Conformational changes biomacromolecules

Dicko, C., Knight, D., Kenney, J. M., and Vollrath, F. (2004b). Secondary structures and conformational changes in flagelliform, cylindrical, major, and minor ampullate silk proteins. Temperature and concentration effects. Biomacromolecules 5, 2105-2115. 

The biochemical applications of UV and visible spectroscopy are determination of concentrations, interactions of ligands with biomaaomolecules and conformational changes caused by experimental perturbations. The sensitivity of UV and visible spectra to the solvent environment of the chromophore leads to shifts in the absorption maximum and the absorption intensity, and it is the basis of solvent perturbation spectra in the structural studies of biomacromolecules (Donovan, 1969). The ideahzed development of environmental (solvent) contribution to the extinction coefficient of a chromophore is described by... 

Spectroscopic observation of perturbations of the chromophores of biomacromolecules has become a valuable method for the determination of the conformation of native and altered structures in solution. When perturbation of the chromophores of a biopolymer is observed, the resulting conformational changes may be detected by measurement with any one of the spectroscopic methods, of which absorption spectroscopy will be considered. To record perturbation of difference spectrum, unperturbed preparation is used as the reference and perturbed preparation as the sample. Perturbation of a chromophore... 

Main applications of ORD or CD spectroscopy are the determination of the secondary structure of biomacromolecules and detection of their conformational changes. The on-line analysis of CD spectroscopic data can be accessed at DICHROWEB (http //public-l.cryst.bbk.ac.uk/cdweb/). 

Many polymeric materials used in biomedical research are biohybrids, meaning a combination of synthetic polymers and biological macromolecules. In addition, the interaction of a biomacromolecule like a peptide and any synthetic polymer is of high interest for potential application, for example, if there are conformational changes or denaturation of the proteins in contact with a polymeric surface and, thus, specific characterization tools not only for the synthetic polymers are of need but also for biomacromolecules. Therefore, in the following, specific techniques are described for the characterization of polypeptides as an example for a typical biological macromolecule. 

The delivery of therapeutic biomacromolecules, such as DNA or proteins that are taken up by endo-somes may be hindered by the endosomal membrane. Actually, the endosomal membrane may protect the body against certain viruses. Anionic polymers that undergo conformational changes and become membrane disruptive in low-pH environments have the potential to assist in the delivery of these biomacromolecules across the endosomal membrane. Endo-somolytic polymers can be synthesized by grafting... 

The adsorption of dh nucleic acids at the mercury electrodes from neutral and acid media is somewhat more complex due to the protonation of bases at the interface. The protonation of base residues in dh nucleic acids results in the surface conformational alternation in this biomacromolecule adsorbed at the mercury electrode polarized to a broad range of potentials around the p.z.c.. This conformational change leads to a more extensive participation of base residues in the adsorption of dh nucleic acids at the mercury electrodes even at short times of the contact of the biomacromolecules with the electrode [110]. 

EPR-based techniques to measure nanometre range distances are nowadays recognized as a valuable tool in studies of structure and conformational changes of biomacromolecules. A typical approach uses some type of nitroxide-based spin labels, which are selectively attached to specific sites.The distances between pairs of these spin labels are then measured by some appropriate pulse EPR technique,most commonly, by the dead-time-free 4-pulse double electron-electron resonance (DEER) experiment. ... 

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