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PDBsum entry 2kf4
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References listed in PDB file
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Key reference
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Title
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Pressure-Dependent structure changes in barnase on ligand binding reveal intermediate rate fluctuations.
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Authors
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D.J.Wilton,
R.Kitahara,
K.Akasaka,
M.J.Pandya,
M.P.Williamson.
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Ref.
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Biophys J, 2009,
97,
1482-1490.
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PubMed id
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Abstract
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In this work we measured 1H NMR chemical shifts for the ribonuclease barnase at
pressures from 3 MPa to 200 MPa, both free and bound to d(CGAC). Shift changes
with pressure were used as restraints to determine the change in structure with
pressure. Free barnase is compressed by approximately 0.7%. The largest changes
are on the ligand-binding face close to Lys-27, which is the recognition site
for the cleaved phosphate bond. This part of the protein also contains the
buried water molecules. In the presence of d(CGAC), the compressibility is
reduced by approximately 70% and the region of structural change is altered: the
ligand-binding face is now almost incompressible, whereas changes occur at the
opposite face. Because compressibility is proportional to mean square volume
fluctuation, we conclude that in free barnase, volume fluctuation is largest
close to the active site, but when the inhibitor is bound, the fluctuations
become much smaller and are located mainly on the opposite face. The timescale
of the fluctuations is nanoseconds to microseconds, consistent with the degree
of ordering required for the fluctuations, which are intermediate between rapid
uncorrelated side-chain dynamics and slow conformational transitions. The
high-pressure technique is therefore useful for characterizing motions on this
relatively inaccessible timescale.
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