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Model calculations are performed on the amide-I infrared (ir) bands of globular proteins by assigning one oscillator with a transition dipole to each peptide group. Coupling between these oscillators is introduced through the transition dipole coupling mechanism. As examples of application of the model, the ir spectra in the amide-I region of eight representative proteins, viz., carbonmonoxy myoglobin, ribonuclease A, α-lactalbumin, lysozyme, flavodoxin, carboxypeptidase A, concanavalin A, and β-trypsin are calculated. Good agreement is obtained between the calculated and observed amide-I band envelopes. Some structure-spectrum correlations are discussed on the basis of the model calculations. The presence of bands with significant ir intensities for myoglobin in the region below 1640 cm−1 is consistent with its x-ray structure having no β sheet. Analysis of the contributions of β sheets to the amide-I band envelopes shows that parallel, antiparallel, and mixed parallel/antiparallel β sheets give rise to strong ir bands at a similar position in the wave number region below 1650 cm−1, and that no band in the region above 1650 cm−1 can be regarded as a reliable marker of antiparallel β sheets. The contributions of non-α-non-β parts spread over a wide wave number region. The differences in the amide-I band envelopes between α-lactalbumin and lysozyme originate most probably from the structural differences between the α-helical parts near the N termini of these proteins.

The Protein Data Bank is a computer-based archival file for macromolecular structures. The Bank stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies. Text included in each data entry gives pertinent information for the structure at hand (e.g. species from which the molecule has been obtained, resolution of diffraction data, literature citations and specifications of secondary structure). In addition to atomic co-ordinates and connectivities, the Protein Data Bank stores structure factors and phases, although these latter data are not placed in any uniform format. Input of data to the Bank and general maintenance functions are carried out at Brookhaven National Laboratory. All data stored in the Bank are available on magnetic tape for public distribution, from Brookhaven (to laboratories in the Americas), Tokyo (Japan), and Cambridge (Europe and worldwide). A master file is maintained at Brookhaven and duplicate copies are stored in Cambridge and Tokyo. In the future, it is hoped to expand the scope of the Protein Data Bank to make available co-ordinates for standard structural types (e.g. a-helix, RNA double-stranded helix) and representative computer programs of utility in the study and interpretation of macromolecular structures.The Protein Data Bank' [1,2] was established in 1971 as a computer-based archival file for macromolecular structures. The purpose of the Bank is to collect, standardize, and distribute atomic co-ordinates and other data from crystallographic studies. As the number of solved protein and nucleic-acid structures has grown to the point where some lo7 characters are necessary to represent the co-ordinate information currently held, the need for such a computer-readable file has become very clear, and demands for the Bank's services have increased accordingly. The Protein Data Bank is one of several data base activities in the field of crystallography, e.g. the Bibliographic

The structures and vibrational frequencies of the acetate ion interacting with a metal ion (Na + , Mg 2+ , and Ca 2+ ) in the unidentate, bidentate, bridging, and pseudobridging forms are studied by ab initio molecular orbital calculations. Effects of a water molecule coordinating to either the acetate ion or the metal ion are also examined. The calculations are carried out by using the self-consistent reaction field method at the Hartree-Fock level with the 6-31+G** basis set. For the species interacting with a divalent metal cation, the lengths of the two CO bonds of the acetate ion are nearly equal in the bidentate form but are significantly different in the unidentate form. The frequency of the COO -antisymmetric stretch of the unidentate species is higher than that of the ionic species, which is in turn higher than that of the bidentate species. The reverse is the case for the COO -symmetric stretch. As a result, the frequency separations (∆ν a-s ) between the COO -antisymmetric and symmetric stretches for the unidentate, bidentate, and ionic species are in the following order: ∆ν a-s (unidentate) > ∆ν a-s (ionic) > ∆ν a-s (bidentate). It is demonstrated that such a correlation between the vibrational frequencies of the COO -group and the types of its coordination to a divalent metal cation is related to changes in the CO bond lengths and the OCO angle. The results of the present study clarify the physical basis of the empirical structure-frequency correlation, which has been used in the analysis of the infrared spectra of Ca 2+ -binding proteins.

