Circular dichroism secondary

Circular dichroism Secondary structure of proteins, interaction between ligands and proteins, binding of metals at active sites in enzymes 1 )... 

CD Spectrum Circular Dichroism Secondary structure, a-helix, p-sheet,.. . 

Ihe rule-based approach to protein structure prediction is obviously very reliant on th quality of the initial secondary structure prediction, which may not be particularly accurate The method tends to work best if it is known to which structural class the protein belongs this can sometimes be deduced from experimental techniques such as circular dichroism... 

The secondary stmcture of the plasminogen molecule, as determined by circular dichroism spectra, is 80% random coil, 20% beta-stmcture, and 0% alpha-helix. Electron microscopy has demonstrated the tertiary stmcture of plasminogen to be a 22- to 24-nm long spiral filament with a diameter of 2.2 to 2.4 nm. 

Optical rotation and circular dichroism have been used for die characterization of optically active polymers. They have been used to determine whether polymers are optically active and whether a secondary structure such as a helix exists. 

Although the total content of carbohydrate fractions of the three components is similar, as reported by Williams et al., 1990, it was found that protein-rich fractions have a significantly lower glucuronic acid content. Circular dichroism studies conducted on different GA fractions showed that only the AGP and GP components have a secondary structure (Renard et al., 2006). The AGP fraction was isolated by gel filtration chromatography and subjected to deglycosylation with hydrofluoric acid (HF) to separate the protein (Qi et al., 1991). About 400 amino acids were contained by the AGP protein fraction ( 33% are... 

Recently, peptoid-based mimics of both SP-C and SP-B have been designed to adopt helical secondary structures, and also mimic (to varying degrees) the sequence patterning of hydrophobic and polar residues found in the natural surfactant proteins. Peptoid-based SP-C mimics of up to 22 monomers in length, were synthesized and characterized by in vitro experimental methods [67, 68] (Fig. 1.8). The secondary structure of all molecules was assessed by circular dichroism and found to be helical. The surface activities of these peptoids, in comparison to the actual SP peptides described above, were characterized by surfactometry using... 

Amino acid sequences of eleven homologous sea anemone polypeptides have been elucidated. All possess three disulfide bonds. The six half-cysteine residues always occur in the same positions (7,8). Initial studies concerning the toxin secondary and tertiary structures relied upon circular dichroism, laser Raman, and, to a lesser extent, fluorescence spectral measurements (15—18). The circular dichroism spectra of the four toxins so far examined are essentially superimpos-able and thus indicate a common secondary structure. The only peak observed, a negative ellipticity at 203 nm, largely results from a non-regular ("random")... 

The conformational changes which have been described so far are probably all relatively small local changes in the structure of H,K-ATPase. This has been confirmed by Mitchell et al. [101] who demonstrated by Fourier transform infrared spectroscopy that a gross change in the protein secondary structure does not occur upon a conformational change from Ei to 3. Circular dichroism measurements, however [102,103], indicated an increase in a-helical structure upon addition of ATP to H,K-ATPase in the presence of Mg and... 

The Ca -ATPase has been crystallized in both conformations [119,152-155]. The two crystal forms are quite different [10,88-93,156-161], suggesting significant differences between the interactions of Ca -ATPase in the Ei and E2 conformations. Since the Ei-E2-transition does not involve changes in the circular dichroism spectrum of the Ca -ATPase [162], the structural differences between the two states presumably arise by hinge-like or sliding motions of domains rather than by a rearrangement of the secondary structure of the protein. 

The availability of the purified transporter in large quantity has enabled investigation of its secondary structure by biophysical techniques. Comparison of the circular dichroism (CD) spectrum of the transporter in lipid vesicles with the CD spectra of water-soluble proteins of known structure indicated the presence of approximately 82% a-helix, 10% ) -turns and 8% other random coil structure [97]. No / -sheet structure was detected either in this study or in a study of the protein by the same group using polarized Fourier transform infrared (FTIR) spectroscopy [98]. In our laboratory FTIR spectroscopy of the transporter has similarly revealed that... 

Of the visible spectroscopic techniques, CD spectroscopy has seen the most rapid and dramatic growth. The far-UV circular dichroism spectrum of a protein is a direct reflection of its secondary structure [71]. An asymmetrical molecule, such as a protein macromolecule, exhibits circular dichroism because it absorbs circularly polarized light of one rotation differently from circularly polarized light of the other rotation. Therefore, the technique is useful in determining changes in secondary structure as a function of stability, thermal treatment, or freeze-thaw. 

