RNA-protein interactions and secondary structures of cowpea chlorotic mottle virus for in vitro assembly

Verduin, B.J.M.; Prescott, B.; Thomas, George J.

doi:10.1021/bi00314a008

Cited by 32 publications

(32 citation statements)

References 41 publications

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“…The use of the 2331 cm-' band as a reference intensity standard for sulfhydryls is not limited to applications involving thiol-thiolate equilibria (Li et al, 1993). Similar intensity standardizations are required for evaluating changes in the hydrogen bonding environments of cysteine sulfhydryls, including those associated with conformational switching in protein assemblies (Verduin et al, 1984). Additionally, quantitative determinations of Raman SH band intensities can be valuable in assessing exposure of protein sulfhydryl groups to chemical probes and monitoring stabilities of cysteine-metal complexes (zinc-finger domains).…”

Section: Discussionmentioning

confidence: 99%

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Cysteine conformation and sulfhydryl interactions in proteins and viruses. 3. Quantitative measurement of the Raman S-H band intensity and frequency

Tůma

Vohník

et al. 1993

Biophysical Journal

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The bond stretching vibration of the cysteine sulfhydryl (SH) group in a typical protein generates a Raman band in the spectral interval 2500-2600 cm-1, a region devoid of interference from any other fundamental mode of vibration of the protein. The relatively high Raman cross section associated with the S-H stretching vibration, the sensitivity of the vibrational frequency to hydrogen bonding interactions and side chain configurations, and the dependence of the Raman intensity on thiol-thiolate equilibria, combine to make the Raman SH band a potentially valuable marker of protein sulfhydryl interactions and a unique indicator of sulfhydryl participation in thiol-disulfide oxidoreductase activity. In order to exploit Raman spectroscopy for these purposes, accurate and precise measurements of Raman SH band profiles are required. We show here that the required precision and accuracy can be achieved by use of the Raman band corresponding to the stretching vibration of in situ nitrogen gas as a quantitative intensity and frequency standard. The Raman Q-branch center of the N2 band occurs at 2330.7 cm-1.

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Section: Discussionmentioning

confidence: 99%

“…Data collection was generally completed within 3 h of sample preparation. Solvent and scattering backgrounds were subtracted from the signal-averaged spectra by difference methods described previously (Verduin et al, 1984). Curve fitting procedures were carried out using software developed in our laboratory (Thomas and Wang, 1988).…”

Section: Raman Standardsmentioning

confidence: 99%

Cysteine conformation and sulfhydryl interactions in proteins and viruses. 3. Quantitative measurement of the Raman S-H band intensity and frequency

Tůma

Vohník

et al. 1993

Biophysical Journal

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“…All spectra were reversible with respect to increases or decreases in pH and pD. Further details of the sample handling required for Raman spectroscopy have been described previously (Verduin et al, 1984).…”

Section: Methodsmentioning

confidence: 99%

A Raman spectroscopic study of hen egg yolk phosvitin: structures in solution and in the solid state

Prescott¹,

Renugopalakrishnan²,

Glimcher³

et al. 1986

Biochemistry

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Laser Raman spectroscopy has been employed to study the structure of the hen egg yolk protein phosvitin in H2O and D2O solutions at neutral and acidic pH (pD) and in the solid state. The Raman data indicate an unusual conformation for phosvitin in neutral aqueous solution, which is deficient in both alpha-helix and conventional beta-sheet conformations. This unusual pH 7 structure is, however, largely converted to a beta-sheet conformation in strongly acidic media (pH less than 2). beta-Sheet is also the predominant secondary structure for phosvitin in the solid state, obtained by lyophilization of the protein from aqueous solution at neutral pH. The imidazolium rings of histidyl residues remain significantly protonated near neutrality, which suggests substantial elevation of the pK for imidazolium ring ionizations of phosvitin in aqueous solution. This may result from extensive ion-pair interactions involving positively charged histidines and negatively charged phosphoserines, which are prevalent in the phosvitin sequence. The present results suggest that antiparallel beta-sheets may not be the secondary structure most characteristic of native phosvitin (physiological pH), even though beta-sheet is the predominant conformation for phosvitin in acidic solutions (pH 1.5) and in the lyophilized solid. Phosvitin appears to be the first protein for which the major component to the Raman amide I band is centered near 1685 cm-1, which is 10-40 cm-1 higher than proteins heretofore examined in aqueous solution by Raman spectroscopy.

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“…We designate this the "D" state. Tyrosines in the D state occur in subunits of several RNA plant viruses (Verduin et al, 1984;Prescott et al, 1985).…”

Section: Determination Of Molecular Environments Of Tyrosinementioning

confidence: 99%

N-Terminal domain of the bacteriophage .lambda. repressor: investigation of secondary structure and tyrosine hydrogen bonding in wild-type and mutant sequences by Raman spectroscopy

et al. 1986

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Laser Raman spectroscopy has been employed to investigate structures of the lambda repressor N-terminal fragment, which recognizes operator DNA. Examination of repressor fragments containing deuterated amide groups and specifically labeled deuteriotyrosines has enabled the assignment of many of the conformation-sensitive Raman bands. By use of Fourier deconvolution and signal averaging techniques, the spectra of both wild-type and mutant sequences have been obtained as a function of the total protein concentration in aqueous solution over the range 5-100 mg/mL. This analysis has permitted monitoring of the monomer-dimer association of the repressor fragment and determination of the effects of dimerization upon individual side-chain interactions and main-chain secondary structure. The spectra are interpreted to reveal the hydrogen-bonding environments of four tyrosines of the N-terminal fragment (Y22, Y60, Y85, and Y88). The fifth tyrosine (Y101) is known from NMR experiments to be exposed to solvent molecules. The results show that in the dimer Y22 and Y85 are each acceptors of a strong hydrogen bond from a positive donor group, while Y88 is the donor of a strong hydrogen bond to a negative acceptor and Y60, like Y101, is involved in both a donor role and an acceptor role. Y60, Y85, and Y88, which are all near the dimer interface, undergo a collective change in hydrogen-bonding environment with dissociation of the dimer. The net effect of this change is the conversion of one acceptor tyrosine, deduced to be Y88, to a combined donor and acceptor role. The Raman results also indicate a predominantly alpha-helical structure for the N-terminal fragment in aqueous solution, with 70 +/- 4% of the residues incorporated into helical domains. The amount of alpha-helix determined from the Raman spectrum is consistent with X-ray and prediction results and is altered neither by the mutations C85----Y85 and C88----Y88 nor by dissociation of the dimer.

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RNA-protein interactions and secondary structures of cowpea chlorotic mottle virus for in vitro assembly

Cited by 32 publications

References 41 publications

Cysteine conformation and sulfhydryl interactions in proteins and viruses. 3. Quantitative measurement of the Raman S-H band intensity and frequency

Cysteine conformation and sulfhydryl interactions in proteins and viruses. 3. Quantitative measurement of the Raman S-H band intensity and frequency

A Raman spectroscopic study of hen egg yolk phosvitin: structures in solution and in the solid state

N-Terminal domain of the bacteriophage .lambda. repressor: investigation of secondary structure and tyrosine hydrogen bonding in wild-type and mutant sequences by Raman spectroscopy

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