Predicting a double mutant in the twilight zone of low homology modeling for the skeletal muscle voltage-gated sodium channel subunit beta-1 (Nav1.4 β1)
The molecular structure modeling of the β1 subunit of the skeletal muscle voltage-gated sodium channel (Nav1.4) was carried out in the twilight zone of very low homology. Structural significance can per se be confounded with random sequence similarities. Hence, we combined (i) not automated computat...
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Published in | Computational and structural biotechnology journal Vol. 13; no. C; pp. 229 - 240 |
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Main Authors | , , , , , , |
Format | Journal Article |
Language | English |
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Research Network of Computational and Structural Biotechnology
2015
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Abstract | The molecular structure modeling of the β1 subunit of the skeletal muscle voltage-gated sodium channel (Nav1.4) was carried out in the twilight zone of very low homology. Structural significance can per se be confounded with random sequence similarities. Hence, we combined (i) not automated computational modeling of weakly homologous 3D templates, some with interfaces to analogous structures to the pore-bearing Nav1.4 α subunit with (ii) site-directed mutagenesis (SDM), as well as (iii) electrophysiological experiments to study the structure and function of the β1 subunit. Despite the distant phylogenic relationships, we found a 3D-template to identify two adjacent amino acids leading to the long-awaited loss of function (inactivation) of Nav1.4 channels. This mutant type (T109A, N110A, herein called TANA) was expressed and tested on cells of hamster ovary (CHO). The present electrophysiological results showed that the double alanine substitution TANA disrupted channel inactivation as if the β1 subunit would not be in complex with the α subunit. Exhaustive and unbiased sampling of "all β proteins" (Ig-like, Ig) resulted in a plethora of 3D templates which were compared to the target secondary structure prediction. The location of TANA was made possible thanks to another "all β protein" structure in complex with an irreversible bound protein as well as a reversible protein-protein interface (our "Rosetta Stone" effect). This finding coincides with our electrophysiological data (disrupted β1-like voltage dependence) and it is safe to utter that the Nav1.4 α/β1 interface is likely to be of reversible nature. |
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AbstractList | The molecular structure modeling of the β1 subunit of the skeletal muscle voltage-gated sodium channel (Nav1.4) was carried out in the twilight zone of very low homology. Structural significance can per se be confounded with random sequence similarities. Hence, we combined (i) not automated computational modeling of weakly homologous 3D templates, some with interfaces to analogous structures to the pore-bearing Nav1.4 α subunit with (ii) site-directed mutagenesis (SDM), as well as (iii) electrophysiological experiments to study the structure and function of the β1 subunit. Despite the distant phylogenic relationships, we found a 3D-template to identify two adjacent amino acids leading to the long-awaited loss of function (inactivation) of Nav1.4 channels. This mutant type (T109A, N110A, herein called TANA) was expressed and tested on cells of hamster ovary (CHO). The present electrophysiological results showed that the double alanine substitution TANA disrupted channel inactivation as if the β1 subunit would not be in complex with the α subunit. Exhaustive and unbiased sampling of “all β proteins” (Ig-like, Ig) resulted in a plethora of 3D templates which were compared to the target secondary structure prediction. The location of TANA was made possible thanks to another “all β protein” structure in complex with an irreversible bound protein as well as a reversible protein–protein interface (our “Rosetta Stone” effect). This finding coincides with our electrophysiological data (disrupted β1-like voltage dependence) and it is safe to utter that the Nav1.4 α/β1 interface is likely to be of reversible nature. The molecular structure modeling of the β1 subunit of