Determination of protein secondary structure has long been a major application of optical spectroscopic studies of biopolymers (Fasman, 1996 Havel, 1996 Mantsch and Chapman, 1996). These efforts have primarily sought to determine the average fractional amount of overall secondary structure, typically represented as helix and sheet contributions, which comprise the extended, coherent structural elements in well-structured proteins. In some cases further interpretations in terms of turns and specific helix and sheet segment types have developed. Only more limited applications of optical spectra to determination of tertiary structure have appeared, and these normally have used fluorescence or near-UV electronic circular dichroism (ECD) of aromatic residues to sense a change in the fold (Haas, 1995 Woody and Dunker, 1996). 

Secondary structural predictions about NPAs, and direct biophysical measurements, have demonstrated that the NPAs are rich in a-helix, with no p-structure either predicted from secondary structure prediction algorithms, or detected by circular dichroism (Kennedy et al, 1995b). In this they are the antithesis of the similarly sized cLBPs and lipocalins. The predictions are that each individual NPA unit protein will fold into four main regions of helix, and it has been speculated that the tertiary structure is as a four-bundle helix protein, similar to other invertebrate carrier proteins (Sheriff et al., 1987). 

The effect of formalin-treatment on the structural properties of RNase A was examined using circular dichroism (CD) spectropolarimetry. A brief introduction to CD spectropolarimetry is provided in Section 15.15.2 for those readers unfamiliar with this biophysical method. The secondary structure of RNase A consists of one long four-stranded anti-parallel p-sheet and three short a-helixes,44 which places RNase A in the a + p structural class of proteins. The effect of a 9-day incubation of RNase A (6.5mg/mL) in 10% formalin on the protein secondary structure was examined with CD spectropolarimetry in the far-UV region (170-240nm) as shown in Figure 15.6a. The resulting... 

The influence of adsorption on the structure of a -chymotrypsin is shown in Fig. 10, where the circular dichroism (CD) spectrum of the protein in solution is compared with that of the protein adsorbed on Teflon and silica. Because of absorbance in the far UV by the aromatic styrene, it is impossible to obtain reliable CD spectra of proteins adsorbed on PS and PS- (EO)8. The CD spectrum of a protein reflects its composition of secondary structural elements (a -helices, / -sheets). The spectrum of dissolved a-chymotrypsin is indicative of a low content of or-helices and a high content of //-sheets. After adsorption at the silica surface, the CD spectrum is shifted, but the shift is much more pronounced when the protein was adsorbed at the Teflon surface. The shifts are in opposite directions for the hydrophobic and hydrophilic surfaces, respectively. The spectrum of the protein on the hydrophilic surface of silica indicates a decrease in ordered secondary structure, i.e., the polypeptide chain in the protein has an increased random structure and, hence, a larger conformational entropy. Adsorption on the hydrophobic Teflon surface induces the formation of ordered structural elements, notably an increase in the content of O -helices (cfi, the discussion in Sect. 3.1.4). 

Fig. 4. Time-induced conformational change of spider silk protein (spidroin) in solution. Solutions of silk proteins at 1% w/v in distilled water were monitored using circular dichroism. The graph shows a change in secondary structure with time. The silk proteins underwent a kinetically driven transition from a partially unfolded structure to a -sheet-rich structure (from Dicko et al., 2004c). ( ) after 0 days, (O) after 1 day, and (A) after 2 days. The conformational change appeared faster at 20°C compared to 5°C, suggesting a hydrophobically driven mechanism. (Copyright 2004 American Chemical Society.)...

Fig. 5. The effect of protein-protein interactions on Nephila edulis major ampullate circular dichroism spectra in solution. A change in secondary structure with increasing concentration is observed. At low concentration (minimal protein-protein interactions) silk proteins appear partially unfolded in solution. At higher concentration (higher protein-protein interactions) silk proteins refold into a helix-like structure, most likely a molten-like globule (from Dicko et al., 2004c). This final molten structure would facilitate local chain rearrangement while preserving the global structure for protein storage and transport. (Copyright 2004 American Chemical Society.)...

Fig. 6. Structural stability of major ampullate silk protein in constrained Nephila edulis. The graph shows a time series of circular dichroism spectra of major ampullate (MA) protein at 1% w/v in distilled water. The spiders prior to dissection were prevented from spinning, but fed and watered for at least 2 weeks. With time, the secondary structure of silk protein is becoming more and more disordered. The arrow indicates increasing time (days). Note that the amino acid composition of the silk protein was similar to that of a native N. edulis spider. Interestingly, silk protein extracted from the constrained spider did not respond to denaturing conditions (detergents, alcohols, pH, and salts Dicko et al, 2004a, 2005).

Wallace, B. A., and Janes, R. W. (2001). Synchrotron radiation circular dichroism spectroscopy of proteins Secondary structure, fold recognition and structural genomics. Curr. Opin. Chem. Biol. 5, 567-571. 

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