Proteins dynamics/flexibility

The secondary and tertiary structures of myoglobin and ribonuclease A illustrate the importance of packing in tertiary structures. Secondary structures pack closely to one another and also intercalate with (insert between) extended polypeptide chains. If the sum of the van der Waals volumes of a protein s constituent amino acids is divided by the volume occupied by the protein, packing densities of 0.72 to 0.77 are typically obtained. This means that, even with close packing, approximately 25% of the total volume of a protein is not occupied by protein atoms. Nearly all of this space is in the form of very small cavities. Cavities the size of water molecules or larger do occasionally occur, but they make up only a small fraction of the total protein volume. It is likely that such cavities provide flexibility for proteins and facilitate conformation changes and a wide range of protein dynamics (discussed later). 

Of great interest to the molecular biologist is the relationship of protein form to function. Recent years have shown that although structural information is necessary, some appreciation of the molecular flexibility and dynamics is essential. Classically this information has been derived from the crystallographic atomic thermal parameters and more recently from molecular dynamics simulations (see for example McCammon 1984) which yield independent atomic trajectories. A diaracteristic feature of protein crystals, however, is that their diffraction patterns extend to quite limited resolution even employing SR. This lack of resolution is especially apparent in medium to large proteins where diffraction data may extend to only 2 A or worse, thus limiting any analysis of the protein conformational flexibility from refined atomic thermal parameters. It is precisely these crystals where flexibility is likely to be important in the protein function. 

Proteins are therefore dynamic, flexible objects whose physical and chemical properties are dominated, not only by their conformation, but also by the continual changes in conformation which are a consequence of their microscopic size22). The marginal stability of most protein conformations suggests that processes at one point in the protein might well have an effect on a portion of the molecule far removed. 

It has been found out that the structure of proteins is flexible and there are many differences between the static spatial image of a protein and a dynamic view of its structure. This divergence is caused by the fact that the repetitive part of a-helices and [3-strands of protein folds, often described as a succession of secondary structures, can assume different local spatial orientation. Two experimental methods can be used to measure the flexibility in precise regions of protein structures (the anatomic mean square displacement, B-factor, measured during crystallographic experiments, and indirectly by NMR experiments which show different local conformation that could correspond directly to different stages of protein structures) (Bornot et al., 2007). 

Investigation of thermostable protein dynamics by indirect methods such as the kinetics of proteolysis and H-D exchange as well as buried chromophore fluorescence quenching, has led to the conclusion that at ambient temperature their globules are essentially less flexible than for non-thermostable proteins (Vetriani et al., 1998 and references therein). 

Remember that proteins (and other biological macromolecules) are quite dynamic, flexible molecules. Even at equilibrium, and just like all chemical equilibrium processes, this equilibrium is dynamic, since thermal motion never stops. For a two-state process, the exchange kinetics may be described by ... 

From the above discussion, it can be concluded that both the effective charge and the hydro-dynamic radius play a major role in the control of the electrophoretic mobility in the separation of proteins by CZE. Since proteins are flexible molecules, the interplay of both factors has to be taken into consideration to explain their mobility in electrophoresis. Eor glycoproteins, a full understanding of the factors that control their separation in CZE is a complex task because the size and flexibility of the glycans constitute an additional cause of structural variability. 

R314 P. Cioni and E. Gabellieri, Protein Dynamics and Pressure What Can High Pressure Tell Us about Protein Structural Flexibility , Biochim. Biophys. Acta, Proteins Proteomics, [online computer file], 2011, 1814, 934. 

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