CD spectrum

5 Determining the percentage of different structural units in a protein from peptide region CD spectra 

The program, CDsstr, is currently available via ftp from alpha.als.orstedu by logging in as anonymous and using your email address as the password. 

Changing directory by typing CD/pub/wcjohnson/CDsstr , then bin to specify binary file transfer, and then typing mget. will retrieve the program files. 

Application of CDsstr to compute protein secondary structure from CD spectra 

2 Create a folder named CDsstr in the root directory of the hard disk (assumed to be drive c in the rest of this protocol),  

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Recent investigation of the effect of substituents in the para position of the phenylalanine ligand on the stability of the ternary complexes has revealed the secpience Br > OH > Q NH2 > H > F". Interestingly, analysis of CD spectra indicates a reduction of the arene-arene interaction" upon addition of 1,4-dioxane to aqueous solutions of the mixed-ligand complexes, in disagreement with previous observations by Sigel" . 

Conformational analysis has been used to find and predict conformations which maximize antibiotic activity, using x-ray crystal stmctures coupled with nmr and cd spectra. An early approach utilized the Dale diamond lattice conformational model (480), which was extended to other diamond lattice models (472,481—483). Other studies have reHed on nmr data (225,484—491). However, extensive correlations between conformation and biological activity have not been successful (486,492). 

The molecular ellipticity is analogous to specific rotation in that two enantiomers have exactly opposite values of 0 at every wavelength. Two enantiomers will thus show CD spectra having opposite signs. A compound with several absorption bands may show both... 

Fig. 2.2. CD spectra of (S)- and (R)-2 amino-l-phenyl-l-propanone hydrochloride. [Reproduced with permission from Helv. Chim. Acta 69 1498 (1986).]...

The substance chaetochromin A, structure A, has been shown by X-ray dif action to have the absolute configuration indicated in the structure. The CD spectra of A and the related compounds cephalochromin (B) and ustilaginoidin (C) are shown in the figure. Deduce the absolute stereochemistry of cephalochromin and ustilaginoidin trom these data, and draw perspective structures indicating the absolute configuration. 

Fig. 2. CD-spectra of (L-Lys HBr) in reversed micellar systems of AOT/octane/H20 at different w0-values 65). T 20 °C...

The conformation of bovine myelin basic protein (MBP) in AOT/isooctane/water reversed micellar systems was studied by Waks et al. 67). This MBP is an extrinsic water soluble protein which attains an extended conformation in aqueous solution 68 but is more density packed at the membrane surface. The solubilization of MBP in the AOT reversed micelles depends on the water/AOT-ratio w0 68). The maximum of solubilization was observed at a w0-value as low as 5.56. The same value was obtained for another major protein component of myelin, the Folch-Pi proteolipid 69). According to fluorescence emission spectra of MBP, accessibility of the single tryptophane residue seems to be decreased in AOT reversed micelles. From CD-spectra one can conclude that there is a higher conformational rigidity in reversed micelles and a more ordered aqueous environment. 

Fig. 13. CD-spectra of random and alternating (L-Leu, L-Lys) u2, u(. a) in water b) in trifluoro-ethanol...

Fig. 14. CD-spectra of alternating (L-Leu-L-Lys) in water-methanol mixtures at different pH of the starting solution "2-"9)...

Fig. 15. CD-spectra of random (L-Leu0,48, L-Lys0,52) in water-methanol mixtures as a function of methanol concentration at 20 °C and pH 7,0. The insert shows [0]2O8 and —[0]2jo dependent on the methanol content112113 ...

These optically active absorption bands are more easily resolved in the corresponding CD spectra (Figs. 8 and 9). 

Neutral salt-soluble collagen as well as add-soluble collagen show a CD spectrum (Fig. 8) having bands at 198 nm, 0 = -53 (MX) (deg cm2 dmol-1), and at 223 nm, 0 = 7500 (deg cm2 dmol-1), the ratio between both being 7 1. Pysh has calculated the CD spectra of a-helix, -structure, polyproline I and II127 ... 

Fig. 8. CD spectra of collagen in 0.01 m acetic add. (A) At 24 °C in the native state, (B) at 44 °C in a randomly coiled state. Data from Piez et al.la)...

Table 5. Formation of the negatively and positive sequences in water and methanol, indicated by the collagen-like CD spectra and by the shape of the temperature transition curve...

Circular Dichroism Measurements. The absolute configurations of the C6 chiral center in tetrahydrobiopterin cofactor and related compounds were determined by comparison of their circular dichroism (CD) spectra with those of... 

Considerably less is known about the chemistry of palladium and platinum 1,1-dithio complexes. Of late, there has been only one report that dealt with the synthesis of a large number of palladium dithiocar-bamates 392). Twenty-five yellow palladium dithiocarbamate complexes were obtained by reaction of PdCla with NaR2dtc in methanol solution. Several other reports have appeared in which a few dithiocarbamate complexes of palladium were synthesized. Thus, the novel [Pd (OH)2dtc 2], which is soluble in water, was isolated 393). The synthesis of optically active palladium(II) complexes of AT-alkyl-a-phen-ethyldithiocarbamates, similar to (XXIV), via the reaction between the optically active amine, CS2, and PdCl2, has been described. From ORD and CD spectra, it has been established that the vicinal contribution of a remote, asymmetric carbon center could give rise to optical activity of the d—d transitions of palladium 394). Carbon disulfide has been shown to insert into the Pt-F bond of [PtF(PPh3)3]HF2, and X-ray studies indicated the structure (XXIX). 

Fig. 10. Absorption, CD, and MOD spectra of the Rieske fragment from bovine heart 6c 1 complex. Top panel) absorption spectra (298 K) middle panel) CD spectra...

The CD spectra reveal several distinct features that are highly significant for both Rieske and Rieske-type clusters. The CD spectra of the oxidized proteins show two positive bands between 310 and 350 nm, a negative band at 375-380 nm, and a set of positive bands between 400 and 500 nm. The CD spectra of the reduced proteins show positive bands at 314 nm, a negative band at 384-390 nm and a negative band around 500 nm. 

Fig. 11. Comparison of the difference CD spectra (reduced — oxidized) of the Rieske...

The CD spectra show that the groups with redox-dependent pK values must interact electronically with the [2Fe-2S] cluster Deprotonation of aspartate, glutamate, or tyrosine could be excluded by FTIR spectroscopy (Baymann, F. Link, T. A. Robertson, D. E. Mantele, W., manuscript in preparation)... 

For recombinant resilin, we found that data from the CD spectra (Figure 9.4), x-ray diffraction pattern (Figure 9.5), and NMR were consistent with resilin being an amorphous random network... 

Fig. 1.6 A comparison of the CD spectra of oligopeptoids with achiral Npm side chains (1) and with a-chiral, aromatic sidechains of S and R chirality (2 and 6, respectively). Sample concentration was 60 j,M in acetonitrile. Spectra were acquired at room temperature. Npm = (N-[l-phenylmethyljglycine) Nspe= (S)-N-(l -phenylethyl)glycine Nrpe= (R)-N-(l -phenylethyl)glycine...

Fig. 2.15 Formulae and CD spectra in aqueous solution of jS-peptides with decreasing proportions ofACHC residues from two (83) to zero (85) [175]...

Surprisingly, peptides 72 and 93-99 do not display CD spectra in MeOH characteristic of the expected (M)-3i4 helix but present a new pattern with an intense single peak near 205 nm (with a mean-residue ellipticity as high as 62,083 deg cm dmol for 97) and no zero crossing (Tab. 2.5). 

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