Binding hypothetical

In the previous section we saw that the stability of a nucleus is affected by its neutron/proton ratio. Even among those nuclei that we consider stable, however, there is a variation in the forces which hold the nucleus together. In order to study this variation in nuclear binding energy, let us consider the process of building a nucleus from protons and neutrons. For an example, let us look at the hypothetical reaction... 

Landschulz WH, Johnson PE, McKnight SL (1988) The leucine zipper - a hypothetical structure common to a new class of DNA-binding proteins. Science 240 1759-1764... 

Fig. I.—Hypothetical Transition State for the Cleavage of the Glycosidic Bond of a (GlcNAc) Chito-oligosaccharide Chain at Sub-Site D of the Substrate Binding Cleft of Lysozyme (from Ref. 65, with Permission).

Figure 39-17. Proteins that regulate transcription have several domains. This hypothetical transcription factor has a DNA-binding domain (DBD) that is distinct from a ligand-binding domain (LBD) and several activation domains (ADs) (1-4). Other proteins may lack the DBD or LBD and all may have variable numbers of domains that contact other proteins, including co-regulators and those of the basal transcription complex (see also Chapters 42 and 43).

Proline 195 was suggested by Gangola and Shamoo [210] as a component of the hypothetical Ca binding site. Mutation of Pro 195 to alanine and the mutation of several acidic residues in the same area [129] had no effect on the Ca transport, making this proposition also unlikely. 

The mechanism of the coupling between ATP hydrolysis and Ca transport is determined by the spatial relationship of the phosphorylation and ATP binding domains of the Ca -ATPase to the Ca channel involved in the translocation of calcium. Two alternative coupling mechanisms have been proposed, based on two rather different hypothetical models of the structure of the Ca -ATPase. In the conformational coupling mechanism the energy transfer between ATP hydrolysis and transport involves a mechanical coupling over long distances between... 

Fig. 8 Schematic representation of the binding of a small molecule (left) or a fragment (right) to a hypothetical protein active site...

Figure 4.2 Hypothetical plasma membrane (PM)-associated structure of FR02. Four histidine residues (white spots) predicted to coordinate two intramembraneous haem groups (white bars) are indicated, as are the tetrapeptide binding sites for FAD and N AD(P)H. The sites of mutations in the FRO gene are indicated (frdl-l,frdl-3) i, inside cell o, outside cell. Reprinted with permission from Nature (Robinson et al., 1999). Copyright (1999) Macmillan Magazines Limited.

Figure 5.7 Only one of the two amino acid enantiomers shown can achieve three-point binding with the hypothetical binding site (e.g., in an enzyme). 

Fig. 6.21. Principle of detection of lipopolysaccharide (LPS) with the CD14-derived probe. It relies on the formation of a ground state complex between fluorescein and rhodamine in aqueous solution with quenching of donor and acceptor fluorescence. Spectrum A shows hypothetical fluorescence emission spectra of this complex. After LPS binding, the peptide sequence gets straightened prohibiting the close contact between the two fluorophores and leading to the recovery of red fluorescence (Spectra B).

Figure 7.2 Schematic showing the relationship of the native antigen to the peptide mimic. The native antigen (a protein) is shown as a winding, twisted line, so as to represent a hypothetical three-dimensional structure. The peptide represents the antibody-binding epitope (shown in dotted lines) of the native antigen. The epitope can represent a linear sequence of the native protein. Alternatively, the epitope can be formed by amino acids that are not immediately adjacent to each other in the primary sequence but brought together by the three-dimensional folding of the protein. Adapted with permission from Sompuram et al.6...

Figure 5 shows a hypothetical plot of the microscopic Kd values versus fractional occupancy of SBA binding to Tn-PSM. The horizontal dashed line is the observed Kd value of 0.2 nM obtained from the ITC experiments (Table I). However, due to... 

Fig. 5. Hypothetical plot (solid line) of the microscopic KA values of SBA binding to Tn-PSM from 0% to 100% occupancy (0 540 aGaINAc residues). The dashed line represents the observed Ktl value of 0.2 nM for SBA binding to Tn-PSM derived from the ITC data in Table I. Crosslinking begins at about 25% occupancy of Tn-PSM by SBA.

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