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

Oberg, Keith A.; Ruysschaert, Jean‐Marie; Goormaghtigh, Erik

doi:10.1111/j.1432-1033.2004.04220.x

Cited by 167 publications

(131 citation statements)

References 53 publications

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“…This initial position specifically corresponds to antiparallel b-sheet [37] and its shift to higher wavenumbers is in agreement with the progressive decrease of the 1,695 cm -1 peak upon aggregation.…”

Section: Secondary Structure Changes Occurring During Aggregationsupporting

confidence: 84%

Transformation of amyloid β(1–40) oligomers into fibrils is characterized by a major change in secondary structure

Sarroukh

Cerf

Derclaye

et al. 2010

Cell. Mol. Life Sci.

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137

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Alzheimer's disease (AD) is a neurodegenerative disorder occurring in the elderly. It is widely accepted that the amyloid beta peptide (Ab) aggregation and especially the oligomeric states rather than fibrils are involved in AD onset. We used infrared spectroscopy to provide structural information on the entire aggregation pathway of Ab(1-40), starting from monomeric Ab to the end of the process, fibrils. Our structural study suggests that conversion of oligomers into fibrils results from a transition from antiparallel to parallel b-sheet. These structural changes are described in terms of H-bonding rupture/formation, b-strands reorientation and b-sheet elongation. As antiparallel b-sheet structure is also observed for other amyloidogenic proteins forming oligomers, reorganization of the b-sheet implicating a reorientation of b-strands could be a generic mechanism determining the kinetics of protein misfolding. Elucidation of the process driving aggregation, including structural transitions, could be essential in a search for therapies inhibiting aggregation or disrupting aggregates.

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Section: Secondary Structure Changes Occurring During Aggregationsupporting

confidence: 84%

Transformation of amyloid β(1–40) oligomers into fibrils is characterized by a major change in secondary structure

Sarroukh

Cerf

Derclaye

et al. 2010

Cell. Mol. Life Sci.

Self Cite

137

119

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“…The combo had the highest percentage of discrimination with 82%, (Beekes et al, 2007;Cai and Singh, 2004;Khaustova et al, 2010;Krimm and Bandekar, 1986;Oberg et al, 2004;Stuart, 1997).…”

Section: Resultsmentioning

confidence: 99%

Analysis of saliva by Fourier transform infrared spectroscopy for diagnosis of physiological stress in athletes

2015

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Introduction: Saliva is the most promising biofluid to monitor the physiological state of athletes, because this method is not invasive and has low contamination risks. The characterization of saliva by Fourier transform infrared spectroscopy (FT-IR) has been studied as an alternative technique to the standard clinical analysis. However, methodological procedures for saliva analysis are not completely clear, especially in terms of influence of storage conditions and sample preparations for infrared analysis. Thawed saliva includes a precipitate, which may influence the infrared spectral analysis. Thus, the purpose of this study was to show the spectral differences of the precipitate, supernatant, and a combo, as well as the best way to classify the physiological state of the athletes by FT-IR. Methods: The saliva collection was performed before, immediately after, and two hours after a handball match. After the storage of samples at -20 ○ C, it was possible to identify two phases (precipitate and supernatant) and to determine the biochemical differences between the spectra of each phase, which were distinctly analyzed by the second derivative and deconvolution bands. Results: The precipitate and supernatant results showed characteristic bands, especially in the protein regions. All FT-IR spectra were also statistically classified by linear discriminant analysis (LDA), using principal component analysis (PCA). The LDA precipitate and supernatant had lower value when compared to combo spectra (Combination of precipitate and supernatant) with 82%, showing that this combination is the best way to discriminate spectra of saliva samples collected before, immediately after, and 2 h after physical effort. Discussion: The results showed that it is possible to differentiate biochemically the two salivary phases, as well as the importance of the homogenization process of saliva samples to classify the physiological status of athletes using FT-IR.

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“…A possible explanation for the amyloidogenic properties of apoA-I IOWA would thus be an increased β-strand structure content in the active conformer. Fourier transform infrared (FTIR) spectroscopy was used to quantify the β-strand content in lipid-free apoA-I IOWA (25). To examine the β-strand contribution to lipidfree apoA-I WT and apoA-I IOWA secondary structure, spectra were obtained in the amide I region (1620-1700 cm −1 ; Figure 2).…”

Section: Resultsmentioning

confidence: 99%

Mapping the Structural Transition in an Amyloidogenic Apolipoprotein A-I

Lagerstedt

Cavigiolio²,

Roberts³

et al. 2007

Biochemistry

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The single amino acid mutation G26R in human apolipoprotein A-I (apoA-I IOWA ) leads to the formation of β-secondary structure rich amyloid fibrils in vivo. Here we show that full-length apoA-I IOWA has a decreased lipid binding capability, an increased amino terminal sensitivity to protease, and a propensity to form annular protofibrils visible by electron microscopy. The molecular basis for the conversion of apolipoprotein A-I to a pro-amyloidogenic form was examined by electron paramagnetic resonance spectroscopy. Our recent findings [Lagerstedt, J. O., Budamagunta, M. S., Oda, M. N., and Voss, J. C. (2007) J Biol Chem, 282,[9143][9144][9145][9146][9147][9148][9149] indicate that Gly26 in native apo-protein separates a preceding β-strand structure (residues 20-25) from a downstream largely α-helical region. The current study demonstrates that the G26R variant promotes a structural transition of positions 27-56 to a mixture of coil and β-strand secondary structure. Microscopy and staining by amyloidophilic dyes suggest that this alteration extends throughout the protein within one week of incubation in vitro, leading to insoluble aggregates of distinct morphology. The severe consequences of the Iowa mutation likely arise from the combination of losing the contribution of the native Gly residue in terminating β-strand propagation and the promotion of β structure when an Arg is introduced adjacent to succeeding residue of identical charge and size, Arg27.Apolipoprotein A-I (apoA-I) 1 is the primary protein component of high density lipoprotein (HDL), where it plays a key role in reverse cholesterol transport, a primary mediator of cholesterol efflux and phospholipid metabolism. In reverse cholesterol transport, apoA-I interacts with several members of this pathway, including ATP-binding cassette transporters (ABCA1, ABCG1, and ABCG4), lecithin:cholesterol acyltransferase (LCAT), and † This work was supported by National Institutes of Health grants HL77268, HL78615 and HL073826-01, and by the American Heart Association Scientist Development Grant 0235222N. This investigation was conducted in a facility constructed with support from Research Facilities Improvement Program Grant Number C06 RR-12088-01 from the National Center (1) ]. The conformational adaptability of apoA-I (2),(3, 4) facilitates the processing of HDL by these distinct receptors and enzymes. For example with lipid binding, apoA-I undergoes a substantial change in structure, wherein the apoA-I helix bundle unfurls into an extended alpha helical "looped belt" conformation that resides on the periphery of the lipid particle [reviewed in (3, 5)]. This structural plasticity has made apoA-I difficult to examine and only recently has detailed structural information become available. Notably, the crystal structure of lipid-free apoA-I provides important new insight into the organization of the lipid-free protein, illuminating a N-terminal four-helix bundle followed by a more flexible C-terminal domain (6). However, features of the structure, parti...

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

Cited by 167 publications

References 53 publications

Transformation of amyloid β(1–40) oligomers into fibrils is characterized by a major change in secondary structure

Transformation of amyloid β(1–40) oligomers into fibrils is characterized by a major change in secondary structure

Analysis of saliva by Fourier transform infrared spectroscopy for diagnosis of physiological stress in athletes

Mapping the Structural Transition in an Amyloidogenic Apolipoprotein A-I

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