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Part 1: Document Description
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Citation |
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Title: |
Collagen breaks at weak sacrificial bonds taming its mechanoradicals [Data] |
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Identification Number: |
doi:10.11588/data/HJ6SVM |
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Distributor: |
heiDATA |
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Date of Distribution: |
2023-03-24 |
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Version: |
1 |
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Bibliographic Citation: |
Rennekamp, Benedikt; Gräter, Frauke, 2023, "Collagen breaks at weak sacrificial bonds taming its mechanoradicals [Data]", https://doi.org/10.11588/data/HJ6SVM, heiDATA, V1, UNF:6:Da6omTKjrSvNcDwyJxuHOg== [fileUNF] |
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Citation |
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Title: |
Collagen breaks at weak sacrificial bonds taming its mechanoradicals [Data] |
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Identification Number: |
doi:10.11588/data/HJ6SVM |
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Authoring Entity: |
Rennekamp, Benedikt (Heidelberg Institute for Theoretical Studies, Heidelberg, Germany) |
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Gräter, Frauke (Heidelberg Institute for Theoretical Studies, Heidelberg, Germany) |
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Distributor: |
heiDATA |
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Access Authority: |
Gräter, Frauke |
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Holdings Information: |
https://doi.org/10.11588/data/HJ6SVM |
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Study Scope |
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Keywords: |
Chemistry, Computer and Information Science, Medicine, Health and Life Sciences, Physics, Molecular Dynamics, Mechanoracials, Collagen, KIMMDY |
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Abstract: |
This dataset contains input files for MD simulations, derived breakage counts from these simulations that are used to generate the figures in the publication, and the experimental, uncropped SDS-PAGE gels of the presented results in the related publication. <p /> <p /> Abstract of related publication:<p /> Collagen is a force-bearing, hierarchical structural protein important to all connective tissue. In tendon collagen, high load even below macroscopic failure level creates mechanoradicals by homolytic bond scission, similar to polymers. The location and type of initial rupture sites critically decide on both the mechanical and chemical impact of these micro-ruptures on the tissue, but are yet to be explored. We here use scale-bridging simulations supported by gel electrophoresis and mass spectrometry to determine breakage points in collagen. We find collagen crosslinks, as opposed to the backbone, to harbor the weakest bonds, with one particular bond in trivalent crosslinks as the most dominant rupture site. We identify this bond as sacrificial, rupturing prior to other bonds while maintaining the material’s integrity. Also, collagen’s weak bonds funnel ruptures such that the potentially harmful mechanoradicals are readily stabilized. Our results suggest this unique failure mode of collagen to be tailored towards combatting an early onset of macroscopic failure and material ageing. |
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Methodology and Processing |
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Sources Statement |
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Data Access |
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Other Study Description Materials |
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Related Publications |
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Citation |
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Title: |
Benedikt Rennekamp, Christoph Karfusehr, Markus Kurth, Aysecan Ünal, Debora Monego, Kai Riedmiller, Ganna Gryn’ova, David M. Hudson, Frauke Gräter: Collagen breaks at weak sacrificial bonds taming its mechanoradicals. Nat Commun 14, 2075 (2023). |
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Identification Number: |
10.1038/s41467-023-37726-z |
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Bibliographic Citation: |
Benedikt Rennekamp, Christoph Karfusehr, Markus Kurth, Aysecan Ünal, Debora Monego, Kai Riedmiller, Ganna Gryn’ova, David M. Hudson, Frauke Gräter: Collagen breaks at weak sacrificial bonds taming its mechanoradicals. Nat Commun 14, 2075 (2023). |
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Citation |
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Title: |
Benedikt Rennekamp, Christoph Karfusehr, Markus Kurth, Aysecan Ünal, Debora Monego, Kai Riedmiller, Ganna Gryn’ova, David M. Hudson, Frauke Gräter: "Collagen breaks at weak sacrificial bonds taming its mechanoradicals". bioRxiv 2022. |
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Identification Number: |
10.1101/2022.10.17.512491 |
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Bibliographic Citation: |
