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Fig. 4. Comparative modeling and calculation of surface electrostatic potential for
L5 and L13–16. Structure-based alignments from
Fig. 3 were used as input in
the MODELLER version 9v1 (Sali and
Blundell, 1993) to develop Lospin models, which were subsequently
verified as described in Materials and methods. Electrostatic potential of the
template, 1AXZi (`A', native antithombin), 1BY7 (`B', plasminogen activator
inhibitor-2, negative control) and Lospin models were calculated as described
in Materials and methods and visualized using PyMol 0.99rev10
[(DeLano, 2002)
www.pymol.org]
at ±5kt/e of positive and negative contour fields. Structures D, E and
F denote Lospins 5, 13 and 16 models. Basic patches are indicated and marked
by a solid circle. C=Lospin 7 (control, has no basic residues on the
-helix D). Structures are shown back to front.
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