Protein Structural Heterogeneity

A general method is needed to examine the structure between redox centers to determine if the bamer for any given productive or unproductive reaction is larger or smaller than average. A full quantum mechanical calculation being impossibly complex, various methods of different degrees of complexity using different sets of approximations have been used. 

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An even more fundamental reason why protein structural heterogeneity is not selected to assist or retard electron tunneling arises from the... 

Takeuchi, A., Ohtsuki, C., Miyazaki, T., Kamitakahara, M., Ogata, S., Yamazaki, M., Furutani, Y., Kinoshita, H. and Tanihara, M. (2005) Heterogeneous nudeation of apatite on protein Structural effect of silk seridn. Journal of the Royal Society Interface, 2, 373-378. 

Asakura, T., and Yao, J. M. (2002). C-13 CP/MAS NMR study on structural heterogeneity in Bombyx mori silk fibre and their generation by stretching. Protein Sci. 11, 2706-2713. 

In the majority of cases, fluorescent labels and probes, when studied in different liquid solvents, display single-exponential fluorescence decay kinetics. However, when they are bound to proteins, their emission exhibits more complicated, nonexponential character. Thus, two decay components were observed for the complex of 8-anilinonaphthalene-l-sulfonate (1,8-ANS) with phosphorylase(49) as well as for 5-diethylamino-l-naphthalenesulfonic acid (DNS)-labeled dehydrogenases.(50) Three decay components were determined for complexes of 1,8-ANS with low-density lipoproteins.1 51 1 On the basis of only the data on the kinetics of the fluorescence decay, the origin of these multiple decay components (whether they are associated with structural heterogeneity in the ground state or arise due to dynamic processes in the excited state) is difficult to ascertain. 

It is also well known that proteins differ in their abilities to be chemically stained and it would be very difficult to devise a set of calibration curves for every protein on an array. The heterogeneity of protein structure makes it unlikely that a general protein labeling strategy can be applied to arrays (Kodadek, 2001). Direct labeling may also alter protein structure, leading to denaturation or the inability to form a complex with a specific capture agent. While antibody stability on arrays appears adequate, other proteins may... 

A new line of research involving blue copper proteins deals with their unfolding and their structural heterogeneity. The thermal unfolding of amicyanin was studied with calorimetric and spectroscopic methods. It was found to be irreversible and the kinetic data were analyzed in a three state model. 

The excited-state kinetics of the chromoprotein were found to differ markedly from the one of the isolated chromophore in solution. A strong and fast biexponential decay is observed and seems to sign a specific deactivation channel, still to be properly identified. This process might well be an electron transfer from the chromophore to the protein, as earlier works had suggested [12]. It is additionally possible to suggest that the nonexponential nature of the fast decay could reveal a structural heterogeneity in the oxyblepharismin-protein complex. 

The ability of MIR to monitor fundamental vibrations of several functional groups provides a new tool for researchers to look at minor compounds in cheese. Some of its early applications were focused on the analysis of macromolecules in cheese such as fat, moisture, and protein (Chen et ah, 1998 McQueen et ah, 1995). More recently, the chemical parameters of cheese (Martfn-del-Campo et ah, 2007), composition (Rodriguez-Saona et ah, 2006), protein structure and interactions during ripening (Mazerolles et ah, 2001), and ripening of Swiss cheese (Martin-del-Campo et ah, 2009) were analyzed with improved techniques. Almost all attempts have been directed toward the determination of macromolecules in cheese. This is mainly because of difficulties in sampling procedures and the heterogeneous nature of cheese (McQueen et ah, 1995) that make analysis of minor compounds difficult. 

Using this approach, hydrophilic (neutral or ionic) comonomers, such as end-captured short polyethylene oxide (PEO) chains (macromonomer), l-vinyl-2-pyrrolidone (VP), acrylic acid (AA) and N,N-dimethylacrylamide (DMA), can be grafted and inserted on the thermally sensitive chain backbone by free radical copolymerization in aqueous solutions at different reaction temperatures higher or lower than its lower critical solution temperature (LCST). When the reaction temperature is higher than the LOST, the chain backbone becomes hydrophobic and collapses into a globular form during the polymerization, which acts as a template so that most of the hydrophilic comonomers are attached on its surface to form a core-shell structure. The dissolution of such a core-shell nanostructure leads to a protein-like heterogeneous distribution of hydrophilic comonomers on the chain backbone. 

Study of enzyme structure often means elucidation of protein structure. In the early stage of enzyme studies, protein was considered to be the heterogeneous macromolecule that could be never determined by methods available in those days. In 1926, Svedberg developed an ultracentrifugation technique to determine molecular weight of macro-... 

Current trends involve the computation of structurally heterogeneous conformer ensembles whose diversity is aimed to reflect the observed dynamics of the molecule at a specific time scale. This is in contrast with the traditional structure determination/representation, where a single static conformer is both expected to correspond to experimental data and be sufficient to explain biological function/ Thus, the recently emerging "dynamical ensembles" of proteins represent new kinds of protein structural models. We will discuss the impact of this paradigm shift in detail below. 

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