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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
Published on: January 16, 2016
Domain motion and interdomain hot spots in a multidomain enzyme
Gwo-Yu Chuang1, Ritcha Mehra-Chaudhary, Chi-Ho Ngan
1Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA.
Computational solvent mapping reveals subtle conformational changes in Pseudomonas aeruginosa phosphomannomutase/phosphoglucomutase (PMM/PGM). This method is more sensitive than traditional structure superposition for detecting ligand-induced shifts in enzyme active sites and interdomain regions.
Area of Science:
- Enzymology
- Structural Biology
- Computational Biology
Background:
- Pseudomonas aeruginosa phosphomannomutase/phosphoglucomutase (PMM/PGM) is a four-domain enzyme.
- Substrate binding and catalysis involve significant C-terminal domain movement.
Purpose of the Study:
- Analyze conformational changes in PMM/PGM using computational solvent mapping.
- Compare 10 different enzyme structures to identify hot spots and binding site alterations.
Main Methods:
- Employed computational solvent mapping to probe protein surfaces and identify hot spots.
- Analyzed differences in interdomain and active site crevices across various enzyme conformers.
- Developed a statistical method to assess the significance of domain movements in X-ray structures.
Main Results:
- Identified an active site hot spot consistent with binding both glucose and mannose phosphosugars.
- Discovered eight additional hot spots at domain interfaces and hinge regions.
- Observed variations in hot spot locations and nature correlating with ligand-induced conformational changes (open, half-open, closed states).
- Demonstrated that computational solvent mapping is more sensitive than RMSD for detecting subtle binding site and crevice changes.
Conclusions:
- Computational solvent mapping effectively reveals sub-resolution conformational differences in multidomain proteins.
- The method provides a sensitive approach to detect ligand-induced changes in enzyme binding sites.
- The study presents a general statistical method for analyzing domain movements in protein structures.
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