Homology modeling of major intrinsic proteins in rice, maize and Arabidopsis: comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters

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

Genome-wide analysis of major intrinsic proteins in the tree plant Populus trichocarpa: Characterization of XIP subfamily of aquaporins from evolutionary perspective

10.1186/1471-2229-9-134BMC Plant Biology913

Anion-selective Formate/nitrite transporters: taxonomic distribution, phylogenetic analysis and subfamily-specific conservation pattern in prokaryotes

Abstract Background The monovalent anions formate, nitrite and hydrosulphide are main metabolites of bacterial respiration during anaerobic mixed-acid fermentation. When accumulated in the cytoplasm, these anions become cytotoxic. Membrane proteins that selectively transport these monovalent anions across the membrane have been identified and they belong to the family of Formate/Nitrite Transporters (FNTs). Individual members that selectively transport formate, nitrite and hydrosulphide have been investigated. Experimentally determined structures of FNTs indicate that they share the same hourglass helical fold with aquaporins and aquaglyceroporins and have two constriction regions, namely, cytoplasmic slit and central constriction. Members of FNTs are found in bacteria, archaea, fungi and protists. However, no FNT homolog has been identified in mammals. With FNTs as potential drug targets for many bacterial diseases, it is important to understand the mechanism of selectivity and transport across these transporters. Results We have systematically searched the sequence databases and identified 2206 FNT sequences from bacteria, archaea and eukaryotes. Although FNT sequences are very diverse, homology modeling followed by structure-based sequence alignment revealed that nearly one third of all the positions within the transmembrane region exhibit high conservation either as a group or at the level of individual residues across all three kingdoms. Phylogenetic analysis of prokaryotic FNT sequences revealed eight different subgroups. Formate, nitrite and hydrosulphide transporters respectively are clustered into two (FocA and FdhC), three (NirC-α, NirC-β and NirC-γ) and one (HSC) subfamilies. We have also recognized two FNT subgroups (YfdC-α and YfdC-β) with unassigned function. Analysis of taxonomic distribution indicates that each subfamily prefers specific taxonomic groups. Structure-based sequence alignment of individual subfamily members revealed that certain positions in the two constriction regions and some residues facing the interior show subfamily-specific conservation. We have also identified examples of FNTs with the two constriction regions formed by residues that are less frequently observed. We have developed dbFNT, a database of FNT models and associated details. dbFNT is freely available to scientific community. Conclusions Taxonomic distribution and sequence conservation of FNTs exhibit subfamily-specific features. The conservation pattern in the central constriction and cytoplasmic slit in the open and closed states are distinct for YfdC and NirC subfamilies. The same is true for some residues facing the interior of the transporters. The specific residues in these positions can exert influence on the type of solutes that are transported by these proteins. With FNTs found in many disease-causing bacteria, the knowledge gained in this study can be used in the development and design of anti-bacterial drugs

ATCUN-like metal-binding motifs in proteins: identification and characterization by crystal structure and sequence analysis

The amino terminal Cu(II)- and Ni(II)-binding (ATCUN) motif is a small metal-binding site found in the N-terminus of many naturally occurring proteins. The ATCUN motif has been implicated in DNA cleavage and has been shown to have antitumor activity. In proteins, the ATCUN motif is formed from a histidine in the third position, its preceding residue and the free N-terminus. Four nitrogen atoms from these three residues act as metal ligands. Knowledge of metal-binding geometry helps in the design of metal-binding peptides and in understanding of the mechanisms of metal-mediated functions. Since the N-terminus region of ATCUN-containing proteins is highly disordered, no geometrical features can be derived from the protein structures. However, the crystal structure of a small metal-bound ATCUN peptide shows that the nitrogen ligands form a distorted square planar geometry. Distance constraints derived from this designed peptide were used to search 1949 polypeptide chains to find ATCUN-like motifs in any position along the polypeptide chain. Only ≈1.9% and ≈0.3% of histidines are involved in partial and full ATCUN-like geometric features, respectively. These two datasets were compared with the dataset of all histidines. None of the ATCUN-like motifs occur in the middle of an α-helix or a β-strand. Further sequence analysis revealed total conservation of ATCUN histidines in four proteins including the transcription factor TBX3, implicated in Ulnar-Mammary Syndrome. Our analysis suggests that the ATCUN-like motif in TBX3 is a potential metal-binding site, although a structural role was not completely ruled out. Metal-binding activity in TBX3, if confirmed, will help us to understand the role of metals in transcriptional regulation and is likely to cast light on the causes of some serious genetic disorders. A conformational role is suggested for ATCUN-like motifs in other proteins

