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Int J Mol Sci. 2016 Apr 21;17(4). pii: E599. doi: 10.3390/ijms17040599.

In Silico Structure and Sequence Analysis of Bacterial Porins and Specific Diffusion Channels for Hydrophilic Molecules: Conservation, Multimericity and Multifunctionality.

Author information

1
Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital and University of Oslo, PO box 28, N-1478 Lørenskog, Norway. h.s.vollan@studmed.uio.no.
2
Norwegian Institute of Public Health, Box 4404 Nydalen, N-0403 Oslo, Norway. h.s.vollan@studmed.uio.no.
3
Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital and University of Oslo, PO box 28, N-1478 Lørenskog, Norway. t.m.tannas@medisin.uio.no.
4
Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands. vriend@cmbi.ru.nl.
5
Norwegian Institute of Public Health, Box 4404 Nydalen, N-0403 Oslo, Norway. geir.bukholm@fhi.no.
6
Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Pb 5003, N-1430 Ås, Norway. geir.bukholm@fhi.no.

Abstract

Diffusion channels are involved in the selective uptake of nutrients and form the largest outer membrane protein (OMP) family in Gram-negative bacteria. Differences in pore size and amino acid composition contribute to the specificity. Structure-based multiple sequence alignments shed light on the structure-function relations for all eight subclasses. Entropy-variability analysis results are correlated to known structural and functional aspects, such as structural integrity, multimericity, specificity and biological niche adaptation. The high mutation rate in their surface-exposed loops is likely an important mechanism for host immune system evasion. Multiple sequence alignments for each subclass revealed conserved residue positions that are involved in substrate recognition and specificity. An analysis of monomeric protein channels revealed particular sequence patterns of amino acids that were observed in other classes at multimeric interfaces. This adds to the emerging evidence that all members of the family exist in a multimeric state. Our findings are important for understanding the role of members of this family in a wide range of bacterial processes, including bacterial food uptake, survival and adaptation mechanisms.

KEYWORDS:

bacteria; entropy-variability analysis; multiple sequence analysis; porins; specific diffusion channels; structure analysis; β-barrel membrane proteins

PMID:
27110766
PMCID:
PMC4849052
DOI:
10.3390/ijms17040599
[Indexed for MEDLINE]
Free PMC Article

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