Peptides amide vibrational modes

Coherent transport of vibrational energy is further limited by vibrational energy relaxation. Experiments on the amide I band of different peptides (NMA, apamin, scyllatoxin BPTI, and the cyclic pentapeptide) revealed a vibrational relaxation rate of approximately Ti = 1.2 ps, which is essentially independent of the particular peptide (30,53). A similar value has recently been reported for myoglobin at room temperature, with only a weak dependence of the relaxation rate on temperature down to cryogenic temperatures (140). In other words, vibrational relaxation of the amide I mode reflects an intrinsic property of the peptide group itself rather than a specific characteristic of the primary or secondary structural motifs of the... 

Detailed analyses of the vibrational spectra of raacromolecules, however, have provided a deeper understanding of structure and interactions in these systems (Krimm, 1960). An important advance in this direction for proteins came with the determination of the normal modes of vibration of the peptide group in A -methylacetamide (Miyazawa et al., 1958), and the characterization of several specific amide vibrations in polypeptide systems (Miyazawa, 1962, 1967). Extensive use has been made of spectra-structure correlations based on some of these amide modes, including attempts to determine secondary structure composition in proteins (see, for example, Pezolet et al., 1976 Lippert et al., 1976 Williams and Dunker, 1981 Williams, 1983). 

The peptide backbone vibration (amide 1) and the ring-breathing mode of phenylalanine at 1004 cm are not enhanced in this chromosome. An interpretation of this missing enhancement is that only the DNA has a strong interaction with the surface. The protein contents do not interact directly with the surface. These Micro-SERS investigations have shown that SERS can clarify structural changes of chromosomes in the adsorbed state. 

To study the vibrational energy relaxation of the amide I mode in N-methylacetamide, we employed the OPLS all-atom force field to model the solute and the flexible simple-point-charge (SPC) water modeF with doubled hydrogen masses to model the solvent D2O. To investigate the photoinduced heat transfer in photoswitchable peptides, we used the GROMOS96 united atom force field 43al. Additional force field parameters for the azobenzene unit were derived from density functional theory as described in Ref. [32]. We employed a united-atom modeP to describe the DMSO solvent, the SPC modeP to describe water, and the rigid all-atom model of Ref [57] to describe the chloroform solvent. 

As a first simple example, we apply the above explained methodology to study the vibrational energy redistribution of A-methylacetamide (NMA) in D2O following the laser excitation of the amide I mode in its first excited state. NMA has been used in numerous studies as a model system the peptide bond that links the various amino acids in a protein. The vibrational life time of the C=0 vibration of NMA has been studied experimentally in Ref [58], revealing a typical lifetime on the order of 1 ps (the decay is observed to occur in a biexponential, or nonexponential, manner). The relaxation rate does not change much whether the peptide bond is isolated (i.e., in NMA) or whether it is part of a larger peptide or protein. Furthermore, the decay is hardly affected by temperature, and increases by less then a factor of two when decreasing the temperature below 100 K. 

The infrared spectra of proteins and polypeptides comprise essentially four strong vibrational modes associated with the peptide link. These are the Amide A band near 3300 cm (vn-h)> the Amide I band near 1650 cm (vc=o), the Amide II band near 1550 cm " and the Amide III band near 1250 cm The latter two modes are both associated with combined stretch-... 

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).

Fig. 5. Comparison of ab initio, DFT/BPW91/6-31G -computed IR and VCD spectra over the amide I, II, and III regions for model peptides (of the generic sequence Ac-Alaw-NHCH3). These are designed to reproduce the major structural features of an o -helix (top left, n— 6, in which the center residue is fully H-bonded), a 3i helix (PLP Il-like, top right, n— 4), and an antiparallel /1-sheet (n= 2, 3 strands, central residue fully H-bonded) in planar (bottom left) and twisted (bottom right) conformations. The computations also encompass all the other vibrations in these molecules, but those from the CH3 side chains were shifted by H/D exchange (CH3) to reduce interference with the amide modes.

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