Circular dichroic

Measuring Protein Sta.bihty, Protein stabihty is usually measured quantitatively as the difference in free energy between the folded and unfolded states of the protein. These states are most commonly measured using spectroscopic techniques, such as circular dichroic spectroscopy, fluorescence (generally tryptophan fluorescence) spectroscopy, nmr spectroscopy, and absorbance spectroscopy (10). For most monomeric proteins, the two-state model of protein folding can be invoked. This model states that under equihbrium conditions, the vast majority of the protein molecules in a solution exist in either the folded (native) or unfolded (denatured) state. Any kinetic intermediates that might exist on the pathway between folded and unfolded states do not accumulate to any significant extent under equihbrium conditions (39). In other words, under any set of solution conditions, at equihbrium the entire population of protein molecules can be accounted for by the mole fraction of denatured protein, and the mole fraction of native protein,, ie. 

A gene encoding this sequence was synthesized and the corresponding protein, called Janus, was expressed, purified, and characterized. The atomic structure of this protein has not been determined at the time of writing but circular dichroic and NMR spectra show very clear differences from B1 and equally clear similarities to Rop. The protein is a dimer in solution like Rop and thermodynamic data indicate that it is a stably folded protein and not a molten globule fold like several other designed proteins. 

Bonding effects in circularly dichroic cobalt(III) complexes. L. T. Katzin and I. Eliezer, Coord. Chem. Rev., 1972,7, 331-343 (20). 

N. Harada and K. Nakanishi, Circular Dichroic Spectroscopy-Exdton Coupling in Organic and Bioorganic Stereochemistry, Univ. Science Books, Mill Valley, CA, 1982. 

The conformations of L-adenylyl-(3 5 )-L-adenosine (28) and L-adenylyl-(2 -> 5 )-L-adenosine (29), as deduced from circular dichroic spectra, are different from the corresponding DD-dinucleotides. < The n.m.r. and u.v. absorption spectra of (28) and (29) are the same as the DD-dimers and their chromatographic and electrophoretic properties appear identical. While (28) and (29) are resistant to enzymic hydrolysis they form complexes with polyU. 

Since the discovery of the double hehcal structure of deoxyribonucleic acid (DNA) by Watson and Crick in 1953 [1], there has been considerable belief that the canonical right-handed B-DNA may adopt a wide range of different conformations depending on the nucleotide sequences and environmental conditions. This speculation turned out to be a reahty [2-10]. hi hving systems, the conformational flexibility of DNA resides primarily in the polymorphs of the DNA double hehx (including right-handed and left-handed double hehcal DNA) and occurs under various environmental conditions [4j. The main family of DNA forms identified, based on circular dichroic and... 

Spectrophotometric and spectrofluorimetric methods provide a wealth of information concerning structural determinations (identification, purity and precise measurement of concentration) and chemical changes in alkaloids. These techniques yield both quantitative and qualitative data on the effect of solvents, pH and other physiological conditions [141-143]. X-ray crystallography, H and NMR spectroscopy, infrared spectroscopy (IR) and circular dichroic spectroscopy were also used to study the physical properties... 

Binding of berberine caused changes in the circular dichroic spectrum of all B-DNAs with an increase of molar ellipticity of the 270 nm band the molar ellipticity value at saturation depended strongly on the base composition of DNA being larger for the AT-rich DNA than the GC-rich DNA. However, the generation of berberine-associated extrinsic circular dichro-ism bands was not dependent on the base composition or sequence of base pairs. 

Fig. 10 Extrinsic circular dichroic spectra of berberine-B-DNA (a) and berberine-H -DNA (b) complexes. Reprinted in part from [186] with permission from Elsevier...

Fig. 12 Representative circular dichroic spectrum of poly(A) treated with various concentrations of berberine (a), palmatine (b) and coralyne (c). a Reprinted from [206], b reprinted from [208] and c reprinted from [187] with permission from Elsevier...

In order to develop compounds that can selectively target duplex RNA, Sinha et al. [ 194] studied the interaction of berberine with two different conformations of poly(rC) poly(rG) structures. Poly(rC) poly(rG) has been shown [15,215] to exist in two conformations depending on the pH of the solution, the A-form at physiological pH and the protonated form at pH 4.3. These two conformations have been characterized to have clearly defined but distinctly different circular dichroic and absorption spectral characteristics. Both the A-form and the protonated form of the RNA induced moderate hypochromic change and bathochromic shifts in the absorption maxima peaks at 344 nm and 420 nm of the alkaloid with three isosbestic points centered around 357,382 and 448 nm. Binding of berberine to both forms enhanced the fluorescence intensity, which was higher with the protonated form than with the A-from, suggesting clear differences in the nature of orientation... 

