Aromatic and Cystine Side-Chain Circular Dichroism in Proteins

Woody, Robert W.; Dunker, A. Keith

doi:10.1007/978-1-4757-2508-7_4

Cited by 188 publications

(205 citation statements)

References 270 publications

(314 reference statements)

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“…The spectral changes of A␤ in the absence of BSBps monitored over 50 h can be ascribed to an overall decrease of the negative molar ellipticity at around 198 nm, typical of turnscontaining structure regions (46), accompanied by an increase of the negative molar ellipticity at around 215 nm, characteristic of ␤-sheet structure.…”

Section: Resultsmentioning

confidence: 97%

Computational and Experimental Studies on β-Sheet Breakers Targeting Aβ1–40 Fibrils

Minicozzi

Chiaraluce

Consalvi

et al. 2014

Journal of Biological Chemistry

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Background: ␤-Amyloid aggregates are at the basis of Alzheimer disease development. Short synthetic peptides are seen to inhibit polymerization. Results: Various synthetic peptides have been studied by MD simulations and tested experimentally. Conclusion:Combined results indicate Ac-LPFFN-NH 2 as an effective lead compound able to slow down A␤ 1-40 aggregation. Significance: Designing potential A␤ aggregation inhibitors will help fight Alzheimer disease.

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Section: Resultsmentioning

confidence: 97%

Computational and Experimental Studies on β-Sheet Breakers Targeting Aβ1–40 Fibrils

Minicozzi

Chiaraluce

Consalvi

et al. 2014

Journal of Biological Chemistry

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“…33 In the near-UV CD spectra (Figure 8), the partially resolved band at 283 nm is attributed to the exposed Tyr residue(s) of the enzyme. 32 Therefore, the 10% decrease in the intensity of this band caused by the 9-day incubation with 10% formalin may also reflect changes affecting the Tyr residues. The decrease in intensity could be explained by either a partial exposure of buried Tyr25 and/or an increase in the distance between Tyr73 and Tyr115 within the RNase A tertiary structure.…”

Section: Effect Of Formalin On the Secondary And Tertiary Structure Omentioning

confidence: 99%

“…The decrease in intensity could be explained by either a partial exposure of buried Tyr25 and/or an increase in the distance between Tyr73 and Tyr115 within the RNase A tertiary structure. 32,34 In native proteins, Tyr fluorescence emission at 304 nm may be quenched by factors such as the presence of nearby charged amino-acid residues or the involvement of the Tyr hydroxyl group in hydrogen bond formation. 35 In our experiments, formaldehyde-induced modifications can, in principle, alter Tyr emission by either chemically modifying the Tyr residue's microenvironment or by changing the secondary or tertiary structure of the enzyme.…”

Section: Effect Of Formalin On the Secondary And Tertiary Structure Omentioning

confidence: 99%

Modeling formalin fixation and antigen retrieval with bovine pancreatic ribonuclease A: I—Structural and functional alterations

Rait

O'Leary

Mason

2004

Laboratory Investigation

129

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Understanding the chemistry of protein modification by formaldehyde is central to developing improved methods to recover proteins from formalin-fixed paraffin-embedded tissues for proteomic analysis and to improve protein immunoreactivity for immunohistochemical studies. We used biophysical techniques to investigate the effects of formaldehyde treatment on bovine pancreatic ribonuclease A (RNase A). Treatment of RNase A with formaldehyde was shown by gel electrophoresis to lead to the rapid formation of intra-and intermolecular protein cross-links. Thermal studies revealed that these protein cross-links significantly increased the thermal denaturation temperature of RNase A preparations. Analysis of formaldehyde-treated RNase A oligomers isolated by gel chromatography revealed that intramolecular protein cross-links are primarily responsible for the increase in protein thermostability. Formaldehyde treatment also lowered the isoelectric point of the enzyme from 9.45 to the 6.0-7.4 range. Optical spectroscopic studies demonstrated that the formaldehyde-induced modifications did not significantly alter the secondary or tertiary structure of RNase A. Heating formaldehyde-treated RNase A at 651C resulted in a significant reversal of the protein intra-and intermolecular cross-links and led to a partial restoration of enzymatic activity.

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“…It remains possible that these differences reflect the internal consistency of the spectra in each respective basis set rather than the expected general accuracy of the methods. In a recent paper, Sreerama & Woody [6] investigated the effect of the number of reference proteins (29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44)(45)(46)(47)(48) on the accuracy of the prediction obtained by three publicly available CD analysis software programs.…”

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confidence: 99%

The optimization of protein secondary structure determination with infrared and circular dichroism spectra

Oberg

Ruysschaert

Goormaghtigh

2004

European Journal of Biochemistry

167

116

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We have used the circular dichroism and infrared spectra of a specially designed 50 protein database [Oberg, K.A., Ruysschaert, J.M. & Goormaghtigh, E. (2003) Protein Sci. 12, 2015-2031 in order to optimize the accuracy of spectroscopic protein secondary structure determination using multivariate statistical analysis methods. The results demonstrate that when the proteins are carefully selected for the diversity in their structure, no smaller subset of the database contains the necessary information to describe the entire set. One conclusion of the paper is therefore that large protein databases, observing stringent selection criteria, are necessary for the prediction of unknown proteins. A second important conclusion is that only the comparison of analyses run on circular dichroism and infrared spectra independently is able to identify failed solutions in the absence of known structure. Interestingly, it was also found in the course of this study that the amide II band has high information content and could be used alone for secondary structure prediction in place of amide I.

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Aromatic and Cystine Side-Chain Circular Dichroism in Proteins

Cited by 188 publications

References 270 publications

Computational and Experimental Studies on β-Sheet Breakers Targeting Aβ1–40 Fibrils

Computational and Experimental Studies on β-Sheet Breakers Targeting Aβ1–40 Fibrils

Modeling formalin fixation and antigen retrieval with bovine pancreatic ribonuclease A: I—Structural and functional alterations

The optimization of protein secondary structure determination with infrared and circular dichroism spectra

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