Protein fitting

For a globular protein of approximately spherical shape, the isotropic tumbling rate can be characterized by the rotational diffusional correlation time, tc, as described above. Assuming that the protein fits in a sphere of radius r, then the viscosity (rf) and temperature (T) of the sample determines rc. 

Fig. 3. A 9-A resolution reconstruction of Semliki Forest virus, (a) Density isosurface view of the reconstruction down an icosahedral 2-fold axis. One trimeric spike is boxed, and shown close up in a similarly boxed inset panel between parts (a) and (b). (b) The central section of the SFV reconstruction, showing the inner capsid, membrane bilayer, and outer E1-E2-E3 layer composed primarily of trimeric spikes, one of which is again boxed. The thick arrow points along a 2-fold axis, (c) A close-up view of the capsid layer from the virion interior, with the capsid protein fitted into the reconstructed electron density. This view is along a 2-fold axis, as marked in (b). (d) A close-up surface-rendered view across the viral surface through a 2-fold axis, showing the layers visible in (b). Showing the density at a single contour level highlights the different extents to which the layers of the virus are ordered.

Fig. 7.18. Role of heat shock proteins in folding. A. The Hsp70 family of proteins prevent folding of the nascent chain and promote unfolding. The ATPase domain of the protein has the actin fold. B. The Hsp60 class of protein has a barrel shape into which the protein fits. It acts as a template, binding and rebinding portions of the unfolded protein until folding is completed. It hydrolyzes many ATP bonds to provide energy for the process.

Figure 2.8 Cross-section of the connector of the SPPl bacteriophage. The connector is a complex of the portal protein and two-head completion proteins, (courtesy of Dr. Orlova) The section shows the X-ray structure of the portal protein fitted into a cryo-EM map. The X-ray structure has been modified from 13-mer into 12-mer, because the connector within the bacteriophage capsid has 12-fold symmetry whereas the portal protein before incorporation into the procapsid has 13-fold symmetry. The excellent fit of density confirms the 10 A resolution of the EM map...

Figure 8.15. Stereo view of yeast cytochromes b and Cl of Complex III showing Qo and heme Ci binding sites for the FeS center of the Rieske Iron Protein. Neutral residues are given in light gray, aromatic residues in black, other hydrophobic residues in gray, and charged residues in white in order to show visually the relative hydrophobicity of the two sites. Note at the Qo site that ubiquinol would reside at the base of a hydrophobic pit into which the hydrophobic FeS tip of the Rieske Iron Protein fits (see Figure 8.16), whereas the heme Cj site is not as hydrophobic. Also note that the hydrophobic residues L263 and V264...

It should also be noted that large-scale processes involving biological systems (such as waste water treatment and production of protein) fit the definition as well as traditional chemical processes such as the production of fertilisers and pharmaceuticals. 

Fig. 5 Exploring protein fitness landscape by directed evolution to modify specificity or create new functions and modulating biophysical properties such as thermostability, tolerance to solvents, flexibility...

Bloom, J.D. and Arnold, F.H. (2009) In the light of directed evolution pathways of adaptive protein evolution. Proc. Natl. Acad. Sci. U.S.A., 106, 9995-10000. Romero, P.A. and Arnold, F.H. (2009) Exploring protein fitness landscapes by directed evolution. Nat. Rev. Mol. Cell Biol, 10, 866-876. 

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Figure 34 Mixed representation of the p53 DNA complex. The p53 protein and the DNA is shown as capped stick model, the protein backbone is represented as ribbon model. Parts of the molecular surface indicate the p53 protein DNA interface region. The surfaces are color coded with respect to the electrostatic potential calculated by a finite difference algorithm solving the Poisson-Boltzmann equation - (blue, negative gray, neutral red. positive). The electropositive parts of the p53 protein fit perfectly in the major and minor groove of the almost electronegative DNA...

Other sensitive methods for copper determinafion involve elemental analysis by using atomic absorption spectrometry (AAS) and mass spectrometry (MS) to directly measure copper content in the protein, fit pure protein preparations of known concentration, the molecular weight of the protein is predicted by using amino acid sequence and compared with the measured molecular weight derived from MS by comparison, the number of copper atoms per monomer can be calculated. MS can also determine the absolute ratios of copper to protein constituents (C, N, and O) to determine specific copper loading in the MCO. Other methods, such as separation based on molecular weight and comparison with known standards (acrylamide gel or size-exclusion chromatography), are not as accurate. Additional care must be taken to ensure that adventitiously bound copper on the protein surface is eliminated since it will absorb like the type 1 (Tl) copper and complicate—or even invalidate— determination. 

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