Homology modeling of major intrinsic proteins in rice, maize and : comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters-1

<p><b>Copyright information:</b></p><p>Taken from "Homology modeling of major intrinsic proteins in rice, maize and : comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters"</p><p>http://www.biomedcentral.com/1472-6807/7/27</p><p>BMC Structural Biology 2007;7():27-27.</p><p>Published online 19 Apr 2007</p><p>PMCID:PMC1866351.</p><p></p> the residues forming the ar/R tetrad from the superposed structures are shown in ball-and-stick model. Residue names in one letter code are given for SoPIP2;1 in green and for GlpF in blue. The transmembrane segments and the loop regions to which these residues belong are indicated. The projection shown for each filter is viewed perpendicular to the membrane plane from the extracellular side

Homology modeling of major intrinsic proteins in rice, maize and : comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters-2

<p><b>Copyright information:</b></p><p>Taken from "Homology modeling of major intrinsic proteins in rice, maize and : comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters"</p><p>http://www.biomedcentral.com/1472-6807/7/27</p><p>BMC Structural Biology 2007;7():27-27.</p><p>Published online 19 Apr 2007</p><p>PMCID:PMC1866351.</p><p></p>pose was generated by the T-Coffee program [81]. As observed in and maize, rice MIPs also can be classified into four subfamilies. OsPIPs, OsTIPs, OsNIPs and OsSIPs respectively indicate plasma membrane intrinsic proteins, tonoplast intrinsic proteins, Nod26-like intrinsic proteins and small basic intrinsic proteins from rice. Thirty three out of thirty nine sequences have been identified by Sakurai et al. [43]. The additional six sequences identified in this study are shown within gray boxes

Homology modeling of major intrinsic proteins in rice, maize and : comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters-3

<p><b>Copyright information:</b></p><p>Taken from "Homology modeling of major intrinsic proteins in rice, maize and : comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters"</p><p>http://www.biomedcentral.com/1472-6807/7/27</p><p>BMC Structural Biology 2007;7():27-27.</p><p>Published online 19 Apr 2007</p><p>PMCID:PMC1866351.</p><p></p>and TM4–TM6 (right) are shown. The backbone is drawn in ribbon representation and the interfacial residues are depicted as space-filling models. Residue numbers of interfacial residues correspond to the PDB structure

Homology modeling of major intrinsic proteins in rice, maize and : comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters-6

<p><b>Copyright information:</b></p><p>Taken from "Homology modeling of major intrinsic proteins in rice, maize and : comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters"</p><p>http://www.biomedcentral.com/1472-6807/7/27</p><p>BMC Structural Biology 2007;7():27-27.</p><p>Published online 19 Apr 2007</p><p>PMCID:PMC1866351.</p><p></p>s B and E are shown. Right: Residues forming the Ar/R selectivity filters of modeled and the X-ray structures are shown after superposition in ball-and-stick representation. The transmembrane segments and the loop regions to which these residues belong are indicated. There is an excellent agreement between the modeled and the X-ray structures in the transmembrane region

Homology modeling of major intrinsic proteins in rice, maize and : comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters-4

<p><b>Copyright information:</b></p><p>Taken from "Homology modeling of major intrinsic proteins in rice, maize and : comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters"</p><p>http://www.biomedcentral.com/1472-6807/7/27</p><p>BMC Structural Biology 2007;7():27-27.</p><p>Published online 19 Apr 2007</p><p>PMCID:PMC1866351.</p><p></p>osed individually on glycerol transporter GlpF (blue) and only the residues forming the ar/R tetrad from the superposed structures are shown in ball-and-stick model. Residue names in one letter code are given for OsTIP4;2 in red, for OsNIP2;1 in pink and for GlpF in blue. The transmembrane segments and the loop regions to which these residues belong are indicated. The projection shown for each filter is viewed perpendicular to the membrane plane from the extracellular side