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Protein molecules, vibration modes

Since the stochastic Langevin force mimics collisions among solvent molecules and the biomolecule (the solute), the characteristic vibrational frequencies of a molecule in vacuum are dampened. In particular, the low-frequency vibrational modes are overdamped, and various correlation functions are smoothed (see Case [35] for a review and further references). The magnitude of such disturbances with respect to Newtonian behavior depends on 7, as can be seen from Fig. 8 showing computed spectral densities of the protein BPTI for three 7 values. Overall, this effect can certainly alter the dynamics of a system, and it remains to study these consequences in connection with biomolecular dynamics. [Pg.234]

There are many systems of different complexity ranging from diatomics to biomolecules (the sodium dimer, oxazine dye molecules, the reaction center of purple bacteria, the photoactive yellow protein, etc.) for which coherent oscillatory responses have been observed in the time and frequency gated (TFG) spontaneous emission (SE) spectra (see, e.g., [1] and references therein). In most cases, these oscillations are characterized by a single well-defined vibrational frequency, It is therefore logical to anticipate that a single optically active mode is responsible for these features, so that the description in terms of few-electronic-states-single-vibrational-mode system Hamiltonian may be appropriate. [Pg.303]

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... [Pg.76]

Relaxation rate, which looks into the low-frequency vibrational modes of protein molecules, is considered to play a significant role in biological process. A fractal-related parameter, called the fracton dimension, d-p, has been used to describe the relaxation rate at low temperature.f ... [Pg.1801]

In describing the normal modes of a protein, it is instructive to compare them conceptually with those of a simple model of a polymer, such as a chain of atoms, both periodic and aperiodic. In a harmonic periodic chain, the normal modes carry energy without resistance from one end of the ID crystal to the other. On the other hand, the vast majority of normal modes of an aperiodic chain are spatially localized [138]. Protein molecules, which are of course not periodic, can be better characterized as an aperiodic chain of atoms, and most normal modes of proteins are likewise localized in space [111,112,126-128]. If a normal mode a is exponentially localized, then the vibrational amplitude of atoms in mode a decays from the center of excitation, Ro, as... [Pg.229]

In the second part of the chapter, we have examined the spread of vibrational energy through coordinate space in systems that are large on the molecular scale—in particular, clusters of hundreds of water molecules and proteins—and computed thermal transport coefficients for these systems. The coefficient of thermal conductivity is given by the product of the heat capacity per unit volume and the energy diffusion coefficient summed over all vibrational modes. For the water clusters, the frequency-dependent energy diffusion coefficient was... [Pg.249]

While the structure and force field uniquely determine the vibrational frequencies of the molecule, the structure cannot in general be obtained directly from the spectrum. However, to a useful approximation, the atomic displacements in many of the vibrational modes of a large molecule are concentrated in the motions of atoms in small chemical groups, and these localized modes are to a good approximation transferable between molecules. Therefore, in the early studies of peptides and proteins (Sutherland, 1952), efforts were directed mainly to the identification of such characteristic frequencies and the determination of their relation to the structure of the molecule. This kind of analysis depended on empirical correlations of the spectra of chemically similar molecules. [Pg.183]

Even with the ability to calculate vibrational frequencies of a given structure of a protein molecule, still other problems will have to be resolved. We saw in Section II,B that a molecule with N atoms has, in general, 3N — 6 normal modes of vibration. For a regular repeating structure, such as a helix, the number of interest to us does not increase indefinitely with the length of the structure, since the IR- and Raman-active modes of an infinite structure consist of only three sets of phase-related values for the modes of a single chemical repeat unit (see Section II,B,3). No such restriction exists for an arbitrary protein molecule, and we must therefore expect all 3N — 6 modes to be potentially active. It therefore becomes very important to have some idea as to which modes can be expected to be strong and which weak, i.e., to be able to predict... [Pg.341]


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See also in sourсe #XX -- [ Pg.1801 ]




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