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Homology modeling of representative subfamilies of Arabidopsis major intrinsic proteins. Classification based on the aromatic/arginine selectivity filter.
Plant Physiol. 2004 Jun; 135(2):1059-68.PP

Abstract

Major intrinsic proteins (MIPs) are a family of membrane channels that facilitate the bidirectional transport of water and small uncharged solutes such as glycerol. The 35 full-length members of the MIP family in Arabidopsis are segregated into four structurally homologous subfamilies: plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), nodulin 26-like intrinsic membrane proteins (NIPs), and small basic intrinsic proteins (SIPs). Computational methods were used to construct structural models of the putative pore regions of various plant MIPs based on homology modeling with the atomic resolution crystal structures of mammalian aquaporin 1 and the bacterial glycerol permease GlpF. Based on comparisons of the narrow selectivity filter regions (the aromatic/Arg [ar/R] filter), the members of the four phylogenetic subfamilies of Arabidopsis MIPs can be classified into eight groups. PIPs possess a uniform ar/R signature characteristic of high water transport aquaporins, whereas TIPs are highly diverse with three separate conserved ar/R regions. NIPs possess two separate conserved ar/R regions, one that is similar to the archetype, soybean (Glycine max) nodulin 26, and another that is characteristic of Arabidopsis NIP6;1. The SIP subfamily possesses two ar/R subgroups, characteristic of either SIP1 or SIP2. Both SIP ar/R residues are divergent from all other MIPs in plants and other kingdoms. Overall, these findings suggest that higher plant MIPs have a common fold but show distinct differences in proposed pore apertures, potential to form hydrogen bonds with transported molecules, and amphiphilicity that likely results in divergent transport selectivities.

Authors+Show Affiliations

Department of Biochemistry, Cellular, and Molecular Biology and Center of Excellence in Structural Biology, The University of Tennessee, Knoxville, Tennessee 37996, USA.No affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, U.S. Gov't, P.H.S.

Language

eng

PubMed ID

15181215

Citation

Wallace, Ian S., and Daniel M. Roberts. "Homology Modeling of Representative Subfamilies of Arabidopsis Major Intrinsic Proteins. Classification Based On the Aromatic/arginine Selectivity Filter." Plant Physiology, vol. 135, no. 2, 2004, pp. 1059-68.
Wallace IS, Roberts DM. Homology modeling of representative subfamilies of Arabidopsis major intrinsic proteins. Classification based on the aromatic/arginine selectivity filter. Plant Physiol. 2004;135(2):1059-68.
Wallace, I. S., & Roberts, D. M. (2004). Homology modeling of representative subfamilies of Arabidopsis major intrinsic proteins. Classification based on the aromatic/arginine selectivity filter. Plant Physiology, 135(2), 1059-68.
Wallace IS, Roberts DM. Homology Modeling of Representative Subfamilies of Arabidopsis Major Intrinsic Proteins. Classification Based On the Aromatic/arginine Selectivity Filter. Plant Physiol. 2004;135(2):1059-68. PubMed PMID: 15181215.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Homology modeling of representative subfamilies of Arabidopsis major intrinsic proteins. Classification based on the aromatic/arginine selectivity filter. AU - Wallace,Ian S, AU - Roberts,Daniel M, Y1 - 2004/06/04/ PY - 2004/6/8/pubmed PY - 2004/8/31/medline PY - 2004/6/8/entrez SP - 1059 EP - 68 JF - Plant physiology JO - Plant Physiol VL - 135 IS - 2 N2 - Major intrinsic proteins (MIPs) are a family of membrane channels that facilitate the bidirectional transport of water and small uncharged solutes such as glycerol. The 35 full-length members of the MIP family in Arabidopsis are segregated into four structurally homologous subfamilies: plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), nodulin 26-like intrinsic membrane proteins (NIPs), and small basic intrinsic proteins (SIPs). Computational methods were used to construct structural models of the putative pore regions of various plant MIPs based on homology modeling with the atomic resolution crystal structures of mammalian aquaporin 1 and the bacterial glycerol permease GlpF. Based on comparisons of the narrow selectivity filter regions (the aromatic/Arg [ar/R] filter), the members of the four phylogenetic subfamilies of Arabidopsis MIPs can be classified into eight groups. PIPs possess a uniform ar/R signature characteristic of high water transport aquaporins, whereas TIPs are highly diverse with three separate conserved ar/R regions. NIPs possess two separate conserved ar/R regions, one that is similar to the archetype, soybean (Glycine max) nodulin 26, and another that is characteristic of Arabidopsis NIP6;1. The SIP subfamily possesses two ar/R subgroups, characteristic of either SIP1 or SIP2. Both SIP ar/R residues are divergent from all other MIPs in plants and other kingdoms. Overall, these findings suggest that higher plant MIPs have a common fold but show distinct differences in proposed pore apertures, potential to form hydrogen bonds with transported molecules, and amphiphilicity that likely results in divergent transport selectivities. SN - 0032-0889 UR - https://www.unboundmedicine.com/medline/citation/15181215/Homology_modeling_of_representative_subfamilies_of_Arabidopsis_major_intrinsic_proteins__Classification_based_on_the_aromatic/arginine_selectivity_filter_ L2 - https://academic.oup.com/plphys/article-lookup/doi/10.1104/pp.103.033415 DB - PRIME DP - Unbound Medicine ER -