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.

Publisher Summary This chapter discusses some recent developments in the estimation of various conformations in a protein molecule from its circular dichroism (CD) spectrum in the ultraviolet region Optical rotatory dispersion (ORD) and CD are two chiroptical phenomena, which differentiate two enantiomers They are caused by different interactions of left- and right-circularly polarized light with chiral molecules Chirality is a geometric property of molecules; the corresponding substances are therefore optically active At present CD has replaced ORD for the conformational analysis of proteins because CD bands that are characteristic of various secondary structures can be directly observed The very simplicity of the CD method and the short time required for the measurements are extremely attractive It is often advantageous to compare the CD analysis with empirical predictions of secondary structure of proteins from sequences, if such are available All current methods for CD analysis are developed to determine not only the helix and β-form but also the β-turn and unordered forms

Calculation of protein conformation from circular dichroism.

Analysis of the circular dichroism spectrum of proteins using the convex constraint algorithm: A practical guide

Circular dichroism studies of distorted alpha-helices, twisted beta-sheets, and beta turns.

In this chapter, the basic phenomenon of circular dichroism (CD) will be described. The central theoretical parameter of rotational strength will then be defined. The mechanisms by which electronic transitions contribute to CD, i.e., acquire rotational strength, will then be discussed qualitatively, after which the methods by which CD is calculated will be described. The most important group in the electronic spectroscopy of proteins, the peptide group, will then be discussed. Finally, theoretical studies of the principal types of peptide secondary structure will be surveyed. The reader should note that aromatic and disulfide groups are not discussed in this chapter, but are covered in a separate chapter (Woody and Dunker, Chapter 4), along with experimental studies of these important protein chromophores.

Theory of Circular Dichroism of Proteins

Conformational energy calculations indicate that the peptide backbones of the low-energy conformations of the cyclized dipeptide derivatives cyclo (L-alanyl-L-alanyl-epsilon-aminocaproyl) and cyclo (L-alanyl-D-alanyl-epsilon-aminocaproyl) are constrained to form beta-bends of types I + III and II, respectively. Thus, the two compounds can serve as models for the spectroscopic properties of beta-bends of these types. The coupling constants obtained from 1H n.m.r. spectra in DMSO-d6 are consistent with the dihedral angeles of the computed lowest-energy conformations. Differences in 13C chemical shifts between the two compounds can be correlated with differences in shielding by C=O groups in bends of various types. 1H and 13C chemical shifts suggest association of cyclo (L-Ala-L-Ala-Aca) but not of cyclo (L-Ala-D-Ala-Aca) in dimethylsulfoxide. The different tendencies to associate can be explained in terms of the difference in conformation. The circular dichroism spectra of the two compounds are quite different. In methanol, trifluoroethanol and water, the L-Ala-L-Ala derivative has a positive extremum near 190 nm and two negative extrema near 206 and 220 nm, whereas the L-Ala-D-Ala derivative has a positive extremum at about 203 nm and negative extrema at about 187 and 229 nm. The spectra can be used to estimate the contribution of various bend types in a related series of compounds. A normal mode analysis of the vibrations of the computed low-energy conformations was compared with solid state infrared and Raman spectra, in order to determine the predominant conformations. The bend types determined by this comparison fully agree with the predictions of the theoretical computations for both derivatives.

Conformations of cyclo(L‐alanyl‐L‐alanyl‐ε‐aminocaproyl) and of cyclo(L‐alany1‐D‐alanyl‐ε‐aminocaproyl); cyclized dipeptide models for specific types of β‐bends

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Conformations of cyclo(L‐alanyl‐L‐alanyl‐ε‐aminocaproyl) and of cyclo(L‐alany1‐D‐alanyl‐ε‐aminocaproyl); cyclized dipeptide models for specific types of β‐bends