Benedikt Rennekamp, Christoph Karfusehr, Markus Kurth, Aysecan Ünal, Debora Monego, Kai Riedmiller, Ganna Gryn’ova, David M. Hudson, Frauke Gräter: "Collagen breaks at weak sacrificial bonds taming its mechanoradicals". bioRxiv 2022. |
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File Description--f11830 |
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File: band_intensity_ratios.tab |
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Notes: |
UNF:6:S95mPa3RP/VaqaLglrWHzQ== |
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File Description--f11825 |
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File: sequence_coverage.tab |
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Notes: |
UNF:6:taKn1oAMU03W4FAWycA4aQ== |
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File Description--f11819 |
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File: Values_control_sample1_nobackground_inverted.tab |
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Notes: |
UNF:6:SHDy3Ojv+10Ux/X0XTDQeA== |
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File Description--f11829 |
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File: Values_control_sample2_nobackground_inverted.tab |
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Notes: |
UNF:6:Aj6Vj6piFXXgsdx4RlPcxQ== |
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File Description--f11822 |
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File: Values_control_sample3_nobackground_inverted.tab |
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Notes: |
UNF:6:Vdasz6//1T9HG1zPklOnMw== |
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File Description--f11827 |
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File: Values_control_sample4_nobackground_inverted.tab |
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Notes: |
UNF:6:3CULJDEhZjsO5M1F16nf8Q== |
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File Description--f11824 |
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File: Values_stressed500ug_sample1_inverted.tab |
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Notes: |
UNF:6:iP5vpkdsErDD694B1jWFVA== |
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File Description--f11832 |
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File: Values_stressed500ug_sample2_inverted.tab |
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Notes: |
UNF:6:g6UEqw9i4uxMobl4CYAvUQ== |
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File Description--f11820 |
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File: Values_stressed500ug_sample3_inverted.tab |
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Notes: |
UNF:6:PkHn4R9TkTJrja1jDVyW8Q== |
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File Description--f11833 |
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File: Values_stressed500ug_sample4_inverted.tab |
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Notes: |
UNF:6:bqkE9U+jWoqdlDzKFeSPHQ== |
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File Description--f11826 |
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File: bands_relative_ratios.tab |
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Notes: |
UNF:6:xaxeo/rLDV2r+v0PrOBcUQ== |
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List of Variables: |
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Variables |
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f11830 Location: |
Variable Format: character Notes: UNF:6:jEhHk4l+b2+6ibeJ/iOBcA== |
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f11830 Location: |
Variable Format: character Notes: UNF:6:ZxctETCGBIPZ8wxVXho9Vg== |
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f11830 Location: |
Summary Statistics: Min. 0.04; StDev 0.1165809726688099; Max. 0.51; Mean 0.2520833333333333; Valid 24.0 Variable Format: numeric Notes: UNF:6:g6zfjJOHPXZmVeMZ6OvQXA== |
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f11830 Location: |
Variable Format: character Notes: UNF:6:wkjUlJzLiRPIkmz0zh8LFw== |
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Column1;sample;band;experiment_type;chain;resid;aminoacid;Coverage |
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f11825 Location: |
Variable Format: character Notes: UNF:6:taKn1oAMU03W4FAWycA4aQ== |
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f11819 Location: |
Summary Statistics: Valid 627.0; Max. 626.0; Min. 0.0; StDev 181.14358945322905; Mean 313.0 Variable Format: numeric Notes: UNF:6:vWag6loR3dsOrjahuWX2IQ== |
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f11819 Location: |
Summary Statistics: StDev 22.587639680383088; Valid 627.0; Max. 153.324; Min. 0.0; Mean 9.072636363636374 Variable Format: numeric Notes: UNF:6:/18maWMmlCzO1DJQo9fr+A== |
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f11829 Location: |
Summary Statistics: Valid 627.0; Min. 0.0; Max. 626.0; Mean 313.0; StDev 181.14358945322905 Variable Format: numeric Notes: UNF:6:vWag6loR3dsOrjahuWX2IQ== |
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f11829 Location: |
Summary Statistics: Valid 627.0; Max. 158.946; Min. 0.0; Mean 9.492403508771922; StDev 24.10033003773965 Variable Format: numeric Notes: UNF:6:Lmd3+YPYXw0SyTKXM/rAfQ== |
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f11822 Location: |
Summary Statistics: Mean 313.0; Max. 626.0; Valid 627.0; Min. 0.0; StDev 181.14358945322905; Variable Format: numeric Notes: UNF:6:vWag6loR3dsOrjahuWX2IQ== |
