The Use of Computed Optical Rotatory Dispersion Curves for the Evaluation of Protein Conformation<sup>*</sup>

Greenfield, Norma J.; Davidson, Bert J.; Fasman, Gerald D.

doi:10.1021/bi00858a009

Cited by 221 publications

(107 citation statements)

References 30 publications

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“…As a more applied example, we investigate the dependence of the alanine Raman and ROA spectra on the /, w, and v-angles driving the rotations of the NH 3 1 , CO 2 2 , and CH 3 groups (see Fig. 9).…”

Section: Alanine Zwitterionmentioning

confidence: 99%

“…For the same reason, positive values of w (e.g. 1408) are not probable, as the oxygen pointing out of the NH 3 1 group would interfere with the CH 3 residue (see Fig. 12).…”

Section: Alanine Zwitterionmentioning

confidence: 99%

“…Thus the optical rotatory dispersion (ORD) or circular dichroism (CD) became standard analytical tools in chemistry and molecular biology. 3,4 The extension of the optical activity techniques into the vibrational domain opened further possibilities, as the vibrational transitions are numerous and better resolved than the electronic ones. The vibrational circular dichroism (VCD) 5 and the Raman optical activity (ROA) 6 gave unique information about structure of many organic compounds, proteins, or nucleic acids.…”

Section: Introductionmentioning

confidence: 99%

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Molecular dynamics with restrictions derived from optical spectra

2008

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The information about molecular structure coded in the optical spectra must often be deciphered by complicated computational procedures. A combination of spectral modeling with the molecular dynamic simulations makes the process simpler, by implicit accounting for the inhomogeneous band broadening and Boltzmann averaging of many conformations. Ideally, geometries of studied systems can be deduced by a direct confrontation of such modeling with the experiment. In this work, the comparison is enhanced by restrictions to molecular dynamics propagations based on the Raman and Raman optical activity spectra. The methodology is introduced and tested on model systems comprising idealized H 2 O 2 , H 2 O 3 molecules, and the alanine zwitterion. An additional gradient term based on the spectral overlap smoothed by Fourier transformation is constructed and added to the molecular energy during the molecular dynamics run. For systems with one prevalent conformation the method did allow to enrich the Boltzmann ensemble by a spectroscopically favored structure. For systems with multiconformational equilibria families preferential conformations can be selected. An alternative algorithm based on the comparison of the averaged spectra with the reference enabling iterative updates of the conformer probabilities provided even more distinct distributions in shorter times. It also accounts for multiconformer equilibria and provided realistic spectra and conformer distribution for the alanine.

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Section: Alanine Zwitterionmentioning

confidence: 99%

“…For the same reason, positive values of w (e.g. 1408) are not probable, as the oxygen pointing out of the NH 3 1 group would interfere with the CH 3 residue (see Fig. 12).…”

Section: Alanine Zwitterionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Molecular dynamics with restrictions derived from optical spectra

2008

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“…Fig.3 shows the CD spectra of both Hb trout I and IV at p H 8.2 and 25 "C. At this pH, where both components are fully oxygenated in air, the shape of the CD spectrum is markedly different, especially in the region around 222nm, which typically corresponds to the n -7t transition of the peptide bond in alpha-helical conformation [13]. Hb trout IV resembles, both in the shape of the spectrum and in the absolute values of 8 (reduced ellipticity), human oxyhemoglobin.…”

Section: Circular Dichroismmentioning

confidence: 99%

Studies on the Properties of Fish Hemoglobins Molecular Properties and Interaction with Third Components of the Isolated Hemoglobins from Trout (Salmo irideus)

