Proteins zooming

In order to represent 3D molecular models it is necessary to supply structure files with 3D information (e.g., pdb, xyz, df, mol, etc.. If structures from a structure editor are used directly, the files do not normally include 3D data. Indusion of such data can be achieved only via 3D structure generators, force-field calculations, etc. 3D structures can then be represented in various display modes, e.g., wire frame, balls and sticks, space-filling (see Section 2.11). Proteins are visualized by various representations of helices, / -strains, or tertiary structures. An additional feature is the ability to color the atoms according to subunits, temperature, or chain types. During all such operations the molecule can be interactively moved, rotated, or zoomed by the user. 

Nanotechnology offers the promise of specific targeting in medicine because its size is on the same scale as cells and proteins it needs to find. Instead of flooding the body with medication, medical applications of nanotechnology zooms in on the problem areas. Nanotechnology seeks to hunt down the bad guys while leaving the peaceful population alone. 

Westbrook, J.A., Yan, J.X., Wait, R., Welson, S.Y., Dunn, M.J. (2001). Zooming-in on the proteome very narrow-range immobilised pH gradients reveal more protein species and isoforms. Electrophoresis, 22(14), 2865-2871. 

Eight significantly regulated proteins are indicated by arrows and respective spot number. In the zoomed sections two differentially regulated proteins white box) are displayed in 3D view obtained with the DeCyder software. 

Figure 7. Enlarged zoom on retinol binding protein in renal insufficiency after two-dimensional polyacrylamide gel electrophoresis. First dimension immobiUzed pH 3 to 10 gradient, second dimension 9 to 16% gradient polyacrylamide gel. Retinol binding protein appeared as two large spots. This particular pattern modification is related to the accumulation, in renal failure, of a truncated variant of retinol binding protein (-266 Da) (arrow on the left) relative to the normal form (arrow on the right) (Kieman et al., 2002).

Figure 9.5 Isotopic distributions of intact Ub ions (charge state +10) before (a) and after (b, c, and d) precursor ion isolation (under exchange-out conditions). Panel (a) shows the extent of H retention on partially exchanged Ub (Ub ) by overlaying its spectrum with spectra of unlabeled (Ub), completely exchanged Ub (endpoint) and fully deuterated (Ub ) protein ions on a zoom-out scale. Panel (b) shows broadband isolation of Ub ions, and panels (c) and (d) illustrate Isolation of Ub ions representing con-formers C-l and C-2, respectively (the isolation windows are shown In panel (a)). Reproduced with permission from [25]...

Figure 12.15 AFM images of (a) a GFP protein array deposited with a 220 nm aperture NADIS tip (spot diameters 150 nm) (b) the same with a 110 nm aperture NADIS tip (spot diameters 30 nm) (c) zoom on a 25 nm spot and height profile (d) NP array obtained with a 300 nm aperture NADIS tip (e) the same with a 130 nm aperture tip and (f) zoom on spots with one and two NPs.

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