Conformational variability of matrix metalloproteinases: beyond a single 3D structure

Area of Science:

• Structural Biology
• Biochemistry
• Enzymology

Background:

• Matrix metalloproteinases (MMPs) are crucial enzymes involved in extracellular matrix remodeling.
• Understanding MMP-12 structure is key to developing targeted inhibitors.
• Previous studies resolved MMP-12 structures with inhibitors, but solution dynamics remained unclear.

Purpose of the Study:

• To elucidate the structural dynamics of the matrix metalloproteinase 12 catalytic domain.
• To compare crystalline structures with solution dynamics using NMR.
• To investigate the role of protein flexibility in MMP-12 function and inhibitor design.

Main Methods:

• X-ray diffraction was used to solve crystal structures of MMP-12 catalytic domain with acetohydroxamic acid and N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid at 1.0 and 1.3 Å resolution.
• Nuclear Magnetic Resonance (NMR) spectroscopy was employed to determine the solution structure of the N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid adduct.
• Comparison of X-ray and NMR structures, alongside analysis of residual dipolar couplings and thermal motion.

Main Results:

• Crystal structures of MMP-12 catalytic domain with inhibitors were determined at high resolution.
• Solution NMR revealed structural similarity but notable differences in flexible loops compared to crystal structures.
• NMR data indicated dynamic behavior and conformational equilibria in MMP-12 loops across various timescales (10^-9 s to ms).

Conclusions:

• Matrix metalloproteinase 12 exhibits significant backbone flexibility and conformational heterogeneity.
• This flexibility, potentially underestimated by static crystal structures, is likely essential for substrate binding and broad substrate specificity.
• Protein flexibility may present challenges in designing selective MMP-12 inhibitors.