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Homology modeling of major intrinsic proteins in rice, maize and Arabidopsis: comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters.
BMC Struct Biol. 2007 Apr 19; 7:27.BS

Abstract

BACKGROUND

The major intrinsic proteins (MIPs) facilitate the transport of water and neutral solutes across the lipid bilayers. Plant MIPs are believed to be important in cell division and expansion and in water transport properties in response to environmental conditions. More than 30 MIP sequences have been identified in Arabidopsis thaliana, maize and rice. Plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), Nod26-like intrinsic protein (NIPs) and small and basic intrinsic proteins (SIPs) are subfamilies of plant MIPs. Despite sequence diversity, all the experimentally determined structures belonging to the MIP superfamily have the same "hour-glass" fold.

RESULTS

We have structurally characterized 39 rice and 31 maize MIPs and compared them with that of Arabidopsis. Homology models of 105 MIPs from all three plant species were built. Structure-based sequence alignments were generated and the residues in the helix-helix interfaces were analyzed. Small residues (Gly/Ala/Ser/Thr) are found to be highly conserved as a group in the helix-helix interface of MIP structures. Individual families sometimes prefer one or another of the residues from this group. The narrow aromatic/arginine (ar/R) selectivity filter in MIPs has been shown to provide an important constriction for solute permeability. Ar/R regions were analyzed and compared between the three plant species. Seventeen TIP, NIP and SIP members from rice and maize have ar/R signatures that are not found in Arabidopsis. A subgroup of rice and maize NIPs has small residues in three of the four positions in the ar/R tetrad, resulting in a wider constriction. These MIP members could transport larger solute molecules.

CONCLUSION

Small residues are group-conserved in the helix-helix interface of MIP structures and they seem to be important for close helix-helix interactions. Such conservation might help to preserve the hour-glass fold in MIP structures. Analysis and comparison of ar/R selectivity filters suggest that rice and maize MIPs could transport more diverse solutes than Arabidopsis MIPs. Thus the MIP members show conservation in helix-helix interfaces and diversity in aromatic/arginine selectivity filters. The former is related to structural stability and the later can be linked to functional diversity.

Authors+Show Affiliations

Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India. anjalib@iitk.ac.in <anjalib@iitk.ac.in>No affiliation info available

Pub Type(s)

Comparative Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

17445256

Citation

Bansal, Anjali, and Ramasubbu Sankararamakrishnan. "Homology Modeling of Major Intrinsic Proteins in Rice, Maize and Arabidopsis: Comparative Analysis of Transmembrane Helix Association and Aromatic/arginine Selectivity Filters." BMC Structural Biology, vol. 7, 2007, p. 27.
Bansal A, Sankararamakrishnan R. Homology modeling of major intrinsic proteins in rice, maize and Arabidopsis: comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters. BMC Struct Biol. 2007;7:27.
Bansal, A., & Sankararamakrishnan, R. (2007). Homology modeling of major intrinsic proteins in rice, maize and Arabidopsis: comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters. BMC Structural Biology, 7, 27.
Bansal A, Sankararamakrishnan R. Homology Modeling of Major Intrinsic Proteins in Rice, Maize and Arabidopsis: Comparative Analysis of Transmembrane Helix Association and Aromatic/arginine Selectivity Filters. BMC Struct Biol. 2007 Apr 19;7:27. PubMed PMID: 17445256.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Homology modeling of major intrinsic proteins in rice, maize and Arabidopsis: comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters. AU - Bansal,Anjali, AU - Sankararamakrishnan,Ramasubbu, Y1 - 2007/04/19/ PY - 2006/12/21/received PY - 2007/04/19/accepted PY - 2007/4/21/pubmed PY - 2008/11/14/medline PY - 2007/4/21/entrez SP - 27 EP - 27 JF - BMC structural biology JO - BMC Struct Biol VL - 7 N2 - BACKGROUND: The major intrinsic proteins (MIPs) facilitate the transport of water and neutral solutes across the lipid bilayers. Plant MIPs are believed to be important in cell division and expansion and in water transport properties in response to environmental conditions. More than 30 MIP sequences have been identified in Arabidopsis thaliana, maize and rice. Plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), Nod26-like intrinsic protein (NIPs) and small and basic intrinsic proteins (SIPs) are subfamilies of plant MIPs. Despite sequence diversity, all the experimentally determined structures belonging to the MIP superfamily have the same "hour-glass" fold. RESULTS: We have structurally characterized 39 rice and 31 maize MIPs and compared them with that of Arabidopsis. Homology models of 105 MIPs from all three plant species were built. Structure-based sequence alignments were generated and the residues in the helix-helix interfaces were analyzed. Small residues (Gly/Ala/Ser/Thr) are found to be highly conserved as a group in the helix-helix interface of MIP structures. Individual families sometimes prefer one or another of the residues from this group. The narrow aromatic/arginine (ar/R) selectivity filter in MIPs has been shown to provide an important constriction for solute permeability. Ar/R regions were analyzed and compared between the three plant species. Seventeen TIP, NIP and SIP members from rice and maize have ar/R signatures that are not found in Arabidopsis. A subgroup of rice and maize NIPs has small residues in three of the four positions in the ar/R tetrad, resulting in a wider constriction. These MIP members could transport larger solute molecules. CONCLUSION: Small residues are group-conserved in the helix-helix interface of MIP structures and they seem to be important for close helix-helix interactions. Such conservation might help to preserve the hour-glass fold in MIP structures. Analysis and comparison of ar/R selectivity filters suggest that rice and maize MIPs could transport more diverse solutes than Arabidopsis MIPs. Thus the MIP members show conservation in helix-helix interfaces and diversity in aromatic/arginine selectivity filters. The former is related to structural stability and the later can be linked to functional diversity. SN - 1472-6807 UR - https://www.unboundmedicine.com/medline/citation/17445256/Homology_modeling_of_major_intrinsic_proteins_in_rice_maize_and_Arabidopsis:_comparative_analysis_of_transmembrane_helix_association_and_aromatic/arginine_selectivity_filters_ L2 - https://bmcstructbiol.biomedcentral.com/articles/10.1186/1472-6807-7-27 DB - PRIME DP - Unbound Medicine ER -