Conformational difference

Conformational Isomers. A molecule in a conformation into which its atoms return spontaneously after small displacements is termed a conformer. Different arrangements of atoms that can be converted into one another by rotation about single bonds are called conformational isomers (see Fig. 1.1). A pair of conformational isomers can be but do not have to be mirror images of each other. When they are not mirror images, they are called diastereomers. 

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 ... 

Tomato bushy stunt virus is a T = 3 plant virus with 180 chemically identical subunits. Each polypeptide chain is divided into several domains. The subunits preserve quasi-equivalent packing in most contact regions by conformational differences of the protein chains, especially a large change in... 

The catalytically active enzyme substrate complex is an interactive structure in which the enzyme causes the substrate to adopt a form that mimics the transition-state intermediate of the reaction. Thus, a poor substrate would be one that was less effective in directing the formation of an optimally active enzyme transition-state intermediate conformation. This active conformation of the enzyme molecule is thought to be relatively unstable in the absence of substrate, and free enzyme thus reverts to a conformationally different state. 

The parameter redundancy is also the reason that care should be exercised when trying to decompose energy differences into individual terms. Although it may be possible to rationalize the preference of one conformation over another by for example increased steric repulsion between certain atom pairs, this is intimately related to the chosen functional form for the non-bonded energy, and the balance between this and the angle bend/torsional terms. The rotational banier in ethane, for example, may be reproduced solely by an HCCH torsional energy term, solely by an H-H van der Waals repulsion or solely by H-H electrostatic repulsion. Different force fields will have (slightly) different balances of these terms, and while one force field may contribute a conformational difference primarily to steric interactions, another may have the... 

An interesting use of the Camps quinoline synthesis is in the ring contraction of macrocycles. Treatment of 9 member ring 24 with sodium hydroxide in water furnished quinolin-4-ol 25, while 26 furnishes exclusively quinolin-2-ol 27 under the same reaction conditions (no yield was given for either reaction). The reaction does not work with smaller macrocycles. The authors rationalize the difference in reactivity based upon ground state conformation differences, but do not elaborate. 

McCapra et al. (1994) and McCapra (1997) suggested that the color variation could be caused by the conformational difference of the oxyluciferin molecule, when the plane of thiazolinone is rotated at various angles against the plane of benzothiazole on the axis of the 2-2 bond the red light would be emitted at 90° angle, reflecting its minimum structural energy. 

Interactions with xanthan were investigated for some GAX fractions of wheat bran [109]. Whereas, for lowly substituted GaMs a synergy in viscosity was observed at low total polymer concentrations, yielding a maximum of the relative viscosity at nearly equal proportions of both polysaccharides [124], the xanthan/xylan mixtures at the same experimental conditions showed no synergy. The observed decrease in the relative viscosity values upon addition of the xylan indicates that a certain interaction with xanthan takes place, but that it leads to a contraction in the hydrodynamic volume. The authors suggested that structural and conformational differences between GaM and GAX might be the reason for this observation. 

In addition to this large movement of the Rieske protein, small but nevertheless significant conformational differences within the functional domain are observed. The structure of the functional domain of the Rieske subunit in the PGi22 crystal form showing the ci positional state is the same as that of the water soluble fragment... 

Protein conformation Differences in conformation of different proteins may facilitate or hinder access of processing enzymes to identical oligosaccharide chains. 

LI ligase s large intrinsic flexibility was revealed by the recent crystal structure of the ligation product of a reduced size variant with two vastly different conformers, differing by reorientation of one of the stems by around 80 A, that were resolved in the same asymmetric cell [106], Based on the presence/absence of specific contacts between distant conserved parts including the ligation site and a totally conserved residue, U38, one of the conformers was postulated to represent the catalytically active or on conformation, the other the inactive or off one [106],... 

First of all, most natively bright green or red GFPs crystallize with a nearly coplanar cis chromophore conformation, while all nonfluorescent chromoproteins seem to bear a trans and noncoplanar chromophore [38, 49]. For AvGFP, there is, up to now, no indication of a chromophore conformation different from the cis isomer. However, various other situations have been reported in the GFP family,... 

In summary, although subtle conformational differences between the various cycloamyloses and the effect of intramolecular hydrogen bonds on their solution conformations remain to be accurately resolved, overall structural features have been clearly defined. This is particularly advantageous and, in fact, a prerequisite if the cycloamyloses are to be profitably used as models for enzymatic or other catalytic processes. In subsequent sections of this article, various aspects of binding and catalysis will be explained on the basis of the chemical nature and geometrical dimensions of the cycloamylose cavity which is, in fact, their active site. 

Molecular mechanics (MM) calculations have been employed for determining dihedral angles and to establish a comparison with values calculated from coupling constants, during conformational studies of tricyclic and tetracyclic quinolizidine alkaloids. The MM results had to be treated with care, as they sometimes predicted ring conformations different to those supported by experimental data <1999JST215>. 

Analogous to the DuP 747 study, complete crystallographic information was not possible on the fosinopril sodium polymorphic system [25], Two known polymorphs (A and B) were studied via a multidisciplinary approach (XRD, IR, NMR, and thermal analysis). Complementary spectral data from IR and solid state 13C NMR revealed that the environment of the acetal sidechain of fosinopril sodium differed in the two forms. In addition, possible cis-trans isomerization about the CgN peptide bond may exist. These conformational differences are postulated as the origin of the observed polymorphism in fosinopril sodium in the absence of the crystallographic data for form B (single crystals not available). 

The use of solid state NMR for the investigation of polymorphism is easily understood based on the following model. If a compound exists in two, true polymorphic forms, labeled as A and B, each crystalline form is conformationally different. This means for instance, that a carbon nucleus in form A may be situated in a slightly different molecular geometry compared with the same carbon nucleus in form B. Although the connectivity of the carbon nucleus is the same in each form, the local environment may be different. Since the local environment may be different, this leads to a different chemical shift interaction for each carbon, and ultimately, a different isotropic chemical shift for the same carbon atom in the two different polymorphic forms. If one is able to obtain pure material for the two forms, analysis and spectral assignment of the solid state NMR spectra of the two forms can lead to the origin of the conformational differences in the two polymorphs. Solid state NMR is thus an important tool in conjunction with thermal analysis, optical microscopy, infrared (IR) spectroscopy, and powder... 

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