Figure 7.2 Representative orientations of HRP taken from docking calculations of (A) nonglycosylated HRP and (B,C) glycosylated HRP. (B) Extended carbohydrates, solution conditions and (C) folded-back carbohydrate, dry conditions. The surface of graphite used in the calculations is represented by a black plane in the bottom of the diagram. Coloring and molecular representation (surface, ribbon, and ball and stick) are identical to those used in Figure 7.1. The result of 250 docking runs suggests that the molecules come to rest on the surface in nonrandom orientations with preferentially maximal surface area in contact.

doi:10.1201/9780203908907-73

Chapter

Figure 7.2 Representative orientations of HRP taken from docking calculations of (A) nonglycosylated HRP and (B,C) glycosylated HRP. (B) Extended carbohydrates, solution conditions and (C) folded-back carbohydrate, dry conditions. The surface of graphite used in the calculations is represented by a black plane in the bottom of the diagram. Coloring and molecular representation (surface, ribbon, and ball and stick) are identical to those used in Figure 7.1. The result of 250 docking runs suggests that the molecules come to rest on the surface in nonrandom orientations with preferentially maximal surface area in contact.

Chapter

Figure 7.2 Representative orientations of HRP taken from docking calculations of (A) nonglycosylated HRP and (B,C) glycosylated HRP. (B) Extended carbohydrates, solution conditions and (C) folded-back carbohydrate, dry conditions. The surface of graphite used in the calculations is represented by a black plane in the bottom of the diagram. Coloring and molecular representation (surface, ribbon, and ball and stick) are identical to those used in Figure 7.1. The result of 250 docking runs suggests that the molecules come to rest on the surface in nonrandom orientations with preferentially maximal surface area in contact.

ABSTRACT

The [3Fe-4S] cluster in A.v. FdI is buried approximately 8 Å below the protein surface and the intervening space contains no water molecules (or spaces to accommodate them). These structural properties make A.v. FdI a valuable model system for studying the mechanism of discrete proton-transfer events inside a protein. Extensive studies have been made using protein film voltammetry-exploiting the fact that interfacial electron exchange is sufficiently facile (k0 is typically about 500 s−1) so that scan rates exceeding 100 V s−1 are able to reveal the coupled kinetics [60-63]. Figure 8 (top; see color plate) shows the structure in the vicinity of the [3Fe-4S] cluster. A clue to how protons are passed between the cluster and solvent was the knowledge that the carboxylate group from aspartate-15 (D15), which is salt-bridged with the −NH4+ from lysine (K)-84, lies some 5 Å from the cluster, and that this group moves away slightly when the cluster is reduced at pH values above 8 [42]. Aspartate (and glutamate) carboxylates are well known as proton-transfer agents in proteins, as is clear from recent studies of the lightdriven proton pump bacteriorhodopsin [64].