Similarity distance

Abstract. A smooth empirical potential is constructed for use in off-lattice protein folding studies. Our potential is a function of the amino acid labels and of the distances between the Ca atoms of a protein. The potential is a sum of smooth surface potential terms that model solvent interactions and of pair potentials that are functions of a distance, with a smooth cutoff at 12 Angstrom. Techniques include the use of a fully automatic and reliable estimator for smooth densities, of cluster analysis to group together amino acid pairs with similar distance distributions, and of quadratic progrmnming to find appropriate weights with which the various terms enter the total potential. For nine small test proteins, the new potential has local minima within 1.3-4.7A of the PDB geometry, with one exception that has an error of S.SA. 

As an example, Figure 7-21 shows that the — 3 orbitals of the copper atom have their maximum electron densities at similar distances from the nucleus. The same regularity holds for all other atoms. The quantum numbers other than tt affect orbital size only slightly. We describe these small effects in the context of orbital energies in Chapter 8. 

Studies of base-base CT in B-form DNA duplexes versus A-form DNA R-NA hybrids also confirmed our fundamental tenet that the pathway of efficient charge transfer will be the well-stacked pathway. In A-form duplexes considerable intra- and interstrand stacking exists. Not surprisingly then, in DNA RNA hybrids we observed a similar distance dependence for the yields of intra- and interstrand CT [105]. So, the distinction between intra- and interstrand CT observed in B-DNA duplexes truly correlates with differences in base stacking. 

Intramolecular Ru(II) to Cu(II) ET rates have been measured in two other blue copper proteins, stellacyanin [42, 43] and azurin [9, 13, 28]. Pseudomonas aeruginosa azurin has been ruthenated at His83 [13] (Fig. 5). The intramolecular Ru(II) to Cu(II) ET rate of 1.9 s was found to be independent of temperature [28]. The Cu reorganization enthalpy was estimated to be < 7 kcal/mol [13, 28], a value confirming that blue copper is structured for efficient ET. Again, a blue copper ET rate is low in comparison with heme protein rates over similar distances (at similar driving forces) (Table 1). 

A model of the full SCF/E2 complex [112] shows that the end of Skp2 which binds the substrate is pointed toward the Rbxl-bound E2, with a 50-A gap between the two. Models based on two other SCF structures show similar distances between the F-box protein and the E2 [109, 115]. Whether this gap can be bridged by the bound substrate is currently unclear. It has been suggested that the E2 may bind to Rbxl somewhat differently than UbcH7 is observed to bind in the c-Cbl RING/ UbcH7 complex, but it is not obvious that this can lead to a 20 A movement of the E2 toward the bound substrate as suggested [109]. 

The analysis of the EXAFS of alloy catalyst particles is inherently more complicated than that of single metals. In the case of PtRu catalysts there is an added complication that the backscattering from Pt and Ru neighbors at similar distances interfere with one another, giving rise to beats in the EXAFS data. This phenomenon was first described by McBreen and Mukerjee ° for a poorly alloyed 1 1 atomic ratio PtRu/C catalyst. The presence of beats in the EXAFS data is more apparent in the EXAFS obtained at the Pt L3 edge for a well mixed 1 1 PtRu/C catalyst than in that of a poorly mixed catalyst of the same composition, as shown in Figure 27 compare panels a and c. Pandya et al. showed that the beats occur because the difference in the backscattering phase shifts from Pt and Ru is... 

Similarity Distance In the case of a nonlinear method such as the k Nearest Neighbor (kNN) QSAR [41], since the models are based on chemical similarity calculations, a large similarity distance could signal query compounds that are too dissimilar to the... 

Further reaction of 53 with diphenyl phosphate afforded a phospho-diester-bridged dinuclear magnesium(II) complex 54. The Mg-Mg distance of 4.11 A is comparable to similar distances in the Klenow fragment of E. coli DNA polymerase I (3.9 A) (39), rat DNA polymerase j8 (4 A) (46), and inositol monophosphatase (3.8 A) (35). The flexibility of the bridging carboxylates in 52 is manifested by the ca. 0.75-A range of Mg-Mg distances in these complexes, which can readily adjust the metal coordination environment. 

Figure 1 shows Fourier transforms of EXAFS spectra of a few samples prepared. The radial distribution functions of these samples are different from that of nickel oxide or cobalt oxide [7]. All the Fourier transforms showed two peaks at similar distances (phase uncorrected) the peak between 1 and 2 A is ascribed to the M-0 bond (M divalent cation) and the peak between 2 and 3 A is ascribed to the M-O-M and M-O-Si bonds. The similar radial distribution functions in Figure 1 indicate that the local structures of X-ray absorbing atoms (Ni, Co, and Zn) are similar. No other bonds derived from metal oxides (nickel, cobalt and zinc oxides) were observed in the EXAFS Fourier transforms of the samples calcined at 873 K, which suggests that the divalent cations are incorporated in the octahedral lattice. 

The key finding of the preliminary investigations of such molecules is that the non-protein diporphyrin models can react many times faster (ca. 104) than similar protein-protein systems at similar distances between the reaction sites and similar AG°. This result minimally suggests that the protein matrix does not accelerate the electron transfer rate [104], although a final conclusion cannot be drawn on the basis of these very limited data. Further studies in this area are necessary. 

The establishment of fast electron transfer over these distances of up to 25 A is important, as similar distances are involved in certain natural redox partners. Thus cytochrome c and cytochrome c peroxidase form a complex in which the heme edge-to-edge separation is about 16 A. 

Finely powdered solid samples of ketodiester 1 (5 mg) were placed evently between two microscope slides (which also acted as a X >305 nm filter) and placed at a similar distance from a medium-pressure Hg Hanovia lamp. After 4 h of irradiation, compound 2 was obtained in 87% yield. 

The ability to separate the fiber-optic tip and sample by as much space as required makes Raman sampling extremely flexible. For example, 15-foot immersion probes to insert in the top of chemical reactors have been made. The laser beam travels down the 15-foot probe shaft, finally coming to a focus just outside of the optical window at the probe s tip. A photo of such a probe is shown in Figure 5.4(a). Non-contact probes could also be made to come to a focus at similar distances, but then the beam must be enclosed to address safety concerns. 

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