Resolution modeling

Lederer, F., et al. Improvement of the 2.5 A resolution model of cytochrome bsea by redetermining the primary stmcture and using molecular graphics. 

Although their medium-resolution model was successful for a-helical proteins, folding P-hairpin structures have been difficult. In general, many off-lattice approaches have been tested, and although definitive proof does not exist in most cases, there appears to be a growing consensus that such off-lattice models are not sufficient. 

Low resolution models (20-30 A) based on diffraction analysis of membrane crystals of Na,K-ATPase [34,35,39] and Ca-ATPase [40,41] show that the cytoplasmic protrusions of the proteins are remarkably similar. A notable difference is a 10-20 A... 

Rawjee, Y. Y and Vigh, Gy., A peak resolution model for the capillary electrophoretic separation of the enantiomers of weak acids with hydroxypropyl (3-cyclodextrm-containing background electrolytes, Anal. Chem., 66, 619, 1994. 

At the antipodes of the latter description, there is a continuous need for better low-resolution models that involve, for instance, coarse graining of molecules, or implicit solvation. This need is motivated by the expectation that the free energy of a large system can be calculated with sufficient accuracy without requiring that all its components be described at the atomic level. In many cases, this is equivalent to the assumption that a mean-field approximation works, or that many fast degrees of freedom can be removed from the system, yet without any appreciable loss of... 

FIGURE 5-1 3 (A, B) Structure of a glutamate transporter. This bacterial glutamate transporter provides the first high-resolution model of a glutamate transporter [88]. The X-ray data indicate a trimeric structure. (A) A view of the trimer extracellularly and perpendicular to the bilayer. 

Oliveira, L., Paiva, A. C., and Vriend, G. (1999) A low resolution model for the interaction of G proteins with G protein-coupled receptors. Prot. Eng. 12,1087-1095. 

Recently, a low-resolution model of the chromatin core particle has been derived from a combination of single-crystal X-ray diffraction and electron microscopic data (Finch et al., 1977). The particle is described as a flat cylinder 110 A in diameter and 57 A in height. A similar shape and similar dimensions were found to be consistent with the low-angle neutron scattering from core particles in solution (Pardon et al., 1977 Suau et al., 1977). Some conclusions may be drawn concerning the conformation of the DNA. Presumably, the strong 28 A periodicity apparent in the crystal data (Finch et al., 1977) corresponds to the pitch of the DNA superhelix wound about the histone core. X-Ray and spectroscopic data suggest that the DNA super-... 

Note added IN Proof Klug et al. (1980) obtained regular fibers by the assembly of histone octamers at high salt. From image reconstruction of these histone fibers a 22-A resolution model was proposed for the histone octamer, which has a 2-fold axis of symmetry and is wedge-shaped. From this structure and the results of various cross-linking data an arrangement of the individual histones within the octamer has been proposed. 

Several steps were needed to determine the structure of the core particle to higher resolution (Fig. Id). The X-ray phases of the low-resolution models were insufficient to extend the structure to higher resolution, since the resolution of the early models of the NCP was severely limited by disorder in the crystals. The disorder was presumed to derive from both the random sequences of the DNA and from heterogeneity of the histone proteins caused by variability in post-translational modification of the native proteins. One strategy for developing an atomic position model of the NCP was to develop a high-resolution structure of the histone core. This structure could then be used with molecular replacement techniques to determine the histone core within the NCP and subsequently identify the DNA in difference Fourier electron density maps. 

The crystallization and structural determination of the histone octamer was first reported in 1984 [34], However, the overall dimensions of the 3.3 A structure [15] did not appear to fit within the known X-ray structures of the nucleosome core particle [12,13], In an elegant analysis [16], re-examination of the original phasing of the histone octamer data revealed misplacement of the heavy atom site by 2.7 A. The structure was resolved, after which it was possible to build molecular models of the individual histones into the 3.1 A resolution electron density map of the histone core of the nucleosome [17]. Figure 2 shows the first atomic resolution model of the core histone octamer. Several additional publications followed in which the histone octamer structure formed the basis for constructing models of the NCP [17-21],... 

E. coli has a specific three-dimensional conformation featuring extensive intrachain base pairing. The predicted secondary structure of the rRNAs (Fig. 27-10) has largely been confirmed in the high-resolution models, but fails to convey the extensive network of tertiary interactions evident in the complete structure. 

A detailed view of the kinesin-microtubule complex has been obtained by combining high-resolution structures of the individual components from X-ray crystallography (kinesin) and electron diffraction (tubulin Lowe et al., 2001 Nogales et al, 1998) with low-resolution models of kinesin-decorated microtubules obtained by cryoelectron microscopy and image reconstruction (Hirose et al, 1999 Hoenger et al., 2000 Kikkawa et al, 2001 Kozielski et al., 1998 Rice et al., 1999 Skiniotis et al., 2003 Wendt... 

Kikkawa, M., Okada, Y., and Hirokawa, N. (2000). 15 A resolution model of the monomeric kinesin motor, KIF1A. Cell 100, 241-252. 

Statistical (with observational data taken into account) scaling (reducing to a higher spatial resolution) of numerical modeling results obtained using low-resolution models. 

---