Calculations of the CD spectrum of bovine pancreatic ribonuclease

Abstract

CD spectra of bovine pancreatic ribonuclease A (RNase A) and its subtilisin-modified from (RNase S) have been calculated, based upon high-resolution structures from x-ray diffraction. All known transitions in the peptide and side-chain groups, especially the aromatic and disulfide groups, have been included. Calculations have been performed with both the matrix method and with first-order perturbation theory. A newly developed method for treating the electrostatic interactions among transition charge densities and between static charge distributions and transition charge densities is used. The effects of local electrostatic fields upon the group transition energies are included for all transitions. Rotational strengths generated by the matrix method were combined with Gaussian band shapes to generate theoretical CD spectra. The calculated spectra reproduce the signs and approximate magnitudes of the near-uv CD bands of both RNase A and S. Agreement is most satisfactory for the negative 275 nm band, dominated by tyrosine contributions. In agreement with two previous studies by other workers, coupling between Tyr 73 and Tyr 115 is the single most important factor in this band. The positive band observed near 240 nm is dominated by disulfide contributions, according to our results. The far-uv CD spectrum is poorly reproduced by the calculations. The observed 208 nm band, characteristic of alpha-helices, is absent from the calculated spectrum, probably because the helices in RNase are short. A strong positive couplet centered near 190 nm is predicted but not observed. Possible reasons for these incorrect predictions of the current theoretical model in the far-uv are discussed.

Individual contributions of the aromatic chromophores to the near-UV Circular Dichroism in class A β-lactamases: A comparative computational analysis

“…6 important role of the coupling between Y73 and Y115 to tyrosine Lb rotational strengths which was experimentally confirmed (13). The method is also used to calculate CD spectra of myoglobin, lactate dehydrogenase and other proteins (12,(40)(41)(42)(43)44 ).…”

“…Experimental excitation energies and electric transition dipole moments were used for the excited states of the model chromophores as described in (13)(14)(15). The method uses the protein X-ray structures thus allowing the orientation and distances between the chromophores within the protein to be taken into account.…”

“…A Combination of CD measurements and computational approaches leads to a fast and accurate understanding of the absolute configuration of small molecules (9-11) In addition, deeper atomistic insights into specific interactions between protein chromophores and the influence of structural and electrostatic effects can be attained via this dual approach (4,(12)(13)(14)(15)(16)(17)(18)(19). The CD spectrum of TEM-1 β-lactamase was calculated in good agreement with the experimental one (17).…”

“…(4,13,16,17,30,36,45).To generate a CD-spectrum, the calculated rotational strengths were combined with Gaussian band shape functions as was reported by Kurapkat and co-workers (13). The visualization of the enzyme structures was done with VMD 1.8.4 (46).…”

6-Methoxy-3,3’,3’-Trimethylspiro[2H-1-Benzopyran-2,1’[2]Oxaindan]: Separation Of Enantiomers, Circular Dichroism Measurements And Determination Of The Absolute Configuration

“…Two different approaches have been used to obtain the half bandwidths (Γ ) of the Gaussians. First we used the empirical formula Γ = κ · λ 1.5 cal , where λ cal is the calculated transition wavelength and the parameter κ has been assumed to be 0.00375 c) [22]. The resulting CD spectrum is shown in Figure 5a.…”