Quantitative IR spectrophotometry of peptide compounds in water (H<sub>2</sub>O) solutions. III. Estimation of the protein secondary structure

Kalnin, N.N.; Baikalov, Igor; Venyaminov, Sergei Yu.

doi:10.1002/bip.360301311

Cited by 144 publications

(104 citation statements)

References 25 publications

(4 reference statements)

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“…This secondary structure content is qualitatively confirmed by the shape of the amide I band in the IR spectrum of Ara h 1 ( Fig. 2A, solid line) where a maximum is observed at 1638 cm Ϫ1 , indicative for a high degree of ␤-structures (26,27). Also, a clear shoulder around 1660 cm Ϫ1 is apparent, indicating a comparable amount of helical structures (28).…”

Section: Ige Binding Experimentssupporting

confidence: 58%

Heat-induced Conformational Changes of Ara h 1, a Major Peanut Allergen, Do Not Affect Its Allergenic Properties

Koppelman

Bruijnzeel-Koomen

Hessing

et al. 1999

Journal of Biological Chemistry

154

143

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Ara h 1, a major peanut allergen was isolated, and its structure on secondary, tertiary, and quaternary level at ambient temperature was investigated using spectroscopic and biochemical techniques. Ara h 1 appeared to be a highly structured protein on a secondary level, possesses a clear tertiary fold, and is present as a trimeric complex. Heat treatment of purified Ara h 1 results in an endothermic, irreversible transition between 80 and 90°C, leading to an increase in ␤-structures and a concomitant aggregation of the protein. Ara h 1 from peanuts that were heat-treated prior to the purification procedure exhibited a similar denatured state with an increased secondary folding and a decreased solubility. The effect of heat treatment on the in vitro allergenic properties of Ara h 1 was investigated by means of a fluid-phase IgE binding assay using serum from patients with a clinically proven peanut allergy. Ara h 1 purified from peanuts heated at different temperatures exhibited IgE binding properties similar to those found for native Ara h 1, indicating that the allergenicity of Ara h 1 is heat-stable. We conclude that the allergenicity of Ara h 1 is unaffected by heating, although native Ara h 1 undergoes a significant heat-induced denaturation on a molecular level, indicating that the recognition of conformational epitopes of Ara h 1 by IgE either is not a dominant mechanism or is restricted to parts of the protein that are not sensitive to heat denaturation.

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Section: Ige Binding Experimentssupporting

confidence: 58%

Heat-induced Conformational Changes of Ara h 1, a Major Peanut Allergen, Do Not Affect Its Allergenic Properties

Koppelman

Bruijnzeel-Koomen

Hessing

et al. 1999

Journal of Biological Chemistry

154

143

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“…There is consensus in the literature that band narrowing does not improve statistical analysis results [20] therefore such procedures were not re-evaluated here. The subtraction of side-chain spectra before analysis has been used in only one study [10]. Normalization of IR spectra is required before analysis.…”

Section: Methods For Evaluating Analysis Performancementioning

confidence: 99%

“…There are eight assignments made by DSSP. Six are familiar to protein chemists: a-helix (denoted by H), 3 10 -helix (G), p-helix (I), b-sheet (E), turn (T), and unassigned structure (indicated by a blank space in the DSSP program output, but which we denote with C). Unassigned structure has been referred to by many names, such as irregular, other, disordered or coil.…”

Section: Protein Secondary Structure Tabulation From Dssp Outputmentioning

confidence: 99%

“…Because of their effectiveness in systems where there are strongly overlapping bands, these chemometric methods have also proved effective in the analysis of protein spectra [1][2][3][4][5][6][7][8][9][10][11][12]. In contrast to most typical applications of statistical analysis methods, the reported accuracy in protein studies, especially those that treat infrared (IR) spectra, varies widely.…”

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confidence: 99%

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

Oberg

Ruysschaert

Goormaghtigh

2004

European Journal of Biochemistry

164

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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“…The relative area of an infrared absorption band can, as a first approximation, be assumed to be a measure of the relative amount of that particular component. However, this assumption does not take into account absorption by amino acid side chains, or the slightly different extinction coefficients of different structural motifs (31)(32)(33). The most conspicuous difference between the FTIR spectra of the phosphorylated and the non-phosphorylated peptides is that the phosphorylated peptide contains a definite contribution from ␣-structure that is absent from that of the non-phosphorylated form (Table I).…”

