Structure-based factor

In a random porous network with fixed geometry and topology, the structure-based factor/(Xw) exhibits a percolation-type dependence on Xw. ... 

The main unknown in Equation 2.1 is the structure-based factor/ (X ). Assuming normal percolation behavior with X = 0.4, Xc = 0.1 and v = 2, gives/(X ) 0.1 and Oppf 0.05 S cm (at 25 C). This conductivity estimate is close to experimental values for Nafion and similar PEMs. Pore network reorganization as a result of swelling, including the merging of pores, could result in larger values of/(Xw). 

Fig. 5. Structure-based alignment of the sequences of the water-soluble Rieske fragment from bovine heart bci complex (ISF), the water-soluble Rieske fragment from spinach b f complex (RFS), and of the Rieske domain of naphthalene dioxygenase (NDO) and of the metal binding loops of rubredoxin (RXN) and transcriptional factor TFIIS (TFI). The numbering of the j3 strands is the same for the ISF and RFS. The metal binding ligands are highlighted the asterisks indicate those residues that are fully conserved between the three Rieske proteins.

This structure-based strategy was found to be very successful. All compounds in this series maintained excellent 5-HT1A affinity and a broad 5-HT /aj selectivity window while significantly reducing hERG binding by factors ranging from fivefold to more than 10-fold. 

Hilser, V.J. and E. Freire. 1996. Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors. 

While the x-ray structure of native Factor Xa has been reported [4] the nature of its crystal packing, specifically the fact that the active site of one Factor Xa molecule is blocked by the N-terminus of a second resulting in a continuous polymeric structure, apparently has precluded diffusing inhibitors into the preformed crystals to obtain complexes. Complexes with inhibitors cocrystallized with Factor Xa also have not been reported [81]. Thus, efforts to do structure-based design with this enzyme have relied on molecular modeling. 

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