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Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions
Pedro Ojeda-May1,2, Ameeq Ui Mushtaq1, Per Rogne1
1Department of Chemistry, Umeå University, Umeå SE-90187, Sweden.
Biochemistry
|July 12, 2021
Summary
Enzymes use protein motions for catalysis. This study shows active site dynamics in adenylate kinase link catalytic steps to enzyme conformational changes, influencing reaction barriers and enzyme opening.
Area of Science:
- Biochemistry
- Enzymology
- Structural Biology
Background:
- Enzymes utilize diverse protein motions for catalysis.
- The role of collective protein motions in enzyme catalysis is not fully understood.
- Understanding these dynamics is crucial for enzyme mechanism elucidation.
Purpose of the Study:
- To investigate the catalytic mechanism of adenylate kinase.
- To determine the role of catalytic residues in catalysis and enzyme conformational changes.
- To link enzyme active site dynamics to overall enzyme function.
Main Methods:
- Molecular dynamics simulations
- Enzyme kinetics assays
- X-ray crystallography
- Nuclear magnetic resonance (NMR) spectroscopy
Main Results:
- Active site motions (picoseconds to nanoseconds) modulate free energy landscapes of subdomain motions.
- Catalytic reaction is linked to slow conformational dynamics via active site motions.
- Post-catalytic conformational rearrangement accelerates enzyme opening.
Conclusions:
- Enzymatic catalysis is intrinsically linked to collective protein motions.
- Intermediate-scale motions bridge disparate timescales between catalysis and conformational change.
- Protein dynamics play a critical role in modulating enzyme reaction barriers and conformational states.
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