Spatial conformation

Secondary structure can be described as the local spatial conformation of a polypeptide s backbone, excluding the constituent amino acid s side chains. The major elements of secondary structure are the a-helix and P-strands, as described below. 

The spatial conformation that the ligand-receptor acquires, particularly the spatial disposition that helix 12 of the LBD attains when it binds to estradiol, is key for the subsequent recruitment of the transcription cofactors (Fig. 1.9). Indeed, the arrival of estradiol restructures the entire domain, making helix 12 rotate and close the hole where the leucine zipper sequence of the corepressor had been lodged before (Fig. 1.10). Consequently, both molecules, corepressor and receptor, lose their affinity and their bond is undone. Another structure capable of interacting with gene transcription coactivators is formed at the same place on the receptor (MacGregor et al. 1998 McDonnell et al. 2002). 

The significance of conjugation as a contributor to the substantivity of dyes for cellulose is not always easy to distinguish from the effect of the degree of linearity of the molecule. Almost all direct dye molecules possess flexible chains of aryl nuclei linked by azo or other unsaturated groups. Such structures can readily adopt a near-linear spatial conformation, as... 

Enzyme is a globular protein with an active site which binds to substrate molecules and helps to catalyze a reaction by holding melecules in the correct spatial conformation for the reaction to take place. Enzymes are important to health many diseases are derived fron the lack of enzymes in the body. In enzyme-histochemical chromogenic reactions, a soluble colorless substrate is converted into a water-insoluble colored compound either directly or in a coupled reaction. In immunohistochemistry, enzyme labels are usually coupled to antibodies or to (strept)avidin. 

Single-stranded DNA or RNA may adopt hairpin structures in which the distance between two sequences is much shorter than in the absence of hairpin. Figure B9.4.1 shows two synthetic targets, both containing 45 nucleotides, but only the first one is able to form a hairpin via a loop of four thymines. The second one is used as a control. Both contain the complementary sequences for ethidium-13-mer and 11-mer-coumarin separated by the same number of bases. The efficiency of energy transfer from coumarin to ethidium is dose to zero for the control, whereas it is about 25% in the hairpin structure. This value is low but the spatial conformation of this particular three-way junction is only partially known, and the transfer efhdency depends on the relative orientation and/or distance between coumarin and ethidium. 

The energy required to activate hydrogenase is in the order of 80kJ/mol. Several possible processes have been suggested so far, e.g. a rearrangement of the spatial conformation of the active site or of the surrounding protein in order to allow substrate accessibility to the active site. 

Meanwhile, back at the lab, volunteer experiments in 1961 were ramping up and beginning to operate at full tilt. When Harry Pars supplied us with a synthetic analog of THC for clinical testing, it came as a mixture of eight stereoisomers. (Stereoisomers are different spatial conformations of the same molecule.) It was not yet feasible to separate the eight isomers for our first studies and consequently, we could not yet explore the relative potency of each of them individually. 

The possibility of binding RGD to different receptors is probably caused by a different spatial conformation of RGD due to the vicinity of different amino acids or existence of different synergistic sequences on various extracellular matrix (ECM) molecules. At the same time, one type of integrin can bind more ligands [38-40]. 

Although not obvious from a two-dimensional representation of its structure, carbamazepine has many similarities to phenytoin. The ureide moiety (-N-CO-NH2) in the heterocyclic ring of most antiseizure drugs is also present in carbamazepine. Three-dimensional structural studies indicate that its spatial conformation is similar to that of phenytoin. 

As previously mentioned, certain flavonoids can penetrate into the hydrophobic core of membranes, a feature that mainly relies on their hydrophobic character, which is dictated by flavanoid chemical structure and spatial conformation. When flavonoid hydrophobicity was assessed from the partition coefficient between ra-octanol and an aqueous solution, the following order of hydrophobicity was observed flavone, genistein > eriodictyol, myricetin, quercetin, kaempferol, hesperetin, daidzein > > galangin, morin, flavanone, naringenin, taxifolin (Table 4.1). 

TheA tr is determined by the increase in degrees of freedom for spatial conformation changes in the liquid state as compared to the crystalline state. In crystal lattices, spatial conformation change resulting from the rotation about a Lexible bond is not permitted. Such a rotation, however, is possible in the liquid state. For each Lexible bond, there are three possible conformations due to steric constrain. Thus, the probability of each conformation resulting from one single bond is one-third, and the probability of the fully stretched conformation is... 

Cycleanine has been cleaved, with oxidation, by mercuric acetate in acetic acid to give the salt (27),77 and the thermolytic demethylation of the alkaloid has been shown to proceed sequentially through norcycleanine and isochondodendrine to the tetra-O-demethyl compound.78 The spatial conformation of the alkaloid has been studied by time-dependent n.m.r. spectroscopy.79... 

For closer examination, Stedman wished to determine whether different spatial conformations of the dimethylamino group on the benzylic carbon would result in different activities. Therefore, a synthesis of the a-methyl chiral analogues of... 

In an initial step, a full geometry optimization is performed on the Au-BDT-Au molecule to obtain the most energetically favorable starting conformation. Three spatial conformations are considered for the computation of the current as shown in Figure 5.5. These conformations are selected to represent a variety of experimental conditions. 

Nano Manipulation As the name suggests, this is quite literally a technique for physically manipulating matter at the nanoscale. Scanning probe microscopy (SPM) techniques have been most widely used to achieve this using the scanning probe tip as an implement for assembling atoms, molecules, or nanoparticles according to the desired spatial conformation [166-169],... 

To be able to perform their biological function, proteins fold into one or more specific spatial conformations, driven by a number of non-covalent interactions, including ... 

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