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EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps.


ABSTRACT: In medium-resolution (7-10 A) cryo-electron microscopy (cryo-EM) density maps, alpha helices can be identified as density rods whereas beta-strand or loop regions are not as easily discerned. We are proposing a computational protein structure prediction algorithm "EM-Fold" that resolves the density rod connectivity ambiguity by placing predicted alpha helices into the density rods and adding missing backbone coordinates in loop regions. In a benchmark of 11 mainly alpha-helical proteins of known structure a native-like model is identified in eight cases (rmsd 3.9-7.9 A). The three failures can be attributed to inaccuracies in the secondary structure prediction step that precedes EM-Fold. EM-Fold has been applied to the approximately 6 A resolution cryo-EM density map of protein IIIa from human adenovirus. We report the first topological model for the alpha-helical 400 residue N-terminal region of protein IIIa. EM-Fold also has the potential to interpret medium-resolution density maps in X-ray crystallography.

SUBMITTER: Lindert S 

PROVIDER: S-EPMC3760413 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature

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EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps.

Lindert Steffen S   Staritzbichler René R   Wötzel Nils N   Karakaş Mert M   Stewart Phoebe L PL   Meiler Jens J  

Structure (London, England : 1993) 20090701 7


In medium-resolution (7-10 A) cryo-electron microscopy (cryo-EM) density maps, alpha helices can be identified as density rods whereas beta-strand or loop regions are not as easily discerned. We are proposing a computational protein structure prediction algorithm "EM-Fold" that resolves the density rod connectivity ambiguity by placing predicted alpha helices into the density rods and adding missing backbone coordinates in loop regions. In a benchmark of 11 mainly alpha-helical proteins of known  ...[more]

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