Molecular pocket

Calculations of the distribution functions of sizes of relaxed structures (Figure 5.11b) show that the starch/silica hydrogel at ft=2.34 g/g is characterized by narrower molecular pockets than that at ft =17.9 g/g. The narrowest pockets (nanopores) are found for hydrogel with gelatinized starch alone. Notice that all distributions show complex structures of pockets (voids) between/inside starch molecules that are in agreement with complex structure of unfolding starch macromolecules. 

Zhang J, Luo J, Zhu XX, Junk MJN, Hinderberger D (2009) Molecular pockets derived from cholic acid as chemosensors for metal ions. Langmuir 26 2958-2962... 

Zhang J, Junk MJN, Luo J, Hinderberger D, Zhu XX (2010) 1,2,3-Triazole-containing molecular pockets dtaived from cholic acid the influence of structure on host-guest coordination properties. Langmuir 26 13415—13421... 

Figure 22.5 Qiemical structure of cryptophane A showing methane within its molecular pocket Because methane occupies just 35% of the cavity volume, it may readily disorder within the host [130].

Extraction of a ligand from the binding pocket of a protein. The force (represented by an arrow) applied to the ligand (shown in van der Waals spheres) leads to its dissociation from the binding pocket of the protein (a slice of the protein represented as a molecular surface is shown). 

The simulations also revealed that flapping motions of one of the loops of the avidin monomer play a crucial role in the mechanism of the unbinding of biotin. The fluctuation time for this loop as well as the relaxation time for many of the processes in proteins can be on the order of microseconds and longer (Eaton et al., 1997). The loop has enough time to fluctuate into an open state on experimental time scales (1 ms), but the fluctuation time is too long for this event to take place on the nanosecond time scale of simulations. To facilitate the exit of biotin from its binding pocket, the conformation of this loop was altered (Izrailev et al., 1997) using the interactive molecular dynamics features of MDScope (Nelson et al., 1995 Nelson et al., 1996 Humphrey et al., 1996). 

The molecular surface of receptor site regions cannot be derived from the structure infoi mation of the molecule, bth represents the form ofthe active site of a protein surrounded by a ligand. This surface representation is employed in drug design in order to illustrate the volume of the pocket region or the molecular interaction layers [186. ... 

Heating Kemp s acid with appropriate aromatic diamines yields bis-imides with two convergently oriented carboxylic acid groups on the edges of a hydrophobic pocket. Dozens of interesting molecular complexes have been obtained from such compounds and can be traced in the Journal of the American Chemical Society under the authorship of J. Rebek, Jr., (1985 and later e.g. T. Tjivikua, 1990 B). 

Occlusions, which are a second type of coprecipitated impurity, occur when physically adsorbed interfering ions become trapped within the growing precipitate. Occlusions form in two ways. The most common mechanism occurs when physically adsorbed ions are surrounded by additional precipitate before they can be desorbed or displaced (see Figure 8.4a). In this case the precipitate s mass is always greater than expected. Occlusions also form when rapid precipitation traps a pocket of solution within the growing precipitate (Figure 8.4b). Since the trapped solution contains dissolved solids, the precipitate s mass normally increases. The mass of the precipitate may be less than expected, however, if the occluded material consists primarily of the analyte in a lower-molecular-weight form from that of the precipitate. 

However, all the receptors hitherto discussed are monomolecular species which possess a monomolecular cavity, pocket, cleft, groove or combination of it including the recognition sites to yield a molecular receptor—substrate complex. They can be assembled and preserved ia solution although there are dependences (see below). By way of contrast, molecular recognition demonstrated ia the foUowiag comes from multimolecular assembly and organization of a nonsolution phase such as polymer materials and crystals. 

Molecular characteristics of luciferase. A molecule of the luciferase of G. polyedra comprises three homologous domains (Li et al., 1997 Li and Hastings, 1998). The full-length luciferase (135 kDa) and each of the individual domains are most active at pH 6.3, and they show very little activity at pH 8.0. Morishita et al. (2002) prepared a recombinant Pyrocystis lunula luciferase consisting of mainly the third domain. This recombinant enzyme catalyzed the light emission of luciferin (luminescence A.max 474 nm) and the enzyme was active at pH 8.0. The recombinant enzyme of the third domain of G. polyedra luciferase was crystallized and its X-ray structure was determined (Schultz et al., 2005). A -barrel pocket putatively for substrate binding and catalysis was identified in the structure, and... 

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