Quantitative methods for structural characterization of proteins based on deep UV resonance Raman spectroscopy

Shashilov, Victor A.; Sikirzhytski, Vitali; Popova, Ludmila A; Lednev, Igor K.

doi:10.1016/j.ymeth.2010.05.004

Cited by 62 publications

(91 citation statements)

References 84 publications

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“…56 The Amide I vibration consisting mainly of C=O stretching and a small contribution from out-of-phase C–N stretching is known to be sensitive to the peptide’s secondary structure. 57 The details of AFM and DUVRR experiments are provided in the Supporting Information (SI).…”

Section: Structural Properties Of Aβ40 Fibrilsmentioning

confidence: 99%

Structural and Mechanical Properties of Amyloid Beta Fibrils: A Combined Experimental and Theoretical Approach

Paul

Hoffmann

Wang

et al. 2016

J. Phys. Chem. Lett.

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In this combined experimental (deep ultraviolet resonance Raman (DUVRR) spectroscopy and atomic force microscopy (AFM)) and theoretical (molecular dynamics (MD) simulations and stress–strain (SS)) study, the structural and mechanical properties of amyloid beta (Aβ40) fibrils have been investigated. The DUVRR spectroscopy and AFM experiments confirmed the formation of linear, unbranched and β-sheet rich fibrils. The fibrils (Aβ40)n, formed using n monomers, were equilibrated using all-atom MD simulations. The structural properties such as β-sheet character, twist, interstrand distance, and periodicity of these fibrils were found to be in agreement with experimental measurements. Furthermore, Young’s modulus (Y) = 4.2 GPa computed using SS calculations was supported by measured values of 1.79 ± 0.41 and 3.2 ± 0.8 GPa provided by two separate AFM experiments. These results revealed size dependence of structural and material properties of amyloid fibrils and show the utility of such combined experimental and theoretical studies in the design of precisely engineered biomaterials.

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Section: Structural Properties Of Aβ40 Fibrilsmentioning

confidence: 99%

Structural and Mechanical Properties of Amyloid Beta Fibrils: A Combined Experimental and Theoretical Approach

Paul

Hoffmann

Wang

et al. 2016

J. Phys. Chem. Lett.

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“…Structural Differences between the Refolded Protein and Mature Fibrils of SAA1.1 and SAA2.2-DUVRR spectroscopy is uniquely capable of identifying differences in ␤-sheet secondary structures between globular and fibrillar structures (21) and, therefore, was used to probe the structure of SAA1.1 and SAA2.2 mature fibrils. DUVRR spectra of mature SAA fibrils are superimposed (Fig.…”

Section: Saa22mentioning

confidence: 99%

Pathogenic Serum Amyloid A 1.1 Shows a Long Oligomer-rich Fibrillation Lag Phase Contrary to the Highly Amyloidogenic Non-pathogenic SAA2.2

Srinivasan

Patke

Wang

et al. 2013

Journal of Biological Chemistry

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Background: Murine SAA1.1 is pathogenic and SAA2.2 is non-pathogenic in AA amyloidosis. Results: SAA1.1 and SAA2.2 exhibit different biophysical properties, including fibrillation kinetics and fibril morphology. Conclusion:The distinct biophysical properties of highly homologous SAA proteins may contribute to their different pathogenicity during chronic inflammation. Significance: Structural and kinetic factors, more than their intrinsic amyloidogenicity, may determine the diverse pathogenicity among nearly identical SAA isoforms.

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“…This technique, however, requires site-specific 13 C and/or 15 N labels. Deep UV resonance Raman (DUVRR) spectroscopy is a powerful tool for protein structural characterization at all stages of fibrillation 19–22 . We have recently reported on the application of DUVRR spectroscopy combined with hydrogen-deuterium exchange (HX) for structural characterization of lysozyme fibril cross-β core 23,24 .…”

Section: Introductionmentioning

confidence: 99%

Dissecting Structure of Prion Amyloid Fibrils by Hydrogen–Deuterium Exchange Ultraviolet Raman Spectroscopy

Shashilov

Makarava

et al. 2012

J. Phys. Chem. B

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The molecular mechanisms underlying structural diversity of amyloid fibrils or prion strains formed within the same primary structure is considered to be one of the most enigmatic questions in prion biology. We report here on the direct characterization of amyloid structures using novel spectroscopic technique, hydrogen-deuterium exchange ultraviolet Raman spectroscopy. This method enables us to assess the structural differences within highly ordered cross-β cores of two amyloid states produced within the same amino acid sequence of full-length mammalian prion protein. We found that while both amyloid states consisted of β-structures, their cross β-cores exhibited hydrogen bonding of different strengths. Moreover, Raman spectroscopy revealed that both amyloid states displayed equally narrow crystalline–like bands suggesting uniform structures of cross β-cores within each state. Taken together, these data suggest highly polymorphous fibrils can display highly uniform structure of their cross β-core and belong to the same prion strain.

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Quantitative methods for structural characterization of proteins based on deep UV resonance Raman spectroscopy

Cited by 62 publications

References 84 publications

Structural and Mechanical Properties of Amyloid Beta Fibrils: A Combined Experimental and Theoretical Approach

Structural and Mechanical Properties of Amyloid Beta Fibrils: A Combined Experimental and Theoretical Approach

Pathogenic Serum Amyloid A 1.1 Shows a Long Oligomer-rich Fibrillation Lag Phase Contrary to the Highly Amyloidogenic Non-pathogenic SAA2.2

Dissecting Structure of Prion Amyloid Fibrils by Hydrogen–Deuterium Exchange Ultraviolet Raman Spectroscopy

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