Circular conformation

This concept is demonstrated schematically in Figure 1.11. It can be seen that the initial bias in a system of proteins containing two conformations (square and spherical) lies far toward the square conformation. When a ligand (filled circles) enters the system and selectively binds to the circular conformations, this binding process removes the circles driving the backward reaction from circles back to squares. In the absence of this backward pressure, more square conformations flow into the circular state to fill the gap. Overall, there is an enrichment of the circular conformations when unbound and ligand-bound circular conformations are totaled. 

As discussed in Section 3.3, when complexed 18-crown-6 assumes a circular conformation with CH bonds pointing outside the cavity 48a (Fig. 3.1), while in the free ligand the structure is squashed with the bonds pointing inside. Thus considerable free energy costs of preorganization must be overcome during the... 

Calix[8]arenes are also found to act as a ditopic receptor in most cases. The calixarenes assume various pinched conformations in these complexes, resembhng two calix[4]arene cone units hnked together. Two 1 1 complexes, of Ca° and Eu, have been characterized where a roughly planar circular conformation is observed, with only two of the phenolic O atoms interacting with the metal atom. It is interesting to note that the free jo-t-butylcalix[8]arene has been found to crystallize as a pyridine solvate with a planar, circular conformation in one case, and a pinched conformation in a subsequent report. 

Solid-state X-ray structural studies of the tetrakis HCl salt of 8.5 (i.e., 8.5b) revealed that the molecule does not exist in a planar, circular conformation as represented in Scheme 8.1.1. Rather, as depicted in Figures 8.1.2 and 8.1.3, the molecule adopts a helical twist and overall figure-eight conformation. This twisting makes 8.5b chiral by virtue of conformation and serves to define a pair of enantiomeric atropisomers, at least in the solid state. In solution, detailed H... 

Fixation of Ft(II) compounds on DNA does not cause chain breaks. A single chain break in supercoiled PM2 DNA convertsthe polymer from a compact closed circular conformation to a relaxed open circular form. This conformational change is an extremely sensitive measure of chain scission and it has been used to detect the nicking of DNA by Pt(II) compounds (24, 25, 26). Table II shows the percentage of nicked PM2 DNA molecules which were observed by electron microscopy after fixation of various amounts of the three platinum compounds on the DNA (25) It can be seen that below rb 0.1 none of the compounds cause chain breaks in the DNA. 

The intermediate, 5-aconitate, remains bound to the enzyme during the course of the reaction. There is some evidence that the citrate is complexed to the Fe(II) in the active site of the enzyme in such a way that the citrate curls back on itself in a nearly circular conformation. Several authors have been unable to resist the temptation to call this situation the ferrous wheel. ... 

The crystal structure of OA is characterized by a circular conformation that allows the interaction between its carboxylic group and the hydroxyl at carbon C-24. This spatial conformation exposes the methyl groups of OA at carbons C-10 and C-13 at the surface of the molecule, allowing an interaction with the protein phosphatase pi2-pi3 loop. The whole discussion reported above is based on the currently accepted structure of okadaic acid, although the definitive structural conformation has been recently questioned, requiring possible re-evaluation of the sites of interaction of OA with the phosphatase molecules. 

Several other natural, acyclic carboxylic ionophores are known. Among these, salinomycin is notable for its unusual tricyclic spiroketal ring system. Further, the ester of salinomycin affords complexes that have a helical, rather than circular," conformation.lonomycin " is likewise notable as the first example of a dibasic ion-ophore to be discovered. lonomycin has a high affinity for divalent cations such as Ca and Cd, owing to the presence of an enolized p diketone. 

Calix[8]arenes may adopt 16 main (basic) conformations[41] and numerous intermediate or distorted conformations related to the main ones. There are two extreme conformations the double cone or inverted double cone conformation which may be characterized as a compact one and mimics two joined together in parallel or antiparallel cones of calix[4]arenes and, at the other end, there is an extended nearly planar circular conformation which may be called rosette or pleated loop . This extreme conformations are exemplified by these found for para-sulphonatocalix[8] arene (Fig. 38.26). 

In order to reach a crystalline state, polymers must have sufficient freedom of motion. Polymer crystals nearly always consist of many strands with a parallel packing. Simply putting strands in parallel does not ensure that they will have the freedom of movement necessary to then find the low-energy con-former. The researcher can check this by examining the cross-sectional profile of the polymer (viewed end on). If the profile is roughly circular, it is likely that the chain will be able to change conformation as necessary. 

Dl A. Supercoiling. Supercoiling is a topological property of closed-circular DNA molecules. Circular DNA molecules can exist in various conformations differing in the number of times one strand of the helix crosses the other. These different isomeric conformations are called topoisomers and maybe characterized in terms of the linking number, Ek. A linear DNA molecule having Nbase pairs and h base pairs per turn of the helix, if joined end to end, has the following ... 

G. D. Fasman, ed.. Circular Dichroism and the Conformational Analysis of Biomolecules, Plenum Press, New York, 1996. 

Chirooptical properties give more subtle information on the conformational behavior of biopolymers and peptides in solution. In early experiments, optical rotation and optical rotatory dispersion (ORD) have been recognized as valuable techniques, followed more recently by significant progress and refinements in the equipment which have resulted in the routine measurements of applied circular dichroism (CD). 

Small-angle X-ray scattering (SAXS), circular dichroism (CD), and UV spectroscopy at different temperatures were used to investigate the nature of calf-thymus DNA in aqueous solution, in the presence of [Me Sn] " (n = 1-3) species. The results demonstrate that the [MeSn(IV)] moiety does not influence the structure and conformation of the DNA double helix, and does not degrade DNA, as indicated by agarose gel electrophoresis. Inter alia, the radii of gyration, Rg, of the cross section of native calf-thymus DNA, determined by SAXS in aqueous solution in the presence of [Me Sn] " (n = 1-3) species are constant and independent of the nature and concentration of the [Me Sn] species. 

These y9 -peptides are not expected to adopt a 3i4-helical conformation in an aqueous environment because of the destabihzing effect of cationic charges. The circular dichroism spectrum of a non-labeled analog of 165 does not display the characteristic signature of the 3i4-helix in aqueous solution however it is highly hehcoidal in MeOH. 

---