Geometry proteins

In Section III, we will explore how spatial and temporal control of silk protein geometry and chemistry play a role in /3-sheet assembly. 

As noted earlier, protein structure is stabilised by a series of weak forces which often give rise to the properties which are functionally important (models of active sites and substrate binding are discussed above). On the other hand, because active sites involve a set of subtle molecular interactions involving weak forces, they are vulnerable and can be transformed into less active configurations by small perturbations in environmental conditions. It is therefore not surprising that a multitude of physical and chemical parameters may cause perturbations in native protein-geometry and structure. Thus, enzyme deactivation rates are usually multi-factorial, e.g. enzyme sensitivity to temperature varies with pH and/or ionic strength of the medium. 

The opposite approach of keeping the bulk of the protein geometry fixed to that observed crystallographically while optimizing the geometry of the active site and its immediate surrounds has also been investigated. In a study of plastocyanin and amicyanin, the geometry about the copper(I) centers was well reproduced -391. ... 

The practical approaches for protein geometry refinement rely on iterative local linearizations of the full nonlinear optimization problem. The procedure is to step along the potential surface in a direction that decreases the energy. Such iterative approaches in Cartesian coordinates may be symbolized by... 

Proteins with a metal ion that can be reduced or oxidized provide additional pathways for reaction of both primary and secondary radicals. The fixed location of the iron within the protein geometry strongly limits its accessibility to primary radicals, small secondary radicals, and radical sites on the host protein. These considerations are especially relevant to myoglobin, the globular protein responsible for meat pigmentation. Several distinctive reactions involving myoglobin have been studied in model and meat systems [18, 19]. 

For this, we go to measure and then to protein geometry in the sequence editor window (Fig. 5.50). 

It will open the protein geometry window where we can see the Ramchandian plot for the respective model. We can see the outliers by clicking on the data button at the upside right comer of the protein geometry window (Figs. 5.51 and 5.52). 

Fig. 5.55 Figure showing the protein geometry report ofthe model... 

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