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09:42
Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
Published on: January 16, 2016
Pressure-dependent structure changes in barnase on ligand binding reveal intermediate rate fluctuations
David J Wilton1, Ryo Kitahara, Kazuyuki Akasaka
1Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom.
Biophysical Journal
|September 2, 2009
Summary
High pressure reveals how barnase protein structure changes. Binding a ligand reduces compressibility and shifts structural fluctuations away from the active site, aiding in understanding protein dynamics.
Area of Science:
- Biochemistry
- Structural Biology
- Biophysics
Background:
- Ribonuclease barnase is a protein enzyme.
- Understanding protein dynamics under pressure is crucial for molecular biology.
- Ligand binding significantly alters protein structure and function.
Purpose of the Study:
- To investigate structural changes in barnase under high pressure.
- To determine how ligand binding affects protein compressibility and dynamics.
- To characterize protein motions on nanosecond to microsecond timescales.
Main Methods:
- Measured 1H NMR chemical shifts of barnase at pressures up to 200 MPa.
- Utilized pressure-induced shift changes as restraints for structural analysis.
- Compared structural changes in free barnase versus barnase bound to d(CGAC).
Main Results:
- Free barnase compressed by ~0.7%, with major changes near the ligand-binding site (Lys-27).
- Barnase-d(CGAC) complex showed 70% reduced compressibility; structural changes shifted to the opposite face.
- Volume fluctuations are largest near the active site in free barnase, but shift to the opposite face upon ligand binding.
Conclusions:
- High pressure is a valuable tool for probing protein dynamics.
- Ligand binding rigidifies the active site and alters protein fluctuation sites.
- Protein volume fluctuations are intermediate between side-chain and conformational dynamics.
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