Topology prediction of Brucella abortus Omp2b and Omp2a porins after critical assessment of transmembrane β strands prediction by several secondary structure prediction methods

Jean-Yves Paquet, Carlota Vinals Bassols, Johan Wouters, Jean-Jacques Letesson, Eric Depiereux

Research output: Contribution to journalArticle

Abstract

In order to propose a reliable model for Brucella porin topology, several structure prediction methods were evaluated in their ability to predict porin topology. Four porins of known structure were selected as test- cases and their secondary structure delineated. The specificity and sensitivity of 11 methods were separately evaluated. Our critical assessment shows that some secondary structure prediction methods (PHD, Dsc, Sopma) originally designed to predict globular protein structure are useful on porin topology prediction. The overall best prediction is obtained by combining these three 'generalist' methods with a transmembrane β strand prediction technique. This 'consensus' method was applied to Brucella porins Omp2b and Omp2a, sharing no sequence homology with any other porin. The predicted topology is a 16-stranted antiparallel β barrel with Omp2a showing a higher number of negatively charged residue in the exposed loops than Omp2b. Experiments are in progress to validate the proposed topology and the functional hypotheses. The ability of the proposed consensus method to predict topology of complex outer membrane protein is briefly discussed.

Original languageEnglish
Pages (from-to)747-757
Number of pages11
JournalJournal of biomolecular structure and dynamics
Volume17
Issue number4
Publication statusPublished - 29 Feb 2000

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