the skeletal muscle voltage-gated sodium channel (Na v 1.4) was carried out in the twilight zone of very low homology. Structural significance can per se be confounded with random sequence similarities. Hence, we combined (i) not automated computational modeling of weakly homologous 3D templates, some with interfaces to analogous structures to the pore-bearing Na v 1.4 α subunit with (ii) site-directed mutagenesis (SDM), as well as (iii) electrophysiological experiments to study the structure and function of the β1 subunit. Despite the distant phylogenic relationships, we found a 3D-template to identify two adjacent amino acids leading to the long-awaited loss of function (inactivation) of Na v 1.4 channels. This mutant type (T109A, N110A, herein called TANA) was expressed and tested on cells of hamster ovary (CHO). The present electrophysiological results showed that the double alanine substitution TANA disrupted channel inactivation as if the β1 subunit would not be in complex with the α subunit. Exhaustive and unbiased sampling of “all β proteins” (Ig-like, Ig) resulted in a plethora of 3D templates which were compared to the target secondary structure prediction. The location of TANA was made possible thanks to another “all β protein” structure in complex with an irreversible bound protein as well as a reversible protein–protein interface (our “Rosetta Stone” effect). This finding coincides with our electrophysiological data (disrupted β1-like voltage dependence) and it is safe to utter that the Na v 1.4 α/β1 interface is likely to be of reversible nature. |
Author | Mancilla-Simbro, Claudia Paiz-Candia, Bertin Islas, Ángel A Sánchez-Solano, Alfredo Salinas-Stefanon, Eduardo M Scior, Thomas Millan-Perez Peña, Lourdes |
AuthorAffiliation | b Laboratorio de Biofísica, Instituto de Fisiología, Universidad Autónoma de Puebla, Puebla, Mexico a Facultad de Ciencias Químicas, Universidad Autónoma de Puebla, Puebla, Mexico c Centro de Química, Instituto de Ciencias, Universidad Autónoma de Puebla, Puebla, Mexico |
AuthorAffiliation_xml | – name: c Centro de Química, Instituto de Ciencias, Universidad Autónoma de Puebla, Puebla, Mexico – name: a Facultad de Ciencias Químicas, Universidad Autónoma de Puebla, Puebla, Mexico – name: b Laboratorio de Biofísica, Instituto de Fisiología, Universidad Autónoma de Puebla, Puebla, Mexico |
Author_xml | – sequence: 1 givenname: Thomas surname: Scior fullname: Scior, Thomas organization: Facultad de Ciencias Químicas, Universidad Autónoma de Puebla, Puebla, Mexico – sequence: 2 givenname: Bertin surname: Paiz-Candia fullname: Paiz-Candia, Bertin organization: Facultad de Ciencias Químicas, Universidad Autónoma de Puebla, Puebla, Mexico – sequence: 3 givenname: Ángel A surname: Islas fullname: Islas, Ángel A organization: Laboratorio de Biofísica, Instituto de Fisiología, Universidad Autónoma de Puebla, Puebla, Mexico – sequence: 4 givenname: Alfredo surname: Sánchez-Solano fullname: Sánchez-Solano, Alfredo organization: Laboratorio de Biofísica, Instituto de Fisiología, Universidad Autónoma de Puebla, Puebla, Mexico – sequence: 5 givenname: Lourdes surname: Millan-Perez Peña fullname: Millan-Perez Peña, Lourdes organization: Centro de Química, Instituto de Ciencias, Universidad Autónoma de Puebla, Puebla, Mexico – sequence: 6 givenname: Claudia surname: Mancilla-Simbro fullname: Mancilla-Simbro, Claudia organization: Laboratorio de Biofísica, Instituto de Fisiología, Universidad Autónoma de Puebla, Puebla, Mexico – sequence: 7 givenname: Eduardo M surname: Salinas-Stefanon fullname: Salinas-Stefanon, Eduardo M organization: Laboratorio de Biofísica, Instituto de Fisiología, Universidad Autónoma de Puebla, Puebla, Mexico |
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Keywords | Ig-like Site-directed mutagenesis MD-2 Nav1.4, skeletal muscle voltage-gated sodium channel MD-2, myeloid differentiation factor 2 (MD-2) TLR4, Toll-like receptor type 4 Analogy modeling Trk, tyrosine receptor Patch-clamp CDR1 SDM, site-directed mutagenesis |
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Title | Predicting a double mutant in the twilight zone of low homology modeling for the skeletal muscle voltage-gated sodium channel subunit beta-1 (Nav1.4 β1) |
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