Protein vibrations

Zhu L, Li P, Huang M, Sage J T and Champion P M 1994 Real time observation of low frequency heme protein vibrations using femtosecond coherence spectroscopy Phys. Rev. Lett. 72 301-4... 

Peterson K A, Engholm J R, Rella C W and Sohwettman H A 1997 Piooseoond infrared studies of protein vibrational modes Accelerator-Based Infrared Sources and Applicationseds G P Williams and P Dumas (Bellingham, WA SPIE) pp 149-58 Proc. SPIE vol 3153... 

This is a subject in which the role of sophisticated theoretical work has been especially crucial aheady, and its importance continues to grow. The most controversial aspect of the subject is the question of whether and how protein vibrations are directly linked to the catalysis of hydrogen tunneling by enzymes. The full nature and value of the theoretical work is not covered in the present article, nor are the evidence and concepts that underlie proposals for the involvement of protein dynamics. It is our intention to follow the present article with a later treatment of the theoretical contributions and the dynamical questions. 

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... 

RBCs. Thus the variation in the 1,253/1,578-cm-1 ratio indicates varying contributions of RBCs among the three samples. The band at 1,122 cm-1 is also due to RBCs. These RBC vibrations may appear as a result of preresonance enhancement of heme protein vibrations due to proximity of the exciting line to heme absorption bands. 

Recent progress in confocal micro Raman spectroscopy has made it possible to investigate chromosomes and whole single living cells (Puppels et al., 1990, 1991). A spatial resolution of less than 1 )im was obtained. Different Raman spectra have been recorded of the cytoplasm and the cell nucleus. The spectrum of the nucleus consists of lines attributed to DNA and protein vibrations, strongly ressembling the spectra of isolated chromatin. The search for left-handed Z form DNA in metaphase chromosomes is in progress. 

Fig. 3.7 Spectral changes caused by thrombin (10 nM) binding to NSTBA sensor. The draninant peaks can be assigned to DNA vibrational modes with a lesser contribution from protein vibrational modes. Controls with BSA (10 mg/ml), msulin 600 nM and 1% human serum show no nonspecific protein binding. Lower three traces show spectra of NS, NS plus blocking agent (mercaptohexanol) and the fully assembled NSTBA sensor. Spectra are averages of 10 acquisitions...

The mid-lR region (1800-800cm ) -also referred to as the fingerprint region-contains the stretching vibration of the ester linkage of lipids at around 1740 cm , and the most dominant spectral feature, the amide 1 protein vibration centered around 1655 cm . This vibration is the exciton-coupled C=0 stretching manifold, and consequently, is sensitive for both peptide and protein secondary structure. 

Micheletti, C., Carloni, R, Maritan, A. Accurate and efficient description of protein vibrational dynamics comparing molecular dynamics and Gaussian models. Proteins 2004,55,635. 

All Raman bands measured in DNA fibres or crystals appear in this chromosome Micro-Raman spectrum. In addition, typical vibrations of the protein component were observed (phenylalanine, tyrosine, S—S group and the amide I mode). Recently, Micro-SERS has been applied for the first time to investigate the chromosomes adsorbed at the silver electrode This Micro-SERS spectrum of Chinese hamster metaphase chromosomes shows a number of intense bands. The enhancement factor obtained was estimated to be about 100 for the 790 cm DNA backbone vibration. The most intense bands in this SERS spectrum are located at 730 cm " and 1330 cm and can be attributed to the adsorbed adenine base vibration of the DNA. The characteristic protein vibrations in the normal Raman spectrum are missing in the SERS spectrum. 

As discussed before in the case of nucleic acids the authors have also considered the incidence of the interfacial conformation of the hemoproteins on the appearance of the SERRS signals from the chromophores. Although under their Raman conditions no protein vibration can be observed, the possibility of heme loss or protein denatura-tion are envisaged to explain a direct interaction of the heme chromophores with the electrode surface in the case of the adsorl Mb. extensive denaturation of Cytc at the electrode appears unlikely to the authors on the basis of the close correspondence of the surface and solution spectra. Furthermore, the sluggish electron transfer kinetics measured by cyclic voltammetry in the case of Cytc is also an argument in favour of some structural hindrance for the accessibility to the heme chromophore in the adsorbed state of Cytc. This electrochemical aspect of the behaviour of Cytc has very recently incited Cotton et al. and Tanigushi et al. to modify the silver and gold electrode surface in order to accelerate the electron transfer. The authors show that in the presence of 4,4-bipyridine bis (4-pyridyl)disulfide and purine an enhancement of the quasi-reversible redox process is possible. The SERRS spectroscopy has also permitted the characterization of the surface of the modified silver electrode. It has teen thus shown, that in presence of both pyridine derivates the direct adsorption of the heme chromophore is not detected while in presence of purine a coadsorption of Cytc and purine occurs In the case of the Ag-bipyridyl modified electrode the cyclicvoltammetric and SERRS data indicate that the bipyridyl forms an Ag(I) complex on Ag electrodes with the appropriate redox potential to mediate electron transfer between the electrode and cytochrome c. 

Chin, J. K. limenez, R. Romesberg, P. E., Direct observation of protein vibrations by selective incorporation of spectroscopically observable carbon-deuterium in cytochrome c. J. Am. Chem. Soc. 2001, 123, 2426-2427. 

Like all molecules, proteins vibrate, and as the temperature increases so the vibration increases. Eventually, this vibration disrupts the weak non-covalent forces that hold the protein in its organized structure. When this happens, proteins frequently become insoluble. This is the process of denaturation - a loss of the native structure of the protein. In denatured proteins most of the peptide bonds are accessible to digestive enzymes, and consequently denatured (i.e. cooked) proteins are more readily hydrolysed to their constituent amino acids. Gastric acid is also important, as relatively strong acid will also disrupt hydrogen bonds and denature proteins. 

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