Labeling, labels biophysical

The last example shows that chemical synthesis of proteins can be a useful tool to study pertinent questions in biochemistry. Its main advantage so far relates to its capability to introduce unnatural amino acids, specific isotope labels, biophysical monitors, or very important posttranslational modifications. The latter modification the introduction of a GPI anchor or a GPI anchor mimic onto PrP, has been the subject of further research. These experiments were not solely directed towards specific questions of PrP research but also towards development of a general method to modify proteins with a GPI anchor. 

Englander, S. W., and Mayne, L., 1992. Protein folding studied using hydrogen exchange labeling and two-dimensional NMR. Annual Review of Biophysics and Biomolecular Structure 21 243—265. 

Marsh, D. 1981. Electron spin resonance Spin labels. In Membrane Spectroscopy. Molecular Biology, Biochemistry, and Biophysics, ed. E. Grell, Vol. 31, pp. 51-142. Berlin, Germany Springer-Verlag. 

Somerharju, P. (2002). Pyrene-labeled lipids as tools in membrane biophysics and cell biology. Chem. Phys. Lipids 116, 57-74. 

Abstract To understand how membrane-active peptides (MAPs) function in vivo, it is essential to obtain structural information about them in their membrane-bound state. Most biophysical approaches rely on the use of bilayers prepared from synthetic phospholipids, i.e. artificial model membranes. A particularly successful structural method is solid-state NMR, which makes use of macroscopically oriented lipid bilayers to study selectively isotope-labelled peptides. Native biomembranes, however, have a far more complex lipid composition and a significant non-lipidic content (protein and carbohydrate). Model membranes, therefore, are not really adequate to address questions concerning for example the selectivity of these membranolytic peptides against prokaryotic vs eukaryotic cells, their varying activities against different bacterial strains, or other related biological issues. 

Kubyshkin VS, Komarov IV, Afonin S, Mykhailiuk PK, Grage SL, Ulrich AS (2011) Trifluoromethyl-substituted a-amino acids as solid state 19F-NMR labels for structural studies of membrane-bound peptides. In Gouvemeur V, Miiller K (eds) Fluorine in pharmaceutical and medicinal chemistry from biophysical aspects to clinical applications. Imperial College Press (in press)... 

Biophysical analysis of biomolecules like proteins, nucleic acids, or lipids utilizes intrinsic physical properties of the observed molecule itself or of an associated reporter molecule, which reflect information about structural characteristics, interactions, or reactions of the subject observed. In most cases the analysis (and the labels introduced) only interferes slightly with the interaction of interest and does not induce significant changes in the properties of the reactants. 

New insights into the analysis of hydrophobically post-translational modified proteins could be achieved by the construction of lipidated proteins in a combination of bioorganic synthesis of activated lipopeptides and bacterial expression of the protein backbone (Fig. 19). The physico-chemical properties of such artificial lipoproteins differ substantially from those of the corresponding lipopeptides. The pronounced dominance of the hydrophilic protein moiety (e.g., for the Ras protein 181 amino acids) over a short lipopeptide with one or two hydrophobic modifications provides solubility up to 10 4 mol/1, while the biotinylated or fluorescence labeled lipopeptides exhibit low solubility in aqueous solutions and can be applied in the biophysical experiments only in vesicle integrated form or dissolved in organic solvent. 

Based on our current understanding of ribosomal protein synthesis, several strategies have been developed to incorporate amino acids other than the 20 standard proteinogenic amino acids into a peptide using the ribosomal machinery . This allows for the design of peptides with novel properties. On the one hand, such a system can be used to synthesize nonstandard peptides that are important pharmaceuticals. In nature, such peptides are produced by nonribosomal peptide synthetases, which operate in complex pathways. On the other hand, non-natural residues are a useful tool in biochemistry and biophysics to study proteins. For example, incorporation of non-natural residues by the ribosome allows for site-specific labeling of proteins with spin labels for electron paramagnetic resonance spectroscopy, with... 

The dyes used for probing lipid membranes consist of a fluorophore with a long lipophilic tail. The lipophilic tail inserts itself into the membrane thus locating the fluorophore label on the membrane. These products are used as lipid labels and in cell tracking as part of biophysical studies. There are two main classes of fluorophore, aminostyryls and indocarbocyanines. The most widely used indocarbocya-nine is the 18-carbon derivative of Cy3 known as dil, (3.72). 

Biophysical Confirmation Competitive binding studies, crystallization, labelled NMR... 

The optimal reaction conditions for derivatizing the tagging RNA with a biophysical label depend on the NHS ester used (Fig. 5.6A). Derivatizations with NHS-biotin or NHS-TAMRA can be performed under the same conditions derivatization with NHS-fluorescein was optimal with different conditions. 

The understanding of structure-dynamics-function relationships in oligonucleotides or oligonucleotide/protein complexes calls for biophysical methods that can resolve the structure and dynamics of such systems on the critical nanometer length scale. A modern electron paramagnetic resonance (EPR) method called pulsed electron-electron double resonance (PELDOR or DEER) has been shown to reliably and precisely provide distances and distance distributions in the range of 1.5-8 nm. In addition, recent experiments proved that a PELDOR experiment also contains information on the orientation of labels,... 

Nitroxide radicals are widely used as spin labels in biology, biochemistry and biophysics to gain information about the structure and the dynamics of biomolecules, membranes, and different nanostructures. Their widespread use is related to an unusual stability, which allows researchers to label specific sites and to detect the most informative EPR parameters (g and hyperfme tensors) that are very sensitive to interactions with the chemical surroundings. Figure 2.1 collects all the radicals used in the following to illustrate the different aspects mentioned in the preceding section. 

Kirley, T.L., Spargue, E.D. and Halsall, H.B. (1982) The binding of spin-labeled propranolol and spin labeled progesterone by orosomucoid. Biophysical Chemistry 15,209-216. 

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