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The sequences of the separate subdomains were structurally aligned, and ancestral sequence prediction (based on the alignment and the inferred phylogenetic tree) was carried out using the Fast ML server.
Symmetrical backbones were produced using Rosetta symmetric docking, using the three individual subdomains of Myti Lec-1 as templates, but only subdomain-A gave the highest score to a trefoil-like assembly, so the other models were discarded.
The new protein, called “Mitsuba”, is based on the structure of the natural shellfish lectin Myti Lec-1, a member of a small lectin family that uses unique sequence motifs to bind α-D-galactose.
The three subdomains of Myti Lec-1 each carry one galactose binding site, and the 149-residue protein forms a tight dimer in solution.
Recently, we have experimented with the creation of perfectly symmetrical proteins from natural templates based on the view that many nearly symmetrical ring-shaped proteins have evolved through exactly such an intermediate phase.
This study describes a new artificial β-trefoil lectin that recognises Burkitt’s lymphoma cells, and which was designed with the intention of finding a basis for novel cancer treatments or diagnostics.We have refined the X-ray crystallographic structure of the symmetrical lectin to high resolution, and show that this artificial protein is significantly more stable than the parent protein, despite the loss of the dimer interface., and the structure of the apo-protein (PDB 3WMU) was chosen as the template to create Mitsuba.The sub-domains of Myti Lec-1 (labelled A, B and C from the N- to C-terminus) show more than 50% amino acid sequence similarity, and superposing these regions of the model with each other shows a main-chain root mean square deviation (RMSD) close to 1.0 Å.A key element of the design approach we adopted was to model the evolutionary development of the chosen natural template, and work from the most probable sequence that represented the blade of the presumed symmetrical intermediate.Here we have adopted a similar procedure and applied it to Myti Lec-1, to create a related protein with three identical subdomains, that retains sugar binding activity and the ability to bind selected cell types.