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~~Normal-coordinate calculations were performed for the all-truns, 7-cis, 9-cis, 13-cis, 15-cis, 9, 13-di-cis, 9,13'-di-cis, 9,15-di-cis and 13,15-di-cis isomers of p-carotene. The Raman and infrared bands of the all-trans and 1 5 4 s isomers in the solid state were assigned on the basis of the results of the normal-coordinate calculations. The Raman excitation profiles of the main Raman bands of the above two isomers in cyclohexane solution reported previously were satisfactorily correlated with the calculated vibrational modes and the molecular structures in the excited electronic states. The Raman bands of the 7-cis, 9-cis, l3-cis, 9,13-di-cis, 9,13'-di-cis, 9,15-di-cis and 13,15-di-cis isomers were assigned. The vibrational modes assigned to the Raman bands characteristic of the cis isomers were analysed in detail.In the preceding paper' we discussed various aspects of the Raman spectra of the all-trans and 15-cis isomers of P,P-carotene (abbreviated to f3-carotene) from an experimental point of view. It was shown that for both the all-trans and 15-cis isomers (hereafter called simply all-trans and 15-cis), a few types of excitation profile exist in the resonance enhancement of the Raman intensities. In addition to the Raman bands which are resonant with strong absorptions in the visible region, there are some others which are resonant primarily with absorptions in the ultraviolet or near-ultraviolet region. It has also been found that some Raman bands of 15-cis are characteristic of this isomer (and therefore can be used as the key bands for identification) and that there are many weak bands in the Raman spectra of both all-trans and 15-cis in the solid state, which are not clearly observed in the spectra obtained from solutions.The purpose of this study was to establish the assignments of the Raman (and infrared) bands of all-rrans and 1 5 4 on the basis of normal-coordinate calculations and, at the same time, to clarify the relationship between the vibrational modes and the types of excitation profile. The assignments of the main Raman bands of other isomers, namely, 7-cis, 9 4 3 , 13-cis, 9,13-dicis, 9,13'-di-cis, 9,15-di-cis and 13,15-di-cis, which have been reported by Koyama and c o -w o r k e r~,~~~ will also be discussed. METHODring at both ends of the p-carotene molecule was replaced by the simplified structure, The vibrations of the C1-C4 part of the p-ionone ring were assumed not to mix with the vibrations of the conjugated chain which are undoubtedly responsible for most of the bands in the resonance Raman spectra. This assumption was supported by the similarity between the resonance Raman spectrum of all-trans-p-carotene and those of bixin and lycopene which have no p-ionone ring.For all-trans the values of the bond lengths and bond angles determined by x-ray analysis4 were used (Fig. 2a). The planarity of the conjugated chain between Cg and Cg' was assumed, although a slight deviation from a plane was indicated in the result of x-ray analysis. The equality of the C=C-H and C-C-H angles around ...

The e †ects of hydration on the structure and vibrational force Ðeld of the peptide group were examined by performing ab initio molecular orbital (MO) calculations on N-methylacetamide (NMA) and its clusters with up to three water molecules. The dielectric solvent e †ect was taken into account by the self-consistent reaction Ðeld (SCRF) method. It is shown that the wavenumbers of NMA are strongly a †ected by both the dielectric e †ect and formation of hydrogen bonds. The vibrational force Ðeld of NMA in aqueous solution is well described by taking into account the hydrogen bonding of three water molecules and the dielectric e †ect of the surrounding water solvent. The wavenumber shifts of the amide I, II and III bands induced by formation of hydrogen bonds are approximately additive. There is a strong correlation among the CxO stretching force constant, the CxO bond length and the amide I wavenumber. Calculated changes in the structural parameters induced by hydrogen-bond formation are consistent with changes in the resonance Raman intensities of the amide I, II and III bands. The changes in the CÈN and CxO bond lengths induced by hydrogen-bond formation in the excited electronic (2 1Aº) state are opposite from those in the ground electronic (1 1Aº) state. These opposite structural changes between the two electronic states are rationalized by using a simple Hamiltonian based on a two-state model, which describes the vibronic interaction between the two states involving a mode consisting of a linear combination of the CxO stretching and the CÈN contraction.