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Protein cavity

We can briefly conclude that the mineralization process of iron in ferritin cores is a difficult process to follow experimentally. While we believe that iron is delivered for storage within the protein cavity as Fe(II), and that an oxidation step occurs in the formation of the ferritin iron core, it is not clear what percentage of iron oxidation occurs on the growing surface of the mineral and what at the catalytic ferroxidase... [Pg.198]

Why mammalian ferritin cores contain ferrihydrite-like structures rather than some other mineral phase is less easy to understand, and presumably reflects the way in which the biomineral is built up within the interior of the protein shell together with the geometry of the presumed nucleation sites. The phosphate content in the intracellular milieu can readily be invoked to explain the amorphous nature of the iron core of bacterioferritins and plants. Indeed, when the iron cores of bacterioferritins are reconstituted in the absence of phosphate, they are found to be more highly ordered than their native counterparts, and give electron diffraction lines typical of the ferrihydrite structure. Recently it has been reported that the 12 subunit ferritin-like Dps protein (Figure 19.6), discussed in Chapter 8, forms a ferrihydrite-like mineral core, which would seem to imply that deposition of ferric oxyhydroxides within a hollow protein cavity (albeit smaller) leads to the production of this particular mineral form (Su et al., 2005 Kauko et al., 2006). [Pg.329]

Once the protein interaction pattern is translated from Cartesian coordinates into distances from the reactive center of the enzyme and the structure of the ligand has been described with similar fingerprints, both sets of descriptors can be compared [25]. The hydrophobic complementarity, the complementarity of charges and H-bonds for the protein and the substrates are all computed using Carbo similarity indices [26]. The prediction of the site of metabolism (either in CYP or in UGT) is based on the hypothesis that the distance between the reactive center on the protein (iron atom in the heme group or the phosphorous atom in UDP) and the interaction points in the protein cavity (GRID-MIF) should correlate to the distance between the reactive center of the molecule (i.e. positions of hydrogen atoms and heteroatoms) and the position of the different atom types in the molecule [27]. [Pg.284]

Key words Drug targets, Hot spots, Druggability, Flo-QXP, Pocket finder, Structure superimposition, Target promiscuity, Protein cavity... [Pg.141]

Fig. 1. Geometry concepts tor analyzing protein cavity. The protein bulk is represented in black, probes as little spheres. The convex Hull ot the protein is represented in dash line. The plain vectors emerging trom the probe in grey are pointing towards the bulk solvent, whereas the dash vectors will encounter protein atoms within a radius of 8 A (radius of the influence circle m dot line).Jhe probe in front ot the clett defines the degree of precision in represenfing the molecular surface. Fig. 1. Geometry concepts tor analyzing protein cavity. The protein bulk is represented in black, probes as little spheres. The convex Hull ot the protein is represented in dash line. The plain vectors emerging trom the probe in grey are pointing towards the bulk solvent, whereas the dash vectors will encounter protein atoms within a radius of 8 A (radius of the influence circle m dot line).Jhe probe in front ot the clett defines the degree of precision in represenfing the molecular surface.
Prediction of the conformational change of the protein under binding is a challenge. New structural parameters based on high resolution X-Ray structures have been presented recently (69). Such studies open the door to a more extended analysis of conformational changes of protein cavity when binding with different ligands. [Pg.153]

The convex hull of a set of points is the volume surrounding these points such that any segment between any two of these points stay inside the volume. For proteins, we might relax this definition to include inside the protein volume, the closed protein cavities that are not open to bulk solvent. A more adequate... [Pg.158]

Tripathi A, Kellogg GE (2010) A novel and efficient tool for locating and characterizing protein cavities and binding sites. Proteins 78 825-842... [Pg.162]

These observations suggest that the environment of heme inside the micellar cavity is more asymmetric than that in simple solution this asymmetry is much larger inside the protein cavity [45]. An unsymmetrical structural disposition of the heme complex inside the micellar cavity has been proposed [67]. Besides, the increase in the spread of the heme methyl signals in the five-coordinate 2-methyl imidazole ferrous heme complex might also arise from the decrease in symmetry... [Pg.140]

Levitt, D. G., Banaszak, L. J. (1992) POCKET a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J Mol Graph 10, 229-234. [Pg.172]

It has been suggested [95] that the synthesis of structured porphyrins with controllable steric ambience is a strategic direction in the reproduction of enzyme protein cavities, which control the selectivity and stability of biochemical reactions such as cytochrome P-450. Such an approach to the synthesis of biomimics has considerable potential, especially in their application on mineral matrices silicon dioxide, alumina and zeolites. Data exist on the synthesis of a biomimic [96] with a complex porphyrin complex (5-pentafluorophenyl-10,15,20-tri(2,6-dichlorophenyl)porphyrin (FeMPFDCPP)) covalently linked to aminopropyl silicon dioxide, which is applied in oxidation of ds-cyclooctene, cyclohexene, cyclohexane and adamantane with participation of iodosylbenzene dissolved in dichloromethane. [Pg.278]

More than MePc complexes, MePOR complexes have offered a great contribution to the understanding of monooxygenase and peroxidase enzymes.[75,76] The similarity in behaviour in selective oxidations with synthetic and natural systems has been the impetus for the search of mimicking the protein cavity of natural enzymes. In this context zeolites have always had a privileged role. Next to the in situ synthesis, zeolite adsorption of pre-synthesized FemPOR has been attempted as well. [Pg.216]


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See also in sourсe #XX -- [ Pg.178 ]

See also in sourсe #XX -- [ Pg.142 , Pg.144 , Pg.145 , Pg.149 , Pg.153 , Pg.154 , Pg.158 , Pg.159 ]




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Protein, proteins cavity

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