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f11822 Location: |
Summary Statistics: Mean 9.797035087719292; StDev 25.304805808611654; Max. 161.847; Valid 627.0; Min. 0.0 Variable Format: numeric Notes: UNF:6:tnZ//agxg8MFMUlwyWO8Og== |
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f11827 Location: |
Summary Statistics: Min. 0.0; Max. 626.0; Valid 627.0; Mean 313.0; StDev 181.14358945322905 Variable Format: numeric Notes: UNF:6:vWag6loR3dsOrjahuWX2IQ== |
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f11827 Location: |
Summary Statistics: Max. 153.115; StDev 22.429140485803003; Valid 627.0; Min. 0.0; Mean 9.148452950558207 Variable Format: numeric Notes: UNF:6:066b8ccB0Y9wgcsXLd2QCQ== |
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f11824 Location: |
Summary Statistics: Min. 0.0; Valid 675.0; StDev 195.0; Mean 337.0; Max. 674.0; Variable Format: numeric Notes: UNF:6:AfKEkcEz/h55XQfEOvl4EQ== |
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f11824 Location: |
Summary Statistics: StDev 10.512481078067585; Min. 0.0; Valid 675.0; Mean 6.7029875555555565; Max. 81.0; Variable Format: numeric Notes: UNF:6:IR5jpJF8QwFLtLN7vaMsSw== |
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f11832 Location: |
Summary Statistics: StDev 195.0; Min. 0.0; Max. 674.0; Mean 337.0; Valid 675.0 Variable Format: numeric Notes: UNF:6:AfKEkcEz/h55XQfEOvl4EQ== |
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f11832 Location: |
Summary Statistics: Mean 12.181383703703693; StDev 21.63710524559453; Min. 0.0; Valid 675.0; Max. 145.822 Variable Format: numeric Notes: UNF:6:bLO7N1yT/4C5MC5bNh7GkQ== |
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f11820 Location: |
Summary Statistics: Mean 337.0; Min. 0.0; Valid 675.0; Max. 674.0; StDev 195.0 Variable Format: numeric Notes: UNF:6:AfKEkcEz/h55XQfEOvl4EQ== |
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f11820 Location: |
Summary Statistics: Min. 0.0; Max. 114.303; Mean 7.294674074074076; Valid 675.0; StDev 14.046473358058906 Variable Format: numeric Notes: UNF:6:14qbUTUQEOP3QidP0Khvug== |
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f11833 Location: |
Summary Statistics: StDev 192.4019230673124; Valid 666.0; Max. 665.0; Mean 332.5; Min. 0.0 Variable Format: numeric Notes: UNF:6:523D2G9S1Xn4+cTG5xBbXw== |
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f11833 Location: |
Summary Statistics: Mean 18.364833333333344; StDev 29.271457995403843; Min. 0.0; Valid 666.0; Max. 135.705 Variable Format: numeric Notes: UNF:6:l6IkscrC7qpa0A4c6UaCnQ== |
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f11826 Location: |
Variable Format: character Notes: UNF:6:m1j+gDM1EZyV7rXtiTfRXQ== |
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f11826 Location: |
Variable Format: character Notes: UNF:6:HnX9945ebbY7BNRDT7vOcw== |
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f11826 Location: |
Summary Statistics: Valid 21.0; Max. 0.396; Mean 0.22766666666666668; Min. 0.149; StDev 0.07003522923024766 Variable Format: numeric Notes: UNF:6:m5aPv6RjsZkXZkF4dEKL6Q== |
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f11826 Location: |
Variable Format: character Notes: UNF:6:jniIG7jdbsiyjvMHTHEpQw== |
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f11826 Location: |
Variable Format: character Notes: UNF:6:47qrFppsSniJQAYbgdsZjA== |
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Label: |
readme.txt |
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Notes: |
text/plain |
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Label: |
runs_overwiev.csv |
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Notes: |
text/csv |
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Label: |
run_input_tprfiles_KIMMDY.zip |
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Notes: |
application/zip |
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Label: |
run_input_tprfiles_main.zip |
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Notes: |
application/zip |
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Label: |
data_HLKNL_crosslinks.csv |
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Notes: |
text/csv |
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Label: |
data_HLKNL_crosslinks_force_corrected_SI.csv |
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Notes: |
text/csv |
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Label: |
data_PYD_crosslinks.csv |
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Notes: |
text/csv |
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Label: |
data_PYD_protonated_crosslinks.csv |
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Notes: |
text/csv |
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Label: |
original_control_RTT.jpg |
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Notes: |
image/jpeg |
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Label: |
original_stressed_RTT.jpg |
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Notes: |
image/jpeg |
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Label: |
IMG_20230119_bw_inverted_nobackground_rotated.jpg |
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Notes: |
image/jpeg |
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Label: |
original_20230119.jpg |
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Notes: |
image/jpeg |