Biomacromolecules flexibility

The described bioaffinity separations demonstrate that polyacrylamide spacers aid the selective binding of highly complex and delicate biomacromolecules and their associates. Moreover, these solutes remain biologically active after desorption probably due to the high inertness and flexibility of the surrounding polymer chains fixed on the solid support. The unbound parts of serum usually show no loss of the activities of their constituents. Thus we evaluate the surface of inorganic supports coated with chemisorbed iV-hydroxyethyl polyacrylamide and its derivatives as being biocompatible. 

Ortega, A. Garcia de la Torre, J. 2007. Equivalent Radii and Ratios of Radii from Solution Properties as Indicators of Macromolecular Conformation, Shape, and Flexibility. Biomacromolecules 8, 2464-2475. 

In solution, the flexibility of the polymer chain allows the polymer to collapse into a compact, randomly coiled structure rather than to retain an extended form. A transition between these two forms can be observed depending on solvent quality and temperature and is best known as the rod-to-coil transition of biomacromolecules such as DNA. 

We have seen above that the conjugation of structural and thermodynamic properties of weak H-bonds, namely their directionality combined with their enthalpies of about 5-lOkr at room temperature, allows building well-defined molecular structures that combine stability with flexibility and adaptability or evolution. Snch structures are most important in the organization of macromolecules, especially biomacromolecules for which the appearance or disappearance of such supramolecular organization may completely change their properties, making for instance a living protein irreversibly becomes a bio-inert polypeptide. 

The considerations of the preceding subsections stress the importance of the stractural flexibility provided by the extended and dense H-bond network developed by H2O molecules in macromolecules to ensure the stabihty of some of these macromolecules, particularly biomacromolecules. The representative case is the secondary structure of proteins, which requires the presence of such a network to be stable. This H-bond network does not... 

Molecules are dynamic, undergoing vibrations and rotations continually. Therefore the static picture of molecular structure provided by MM is not realistic. Flexibility and motion are clearly important to the biological functioning of biomacromolecules. These molecules are not static structures, but exhibit a variety of complex motions both in solution and in the crystalline state. Energy minimization concerns only the potential energy term of the total energy and so it treats the biomacromolecule as a static entity. The dynamic properties of the atoms in a macromolecule or the momentum of the atoms in space requires the description of the kinetic term. The momentum (p) is related to the force exerted on the atom (Ft) and the potential energy (V) by... 

Pavan, G.M., Mintzer, M.A., Simanek, E.E., Merkel, O.M., Kissel, T., Danani, A. Computational Insights into the Interactions between DNA and siRNA with Rigid and Flexible Triazine Dendrimers. Biomacromolecules 11(3), 721-730 (2010). doi 10.1021/Bm901298t... 

Fig. 5.4 Challenges for surface recognition of biomacromolecules, (a) A large surface area is required, (b) A preorganized yet flexible receptor (Reprinted with permission from You et al. [50]. Copyright 2009 Elsevier)...

Calixarenes are regular macrocyclic aromatic systems, whose conformation can be largely controlled between the extremes of rigid defined molecular shapes and entirely flexible architectures. Upper and lower rim of cone-shaped calixarenes can be equipped with a large variety of functional groups, which may carry multiple charges. These features qualify calixarenes to be potential ligands for biomacromolecules such as proteins and nucleic acids. 

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