All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences - PubMed (original) (raw)

All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

Sikander Hayat et al. Proc Natl Acad Sci U S A. 2015.

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.

Keywords: de novo 3D structure prediction; evolutionary couplings; hydrogen bonding; maximum-entropy analysis; transmembrane β-barrels.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.

Fig. 1.

EVfold_bb pipeline to de novo fold transmembrane β-barrels. EVFold-PLM is used to generate evolutionary couplings (ECs) from a multiple-sequence alignment of the target protein. Boctopus2 is used to assign β-strands. Alternative strand registrations are compared for successive relative shifts of adjacent strands up to plus or minus three residues. The configuration with the largest sum of EC values is chosen and distance constraints are applied on N–O atoms of alternate residue pairs. In addition, other nonstrand–strand constraints are used to de novo fold the protein. Multiple models are generated and blindly ranked.

Fig. 2.

Fig. 2.

Evolutionary couplings give residue pairs that are hydrogen bonded. From the evolutionary couplings (ECs) (black) predicted between residues (red) on strands 5 and 6 of EstA (Left), a subset of hydrogen-bonded pairs (dashed lines, where N–O distance ≤ 3.4 Å) is extracted. Predicted adjacent β-strands are shifted plus or minus three residues relative to each other to generate alternate configurations of residue pairs (Center). To select the best configuration, the EC strength of all pairs is summed and the highest-scoring configuration is selected; then distance constraints are applied to N–O atoms of alternate residue pairs (Right) to reflect N–H ... O = C hydrogen bonds.

Fig. 3.

Fig. 3.

Blinded benchmark de novo 3D models of transmembrane β-barrels. Shown are predicted contact maps (red, ECs; gray, crystal contacts ≤ 5 Å; blue, gaps in crystal structure) and front and top views of folded structures (red, de novo folded; gray, crystal structure) for six proteins in the dataset.

Fig. 4.

Fig. 4.

ECs predict interactions between loops/plugs and the barrel domain. Interactions between the barrel (245–774) and the plug (121–244) domain in FecA are highlighted in the predicted contact map (red, ECs; gray, crystal contacts ≤ 5 Å). Top 10 interdomain contacts between the barrel (red) and the plug domain (pink) are shown on the crystal structure and have a PPV of 0.9.

Similar articles

Cited by

References

    1. Freeman TC, Jr, Wimley WC. A highly accurate statistical approach for the prediction of transmembrane beta-barrels. Bioinformatics. 2010;26(16):1965–1974. - PMC - PubMed
    1. Imai K, Fujita N, Gromiha MM, Horton P. Eukaryote-wide sequence analysis of mitochondrial β-barrel outer membrane proteins. BMC Genomics. 2011;12:79. - PMC - PubMed
    1. Noinaj N, et al. Structural insight into the biogenesis of β-barrel membrane proteins. Nature. 2013;501(7467):385–390. - PMC - PubMed
    1. Schleiff E, Becker T. Common ground for protein translocation: Access control for mitochondria and chloroplasts. Nat Rev Mol Cell Biol. 2011;12(1):48–59. - PubMed
    1. Pagès JM, James CE, Winterhalter M. The porin and the permeating antibiotic: A selective diffusion barrier in Gram-negative bacteria. Nat Rev Microbiol. 2008;6(12):893–903. - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources