Atomic structure—cont

Lo Conte, L., Chothia, C and Janin, J. (1999) The atomic structure of protein-protein recognition sites../. Mol. Biol. 285,2177-2198. 

L. Lo Conte, C. Chothia, and J. Janin,/. Mol. Biol., 285, 2177-2198 (1999). The Atomic Structure of Protein-Protein recognition Sites. 

FIGURE 11.6 (cont d). (c) View onto a benzene molecule in the crystal structure, showing the intermolecular interactions listed in (b). Carbon and hydrogen atoms drawn with filled circles are those in one asymmetric unit. Positions of all other atoms are generated from these by application of the symmetry operations of the space group. 

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. 

Fig. 52. Stellerite. Projection along [100] of refined structure (a) phase A at RT. Ca atoms are represented by large light gray spheres and W oxygen atoms are the small dark gray spheres, (cont.)...

Fig. 48. (cont.) ZSM-5, mazzite. (b) Mazzite the effect of CP versus DEC C MAS NMR on the templates TMA and diaminohexane occluded in the structure (T = 383 K). There are two resonance lines at <5= 57.6 and 58.1 ppm originating respectively from TMA and TMAOH species present in the gmelite cage and lines at <5 = 41, 26, and 24 ppm are from different types of carbon atoms of the symmetric diaminohexane ions incorporated in the 12-ring channel [98K1]. 

The first band structure calculation for TiC, TiN, and TiO was performed by Bilz (13). He used a simplified linear combination of atomic orbitals (LCAO) method and considered only the M— X bonds as the important ones. From his results he inferred a charge transfer from the metal to the nonmetal atom. A completely opposite point of view was adopted by Costa and Conte (14). These authors ignored the M—X bonds and considered only the M—M bonds. According to their calculations, a transfer of electronic charge from the nonmetal to the metal atom should occur. Lye and Logothetis (15), using optical data to adjust the parameters in their... 

Fig. 2. Structural formula for inhibitors, substrate and transition state analogs, and reaction products bound to ribonucleases. Only polar hydrogen atoms are indicated, (cont.)...

---