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A computational model of the LGI1 protein suggests a common binding site for ADAM proteins.

Leonardi E, Andreazza S, Vanin S, Busolin G, Nobile C, Tosatto SC - PLoS ONE (2011)

Bottom Line: The functional model indicates that epitempin could mediate the interaction between proteins localized to different synaptic sides in a static way, by forming a dimer, or in a dynamic way, by binding proteins at different times.The model was also used to predict effects of known disease-causing missense mutations.Most of the variants are predicted to alter protein folding while several other map to functional surface regions.In agreement with experimental evidence, this suggests that non-secreted LGI1 mutants could be retained within the cell by quality control mechanisms or by altering interactions required for the secretion process.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Padova, Padova, Italy.

ABSTRACT
Mutations of human leucine-rich glioma inactivated (LGI1) gene encoding the epitempin protein cause autosomal dominant temporal lateral epilepsy (ADTLE), a rare familial partial epileptic syndrome. The LGI1 gene seems to have a role on the transmission of neuronal messages but the exact molecular mechanism remains unclear. In contrast to other genes involved in epileptic disorders, epitempin shows no homology with known ion channel genes but contains two domains, composed of repeated structural units, known to mediate protein-protein interactions.A three dimensional in silico model of the two epitempin domains was built to predict the structure-function relationship and propose a functional model integrating previous experimental findings. Conserved and electrostatic charged regions of the model surface suggest a possible arrangement between the two domains and identifies a possible ADAM protein binding site in the β-propeller domain and another protein binding site in the leucine-rich repeat domain. The functional model indicates that epitempin could mediate the interaction between proteins localized to different synaptic sides in a static way, by forming a dimer, or in a dynamic way, by binding proteins at different times.The model was also used to predict effects of known disease-causing missense mutations. Most of the variants are predicted to alter protein folding while several other map to functional surface regions. In agreement with experimental evidence, this suggests that non-secreted LGI1 mutants could be retained within the cell by quality control mechanisms or by altering interactions required for the secretion process.

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EPTP model, structural analysis.A. Top (up) and bottom (down) view of electrostatic surface of EPTP model (negative charge in red and positive charge in blue); B. Top (up) and bottom (down) view of the conserved surface of EPTP model with ConSurf colouring from unconserved (cyan) to strictly conserved (magenta). C. Cartoon of the EPTP model in top and lateral view with ConSurf colouring. Spheres indicate residues found mutated in ADTLE patients with structural mutations indicated in red.
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pone-0018142-g006: EPTP model, structural analysis.A. Top (up) and bottom (down) view of electrostatic surface of EPTP model (negative charge in red and positive charge in blue); B. Top (up) and bottom (down) view of the conserved surface of EPTP model with ConSurf colouring from unconserved (cyan) to strictly conserved (magenta). C. Cartoon of the EPTP model in top and lateral view with ConSurf colouring. Spheres indicate residues found mutated in ADTLE patients with structural mutations indicated in red.

Mentions: The LGI1 structural model has been evaluated for both conserved regions and electrostatic surface (Figure 6). Using the alignment of different sequence families retrieved by BLAST, ConSurf does not reveal any particular conserved region. A conserved feature in all modular sheets from different propeller domains is a set of positions with non-polar side chains, generally non solvent accessible, located in the central part of the strands. Since the major determinant for β-propeller assembly is the packing of these residues, amino acids in these positions are free to be replaced by other amino acids with similar biochemical properties [12]. Interestingly, using only sequences of different LGI family members to build the alignment, ConSurf identifies a highly conserved circular region in the top face of the β-propeller. On the bottom face of the protein there are also some conserved sites that correspond to the WD motif and electrostatic surface analysis identifies an extended positively charged region (Figure 6). The top surface is formed by loops connecting strand D of one blade and strand A of the next (DA loops) and loops connecting strand B with strand C in the same blade (BC loops). The bottom surface is formed by loops connecting strand C and D of a blade (CD loops) and loops connecting strand A and B (AB loops) (Figure 5). The alignment of WD repeat sequences allowed the identification of regions of variable length. In some proteins, one or more of these variable regions can be long enough to form an independently folded domain while other insertions form a reverse turn or loop that protrudes from the bottom of the β-propeller [56]. The LGI1 β-propeller has an insertion in the AB loop of the fourth repeat, not presents in paralogous LGI members, that protrudes from the bottom surface (Fig. 2 and 7). This loop may contain a functional motif that contributes to the functional specificity of LGI1.


