Water Molecular System Dynamics Associated with Amyloidogenic Nucleation as Revealed by Real Time Near Infrared Spectroscopy and Aquaphotomics
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{"title"=>"Water molecular system dynamics associated with amyloidogenic nucleation as revealed by real time near infrared spectroscopy and aquaphotomics", "type"=>"journal", "authors"=>[{"first_name"=>"Eri", "last_name"=>"Chatani", "scopus_author_id"=>"6603232374"}, {"first_name"=>"Yutaro", "last_name"=>"Tsuchisaka", "scopus_author_id"=>"56270251400"}, {"first_name"=>"Yuki", "last_name"=>"Masuda", "scopus_author_id"=>"56270225700"}, {"first_name"=>"Roumiana", "last_name"=>"Tsenkova", "scopus_author_id"=>"55910264500"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"25013915", "doi"=>"10.1371/journal.pone.0101997", "pui"=>"373524551", "issn"=>"19326203", "sgr"=>"84904247195", "scopus"=>"2-s2.0-84904247195"}, "id"=>"c688cae0-5307-3d26-a717-2c8532aca028", "abstract"=>"The formation of amyloid fibrils proceeds via a nucleation-dependent mechanism in which nucleation phase is generally associated with a high free energy resulting in the rate-limiting step. On the basis of this kinetic feature, the nucleation is one of the most crucial phases controlling the pathogenesis of amyloidoses, but little is known about the details of how protein molecules and surrounding environment vary at this stage. Here, we applied near infrared (NIR) spectral monitoring of water structural changes in real time during the nucleation-dependent fibrillation of insulin. Whilst multivariate spectral analysis in the 2050-2350 nm spectral region indicated cross-β formation, characteristic transformations of water structure have been detected in the spectral region 1300-1600 nm corresponding to the first overtone of water OH stretching vibrations. Furthermore, specific water spectral patterns (aquagrams) related to different water molecular conformations have been found along the course of protein nucleation and aggregation. Right in the beginning, dissociation of hydrogen-bonded network in bulk water and coinstantaneous protein and ion hydration were observed, followed by water hydrogen-bonded networks development, presumably forcing the nucleation. These specific transformations of water spectral pattern could be used further as a biomarker for early non-invasive diagnosis of amyloidoses prior to explosive amplification and deposits of amyloid fibrils.", "link"=>"http://www.mendeley.com/research/water-molecular-system-dynamics-associated-amyloidogenic-nucleation-revealed-real-time-near-infrared", "reader_count"=>24, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>6, "Other"=>2, "Student > Master"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>6, "Other"=>2, "Student > Master"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Engineering"=>5, "Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Materials Science"=>1, "Agricultural and Biological Sciences"=>10, "Medicine and Dentistry"=>1, "Physics and Astronomy"=>1, "Chemistry"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>5}, "Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>2}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>10}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Japan"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1589355", "https://ndownloader.figshare.com/files/1589356", "https://ndownloader.figshare.com/files/1589357", "https://ndownloader.figshare.com/files/1589358", "https://ndownloader.figshare.com/files/1589359", "https://ndownloader.figshare.com/files/1589360", "https://ndownloader.figshare.com/files/1589361"], "description"=>"<div><p>The formation of amyloid fibrils proceeds via a nucleation-dependent mechanism in which nucleation phase is generally associated with a high free energy resulting in the rate-limiting step. On the basis of this kinetic feature, the nucleation is one of the most crucial phases controlling the pathogenesis of amyloidoses, but little is known about the details of how protein molecules and surrounding environment vary at this stage. Here, we applied near infrared (NIR) spectral monitoring of water structural changes in real time during the nucleation-dependent fibrillation of insulin. Whilst multivariate spectral analysis in the 2050–2350 nm spectral region indicated cross-β formation, characteristic transformations of water structure have been detected in the spectral region 1300–1600 nm corresponding to the first overtone of water OH stretching vibrations. Furthermore, specific water spectral patterns (aquagrams) related to different water molecular conformations have been found along the course of protein nucleation and aggregation. Right in the beginning, dissociation of hydrogen-bonded network in bulk water and coinstantaneous protein and ion hydration were observed, followed by water hydrogen-bonded networks development, presumably forcing the nucleation. These specific transformations of water spectral pattern could be used further as a biomarker for early non-invasive diagnosis of amyloidoses prior to explosive amplification and deposits of amyloid fibrils.</p></div>", "links"=>[], "tags"=>["Biochemistry", "biophysics", "molecular biology", "molecular", "amyloidogenic", "nucleation", "revealed", "infrared", "spectroscopy"], "article_id"=>1100720, "categories"=>["Biological Sciences"], "users"=>["Eri Chatani", "Yutaro Tsuchisaka", "Yuki Masuda", "Roumiana Tsenkova"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0101997.s001", "https://dx.doi.org/10.1371/journal.pone.0101997.s002", "https://dx.doi.org/10.1371/journal.pone.0101997.s003", "https://dx.doi.org/10.1371/journal.pone.0101997.s004", "https://dx.doi.org/10.1371/journal.pone.0101997.s005", "https://dx.doi.org/10.1371/journal.pone.0101997.s006", "https://dx.doi.org/10.1371/journal.pone.0101997.s007"], "stats"=>{"downloads"=>12, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Water_Molecular_System_Dynamics_Associated_with_Amyloidogenic_Nucleation_as_Revealed_by_Real_Time_Near_Infrared_Spectroscopy_and_Aquaphotomics_/1100720", "title"=>"Water Molecular System Dynamics Associated with Amyloidogenic Nucleation as Revealed by Real Time Near Infrared Spectroscopy and Aquaphotomics", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-07-11 02:56:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1589341"], "description"=>"<p>(A) Raw NIR spectra data set. Two regions over 1300–1600 nm and 2050–2350 nm were focused on to evaluate changes with water and protein structures, respectively. (B) A magnified view at 1300–1600 nm. The direction of absorbance increment is indicated by an arrow. (C) Time-dependency of absorbance. Absorbance increment obtained by averaging absorbance over 1300–1600 nm (closed circles) or 2050–2350 nm (open circles) was plotted against time. The three phases, i.e., phases I (nucleation), II (elongation), and III (equilibrium), are represented.