Crystal structure of human chondroadherin : Solving a difficult molecular-replacement problem using de novo models
(2017) In Acta Crystallographica Section D: Structural Biology 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.
(Less)
- author
- Rämisch, Sebastian
LU
; Pramhed, Anna
LU
; Tillgren, Viveka
LU
; Aspberg, Anders
LU
and Logan, Derek T. LU
- organization
- publishing date
- 2017-01-01
- 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 Biology
- volume
- 73
- issue
- 1
- pages
- 11 pages
- publisher
- John Wiley & Sons Inc.
- external identifiers
-
- scopus:85008213623
- pmid:28045385
- wos:000390566600006
- ISSN
- 2059-7983
- 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
- 2024-07-21 17:46:04
@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.}}, issn = {{2059-7983}}, keywords = {{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 & Sons Inc.}}, series = {{Acta Crystallographica Section D: Structural Biology}}, title = {{Crystal structure of human chondroadherin : Solving a difficult molecular-replacement problem using de novo models}}, url = {{http://dx.doi.org/10.1107/S205979831601980X}}, doi = {{10.1107/S205979831601980X}}, volume = {{73}}, year = {{2017}}, }