Brunori

Giardina

Chiancone

et al. 1973

European Journal of Biochemistry

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This paper reports some physico-chemical and functional properties of two of the isolated hemoglobin components from trout (Salmo irideus) blood (Hb trout I and Hb trout IV).Both hemoglobins in the oxygenated state are tetrameric a t pH between 7 and 7.8 and protein concentration above x 0.1 mg/ml. The tetramer is extremely stable towards dissociation into subunits and the stability constants, estimated by differential gel filtration, are between 10 and 50 times larger than that of human hemoglobin in phosphate buffer. A very small degree of dissociation is also suggested by the very small extent of hybrid formation even in concentrated K I or triethanobmine.The dichroic properties of both Hb trout I and Hb trout IV show distinct features in the wavelength region between 300 and 200 nm. H b trout IV resembles human hemoglobin in the shape of the CO spectrum and in the values of the reduced ellipticity ( 6 ) ; furthermore upon deoxygenation the value of 8 a t 222 nm becomes more negative by about 5O/,. On the other hand H b trout I shows a different circular dichroism spectrum and in particular the ellipticity a t 222 nm is lower than that of H b trout IV. Moreover the spectrum is insensitive to the presence of heme ligands.Hb trout IV binds human haptoglobin (Hp) as shown by quenching of the fluorescence of the tryptophanyl residues of Hp upon addition of hemoglobin. The apparent stoichiometry of complex formation corresponds to two H b tetramers per H p molecule (while for human hemoglobin the stoichiometry corresponds to one tetramer per Hp). A clear cut effect of H p binding is observed on the kinetics of 0, and especially CO combination as studied by flash photolysis.The effect of several third components on the 0, equilibrium of both Hb trout I and IV has been investigated. I n general the effect of adding ions or other molecules to a solution of Hb trout I is very minor. On the other hand Hb trout IV is more susceptible to changes in solvent composition. Of particular importance is the action of ATP, the physiological organic phosphate, which is without effect on Hb trout I, while it has a clear effect on Hb trout IV. The addition of ATP shifts the Root effect, the characteristic property of Hb trout IV, to higher pH values, thereby acting as one of the allosteric effectors.It was shown in the previous papers of this series property of Hb trout IV, i.e. of that component which is present in the blood in larger amounts (%65O/, of the total). On the other hand the 0, binding properties of both Hb trout I and Hb trout I1 are invariant with pH, although the equilibrium curve is markedly cooperative (n = 2.5).The functional differences between the various components have been used to interprete the physiological role played by each of them in the economy of the organism [4]. It is clear that knowledge Eur. J. Biochem. 39 (1973)

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“…The ratios b i were obtained by minimization of the sum 2 , where spectral intensities within ω∈(300.. 0.1800 cm -1 ) were included. The penalty function (last term, with R ) 0.02 and R ) 0.…”

Section: Methodsmentioning

confidence: 99%

Comparison of Quantitative Conformer Analyses by Nuclear Magnetic Resonance and Raman Optical Activity Spectra for Model Dipeptides

et al. 2008

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Interpretation of the Raman optical activity (ROA) of peptides is difficult because of molecular flexibility and interaction with the solvent. Typically, simulations and experiments are compared in terms of a qualitative agreement between the spectra. However, on a series of the Pro-Gly, Gly-Pro, Pro-Ala, and Ala-Pro dipeptides more precise conformer ratios could be obtained with the aid of the density functional computations and numerical decomposition of the spectral shapes. All observed transitions were assigned, and the computed transition frequencies were scaled accordingly. Then the populations predicted by the optical spectroscopy agreed within a few percent with an analysis of the spin-spin coupling constants based on the Karplus equations, which was confirmed also by a comparison of calculated and experimental NMR couplings. The results are supported by molecular dynamics simulations and related to the previous conformational studies of similar molecules.

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The Use of Computed Optical Rotatory Dispersion Curves for the Evaluation of Protein Conformation^*

Cited by 221 publications

References 30 publications

Molecular dynamics with restrictions derived from optical spectra

Molecular dynamics with restrictions derived from optical spectra

Studies on the Properties of Fish Hemoglobins Molecular Properties and Interaction with Third Components of the Isolated Hemoglobins from Trout (Salmo irideus)

Comparison of Quantitative Conformer Analyses by Nuclear Magnetic Resonance and Raman Optical Activity Spectra for Model Dipeptides

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The Use of Computed Optical Rotatory Dispersion Curves for the Evaluation of Protein Conformation*

Cited by 221 publications

References 30 publications

Molecular dynamics with restrictions derived from optical spectra

Molecular dynamics with restrictions derived from optical spectra

Studies on the Properties of Fish Hemoglobins Molecular Properties and Interaction with Third Components of the Isolated Hemoglobins from Trout (Salmo irideus)

Comparison of Quantitative Conformer Analyses by Nuclear Magnetic Resonance and Raman Optical Activity Spectra for Model Dipeptides

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The Use of Computed Optical Rotatory Dispersion Curves for the Evaluation of Protein Conformation^*