We describe a modeling procedure that allowed computing the three dimensional low-resolution folding (3D) of a set of very important human membrane proteins, mitochondrial porins, or voltage-dependent anion selective channels (VDACs) whose structure is not yet known with atomic resolution. Our procedure is a somewhat modified threading procedure that takes advantage of aligning the predicted membrane domains starting from the protein sequence with a suited bacterial template of undetectable sequence homology with the target and of the rather conserved architecture of the membrane protein type known as beta-barrel. By this it was possible to overcome the absence of homologous sequences with known atomic structure in the PDB data base and compute a set of models that are good enough to fit most of the existing experimental data. Our results add to the structural data base, and allow the possibility to have computed models carefully built to design experiments of site directed mutagenesis and/or adopt the models for interpreting phenomelogical-biophysical characterization of transmembrane transport. The repository of VDAC models is available at http://gpcr2.biocomp.unibo.it/~vdac/.
A repository of 3D models of human VDACs
FARISELLI P.;
2008-01-01
Abstract
We describe a modeling procedure that allowed computing the three dimensional low-resolution folding (3D) of a set of very important human membrane proteins, mitochondrial porins, or voltage-dependent anion selective channels (VDACs) whose structure is not yet known with atomic resolution. Our procedure is a somewhat modified threading procedure that takes advantage of aligning the predicted membrane domains starting from the protein sequence with a suited bacterial template of undetectable sequence homology with the target and of the rather conserved architecture of the membrane protein type known as beta-barrel. By this it was possible to overcome the absence of homologous sequences with known atomic structure in the PDB data base and compute a set of models that are good enough to fit most of the existing experimental data. Our results add to the structural data base, and allow the possibility to have computed models carefully built to design experiments of site directed mutagenesis and/or adopt the models for interpreting phenomelogical-biophysical characterization of transmembrane transport. The repository of VDAC models is available at http://gpcr2.biocomp.unibo.it/~vdac/.
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