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Crystal structure of human chondroadherin : Solving a difficult molecular-replacement problem using de novo models

Rämisch, Sebastian LU ; Pramhed, Anna LU ; Tillgren, Viveka LU ; Aspberg, Anders LU and Logan, Derek T. LU (2017) In Acta Crystallographica Section D: Structural Biology2016-01-01+01:00 73(1). p.53-63
Abstract

Chondroadherin (CHAD) is a cartilage matrix protein that mediates the adhesion of isolated chondrocytes. Its protein core is composed of 11 leucine-rich repeats (LRR) flanked by cysteine-rich domains. CHAD makes important interactions with collagen as well as with cell-surface heparin sulfate proteoglycans and α2β1 integrins. The integrin-binding site is located in a region of hitherto unknown structure at the C-terminal end of CHAD. Peptides based on the C-terminal human CHAD (hCHAD) sequence have shown therapeutic potential for treating osteoporosis. This article describes a still-unconventional structure solution by phasing with de novo models, the first of a β-rich protein. Structure determination of hCHAD... (More)

Chondroadherin (CHAD) is a cartilage matrix protein that mediates the adhesion of isolated chondrocytes. Its protein core is composed of 11 leucine-rich repeats (LRR) flanked by cysteine-rich domains. CHAD makes important interactions with collagen as well as with cell-surface heparin sulfate proteoglycans and α2β1 integrins. The integrin-binding site is located in a region of hitherto unknown structure at the C-terminal end of CHAD. Peptides based on the C-terminal human CHAD (hCHAD) sequence have shown therapeutic potential for treating osteoporosis. This article describes a still-unconventional structure solution by phasing with de novo models, the first of a β-rich protein. Structure determination of hCHAD using traditional, though nonsystematic, molecular replacement was unsuccessful in the hands of the authors, possibly owing to a combination of low sequence identity to other LRR proteins, four copies in the asymmetric unit and weak translational pseudosymmetry. However, it was possible to solve the structure by generating a large number of de novo models for the central LRR domain using Rosetta and multiple parallel molecular-replacement attempts using AMPLE. The hCHAD structure reveals an ordered C-terminal domain belonging to the LRRCT fold, with the integrin-binding motif (WLEAK) being part of a regular α-helix, and suggests ways in which experimental therapeutic peptides can be improved. The crystal structure itself and docking simulations further support that hCHAD dimers form in a similar manner to other matrix LRR proteins.The structure of human chondroadherin (hCHAD), a 359-amino-acid protein with 11 leucine-rich repeats, has been solved by molecular replacement using de novo models of a 195-residue segment and the AMPLE pipeline. This demonstrates that even a fairly large β-rich protein is tractable to solution using de novo modelling. The structure of the C-terminal domain of hCHAD reveals the conformation of a medically relevant peptide.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
chondroadherin, collagen binding, de novo models, extracellular matrix, integrin binding, molecular replacement, small leucine-rich repeat proteins, structure prediction
in
Acta Crystallographica Section D: Structural Biology2016-01-01+01:00
volume
73
issue
1
pages
11 pages
publisher
John Wiley and Sons Inc.
external identifiers
  • scopus:85008213623
  • wos:000390566600006
DOI
10.1107/S205979831601980X
language
English
LU publication?
yes
id
5de05dfd-5951-47b8-97e9-a69614cbe968
date added to LUP
2017-03-16 11:52:00
date last changed
2018-06-10 05:17:12
@article{5de05dfd-5951-47b8-97e9-a69614cbe968,
  abstract     = {<p>Chondroadherin (CHAD) is a cartilage matrix protein that mediates the adhesion of isolated chondrocytes. Its protein core is composed of 11 leucine-rich repeats (LRR) flanked by cysteine-rich domains. CHAD makes important interactions with collagen as well as with cell-surface heparin sulfate proteoglycans and α<sub>2</sub>β<sub>1</sub> integrins. The integrin-binding site is located in a region of hitherto unknown structure at the C-terminal end of CHAD. Peptides based on the C-terminal human CHAD (hCHAD) sequence have shown therapeutic potential for treating osteoporosis. This article describes a still-unconventional structure solution by phasing with de novo models, the first of a β-rich protein. Structure determination of hCHAD using traditional, though nonsystematic, molecular replacement was unsuccessful in the hands of the authors, possibly owing to a combination of low sequence identity to other LRR proteins, four copies in the asymmetric unit and weak translational pseudosymmetry. However, it was possible to solve the structure by generating a large number of de novo models for the central LRR domain using Rosetta and multiple parallel molecular-replacement attempts using AMPLE. The hCHAD structure reveals an ordered C-terminal domain belonging to the LRRCT fold, with the integrin-binding motif (WLEAK) being part of a regular α-helix, and suggests ways in which experimental therapeutic peptides can be improved. The crystal structure itself and docking simulations further support that hCHAD dimers form in a similar manner to other matrix LRR proteins.The structure of human chondroadherin (hCHAD), a 359-amino-acid protein with 11 leucine-rich repeats, has been solved by molecular replacement using de novo models of a 195-residue segment and the AMPLE pipeline. This demonstrates that even a fairly large β-rich protein is tractable to solution using de novo modelling. The structure of the C-terminal domain of hCHAD reveals the conformation of a medically relevant peptide.</p>},
  author       = {Rämisch, Sebastian and Pramhed, Anna and Tillgren, Viveka and Aspberg, Anders and Logan, Derek T.},
  keyword      = {chondroadherin,collagen binding,de novo models,extracellular matrix,integrin binding,molecular replacement,small leucine-rich repeat proteins,structure prediction},
  language     = {eng},
  month        = {01},
  number       = {1},
  pages        = {53--63},
  publisher    = {John Wiley and Sons Inc.},
  series       = {Acta Crystallographica Section D: Structural Biology2016-01-01+01:00},
  title        = {Crystal structure of human chondroadherin : Solving a difficult molecular-replacement problem using de novo models},
  url          = {http://dx.doi.org/10.1107/S205979831601980X},
  volume       = {73},
  year         = {2017},
}