Accessing gap-junction channel structure-function relationships through molecular modeling and simulations.

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Published in BMC Cell Biol on January 17, 2017

Authors

F Villanelo1, Y Escalona1, C Pareja-Barrueto1, J A Garate1,2, I M Skerrett3, T Perez-Acle4,5

Author Affiliations

1: Computational Biology Lab. Fundación Ciencia & Vida, Santiago, Chile.
2: Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Playa Ancha, Valparaíso, Chile.
3: State University of New York (SUNY) Buffalo State, Buffalo, NY, 14222, USA.
4: Computational Biology Lab. Fundación Ciencia & Vida, Santiago, Chile. tomas@dlab.cl.
5: Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Playa Ancha, Valparaíso, Chile. tomas@dlab.cl.

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Emerging issues of connexin channels: biophysics fills the gap. Q Rev Biophys (2001) 4.76

Structure of the junction between communicating cells. Nature (1980) 4.68

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Principles that determine the structure of proteins. Annu Rev Biochem (1984) 4.15

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Properties of a nonjunctional current expressed from a rat connexin46 cDNA in Xenopus oocytes. J Gen Physiol (1993) 2.64

The isolation of mouse hepatocyte gap junctions. Preliminary chemical characterization and x-ray diffraction. J Cell Biol (1972) 2.45

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