A computational model of the LGI1 protein suggests a common binding site for ADAM proteins.

Leonardi E, Andreazza S, Vanin S, Busolin G, Nobile C, Tosatto SC - PLoS ONE (2011)

EPTP model, structural analysis.A. Top (up) and bottom (down) view of electrostatic surface of EPTP model (negative charge in red and positive charge in blue); B. Top (up) and bottom (down) view of the conserved surface of EPTP model with ConSurf colouring from unconserved (cyan) to strictly conserved (magenta). C. Cartoon of the EPTP model in top and lateral view with ConSurf colouring. Spheres indicate residues found mutated in ADTLE patients with structural mutations indicated in red.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3066209&req=5

pone-0018142-g006: EPTP model, structural analysis.A. Top (up) and bottom (down) view of electrostatic surface of EPTP model (negative charge in red and positive charge in blue); B. Top (up) and bottom (down) view of the conserved surface of EPTP model with ConSurf colouring from unconserved (cyan) to strictly conserved (magenta). C. Cartoon of the EPTP model in top and lateral view with ConSurf colouring. Spheres indicate residues found mutated in ADTLE patients with structural mutations indicated in red.
Mentions: The LGI1 structural model has been evaluated for both conserved regions and electrostatic surface (Figure 6). Using the alignment of different sequence families retrieved by BLAST, ConSurf does not reveal any particular conserved region. A conserved feature in all modular sheets from different propeller domains is a set of positions with non-polar side chains, generally non solvent accessible, located in the central part of the strands. Since the major determinant for β-propeller assembly is the packing of these residues, amino acids in these positions are free to be replaced by other amino acids with similar biochemical properties [12]. Interestingly, using only sequences of different LGI family members to build the alignment, ConSurf identifies a highly conserved circular region in the top face of the β-propeller. On the bottom face of the protein there are also some conserved sites that correspond to the WD motif and electrostatic surface analysis identifies an extended positively charged region (Figure 6). The top surface is formed by loops connecting strand D of one blade and strand A of the next (DA loops) and loops connecting strand B with strand C in the same blade (BC loops). The bottom surface is formed by loops connecting strand C and D of a blade (CD loops) and loops connecting strand A and B (AB loops) (Figure 5). The alignment of WD repeat sequences allowed the identification of regions of variable length. In some proteins, one or more of these variable regions can be long enough to form an independently folded domain while other insertions form a reverse turn or loop that protrudes from the bottom of the β-propeller [56]. The LGI1 β-propeller has an insertion in the AB loop of the fourth repeat, not presents in paralogous LGI members, that protrudes from the bottom surface (Fig. 2 and 7). This loop may contain a functional motif that contributes to the functional specificity of LGI1.

Bottom Line: The functional model indicates that epitempin could mediate the interaction between proteins localized to different synaptic sides in a static way, by forming a dimer, or in a dynamic way, by binding proteins at different times.The model was also used to predict effects of known disease-causing missense mutations.Most of the variants are predicted to alter protein folding while several other map to functional surface regions.In agreement with experimental evidence, this suggests that non-secreted LGI1 mutants could be retained within the cell by quality control mechanisms or by altering interactions required for the secretion process.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Padova, Padova, Italy.

ABSTRACT
Mutations of human leucine-rich glioma inactivated (LGI1) gene encoding the epitempin protein cause autosomal dominant temporal lateral epilepsy (ADTLE), a rare familial partial epileptic syndrome. The LGI1 gene seems to have a role on the transmission of neuronal messages but the exact molecular mechanism remains unclear. In contrast to other genes involved in epileptic disorders, epitempin shows no homology with known ion channel genes but contains two domains, composed of repeated structural units, known to mediate protein-protein interactions.A three dimensional in silico model of the two epitempin domains was built to predict the structure-function relationship and propose a functional model integrating previous experimental findings. Conserved and electrostatic charged regions of the model surface suggest a possible arrangement between the two domains and identifies a possible ADAM protein binding site in the β-propeller domain and another protein binding site in the leucine-rich repeat domain. The functional model indicates that epitempin could mediate the interaction between proteins localized to different synaptic sides in a static way, by forming a dimer, or in a dynamic way, by binding proteins at different times.The model was also used to predict effects of known disease-causing missense mutations. Most of the variants are predicted to alter protein folding while several other map to functional surface regions. In agreement with experimental evidence, this suggests that non-secreted LGI1 mutants could be retained within the cell by quality control mechanisms or by altering interactions required for the secretion process.

Show MeSH
Related in: MedlinePlus