Virtual conformation

Y, and Z are connected by bonds of fixed length joined at fixed valence angles, that atoms W, X, and Y are confined to fixed positions in the plane of the paper, and that torsional rotation 0 occurs about the X-Y bond which allows Z to move on the circular path depicted. If the rotation 0 is "free such that the potential energy is constant for all values of 0, then all points on the circular locus are equally probable, and the mean position of Z, i.e., the terminus of , lies at point z. The mean vector would terminate at z for any potential function symmetric in 0 for any potential function at all, except one that allows absolutely no rotational motion, the vector will terminate at a point that is not on the circle. Thus, the mean position of Z as seen from W is not any one of the positions that Z can actually adopt, and, while the magnitude ll may correspond to some separation that W and Z can in fact achieve, it is incorrect to attribute the separation to any real conformation of the entity W-X-Y-Z. Mean conformations tiiat would place Z at a position z relative to the fixed positions of W, X, and Y have been called "virtual" conformations.i9,20it is clear that such conformations can never be identified with any conformation that the molecule can actually adopt... 

In a study of mannose oligosaccharides, a single structure fitted the RDC data however, a dynamic ensemble of structures was required to predict the experimental relaxation data.147 The possibility that a single structure could correspond to a virtual conformer should therefore never be ruled out. Its consistency with experimental data sampling motions on different timescales, that is, 1H—XH NOE, 3 7ch and iJcc scalar couplings, or relaxation data, should always be checked.147,156... 

As mentioned earlier, in the event that interresidue NOEs arise from averaging of conformations, the use of ISPA distances as constraints may lead to virtual conformations. Moreover, the ISPA assumption that no spin diffusion is occurring is generally true only when the NOE mixing times are extremely short. In... 

R and M M Hann 2000. The In Silico World of Virtual Libraries. Drug Discovery Today 5 326-336. R and I D Kuntz 1990. Conformational Analysis of Flexible Ligands in Macromolecular eptor Sites. Journal of Computational Chemistry 13 730-748. 

In the absence of an electric field, the dome-closed conformation must be the most stable tip structure, even when spot-welds are considered, since only the perfectly dome-closed tip has no dangling bonds (i.e., it is a true hemifullerene). At the 3000°C temperature of the arc, the rate of tip annealing should be so fast that it is sure to find its most stable structure (i.e., to close as a dome). Clear evidence of this facile closure is the fact that virtually all nanotubes found in the arc deposit are dome-closed. (Even stronger evidence is the observation of only dome-closed nanotubes made at 1200°C by the oven laser vaporization method.) Such considerations constituted the original motivation for the electric field hypothesis. 

Baumgartner and coworkers [145,146] study lipid-protein interactions in lipid bilayers. The lipids are modeled as chains of hard spheres with heads tethered to two virtual surfaces, representing the two sides of the bilayer. Within this model, Baumgartner [145] has investigated the influence of membrane curvature on the conformations of a long embedded chain (a protein ). He predicts that the protein spontaneously localizes on the inner side of the membrane, due to the larger fluctuations of lipid density there. Sintes and Baumgartner [146] have calculated the lipid-mediated interactions between cylindrical inclusions ( proteins ). Apart from the... 

As noted, hemoglobin is an tetramer. Each of the four subunits has a conformation virtually identical to that of myoglobin. Two different types of subunits, a and /3, are necessary to achieve cooperative Oa-binding by Hb. The /3-chain at 146 amino acid residues is shorter than the myoglobin chain (153 residues), mainly because its final helical segment (the H helix) is shorter. The a-chain (141 residues) also has a shortened H helix and lacks the D helix as well (Figure 15.28). Max Perutz, who has devoted his life to elucidating the atomic structure of Hb, noted very early in his studies that the molecule was... 

A model for the allosteric behavior of hemoglobin is based on recent observations that oxygen is accessible only to the heme groups of the a-chains when hemoglobin is in the T conformational state. Perutz has pointed out that the heme environment of /3-chains in the T state is virtually inaccessible because of steric hindrance by amino acid residues in the E helix. This hindrance dis-... 

If the sequence of a protein has more than 90% identity to a protein with known experimental 3D-stmcture, then it is an optimal case to build a homologous structural model based on that structural template. The margins of error for the model and for the experimental method are in similar ranges. The different amino acids have to be mutated virtually. The conformations of the new side chains can be derived either from residues of structurally characterized amino acids in a similar spatial environment or from side chain rotamer libraries for each amino acid type which are stored for different structural environments like beta-strands or alpha-helices. 

Zirconocene dichloride 121 derived from (l-phenylethyl)cyclopentadienyl ligand is formed as a mixture of diastereomers from which the racemic form can be isolated by fractional crystallization. This complex was studied by X-ray diffraction methods and revealed a virtually chiral C2-symmetrical conformation in which the chiral ring-substituents are arranged in a synclinal position relative to the five-membered ring. It was proposed that this conformation is preserved in solution. Using 121 as catalyst the influence of double stereodifferentiation during isospecific polymerization of propylene (Eq. 32) was demonstrated for the first time [142],... 

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