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Collagen, a vital protein that provides strength to various body tissues, has a triple helix structure containing three polypeptide chains. The chains are composed mostly of a tripeptide of glycine (G), proline (P), and hydroxyproline (O). Using molecular dynamics simulations and theoretical analysis, the study examines the mechanical response of collagen triple helix structures, made up of three different tripeptide units, when subjected to different fracture loading modes. The results show that collagen with GPO tripeptide units at their C-terminal are mechanically stronger than the POG and OGP units with a single amino-acid frame shift. Our work shows that the N-terminal has less effect on collagen fracture than the C-terminal. The differences in mechanical response are explained by the heterogenous rigidity of the amino acid backbone and the resulting shear lag effect near the terminal. The findings have potential applications in developing tough synthetic collagen for building materials and may stimulate further studies on the connection between terminal repeats and the mechanical-thermal behavior of other structural proteins such as silk, elastin, fibrin, and keratin.
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Elucidating the Structural Impacts of Protein InDels
The effects of amino acid insertions and deletions (InDels) remain a rather under-explored area of structural biology. These variations oftentimes are the cause of numerous disease phenotypes. In spite of this, research to study InDels and their structural significance remains limited, primarily due to a lack of experimental information and computational methods. In this work, we fill this gap by modeling InDels computationally; we investigate the rigidity differences between the wildtype and a mutant variant with one or more InDels. Further, we compare how structural effects due to InDels differ from the effects of amino acid substitutions, which are another type of amino acid mutation. We finish by performing a correlation analysis between our rigidity-based metrics and wet lab data for their ability to infer the effects of InDels on protein fitness.
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- Award ID(s):
- 2031260
- PAR ID:
- 10379035
- Date Published:
- Journal Name:
- Biomolecules
- Volume:
- 12
- Issue:
- 10
- ISSN:
- 2218-273X
- Page Range / eLocation ID:
- 1435
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3390/biom12101435
