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Start Your Free Trial Today. Load Next Page. More About. Its formation can be considered to be driven by a funnel-like energy landscape. Hence, if the association between any two building blocks in folding or in binding is also a funnel-like energy landscape resulting from a fusion of two funnel landscapes, then the overall folding and binding landscape has a funnel-like shape. Figures 1 and 2 illustrate schematically landscapes of folding and binding.

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The parts themselves are not entirely rigid, although they are relatively so compared with the swiveling region. Swiveling is not a complete rotation in 3D space. Too much freedom is likely to hinder protein function Sun and Sampson, Hence, through evolution, particular residues are likely to have been selected to be at and around the hinge and possibly at interdomain interfacial boundaries, limiting both the extent of the motions and at the same time leading to preferred rotational directions.

The existence of an ensemble of hinge-bent conformational isomers around the rugged bottom of the energy funnel, such as in the case of different crystal forms or as in bound and unbound states, suggests low-energy barriers between them. Hence, while the conformations of the structural parts which move as relatively rigid bodies may be expected to be relatively stable, the interactions at the interdomain boundaries may be of a different nature. Some inkling into this problem may be obtained from thermostable proteins.

Analysis of salt bridges in an extremely thermostable protein and its comparison with its mesophilic counterpart has recently shown that while there was a large difference in the number of salt bridges between this homologous pair of proteins, this difference appears to be confined to salt bridges within the hydrophobic folding units Kumar et al.

Consistently, it has been suggested that breaking a salt bridge involves overcoming a high conformational energy barrier Waldburger et al.

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Below we review some specific examples of hinge-bending conformational isomers in binding which may be the outcome of the presence of the ensemble of conformers around the rugged bottom of the folding funnel. These examples include both allosteric and non-allosteric binding. Allosteric transitions between R relaxed and T taut states in aspartate transcarbamyltransferase Stevens and Lipscomb, , fructose-1,6-bisphosphatase Ke et al.

These transitions mostly involve movements of subunits with respect to each other and positional shifts in the cofactor binding site.

Conformational changes in bound and unbound forms of proteins that do not involve any allosteric cofactors have also been studied. Examples include aspartate receptor Milburn et al. Again, in these cases most of the conformational change involves movements of subunits with respect to one another. In both allosteric and non-allosteric binding, the deceptively rigid snapshot images of protein motion observed by crystallography can actually be explained by the presence of several low barrier conformational isomers in solution around the bottom of the funnel and shifts in chemical equilibrium in favor of the bound states of the proteins upon substrate—ligand binding.

These examples of protein—substrate binding indicate a predominance of the induced fit mechanism. However, the lock-and-key mechanism has also been observed in the case of Fab D1. Unlike other antibody—antigen complexes, this complex exhibits almost perfect complementarity. The rigidity of the antibody molecule indicates the presence of fewer conformational isomers in this case and hence a smoother energy landscape bottom. The immunoglobulins constitute an ideal case for studies of specific versus non-specific binding.

Whereas mature immunoglobulins are highly specific, the germline ones bind a broad range of antigens. Hence a difficult although extremely intriguing question is what the origin of this difference is. Is there also a concomitant difference in the extent of the molecular flexibility, with the germline antibody being more flexible than its mature descendent? In , based on a kinetic analysis, Foote and Milstein proposed that antibodies do not have a single conformation at their combining site. They suggested that differences observed in crystal structures between bound and unbound forms could arise from the direct interactions of the antibody with its antigen through either induced fit or, alternatively, by preferential ligand binding to a pre-existing subpopulation of antibody isomers.

Thus, a few conformations may exist, with the ligands binding preferentially to one form.

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  5. Recently, Wedemeyer et al. They solved the X-ray crystal structures of two antibodies, an affinity matured antibody and its apparent corresponding germline antibody. Nine somatic mutations differentiate between these two molecules. Each of these antibodies was crystallized twice, in its free, unbound form and complexed with a hapten antigen.

    Correspondingly, a comparison between the bound form of the germline and the free form of the mature antibody showed the two to be highly similar. Hence Wedemeyer et al.

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    On the other hand, as they note, this ability of the germline to bind the hapten, reconfiguring its active site in response to binding, reflects conformational flexibility, expanding substantially the structural diversity of the germline repertoire. Taken together, the germline, non-specific antibody exists in a range of conformations. The one that binds the invading antigen is the one whose structure is complementary to that of the antigen.

    If the barriers between the conformers in the ensemble are low, the equilibrium of the population is kept by the low-energy interconversion of the conformations near the one that binds the antigen and thereby drive the reaction in this direction. The more non-specific the antibody, the more flexible it may be expected to be. The more flexible it is, the broader the range of conformations it may adopt.

    https://marxsbotogtendard.ml In non-specific, broad range-binding antibodies, the energy surface at the funnel bottom is rugged, with numerous minima reflecting the large number of conformational isomers, with low barriers between the conformers, allowing fluctuations from one to the other. On the other hand, during antibody maturation, mutational events take place, rigidifying some conformers with favorable geometries. Another well studied example of a broad range of binding is that of the proteolytic enzymes, such as the aspartic proteinase family. A hinge-based motion has been observed there James et al.

    Recently, Lee et al. DNA binding proteins which bind to variable sequences are also likely to display a range of conformations around the bottom of the funnel, while still binding to the DNA with high affinity. This flexibility of the DNA binding domain of the trp repressor is essential for recognition of different operator sequences Gryk et al. To illustrate our point, we discuss two examples. Recently, the crystal structure of the extracellular portion of the rabbit tissue factor r-TF has been solved Muller et al.

    The extracellular portions of both the human tissue factor h-TF Muller et al. However, the two r-TF molecules in the asymmetric unit have been observed to differ in the orientation of the two domains with respect to each other, illustrating an unexpected hinge of Muller et al. Consistently, Huang et al.

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    Rose et al. They found that five domains of the SIV dimer move as rigid bodies with respect to each other. Their interpretation is that the unliganded SIV structure is the outcome of the crystal contacts. Here we argue that the origin of both is the population of hinge-bending conformational isoformers. The conformer which is crystallized is the one whose conformation is optimal for the association, with the equilibrium shifting itself in its direction.

    Recently, Eisenberg and colleagues presented an inspiring hypothesis for the origin of protein oligomerization Bennett et al. Domain-swapped oligomers have been proposed to arise when a segment of a monomeric protein is exchanged by an analogous segment from a sister monomer. Domain swapping can take place in oligomeric proteins, between their subunits or between domains within the same subunit. They further made an attractive proposition that during evolution domain-swapped dimers have been cleaved to form two separate stable monomers, which subsequently associate to form the oligomer.

    These may not bear a clear trace of their evolutionary origin. For some of the domain-swapped cases, such as in the case of bovine seminal ribonuclease BS-RNase , it has been shown that there are two types of dimeric associations: one with swapped N-terminal segment and the other without the swapping. The two conformations co-exist, with the swapping occurring after the non-swapped dimer forms Piccoli et al. Both conformations may be expected to populate the floor of the funnel.

    Swapping will be observed, depending on their relative stabilities and the barrier heights. Figure 2d illustrates schematically the shape of the folding funnel for a swapping case.