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Conformational Dynamics of Matrix Metalloproteinase-1·Triple-Helical Peptide Complexes
Tatyana G Karabencheva-Christova1,2, Christo Z Christov1,2, Gregg B Fields3,4
1Department of Applied Sciences, Faculty of Health and Life Sciences , Northumbria University , Newcastle upon Tyne NE1 8ST , United Kingdom.
The Journal of Physical Chemistry. B
|November 22, 2017
Summary
Molecular dynamics studies reveal that the NMR-derived structure of matrix metalloproteinase-1 (MMP-1) bound to a collagen triple-helical peptide (THP) is catalytically productive, unlike the X-ray structure.
Area of Science:
- Biochemistry
- Structural Biology
- Molecular Dynamics
Background:
- Matrix metalloproteinase-1 (MMP-1) is a key enzyme in collagen degradation.
- Previous studies elucidated MMP-1 interactions with collagen using X-ray crystallography and NMR.
Purpose of the Study:
- To investigate the structural basis of MMP-1 collagenolysis.
- To compare MMP-1-collagen complex structures derived from X-ray crystallography and NMR using molecular dynamics.
Main Methods:
- Molecular dynamics (MD) simulations were performed on MMP-1 complexes.
- Complexes were based on X-ray crystallographic and NMR-derived structures of MMP-1 bound to triple-helical peptides (THPs).
Main Results:
- The NMR-derived MMP-1·THP complex adopted an "open/extended" conformation, facilitating catalysis.
- The X-ray crystallographic MMP-1·THP complex adopted a "closed/collapsed" conformation, hindering catalysis.
- The NMR-derived complex showed greater atomistic interactions and THP destabilization by MMP-1.
Conclusions:
- The NMR-derived structure provides a more accurate model for the initial stages of collagenolysis.
- Specific atomistic interactions in the NMR-derived complex explain favorable energetics for collagen hydrolysis.
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