Water—Cont structure

Table 17.3 (cont.) Structures of tested organic solutes and herbicides, their water solubility and Ln(K ) values. ... 

Figure 3.31 As (due to orientational response of aqueous solvent) versus e, calculated for ET in a large binuclear transition metal complex (D (Ru2+/3+) and A (Co2+/3+) sites bridged by a tetraproline moiety) molecular-level results obtained from a nonlocal polarization response theory (NRFT, solid lines) continuum results are given by dashed lines, referring to numerical solution of the Poisson equation with vdW (cont./vdW) and SAS (cont./SAS) cavities, or as the limit of the NRFT results when the full k-dependent structure factor (5(k)) is replaced by 5(0) 5(k) for bulk water was obtained from a fluid model based on polarizable dipolar spheres (s = 1.8 refers to ambient water (square)). For an alternative model based on TIP3 water (where, nominally, 6 = ), ambient water corresponds to the diamond. (Reprinted from A. A. Milishuk and D. V. Matyushov, Chem Phys., 324, 172. Copyright (2006), with permission from Elsevier).

Fig. 11 Three-dimensional structures of epothilones determined in different environments (O red, S yellow, N dark blue). Top structures of free EpoA determined by X-ray crystallography from dichloromethane/petroleum ether (top left [9 8] (a)) and from methanol/water (top right [143](b)). Bottom structures of EpoA bound to tubulin determined by solution NMR in aqueous medium (bottom left [96]) and by electron crystallography from zinc-stabilized tubulin sheets (bottom right [26]).(a) The crystal structure data have been available from the author to interested research groups since October 1995.(b) H.-J. Hecht, G. Hofle, unpublished results CCDC 241333 and CCDC 241334 contain the crystallographic data of this structure. These data can be obtained free of charge via www.ccdc.cam.ac.uk/conts/retiieving.html (or from the Cambridge Crystallographic Data Centre, 12, Union Road, Cambridge CB2 1EZ, UK fax (+ 44) 1223-336-033 or deposit cede. cam. ac. uk)...

FIGURE 15.9 (cont d). Crystal structure of an aralkylated peptide showing segregation of hydrophobic and hydrophilic portions of molecules into different regions as they pack, (b) Diagram of the molecular packing, and (c) view of the crystal structure. Crystals contain two molecules of water per alkylated peptide molecule (Ref. 61). 

The Voronoi calculation can be performed on protein atoms buried at interfaces as well as inside proteins. However, the procedure has a serious limitation a Voronoi polyhedron can be drawn around an atom only if it is completely surrounded by other atoms. At interfaces, only about one-third of the atoms that contribute to the interface area B have zero accessible surface area. These atoms are located mostly at the center of the interface, which biases the F/Fq ratio in an opposite way to the gap index, which is biased toward the periphery. However, high-resolution X-ray structures usually report positions for immobilized water molecules, which are abundant at interfaces (see Section II,D). These molecules may also be used to close the polyhedra, making the evaluation of Voronoi volumes possible for atoms which are surrounded by both protein atoms and immobilized water molecules (Fig. 4). On average, there are as many such interface atoms as there are completely buried atoms. Thus, a Voronoi calculation taking into account the crystallographic water molecules applies to two-thirds of the interface atoms on average instead of only one-third and up to 90% in specific cases (Lo Conte et al., 1999). 

In the 75 protein-protein complexes of Lo Conte et al. (1999), 96% of the interfaces have V/Vq in the range 0.97-1.06. Thus, the packing of atoms buried at protein-protein interfaces is very similar to that of the protein interior. In 36 complexes with X-ray structures at a resolution of 2.5 A and better, the V/Vq ratios calculated in the presence of water molecules were distributed over a narrow range of 0.97-1.03 (Fig. 5, top). Therefore, their interfaces are packed like the protein core, except that water, which is almost entirely excluded from the protein core, makes an important contribution to the packing at protein-protein interfaces. There is one exception to this rule in the sample analyzed by Lo Conte et al. (1999) the complex between cytochrome peroxidase and cytochrome c [PDB code, Iccp (Pelletier and Kraut, 1992)]. Its interface is small and has only a few buried atoms and a large volume ratio (1.07). In contrast, the 19 protease-inhibitor and the 19 antigen-antibody complexes of this sample have mean V/Vq ratios of 1.00 and 1.01, respectively. Thus, unlike 5c and the gap index, the volume ratio indicates that these two types of interfaces are close-packed and shows no difference in their packing density, at least for their buried atoms. 

Table B. Physico-Chemical Parameters (in relation to the water s natural structure) (cont.)...

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