Maiti M (1986) Application of circular dichroic technique in nucleic acids research. In Chatterjee SN (ed) Physical techniques in biology. Indian Physical Society, Calcutta, p 52... 

Fang JM, Selvi S, Liao JH et al (2004) Fluorescent and circular dichroic detection of monosaccharides by molecular sensors bis[(pyrrolyl)ethynyl]naphthyridine and bis [(indoili)ethynyl]naphthyridine. J Am Chem Soc 126 3559-3566... 

Harada, N. Nakanishi, K. Circular Dichroic Spectroscopy—Exciton Coupling in Organic Stereochemistry, Oxford University Press, Oxford, 1983. 

A prime example of a Refolding model is that of the insulin protofilament (Jimenez et al., 2002). Insulin is a polypeptide hormone composed of two peptide chains of mainly o -helical secondary structure (Fig. 3A Adams et al., 1969). Its chains (21- and 30-amino acids long) are held together by 3 disulfide bonds, 2 interchain and 1 intrachain (Sanger, 1959). These bonds remain intact in the insulin amyloid fibrils of patients with injection amyloidosis (Dische et al., 1988). Fourier transform infrared (FTIR) and circular dichroic (CD) spectroscopy indicate that a conversion to jS-structure accompanies insulin fibril formation (Bouchard et al., 2000). The fibrils also give a cross-jS diffraction pattern (Burke and Rougvie, 1972). 

The inclusion modes of flurbiprofen with beta cyclodextrin and with heptakis(2,3,6-tri-0-methyl)-beta cyclodextrin have been studied by Imai and coworkers. They showed that, although the Cotton effects in the circular dichroic spectra induced by beta cyclodextrin in / (-) and 5(+) flurbiprofen are identical, those induced by heptakis(2,3,6-tri-0-methyl)-beta cyclodextrin differ from each other and from those induced by beta cyclodextrin. C.p.-m.a.s. C-n.m.r. experiments showed that the cyclodextrin ring is probably more distorted in the flurbiprofen inclusion complex with methylated beta cyclodextrin than in that with beta cyclodextrin. 

Sixou et al. (101) showed the circular dichroism of cholesteric CTA solutions in TFA depends on the CTA molecular weight. The intensity of the circular dichroic peak increases with molecular weight. Meeten and Navard (97) studied gel formation and liquid crystallinity in TFA-H2O solutions of CTA. When water was added to a liquid crystalline solution of CTA in TFA a gel phase formed presumably by the formation of crosslinks due to hydrogen bonding. They interpreted their results that liquid crystalline ordering involves both inter- and intramolecular forces. 

Scanu, A. M., The effect of reduction and carboxymethylation on the circular dichroic spectra of pure polypeptide classes of serum high density lipoproteins. BwMm. Biophys. Acta 200, 570-572 (1970). 

Ferreira, D. et al.. Circular dichroic properties of flavan-3,4-diols, J. Nat. Prod., 67, 174, 2004. Cai, Y. et al.. Biological and chemical investigation of dragon s blood from croton species of South America. Part 1. Polyphenolic compounds from Croton lechleri. Phytochemistry, 30, 2033, 1991. Cui, C.B., Davallin, a new tetrameric proanthocyanidin from the rhizomes of Davallia mariesii Moore, Chem. Pharm. Bull, 39, 2179, 1991. 

The compartmentation of cubic phases is geometrically not so well defined as in the case of micelles or vesicles. However, several years ago the very interesting observation was made that cubic phases can incorporate proteins up to 50% of their weight (Ericsson et al, 1983). Usually cubic phases also remain transparent after incorporation of proteins, and in fact it has been possible to carry out circular dichroic investigations of enzymes in such systems, (Larsson, 1989 Portmann et al, 1991 Landau and Luisi, 1993), as shown in Figure 9.19, and even to follow spectroscopically the course of enzymatic reactions (Portmann et al, 1991). 

Pietrini, A. V. and Luisi, P. L. (2002). Circular dichroic properties and average dimensions of DNA-containing reverse micellar aggregates. Biochim. Biophys. Acta, 1562, 57-62. 

Figure 13. Definition of exciton chirality. Summation of the two Cotton effects (broken lines) separated by Davydov splitting A). gives the curves shown in solid lines. Adapted from N. Harada, K. Nakanishi. Circular Dichroic Spectroscopy - Exciton Coupling in Organic Stereochemistry, University Science Books. Mill Valley, California. 1983...

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