Publisher Summary The vibrational spectrum of a molecule is determined by its three-dimensional structure and its vibrational force field. An analysis of this (usually infrared (IR) and Raman) spectrum can therefore provide information on the structure and on intramolecular and intermolecular interactions. The more probing the analysis, the more detailed is the information that can be obtained. Detailed analyses of the vibrational spectra of macromolecules, however, have provided a deeper understanding of structure and interactions in these systems. An important advance in this direction for proteins came with the determination of the normal modes of vibration of the peptide group in N-methylacetamide, and the characterization of several specific amide vibrations in polypeptide systems. Extensive use has been made of spectra-structure correlations based on some of these amide modes, including attempts to determine secondary structure composition in proteins. Polypeptide molecules exhibit many more vibrational frequencies than the amide modes. Over the years, some normal-mode calculations have provided greater insight into the spectra of particular molecules. However, these have often been based on approximate structures or have employed limited force fields. These force fields can now serve as a basis for detailed analyses of spectral and structural questions in other polypeptide molecules. The aim of this chapter is to present these recent developments in the vibrational spectroscopy of peptides, polypeptides, and proteins.

Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins.

Amide modes and protein conformation.

Surface-enhanced Raman (SERS) signatures were measured from single living cells at different times after the uptake of gold nanoparticles. The spectra are indicative of chemical changes in the environment of the nanostructures over time. The increase of the SERS signal strength and parallel TEM studies indicate the formation of nanoaggregates providing optimum SERS enhancement for ultrasensitive probing inside the endosomal compartment. The results have implications for medical and biotechnology applications of SERS nanosensors in cells.

In vivo molecular probing of cellular compartments with gold nanoparticles and nanoaggregates.

The Raman spectra of collagen, gelatin, and elastin are presented. The Raman lines in the latter two spectra are assigned by deuterating the amide N-H groups in gelatin and by studying the superposition spectra of the constituent amino acids. Two lines appear at 1271 and 1248 cm−1 in the spectra of collagen and gelatin that can be assigned to the amide III mode. Possibly, the appearance of two amide III lines is related to the biphasic nature of the tropocollagen molecule, i.e., proline-rich (nonpolar) and proline-poor (polar) regions distributed along the chain. The melting, or collagen-to-gelatin transition, in water-soluble calf skin collagen is studied and the 1248-cm−1 amide III line is assigned to the 31 helical regions of the tropocollagen molecule.

Elastin is thought to be mostly random and the Raman spectrum confirms this assertion. Strong amide I and III lines appear at 1668 and 1254 cm−1, respectively, and only weak scattering is observed at 938 cm−1. These features have been shown to be characteristic of the disordered conformation in proteins.

Raman scattering of collagen, gelatin, and elastin.

Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pd, and Cd

The intensity of Raman scattering from the various Raman active vibrations of poly-(riboadenylic acid), poly(ribocytidylic acid), poly(ribouridylic acid), and poly(riboinosinic acid) in moderately dilute solutions were examined as the temperature was changed to alter their conformation. It was found that certain highly intense, highly polarized Raman bands from the totally symmetric, i.e., in-plane, ring vibrations of the nucleic acid bases become less intense as the chains become more ordered in solution. Since these vibrations occur at frequencies which are markedly different for each type of base, Raman spectroscopy appears to provide a new method for the characterizing of the average conformation of each of the bases in solution. A theory for the resonant Raman effect is given in which it is shown that, a decrease in resonant Raman intensity is to be expected if one obtains a decrease in the intensity of the corresponding ultraviolet absorption band with which the incident light is resonant. If it is assumed that certain Raman bands derive their intensity predominantly from the first few ultraviolet absorption intensities, then a qualitative explanation of our observed conformational dependence of the ordinary Raman intensities can be obtained.

Conformational dependence of the Raman scattering intensities from polynucleotides.

The Raman spectra of the two crystalline modifications of polyglycine, I and II, and of N‐deuterated polyglycine II have been recorded. The results of a normal‐coordinate analysis of polyglycine II and N‐deuterated polyglycine II are presented along with the phonon dispersion curves of polyglycine II. Assignments are made on a number of bands not observed in the infrared. Some previous band assignments are found to be inconsistent with the Raman data.

Raman Spectra and the Phonon Dispersion of Polyglycine

The vibrational frequencies of α-helical poly-L-alanine and its N-deuterated analog have been assigned by normal coordinate analyses. The phonon dispersion curves and frequency distribution of α-poly-L-alanine have been calculated by using a model which includes hydrogen bonding. The frequency distribution was used to interpret the inelastic neutron scattering data and to calculate the heat capacity. The low-frequency chain modes involving accordian-like motions of the whole helix have been calculated and their dispersion investigated by means of a simplified model.

Phonon dispersion curves and normal coordinate analysis of -poly-L-alanine.

Laser Raman spectra of a mixture of yeast t-RNA's are examined as a function of temperature and after total alkaline hydrolysis to mononucleotides; the data are interpreted on the basis of extensive preliminary studies previously reported from this laboratory on the Raman spectral properties of numerous synthetic model compounds. Since the Raman intensities observed are extremely sensitive to conformational changes in the nucleic acid, much useful structural information can be obtained.

Structural changes in t-RNA from changes in the Raman scattering intensities.

From Raman scattering we can measure certain vibrational frequencies of biological polymers, many of which cannot be obtained from infrared spectroscopy because of selection rules, intensity differences, or interference from solvent bands. The frequencies can be used to determine force fields of the polymers, and various spectral features can be used to perform structural studies on the polymers.

Enoch W. Small

Papers

Conformational dependence of the Raman scattering intensities from polynucleotides.

Raman Spectra and the Phonon Dispersion of Polyglycine

Phonon dispersion curves and normal coordinate analysis of -poly-L-alanine.

Structural changes in t-RNA from changes in the Raman scattering intensities.

Characterization of Biological Polymers by Laser Raman Scattering