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Transmembrane beta-barrel protein structure prediction

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Structural Bioinformatics of Membrane Proteins

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Abstract

Transmembrane β-barrel (TMB) proteins are embedded in the outer membranes of mitochondria, Gram-negative bacteria, and chloroplasts. These proteins perform critical functions, including active ion-transport and passive nutrient intake. Therefore, there is a need for accurate prediction of secondary and tertiary structures of TMB proteins. A variety of methods have been developed for predicting the secondary structure and these predictions are very useful for constructing a coarse topology of TMB structure; however, they do not provide enough information to construct a low-resolution tertiary structure for a TMB protein. In addition, while the overall structural architecture is well conserved among TMB proteins, the amino acid sequences are highly divergent. Thus, traditional homology modeling methods cannot be applied to many putative TMB proteins. Here, we describe the TMBpro: a pipeline of methods for predicting TMB secondary structure, β-residue contacts, and finally tertiary structure. The tertiary prediction method relies on the specific construction rules that TMB proteins adhere to and on the predicted β-residue contacts to dramatically reduce the search space for the model building procedure.

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  1. School of Information and Computer Sciences, Institute for Genomics and Bioinformatics, University of California-Irvine, Irvine, CA, USA

    Arlo Randall & Pierre Baldi

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  1. Arlo Randall
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  2. Pierre Baldi
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Randall, A., Baldi, P. (2010). Transmembrane beta-barrel protein structure prediction. In: Structural Bioinformatics of Membrane Proteins. Springer, Vienna. https://doi.org/10.1007/978-3-7091-0045-5_5

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  • DOI: https://doi.org/10.1007/978-3-7091-0045-5_5

  • Publisher Name: Springer, Vienna

  • Print ISBN: 978-3-7091-0044-8

  • Online ISBN: 978-3-7091-0045-5

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