Proteins vibrational studies

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... 

Furthennore, resonance Raman studies of aconitase by Johnson et al. (53) demonstrated homologous spectra for both inactive and active aconitase. This suggests similar vibrational modes and thus similar core structures for the two forms. Finally, a cubane structure for the [3Fe-4S] cluster is supported by recent protein crystallographic studies of inactive aconitase by Robbins and Stout (54). (Recent results from Jensen s group (55) on the redetermination of the crystal structure of the Azotobacter ferredoxin I clearly show that the 3Fe cluster does not have a [3Fe-3S] ring structure, as originally determined (37), but has a [3Fe-4S] cubane structure.)... 

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... 

R.K. Dukor, Protein conformational studies using vibrational spectroscopy Comparison of techniques. Paper presented at 232nd ACS national meeting, biophysical and biomolecular symposium New and emerging techniques for protein characterization, Hilton, San Francisco, 10-14 September 2006... 

The vibrational spectra of molecules dissolved in water are different in significant ways from the spectra of these molecules in the gas phase. The study of water solution spectra is particularly important for molecules of biological significance because their structure and properties are often determined by the presence or absence of water. Computational techniques have been developed that relate computationally determined structure and associated properties such as force constants to experimental information such as vibrational frequencies. Experimental vibrational studies have been used to elucidate information about such problems as the secondary structure of proteins in water solution. A brief review of the computational and experimental techniques is presented. Our work, which builds on the essential combination of theoretical and experimental information, is then reviewed to outline our ideas about using computational studies to investigate the complicated problems of amino acids and proteins in water solution. Finally some suggestions are presented to show how computational techniques can enhance the use of experimental techniques, such as isotopic substitution for the study of complicated molecules. 

Specific vibrational assigmnents often require isotope or (in proteins) mutant studies. 

Sections V-1 and V-2 describe vibrational studies of other metalloporphyrins wilh axial ligands which serve as model compounds of a variety of heme proteins... 

A variety of methods can now be used to probe intermolecular interactions. The structural information on intermolecular interactions obtained from X-ray and neutron diffraction studies can be compared with gas-phase experimental data from pure rotational or rotation-vibrational spectra [1] and the energies obtained from ab initio molecular orbital calculations. It is found that each of these methods generally gives essentially the same result. While most X-ray diffraction studies are on crystals of small molecules, comparisons with the lower-resolution results of protein crystallographic studies give information on interactions in an environment that consists of about 50 % water by volume [8]. 

It has been shown that the most prominent bands are those yielded by aromatic amino-acid residues [84, 87, 88]. A similar picture is obtained when proteins are studied by the SERS spectroscopy [85, 87, 89-92]. The spectra consist of the vibrational modes of amino acid residues that are anchored directly to the electrode surface, i.e. mainly the aromatic amino-acid, cystine and acidic groups. 

W. Qian and S. Krimm,/. Comput. Chem., 32, 1025-1033 (1992). Vibrational Studies of the Disulfide Group in Proteins. VI. General Correlations of SS and CS Stretch Frequencies with Disulfide Bridge Geometry. 

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. 

Resonance Raman studies of the recombinant proteins showed vibrational bands at the 200-430 cm region characteristic of iron-sulfur clusters (124). Most interestingly, on Fe and O isotope sensitive band was detected at 801 cm which could be attributed to either a Fe(IV)=0 species or a monobridged Fe-O-Fe structure. This observation, together with Mossbauer analysis, which indicated a mixed N, 0, and S ligand environment for cluster 2, suggests a Fe-O-Fe or Fe=0 unit as part of the structure for cluster 2. 

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

Vibrational spectroscopy has played a very important role in the development of potential functions for molecular mechanics studies of proteins. Force constants which appear in the energy expressions are heavily parameterized from infrared and Raman studies of small model compounds. One approach to the interpretation of vibrational spectra for biopolymers has been a harmonic analysis whereby spectra are fit by geometry and/or force constant changes. There are a number of reasons for developing other approaches. The consistent force field (CFF) type potentials used in computer simulations are meant to model the motions of the atoms over a large ranee of conformations and, implicitly temperatures, without reparameterization. It is also desirable to develop a formalism for interpreting vibrational spectra which takes into account the variation in the conformations of the chromophore and surroundings which occur due to thermal motions. 

The use of Upid bilayers as a relevant model of biological membranes has provided important information on the structure and function of cell membranes. To utilize the function of cell membrane components for practical applications, a stabilization of Upid bilayers is imperative, because free-standing bilayer lipid membranes (BLMs) typically survive for minutes to hours and are very sensitive to vibration and mechanical shocks [156,157]. The following concept introduces S-layer proteins as supporting structures for BLMs (Fig. 15c) with largely retained physical features (e.g., thickness of the bilayer, fluidity). Electrophysical and spectroscopical studies have been performed to assess the appUcation potential of S-layer-supported lipid membranes. The S-layer protein used in aU studies on planar BLMs was isolated fromB. coagulans E38/vl. 

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. 

Heme complexes and heme proteins have also been the subject of NIS studies. Of specific interest have been three features the in-plane vibrations of iron, which have not been reported by Resonance Raman studies [108], the iron-imidazole stretch, which has not been identified in six-coordinated porphyrins before, and the heme-doming mode, which was assumed to be a soft 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. 

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