Polypeptide chain modes amide

P sheet A mode of protein folding in which two polypeptide chains (/ strands) lie side by side and either parallel or antiparallel with respect to the direction of the NH-Cq-CO group. Hydrogen bonds are formed from a carbonyl group of one chain to an amide nitrogen atom of the other chain and vice versa. 

We illustrate the results of a normal-mode calculation on a small molecule by discussing the normal vibrations of N-methylacetamide (NMA), the simplest molecule containing a trans peptide group analogous to that in a polypeptide chain. A study of this molecule provides insights into the general nature of the so-called amide modes of the peptide group. 

It is worth noting from Table XIII that the approximate force field gives a good reproduction of the frequencies and eigenvectors of the non-CHs modes of the side-chain point-mass model of the a helix. This approximation should therefore be satisfactory for reproducing the amide modes of an a-helical polypeptide chain in, for example, a globular protein. 

The goal of a vibrational spectroscopic study of a polypeptide molecule is to derive structural information from spectral parameters, such as band frequencies, intensities, and polarizations. In the past, the frequencies of the amide modes were the main diagnostic quantities, with structural insights being obtained from correlational studies based on observed spectra of known polypeptide chain structures. 

B. Amide and Skeletal Modes of the Polypeptide Chain 1. NH Stretch Mode... 

Although the so-called amide III mode has been described as the localized counterpart to amide II (Fraser and Price, 1952), and, as we have seen, contains NH ib and CN s in NMA, the situation is in fact much more complex for the polypeptide chain. The main point is that... 

The amide V mode in NMA consists of CN t plus NH ob, although CO ob can make a small contribution (Rey-Lafon et al., 1973). In the polypeptide chain, CN t and NH ob are also the main components but other coordinates contribute significantly. Thus, the frequency of this mode depends not only on the strength of the hydrogen bond (Miyazawa, 1962), but also on the side-chain structure. We present in Table XXXIX the PEDs together with their N O and H — O bond lengths, for observed amide V modes of structures for which the normal-mode calculations have been done. 

For NMA it made sense to define CO ib (amide IV), CO ob (amide VI), CN t (amide VII), and C CN d and CNC d as characteristic modes. Such a classification is too simplistic for a polypeptide chain, where many of these modes, together with NC C d and C b, mix strongly and very differently depending on the main-chain conformation and the side-chain structure. 

The normal-mode calculations on glucagon and BPTI demonstrate that, in order to analyze the vibrational spectra of proteins, we need to be able to predict more than just a density of vibrational states. In particular, we need to know what IR and Raman intensities are to be expected for a normal vibration. While a calculation of Raman intensities has yet to be done, important progress has been made in calculating IR intensities of amide and backbone modes of the polypeptide chain (Cheam and Krimm, 1985). 

We have noted the importance of incorporating calculations of IR intensities in the analysis of spectra. This approach is certain to prove fruitful in a number of areas determination of the dependence of amide mode intensities on conformation influence of size and perfection of structure on intensities correlation of intensities with hydrogen-bond geometry (Cheam and Krimm, 1986). Just as it is possible to develop a conformational (, i/ )-frequency map (Hsu et al., 1976), it should be possible to compute a conformational (, i/ )-intensity map, which could be useful in analyzing the spectra of unordered polypeptide chain structures. Of course, nothing has yet been done on the calculation of Raman intensities of polypeptides, and this area is ripe for future development. 

Since the peptide group, -CONH-, is the most distinctive component of the backbone of the polypeptide chain, it is not surprising that the normal modes of this group, the so-called amide modes, were first studied in the simplest representative molecule, viz., NMA. It is useful to examine the nature of these modes in NMA and in blocked dipeptides since they have sei-ved as important guideposts in the analysis of polypeptide spectra in terms of structure. 

The excellent agreement obtained for )5-PLA would indicate that this force field should be transferable to other APRS polypeptides, of course taking due accoimt of side-chain differences. This has been done for Ca-poly(L-glutamate), Ca-PLG [92], which X-ray and electron diffraction data had indicated to have an APPS structure but which were not extensive enough to provide a definitive conclusion. A proposed model [93] was used as the basis for the vibrational analysis, and the good prediction of the observed bands [92] supports both the model as well as the viability of the force field. The subtle differences between the -PLA and fi-Ca-PVG spectra are accounted for by the normal mode calculation, and emphasize the influence of the side chain on the main-chain modes, particularly on amide III. A similar successful vibrational analysis has been done on an alternating copolymer, APPS poly(L-alanylglycine) [19]. 

Figure I presents FTIR/ATR spectra of live and treated cryptococci H99 (A, B) and d plbl cells (C, D). The spectra of the live and heat treated samples are dominated by the amide I (1639 cm" ) and II (1547 cm" ) bands which are generated by the peptide bond formed between amino acid residues within a polypeptide chain or protein (26). These amide vibrations are attributed to the mannoprotein component of the capsule and cell wall of Cryptococcus (23, 27). The other prominent feature is the broad intense peak centred at -1024 cm" which is attributed to numerous v(C-0) vibrational modes from polysaccharides also present within the capsule and cell wall (28).

The main spectroscopic observation that required explanation was the 60-cm splitting in the infrared-active amide 1 (mainly CO s) modes of antiparallel-chain pleated sheet (APPS) polypeptides. Miyazawa (1960a) proposed that such splittings must be a consequence of the interactions between similar oscillators within the repeat unit of the structure, namely, the four peptide groups in the present case. He showed by a perturbation treatment that the frequencies for the four possible coupled modes would depend on the relative phases of the vibrations and the magnitudes of the interactions between peptide groups according to the relation... 

The APPS structure is the predominant one in synthetic polypeptides, and is a prevalent motif in proteins [2]. (Polyglycine is an exception, which we treat below.) An X-ray diffraction study of the simplest representative polypeptide, /ff-PLA [81], has provided the geometric parameters of the APPS. In addition to those given in Table 5-5, we note that the axial shift between adjacent chains, measured from the position where the hydrogen bond is linear, is 0.27A (as obtained from a TDC analysis of the amide I mode [80]). The vibrational analysis of /9-PLA thus provides the basic spectral characteristics of the APPS. 

Baltzer et al. reported a 42 amino acid containing polypeptide folding into a helix-loop-helix motif in solution, which dimerized in an antiparallel mode to form four-helix bundles. NMR and CD spectroscopy was used to study the structural features of the designed polypeptides. On the basis of this helix-loop-helix motif, a histidine containing peptide KO-42 122 (Figure 45a) was synthesized. On the surface of the folded motif, there are six histidines with assigned p a values in the range of 52-1.2. KO-42 shows catalytic efficiency in acyl-transfer and amidation reactions with /7-nitrophenylesters as substrates. The reactivity of histidine is due to its imidazoyl side chain that... 

The need for caution in the interpretation of polarisation studies is indicated by the recent work of Fraser and Price [59]. They point out that the transition moment of the carbonyl stretching mode responsible for the amide I absorption will be displaced from the CO direction due to interaction with the C—N vibration, and to an orbital following effect. They have calculated the dichroism of an oriented polypeptide in which the chains have the configuration of Pauling and Corey [60] with a 3.7 residue helix, and have shown that if allowance is made for a displacement of the CO transition moment by 20° towards the NO, the dichroic value obtained is very close to that observed experimentally [54]. The objection to the 3.7 helix based on polarisation studies [61] cannot therefore be maintained. 

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