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All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences. Proc Natl Acad Sci U S A 2015 Apr 28;112(17):5413-8

Date

04/11/2015

Pubmed ID

25858953

Pubmed Central ID

PMC4418893

DOI

10.1073/pnas.1419956112

Scopus ID

2-s2.0-84928651779   38 Citations

Abstract

Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand-strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases.

Author List

Hayat S, Sander C, Marks DS, Elofsson A

Author

David S. Marks MD Vice Chair, Professor in the Medicine department at Medical College of Wisconsin




MESH terms used to index this publication - Major topics in bold

Artificial Intelligence
Escherichia coli
Escherichia coli Proteins
Models, Molecular
Protein Structure, Secondary
Protein Structure, Tertiary
Receptors, Cell Surface
Sequence Analysis, Protein