Protein vibrational spectroscopy

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... 

Zhu L, Wang W, Sage J T and Champion P M 1995 Femtosecond time-resolved vibrational spectroscopy of heme proteins J. Raman Spectrosc. 26 527-34... 

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. 

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. 

Stoner-Ma D, Melief EH, Nappa J et al (2006) Proton relay reaction in green fluorescent protein (GFP) polarization-resolved ultrafast vibrational spectroscopy of isotopically edited GFP. J Phys Chem B 110 22009-22018... 

Stoner-Ma D, laye AA, Matousek P, Towrie M, Meech SR, Tonge PJ (2005) Observation of excited-state proton transfer in green fluorescent protein using ultrafast vibrational spectroscopy. I Am Chem Soc 127 2864—2865... 

Selected entries from Methods in Enzymology [vol, page(s)] Biomolecular vibrational spectroscopy, 246, 377 Raman spectroscopy of DNA and proteins, 246, 389 resonance Raman spectroscopy of metalloproteins, 246, 416 structure and dynamics of transient species using time-resolved resonance Raman spectroscopy, 246, 460 infrared spectroscopy applied to biochemical and biological problems, 246, 501 resonance Raman spectroscopy of quinoproteins, 258, 132. 

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... 

There is substantial history regarding the application of conventional vibrational spectroscopy methods to study the intact surface of skin, the extracted stratum corneum and the ceramide-cholesterol-fatty acid mixtures that constitute the primary lipid components of the barrier. The complexity of the barrier and the multiple phases formed by the interactions of the barrier components have begun to reveal the role of each of these substances in barrier structure and stability. The use of bulk phase IR to monitor lipid phase behavior and protein secondary structures in the epidermis, as well as in stratum corneum models, is also well established 24-28 In addition, in vivo and ex vivo attenuated total reflectance (ATR) techniques have examined the outer layers of skin to probe hydration levels, drug delivery and percutaneous absorption at a macroscopic level.29-32 Both mid-IR and near-IR spectroscopy have been used to differentiate pathological skin samples.33,34 The above studies, and many others too numerous to mention, lend confidence to the fact that the extension to IR imaging will produce useful results. 

The vibrational spectroscopy time scale (10-300 x 10 sec) is appropriate for the direct sampling of the fastest motion expected to occur in phospholipid acyl chains, namely trans-gauche isomerization. To date, most Raman ai)d FT-IR studies of phospholipid phase behavior and lipid/protein interaction have focused mainly on qualitative measures of acyl chain organization. For example, the... 

Although X-ray crystallography, NMR, and circular dichroism are extremely valuable techniques for determining the structure of crystalline proteins or proteins in solution, they cannot be used to study proteins adsorbed on surfaces. Vibrational spectroscopy (infrared and Raman) appears to be the best approach available for bridging the gap between adsorbed proteins and proteins in solution. 

Vibrational spectroscopy has been used in the past as an indicator of protein structural motifs. Most of the work utilized IR spectroscopy (see, for example, Refs. 118-128), but Raman spectroscopy has also been demonstrated to be extremely useful (129,130). Amide modes are vibrational eigenmodes localized on the peptide backbone, whose frequencies and intensities are related to the structure of the protein. The protein secondary structures must be the main factors determining the force fields and hence the spectra of the amide bands. In particular the amide I band (1600-1700 cm-1), which mainly involves the C=0-stretching motion of the peptide backbone, is ideal for infrared spectroscopy since it has an large transition dipole moment and is spectrally isolated... 

Krimm S, Bandekar J. Vibrational spectroscopy and conformation of peptides, polypeptides and proteins. Adv Protein Chem 1986 38 181-365. 

Because our research is focused on problems relevant to secondary structure of proteins in solution, this section will briefly review the recent developments in spectroscopic techniques applied to this problem. These techniques are considered low-resolution methods which provide global insight into the overall secondary structure of proteins without being able to establish the precise three-dimensional location of individual structural elements [707], Vibrational spectroscopy has played a pioneering role in studying the conformations of peptides, polypeptides, and proteins [702]. The advent of stable and powerful lasers has led to the development of Fourier transform methods which allows the use of powerful computational techniques for the analysis of spectral data [10,103,104], Laser... 

Vibrational spectroscopy was used to study native chromatin as well as reconstituted DNA-histone complexes. IR (Liquier et al., 1979) and Raman spectra (Goodwin and Brahms, 1978 Savoie et al., 1985) show that the DNA in chromatin adopts a B type conformation. The important role adopted by the a helical parts of the histones in stabilizing the B conformation of histone-DNA complexes was demonstrated by IR (Taillandier et al., 1984b). Raman spectra of chromatin have made it possible to localize histone-DNA interactions in the minor groove and non-histone protein-DNA interactions in the major groove (Goodwin and Brahms, 1978). 

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. 

Cholesterol and membrane proteins, including structural ones such as glycophorin and myelin basic protein and functional ones such as -ATPase, bacteriorhodopsin, and cytochrome c, are important components of biological membranes. Cholesterol-lipid and a number of protein-lipid interactions have therefore been extensively investigated by vibrational spectroscopy. Interactions of hormones and toxins with phospholipid bilayers were also investigated. 

Bernstein HJ, Sunder S (1977) Resonance Raman Spectroscopy and Normal Coordinate Analysis of some Model Compounds of Heme Proteins, chapt 26. In Barnes AJ, Orville-Thomas WJ (eds) Vibrational Spectroscopy - Modem Trends. Elsevier, Amsterdam New York, p 413 Berreman DW (1963) Phys Rev 130 2193 Berreman DW (1972) J Opt Soc Amer 62 502... 

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