Structure proteins comparative studies

Comparative study of LB films of cytochrome P450 wild type and recombinant revealed similar surface-active properties of the samples. CD spectra have shown that the secondary structure of these proteins is practically identical. Improved thermal stability is also similar for LB films built up from these proteins. Marked differences for LB films of wild type and recombinant protein were observed in surface density and the thickness of the deposited layer. These differences can be explained by improved purity of the recombinant sample. In fact, impurity can disturb layer formation, preventing closest packing and diminishing the surface density and the average monolayer thickness. Decreased purity of... 

Native monellin consists of two polypeptide chains, a 45-residue A-chain and a 50-residue B-chain, linked by non-covalent interactions. At neutral pH, it is fairly resistant to heat denaturation with a higher than 80 °C. The crystal structure of native monellin shows a tertiary structure comprising an anti-parallel /1-sheet with five strands and an a-helix. H NMR spectroscopy and hydrogen exchange methods have been used to characterize the alcohol-denaturated state of monellin in order to understand how its secondary structure depends on environmental conditions. " Structural and dynamic studies by NMR have been carried out in order to compare native monellin and a non-sweet analogue in which Asp was replaced by Abu . The three-dimensional structures of the two proteins are found to be very... 

In addition, for solid samples or peptides in nonaqueous solvents, the amide II (primarily in-plane NH deformation mixed with C—N stretch, -1500-1530 cm-1) and the amide A (NH stretch, -3300 cm-1 but quite broad) bands are also useful added diagnostics of secondary structure 5,15-17 Due to their relatively broader profiles and complicated by their somewhat weaker intensities, the frequency shifts of these two bands with change in secondary structure are less dramatic than for the amide I yet for oriented samples their polarization properties remain useful 18 Additionally, the amide A and amide II bands are highly sensitive to deuteration effects. Thus, they can be diagnostic of the degree of exchange for a peptide and consequently act as a measure of protected or buried residues as compared to those fully exposed to solvent 9,19,20 Amide A measurements are not useful in aqueous solution due to overlap with very intense water transitions, but amide II measurements can usefully be measured under such conditions 5,19,20 The amide III (opposite-phase NH deformation plus C—N stretch combination) is very weak in the IR and is mixed with other local modes, but has nonetheless been the focus of a few protein-based studies 5,21-26 Finally, other amide modes (IV-VII) have been identified at lower frequencies, but have been the subject of relatively few studies in peptides 5-8,18,27,28 ... 

In the literature Raman spectroscopy has been used to characterize protein secondary structure using reference intensity profile method (Alix et al. 1985). A set of 17 proteins was studied with this method and results of characterization of secondary structures were compared to the results obtained by x-ray crystallography methods. Deconvolution of the Raman Amide I band, 1630-1700 cm-1, was made to quantitatively analyze structures of proteins. This method was used on a reference set of 17 proteins, and the results show fairly good correlations between the two methods (Alix et al. 1985). 

A growing number of researchers are focusing on the use of top-down proteomics, a relatively new approach compared to bottom-up, in which structure of proteins is studied through measurement of their intact mass followed by direct ion dissociation in the gas phase. The main advantages over the bottom-up approach are that higher sequence coverage is obtained, it permits... 

There are many numerical techniques to predict theoretically the 3D structure of a protein. Among most successful (although beyond the scope of the present paper) are those which compare the amino acid sequence of the protein under study with the sequences of the proteins for which the 3D structure is already known (alignment methods), and create an educated guess of the structure. In the present paper, we focus on the ab novo methods, which rely on considering physical interactions as the main factors determining the 3D structure. 

Kim BC, T Young, E Harder, RA Friesner, BJ Berne (2005) Structure and dynamics of the solvation of bovine pancreatic trypsin inhibitor in explicit water A comparative study of the effects of solvent and protein polarizability. J. Phys. Chem. B 109 (34) 16529-16538... 

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