Proteins backbone vibrations

The Raman frequencies of the protein backbone vibrations are often different than the infrared frequencies and thus infrared assignments are needed for structure determinations from infrared spectra. Such structural information is needed from the... 

In the past, the assignments of the protein backbone vibrations to secondary structures were often made from the spectrum of one compound and no attempts were made to support the assignments by changing the structure of the proteins. In fact structures were often determined from the frequencies and contours of one band. Only recently (4,9,10,11), have resolution enhancement or deconvolution (12) techniques being applied to the infrared spectra of proteins. While these deconvolution techniques appear to be essential for a valid interpretation of protein spectra, it is also necessary to use more than one infrared band and to substantiate assignments. 

Therefore, the purpose of this paper is to first present new work on the assignment of the protein backbone vibrations for a group of proteins in aqueous solution using the deconvoluted spectra for the assignments. These are the first spectra-structure correlations for a group of proteins in aqueous solutions and using deconvoluted spectra. These assignments also... 

In light of tire tlieory presented above one can understand tliat tire rate of energy delivery to an acceptor site will be modified tlirough tire influence of nuclear motions on tire mutual orientations and distances between donors and acceptors. One aspect is tire fact tliat ultrafast excitation of tire donor pool can lead to collective motion in tire excited donor wavepacket on tire potential surface of tire excited electronic state. Anotlier type of collective nuclear motion, which can also contribute to such observations, relates to tire low-frequency vibrations of tire matrix stmcture in which tire chromophores are embedded, as for example a protein backbone. In tire latter case tire matrix vibration effectively causes a collective motion of tire chromophores togetlier, witliout direct involvement on tire wavepacket motions of individual cliromophores. For all such reasons, nuclear motions cannot in general be neglected. In tliis connection it is notable tliat observations in protein complexes of low-frequency modes in tlie... 

Conventional MS in the energy domain has contributed a lot to the understanding of the electronic ground state of iron centers in proteins and biomimetic models ([55], and references therein). However, the vibrational properties of these centers, which are thought to be related to their biological function, are much less studied. This is partly due to the fact that the vibrational states of the iron centers are masked by the vibrational states of the protein backbone and thus techniques such as Resonance Raman- or IR-spectroscopy do not provide a clear picture of the vibrational properties of these centers. A special feature of NIS is that it directly reveals the fraction of kinetic energy due to the Fe motion in a particular vibrational mode. 

In summary, NIS provides an excellent tool for the study of the vibrational properties of iron centers in proteins. In spectroscopies like Resonance Raman and IR, the vibrational states of the iron centers are masked by those of the protein backbone. A specific feature of NIS is that it is an isotope-selective technique (e.g., for Fe). Its focus is on the metal-ligand bond stretching and bending vibrations which exhibit the most prominent contributions to the mean square displacement of the metal atom. 

The plots of the intensities of selected characteristic bands as a function of lateral position (so-called chemical maps) provide information on the amount of the respective molecules or molecular groups in the different morphological structures (Fig. 4.2). The band at 784 cm 1 can be assigned to out-of-plane deformation vibrational modes of the nucleobases cytosine, thymine and uracil and serves as an indicator for the presence of nucleic acids. At 483 cm-1, a C-C-C deformation of carbohydrate polymers such as starch or pectin is present in some of the spectra. To study the distribution of protein compounds, we analysed characteristic signals of the amino acid phenylalanine (1002 cm 1 ring breathe) as well as of the protein amide I band (1651 cm-1) that is brought about by vibrations of the protein backbones. The maximum of the phenylalanine signal co-localizes with a maximum in protein content... 

What information does the difference spectrum provide concerning the intramolecular mechanism of the BR to K transition The frequency shifts observed (Fig 6.6-10) between 1300 and 1100 cm characterize an all-trans to 13-cis isomerization of retinal. The unusually strong out-of-plane vibrations at 960 cm and 814 cm indicate considerable distortion of the terminal part of the chromophore. In summary, the BR-K difference spectrum shows that isomerization forces the chromophore and the protein backbone into a strained conformation, generating tension in the protein, which in turn drives the ensuing reactions. 

Amino acid side chains, particularly those with aromatic groups, exhibit characteristic frequencies that often are very useful in probing the local environment of the group in the protein (Spiro and Gaber, 1977). From our present point of view, however, we are interested in characterizing spectral features of backbone chain conformation. It is therefore important to know the locations of such bands so that their contribution to the spectrum is not confused with amide and backbone vibrations. We discuss below some features (in the nonstretching region) of such side-chain modes these are summarized in Table XL. 

Very few of the infrared studies of proteins have been carried out on aqueous solutions of the proteins. Except for the work of Koenig and Tabb (1), the few aqueous IR studies have been on single proteins. Correspondingly, most of the assignments of the backbone vibrations (the so-called Amide I, II, III, etc. vibrations) have been based on either Raman spectra of aqueous solutions (2) or on infrared spectra of proteins in the solid state (3). Where infrared solution spectra have been obtained, it has mostly been on D2O solutions (4) - not H2O solutions. Since these Amide I, II, III, etc. vibrations involve motion of the protein backbone, they are sensitive to the secondary structure of the protein and thus valid assignments are necessary in order to use infrared spectroscopy for determining the conformations of proteins. 

The frequencies of the infrared peptide backbone vibrations (the so-called Amide vibrations) of proteins can be used to differentiate secondary structures (conformations) in proteins in aqueous solutions. 

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. 

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. 

A number of characteristic SERS bands originate from the amino acid side chains Trp, Tyr and Phe. The peptide backbone vibrations are not enhanced in this protein (low scattering intensity in the spectral range of 1650-1675 cm amide I). The presence of the strong SERS bands of Trp, Tyr and Phe and the absence of the amide vibrations indicate a preferential interaction of these amino acid side chains with the surface. The strong (S—S) vibration at 509 cm in the NSRS spectrum is also missing in the SERS spectrum. This indicates that the disulfide bonds do not interact directly with the surface. 

FTIR measures the wavelength and intensity of the absorption of IR radiation energy by the protein sample. The polypeptide and protein repeat units give rise to nine characteristic IR absorption bands amides A, B, and I-VII. Among these bands, the amide I and II bands are the two most prominent vibrational bands of the protein backbone (Snsi and Byler 1986 Surewicz and Mantsch, 1988). The amide... 

Negative lines in the D Qa /DQa snd D Q0 /DQ0 spectra arise from vibrations associated with the relaxed states DQ and DQ0, respectively. The frequency of the lines detected at 1649cm , 1633cm , and 1604 cm " in the D Q /DQa spectrum, and at 1636 cm " and 1618 cm " in the D Q0 /DQ0 suggests that they most probably arise from either the neutral quinone (C=0 stretch. C=C stretch) or a C=0 stretch (Amide I) of the protein backbone. 

However, these spectra cannot be directly interpreted in terms of the quinone vibrations inasmuch as any bond affected by the photoinduced change of state of the quinone (such as protein backbone or side chains, water, other cofactors...) will also contribute to the difference spectrum. It is thus necessary to reconstitute RCs with chemically modified or isotopically labelled quinones in order to separate the contributions of the quinones from those of the protein. The results of such an approach for the QA /QA vibrations of Rb, sphaeroides reconstituted with a series of 1,4-naphtoquinones (NQ) are presented in this contribution. 

---