Raman amides

Chi Z H, Chen X G, Holtz J S W and Asher S A 1998 UV resonance Raman-selective amide vibrational enhancement quantitative methodology for determining protein secondary structure Biochemistry 27 2854-64... 

It is a supposition that the )9-sheet structure of neurotoxin is an essential structural element for binding to the receptor. The presence of -sheet structure was found by Raman spectroscopic analysis of a sea snake neurotoxin (2). The amide I band and III band for Enhydrina schistosa toxin were at 1672 cm and 1242 cm" respectively. These wave numbers are characteristic for anti-parallel -sheet structure. The presence of -sheet structure found by Raman spectroscopic study was later confirmed by X-ray diffraction study on Laticauda semifasciata toxin b. 

Figure 2. The spectra of the amidated pectins (NIR, FT-IR and Raman shift).

The crystal structure of a CODH/ACS enzyme was reported only in 2002.43,44 It reveals a trio of Fe, Ni, and Cu at the active site (6). The Cu is linked to the Ni atom through two cysteine-S, the Ni being square planar with two terminal amide ligands. Planarity and amide coordination bear some resemblance to the Ni porphinoid in MCR. A two-metal ion mechanism is likely for acetyl CoA synthesis, in which a Ni-bound methyl group attacks an adjacent Cu—CO fragment with formation of a Cu-acyl intermediate. A methylnickel species in CODH/ACS has been identified by resonance Raman spectroscopy.45... 

IR and Raman spectroscopy have been commonly used and, for example, the effects of pressure on the Raman spectrum of a zinc compound with a N2C12 coordination sphere around the metal, have been investigated.28 IR spectroscopy has been utilized in studies of the hydration of zinc in aqueous solution and in the hydrated perchlorate salt.29 Gas phase chemistry of zinc complexes has been studied with some gas phase electron diffraction structures including amide and dithiocarbamate compounds.30-32... 

Silk fibers, a basic system with a uniaxial symmetry, have also been investigated by Raman spectromicroscopy [63] that is one of the rare techniques capable of providing molecular data on such small (3-10 pm diameter) single filaments. The amide I band of the silk proteins has been particularly studied to determine the molecular orientation using the cylindrical Raman tensor approximation. In this work, it was assumed that Co Ci, C2 and the a parameter was determined from an isotropic sample using the following expression of the depolarization ratio... 

Figure 10 shows polarized spectra of two types of silks recorded by Raman spectromicroscopy the dragline silk (the lifeline) of the spider Nephila edulis and the cocoon silk of a wild silkworm Sarnia cynthia ricini. The position of the amide I band at 1,668-1,669 cm-1 for both threads is characteristic of the /i-sheet... 

The heme moiety provides de novo designed heme proteins with an intrinsic and spectroscopically rich probe. The interaction of the amide bonds of the peptide or protein with the heme macrocycle provides for an induced circular dichroism spectrum indicative of protein-cofactor interactions. The strong optical properties of the heme macrocycle also make it suitable for resonance Raman spectroscopy. Aside from the heme macrocycle, the encapsulated metal ion itself provides a spectroscopic probe into its electronic structure via EPR spectroscopy and electrochemistry. These spectroscopic and electrochemical tools provide a strong quantitative base for the detailed evaluation of the relative successes of de novo heme proteins. 

The interpretation of the infrared and Raman spectra of solid salts of amides has been the subject of much disagreement. One must first distinguish solid complexes of amides with carboxylic acids from salts with strong mineral acids. In the first, the interaction is... 

Raman spectra obtained on concentrated protein solutions (ca. 20 mM) are dominated by contributions from the repeating amide group of the polypeptide backbone and from the sldechalns of aromatic amino acids (6). Phenylalanine and tryptophan exhibit particularly Intense ring breathing modes at 1006 and 1014 cm, respectively. An additional strong peak due to tryptophan Is typically observed at 760 cm ... 

Due to limitations in signal-to-noise ratio available for the then common dispersive IR instruments, peptide and protein vibrational spectroscopic studies shifted to emphasize Raman measurements in the 1970s 29-32 Qualitatively the same sorts of empirical correlations as discussed above have been found between frequencies of amide bands in the Raman and secondary structure. However, due to the complementary selection rules for Raman as compared to IR and to the multi-component nature of these polymeric spectral bands, the... 

Characterization of amide vibrational modes as seen in IR and Raman spectra has developed from a series of theoretical analyses of empirical data. The designation of amide A, B, I, II, etc., modes stem from several early studies of the (V-methyl acetamide (NMA) molecule vibrational spectra which continues to be a target of theoretical analysis. 15 27,34 162 166,2391 Experimental frequencies were originally fitted to a valence force field using standard vibrational analysis techniques and subsequently were compared to ab initio quantum mechanical force field results. 

Piperazine-2,5-diones possess two cis amide bonds. In the infrared, the CO stretching bands occur at 1670-1690 cm 1 and the NH stretching frequency at 3180-3195 cm-1. More detailed analysis of IR and Raman spectra have been carried out [84SA(A)481, 84SA(A)503]. 

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