Proteins amide chromophore

Significantly, the bio-inorganic and polymer-containing PM nanocomposites showed no significant shift in the protein amide I and II vibration bands, or in the characteristic 567 nm optical absorption band of the retinal chromophore of BR, indicating that the structural and dynamical properties of the membrane-bound... 

As a second possibility, lipid-protein interaction must be considered. The red shift might be explained in terms of hydrophobic interaction of the hydrocarbon chains of phospholipids with the protein in such a way that the amide chromophores are transferred to a less polar environment (89). Again, the hypothesis can be tested by removal of lipid. The existence of the red shift in lipid-depleted mitochondria and in lipid-free mitochondrial structural protein shows that lipid-protein interaction is not necessary to produce the ORD spectra characteristic of membranes. It is possible that if some molecular rearrangement occurs during the extraction process, a red shift caused by hydrophobic lipid-protein association could be replaced with a red shift arising from hydrophobic protein-protein association. Such an explanation is unlikely, especially in view of the retention of the unit membrane structure in electron micrographs taken of extracted vesicles (30). On the basis of ORD, then, the most reasonable conclusion is that the red shift need not be assigned to lipid-protein association. 

CD spectroscopy is not limited to the study of small molecules, and has become extremely important in the characterization of biomolecules. The secondary structure of proteins can be characterized through studies of the CD associated with the amide chromophores. Using a combination of models and calibration spectra, it is possible to deduce the relative contributions to the overall secondary structure made by a-helix, antiparallel B-sheet, B-turn, and random coil portions of the polypeptide [11]. With the increasing use being made of such agents in the pharmaceutical industry, it... 

For proteins, it is the amide chromophore and the long-range order or lack of it that is responsible for the characteristic spectra of each of the secondary structural elements. A number of approaches have been employed to analyze the ORD or CD spectrum of a protein for the type and content of component secondary structures utilizing a set of basis spectra. The basis spectra are derived from the ORD/CD spectra of proteins from which the secondary structural content has been determined by X-ray crystallography. It is the solution of the linear combination of the basis spectra that gives the relative proportion for each of the secondary structural elements in the protein. 

Hirst, J.D. Improving protein circular dichroism calculations in the far-ultraviolet through reparametrizing the amide chromophore. J. Chem. Phys. 109, 782-788 (1998)... 

Amide derivatives have proved especially useful sugars for study by c.d. spectroscopy. The amide substituent is the same as the chromophore found in proteins, so that its optical properties have been extensively studied both experimentally and theoretically. 2-Acetamido sugars are found in many glycoproteins. The structure of 2-acetamido-2-deoxy-a-D-glucopyranose is given as an example in formula 7. 

Antibodies produced by this procedure were screened for their ability to react with the hapten to form the vinylogous amide 6, which has a convenient UV chromophore near 318nm, clear of the main protein absorption. Two antibodies selected in this way catalysed the expected aldol reaction of acetone with aldehyde 7 by way of the enamine 8 (Scheme 3) the remainder did not. These two effective aldolase mimics have been studied in some detail, and a crystal structure is available for (a Fab fragment of) one of them.126,281... 

Similar curves are obtained with other synthetic polypeptides, and in most cases they are reasonably independent of the nature of the amino acid side chains. In synthetic polypeptides and proteins the observed Cotton effects do not arise from isolated chromophores but are composite curves resulting from several transitions assigned to the amide bonds in the 200-m/x region. The a-helical curve, for example, results from three optically active absorption bands. One around 222 m/ arises from an n — 7T transition of nonbonding electrons, and the other two at 208 and 191 m/ji are attributed to w — tt transitions parallel and perpendicular to the axis of the helix. These transitions of the a-helix and the resulting Cotton effects characteristic of the a-helix are at present of great interest in interpreting ORD curves of membranes. 

The amine, amide and carboxy chromophores that are common to the general family of amino acids, peptides and proteins show absorption features in the short-wavelength part of the ultraviolet range to establish their associated CD features requires more sophisticated spectrometers. Much of the detailed conformational information gained from CD studies depends on data from this wavelength region. 

In protein systems in particular, a distinction between intrinsic and extrinsic Cotton effects has been made 31). The intrinsic effects are the result of internal dissymmetric interactions of protein chromophores such as the amide transitions in helical arrays. Extrinsic effects relate to non-protein substances which are usually optically inactive but exhibit optical activity when conjugated to a protein or to an... 

The excited-state deactivation pathway of PYP model chromophores is foimd to depend strongly on the substituent adjacent to the carbonyl group. The photoisomerization reaction of the deprotonated p-coumaric acid (pCA ) and of its amide analogue (pCNT) in solution does not show any spectroscopically detectable intermediate, which is quite different from PYP. On the contrary, the phenyl thioester derivative pCT exhibits a photophysical behavior in solution surprisingly close to that of the protein during its initial deactivation step. This study highlights the determining role of the thioester bond in the primary molecular events in PYP. 

A few explanations may be approprate here. As a retinal protein, bacte-riorhodopsin contains as chromophore all-frani-retinal which is bound to the protein by a protonated Schiff base. The action of light causes the isomerization of the chromophore to the 13-cis geometry. This is reflected in the BR K difference spectrum by the bands between 1100 and 1300 cm . The strong bands at 1529 and 1515 cm are the ethylenic (C—C) stretching modes of the retinal. Protein bands indicating alterations of the backbone are found around 1550 cm" (amide II) and between 1620 and 1680 cm" (amide I). An interesting feature is observed in the BR M spectrum at 1762.5 cm". This band could be assigned to an aspartic acid (see below) which becomes protonated in M. Because the... 

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