</p>", "links"=>[], "tags"=>["Biochemistry", "biophysics", "molecular biology", "spectra", "insulin", "monitored"], "article_id"=>1100707, "categories"=>["Biological Sciences"], "users"=>["Eri Chatani", "Yutaro Tsuchisaka", "Yuki Masuda", "Roumiana Tsenkova"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101997.g001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_NIR_spectra_of_insulin_solution_monitored_in_the_present_study_/1100707", "title"=>"NIR spectra of insulin solution monitored in the present study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-11 02:56:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1589343"], "description"=>"<p>(A, B) PC2 score plot with monitoring time (A) and its loading (B). The variation of PC2 was 0.463% and the results of other PC components are shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101997#pone.0101997.s001\" target=\"_blank\">Figure S1</a>.</p>", "links"=>[], "tags"=>["Biochemistry", "biophysics", "molecular biology", "spectral", "acquired", "amide", "overtone", "fibril", "insulin", "amyloid"], "article_id"=>1100709, "categories"=>["Biological Sciences"], "users"=>["Eri Chatani", "Yutaro Tsuchisaka", "Yuki Masuda", "Roumiana Tsenkova"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101997.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCA_of_spectral_data_acquired_at_amide_I_overtone_region_for_the_fibril_formation_of_insulin_indicating_945_helix_to_946_sheet_transition_during_the_formation_of_amyloid_fibrils_/1100709", "title"=>"PCA of spectral data acquired at amide I overtone region for the fibril formation of insulin indicating α-helix to β-sheet transition during the formation of amyloid fibrils.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-11 02:56:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1589344"], "description"=>"<p>(A) FTIR absorption spectrum at around the amide I region (solid line). The dashed line represents spectrum of intact insulin without any heating treatment as a reference. The spectra were normalized so that the integrated intensity of the amide I band ranging from 1580 to 1780 cm<sup>−1</sup> is set to be equal. (B) Difference FTIR spectrum plotted by subtracting the spectrum of sample solution after the NIR measurement (A, solid line) from that of intact insulin (A, dashed line). (C) AFM image. The scale bar inside the image represents 1 µm.</p>", "links"=>[], "tags"=>["Biochemistry", "biophysics", "molecular biology", "fibrils", "formed", "optical", "nir", "confirmed", "ftir", "afm"], "article_id"=>1100710, "categories"=>["Biological Sciences"], "users"=>["Eri Chatani", "Yutaro Tsuchisaka", "Yuki Masuda", "Roumiana Tsenkova"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101997.g003", "stats"=>{"downloads"=>1, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Amyloid_fibrils_formed_inside_the_optical_cell_after_the_NIR_measurement_confirmed_by_FTIR_and_AFM_measurements_/1100710", "title"=>"Amyloid fibrils formed inside the optical cell after the NIR measurement confirmed by FTIR and AFM measurements.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-11 02:56:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1589346"], "description"=>"<p>(A, B) PC3 score plot with monitoring time (A) and its loading (B). The variation of PC3 was 0.0005% and the results of other PC components are shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101997#pone.0101997.s003\" target=\"_blank\">Figure S3</a>. PC3 loading presents interplay of opposite spectral changes of hydrogen bonded water species (1360 nm, 1454 nm, and 1470 nm) and water molecular species with free hydrogen bonds (1414 nm) along the examined process of insulin fibril formation.</p>", "links"=>[], "tags"=>["Biochemistry", "biophysics", "molecular biology", "spectral", "acquired", "overtone", "fibril", "insulin", "conformational"], "article_id"=>1100712, "categories"=>["Biological Sciences"], "users"=>["Eri Chatani", "Yutaro Tsuchisaka", "Yuki Masuda", "Roumiana Tsenkova"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101997.g004", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCA_of_spectral_data_acquired_at_water_first_overtone_region_for_the_fibril_formation_of_insulin_indicating_conformational_changes_of_water_molecules_/1100712", "title"=>"PCA of spectral data acquired at water first overtone region for the fibril formation of insulin indicating conformational changes of water molecules.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-11 02:56:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1589349"], "description"=>"<p>In the nucleation phase, free water molecules, free OH and protein hydrating water molecular species were initially dominating, but afterwards hydrogen-bonded water networks were developed, which was considered essential for nucleation by interlinking protein molecules. In the elongation phase, the hydrogen bonds were decayed gradually towards the state observed in bulk water, and slight increase of hydrating water onto amyloid fibrils was also observed. The aquagram patterns at 6, 10, 18 min are also represented at corresponding stages of the fibril formation.</p>", "links"=>[], "tags"=>["Biochemistry", "biophysics", "molecular biology", "multi-step", "structures", "fibril"], "article_id"=>1100714, "categories"=>["Biological Sciences"], "users"=>["Eri Chatani", "Yutaro Tsuchisaka", "Yuki Masuda", "Roumiana Tsenkova"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101997.g006", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_illustration_representing_multi_step_transformation_of_water_structures_during_the_fibril_formation_/1100714", "title"=>"Schematic illustration representing multi-step transformation of water structures during the fibril formation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-11 02:56:50"}

PMC Usage Stats | Further Information

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Relative Metric

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