Section: CD Nmr and Ftir Spectroscopy Of Lhc Iimentioning

confidence: 99%

Phosphorylation Controls the Three-dimensional Structure of Plant Light Harvesting Complex II

Nilsson¹,

Štys²,

Drakenberg³

et al. 1997

Journal of Biological Chemistry

100

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The most abundant chlorophyll-binding complex in plants is the intrinsic membrane protein light-harvesting complex II (LHC II). LHC II acts as a light-harvesting antenna and has an important role in the distribution of absorbed energy between the two photosystems of photosynthesis. We used spectroscopic techniques to study a synthetic peptide with identical sequence to the LHC IIb N terminus found in pea, with and without the phosphorylated Thr at the 5th amino acid residue, and to study both forms of the native full-length protein. Our results show that the N terminus of LHC II changes structure upon phosphorylation and that the structural change resembles that of rabbit glycogen phosphorylase, one of the few phosphoproteins where both phosphorylated and non-phosphorylated structures have been solved. Our results indicate that phosphorylation of membrane proteins may regulate their function through structural protein-protein interactions in surface-exposed domains. Light harvesting complex II (LHC II)1 is a major chlorophyllcontaining protein complex that accounts alone for half of the pigments involved in photosynthesis in plants. It is located mainly in appressed regions of the thylakoid membrane where it acts as the light-harvesting antenna for photosystem II (PS II). Reversible phosphorylation of LHC II is an established mechanism for redistribution of absorbed light energy between PS II and PS I. Phosphorylation of LHC II (giving LHC II(P)) is triggered by conditions where the plastoquinone pool of the photosynthetic electron transport chain becomes reduced (1). The kinase responsible for the phosphorylation of LHC II is not yet identified, although it is suggested that it is located in the core of photosystem II (2) or in contact with the cytochrome b 6 f complex (3, 4). LHC II(P) is found in the unappressed regions of the chloroplast thylakoid membrane and there acts as a lightharvesting antenna for photosystem I (PS I) (5-7). From electron crystallography of 2-dimensional crystals, a structure for the major part of non-phosphorylated LHC II has been described at 3.4-Å resolution (8). This structure reveals no information regarding the N-terminal domain that contains the phosphorylation site at position 5 (Thr); the protein backbone was traced only to residue 26 where it ends up close to the lipid membrane, consistent with the fact that the sequence between residues 21 and 29 (RVKYLGPF) (9) consists mainly of hydrophobic, aromatic, or charged amino acids. Aromatic residues are located at the membrane surface in structures of membrane proteins (10 -13), and residues Trp-16 and Tyr-17 of LHC II may also then form a point of contact with the membrane. LHC II has been shown to lose its ability to trimerize when more than the first 15 amino acids are removed from the apoprotein (14). At this site, specific lipid-protein interactions between the amino side chains and the lipid phosphatidylglycerol are involved in stabilization of the trimers (15), which implies that only the first 15 amino acid residues at the...

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Quantitative IR spectrophotometry of peptide compounds in water (H₂O) solutions. III. Estimation of the protein secondary structure

Cited by 144 publications

References 25 publications

Heat-induced Conformational Changes of Ara h 1, a Major Peanut Allergen, Do Not Affect Its Allergenic Properties

Heat-induced Conformational Changes of Ara h 1, a Major Peanut Allergen, Do Not Affect Its Allergenic Properties

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

Phosphorylation Controls the Three-dimensional Structure of Plant Light Harvesting Complex II

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Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. III. Estimation of the protein secondary structure

Cited by 144 publications

References 25 publications

Heat-induced Conformational Changes of Ara h 1, a Major Peanut Allergen, Do Not Affect Its Allergenic Properties

Heat-induced Conformational Changes of Ara h 1, a Major Peanut Allergen, Do Not Affect Its Allergenic Properties

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

Phosphorylation Controls the Three-dimensional Structure of Plant Light Harvesting Complex II

Contact Info

Product

Resources

About

Quantitative IR spectrophotometry of peptide compounds in water (H₂O) solutions. III. Estimation of the protein secondary structure