; D008958:Models, Molecular; D015221:Potassium Channels / Q000737:chemistry / Q000648:ultrastructure; D017433:Protein Structure, Secondary; D055672:Static Electricity; D013816:Thermodynamics
D001426:Bacterial Proteins; C409972:GYPA protein, human; D006021:Glycophorins; D007473:Ion Channels; D008565:Membrane Proteins; D015221:Potassium Channels; C116377:Tb-MscL protein, Mycobacterium tuberculosis; C107790:prokaryotic potassium channel