Advanced Statistical and Numerical Methods for Spectroscopic Characterization of Protein Structural Evolution

Shashilov, Victor A.; Lednev, Igor K.

doi:10.1021/cr900152h

Cited by 61 publications

(50 citation statements)

References 200 publications

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“…17−19 The typical protein DUVRR spectrum is dominated by amide bands, which characterize the polypeptide backbone conformation, and aromatic amino acid bands, which report on their local environment. 19 The DUVRR spectra of both pH 2.0 and pH 6.0 HET-s (218−289) prion fibrils show sharp, intense Amide I and II bands as well as a high intensity of the C α −H band that are indicative of an extended β-sheet conformation ( Figure 3). It was found that the positions and relative intensities of all bands remained the same, which shows that the secondary cross-β core structure of HET-s (218−289) prion fibrils does not change upon reversal of the filament supramolecular chirality.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

Rapid Filament Supramolecular Chirality Reversal of HET-s (218–289) Prion Fibrils Driven by pH Elevation

et al. 2015

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Amyloid fibril polymorphism is not well understood despite its potential importance for biological activity and associated toxicity. Controlling the polymorphism of mature fibrils including their morphology and supramolecular chirality by postfibrillation changes in the local environment is the subject of this study. Specifically, the effect of pH on the stability and dynamics of HET-s (218-289) prion fibrils has been determined through the use of vibrational circular dichroism (VCD), deep UV resonance Raman, and fluorescence spectroscopies. It was found that a change in solution pH causes deprotonation of Asp and Glu amino acid residues on the surface of HET-s (218-289) prion fibrils and triggers rapid transformation of one supramolecular chiral polymorph into another. This process involves changes in higher order arrangements like lateral filament and fibril association and their supramolecular chirality, while the fibril cross-β core remains intact. This work suggests a hypothetical mechanism for HET-s (218-289) prion fibril refolding and proposes that the interconversion between fibril polymorphs driven by the solution environment change is a general property of amyloid fibrils.

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Section: ■ Materials and Methodsmentioning

confidence: 99%

Rapid Filament Supramolecular Chirality Reversal of HET-s (218–289) Prion Fibrils Driven by pH Elevation

et al. 2015

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“…Further analysis of the Amide 1 band is required in order to obtain the types and amounts of secondary structure present; this is achieved through Fourier deconvolution and second derivative, curve fitting and spectral subtraction, for example. Multivariate analysis and other statistical methods are also increasingly being applied to the analysis of protein spectra because of their usefulness in interpreting the wealth and complexity of information contained within the spectra [21,22,23].…”

Section: Ftir Spectra Of Proteins -The Amide Bandsmentioning

confidence: 99%

Recent applications of ATR FTIR spectroscopy and imaging to proteins

Glassford¹,

Byrne²,

Kazarian³

2013

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

289

169

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Attenuated Total Reflection (ATR) Fourier Transform Infrared (FTIR) spectroscopy is a label-free, non-destructive analytical technique that can be used extensively to study a wide variety of different molecules in a range of different conditions. The aim of this review is to discuss and highlight the recent advances in the applications of ATR FTIR spectroscopic imaging to proteins. It briefly covers the basic principles of ATR FTIR spectroscopy and ATR FTIR spectroscopic imaging as well as their advantages to the study of proteins compared to other techniques and other forms of FTIR spectroscopy. It will then go on to examine the advances that have been made within the field over the last several years, particularly the use of ATR FTIR spectroscopy for the understanding and development of protein interaction with surfaces. Additionally, the growing potential of Surface Enhanced Infrared spectroscopy (SEIRAS) within this area of applications will be discussed. The review includes the applications of ATR FTIR imaging to protein crystallization and for highthroughput studies, highlighting the future potential of the technology within the field of protein structural studies and beyond.

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“…19,20 Coupling of hydrogen-deuterium exchange (H/D exchange) with deep UV Raman (DUVRR) spectroscopy allows one to elucidate fibril core structural organization and determine the psi (Ψ) dihedral angle of the protein backbone. 18,[21][22][23] In addition, DUVRR provides valuable information about the local environment near aromatic amino acids, such as phenylalanine and tyrosine. This can be utilized to monitor the changes in protein secondary structure that occur upon protein aggregation.…”

Section: Introductionmentioning

confidence: 99%

Exploring the structure and formation mechanism of amyloid fibrils by Raman spectroscopy: a review

Kurouski

Duyne

Lednev

2015

Analyst

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200

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Amyloid fibrils are β-sheet rich protein aggregates that are strongly associated with various neurodegenerative diseases. Raman spectroscopy has been broadly utilized to investigate protein aggregation and amyloid fibril formation and has been shown to be capable of revealing changes in secondary and tertiary structures at all stages of fibrillation. When coupled with atomic force (AFM) and scanning electron (SEM) microscopies, Raman spectroscopy becomes a powerful spectroscopic approach that can investigate the structural organization of amyloid fibril polymorphs. In this review, we discuss the applications of Raman spectroscopy, a unique, label-free and non-destructive technique for the structural characterization of amyloidogenic proteins, prefibrilar oligomers, and mature fibrils.

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Advanced Statistical and Numerical Methods for Spectroscopic Characterization of Protein Structural Evolution

Cited by 61 publications

References 200 publications

Rapid Filament Supramolecular Chirality Reversal of HET-s (218–289) Prion Fibrils Driven by pH Elevation

Rapid Filament Supramolecular Chirality Reversal of HET-s (218–289) Prion Fibrils Driven by pH Elevation

Recent applications of ATR FTIR spectroscopy and imaging to proteins

Exploring the structure and formation mechanism of amyloid fibrils by Raman spectroscopy: a review

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