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PDBsum entry 2nvh
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Contents |
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* Residue conservation analysis
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DOI no:
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Proc Natl Acad Sci U S A
103:19749-19753
(2006)
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PubMed id:
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Determination of solvent content in cavities in IL-1beta using experimentally phased electron density.
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M.L.Quillin,
P.T.Wingfield,
B.W.Matthews.
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ABSTRACT
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The extent to which water is present within apolar cavities in proteins remains
unclear. In the case of interleukin-1beta (IL-1beta), four independent
structures solved by x-ray crystallography indicate that water is not present in
the central apolar cavity. In contrast, results from NMR spectroscopy suggest
that water has high occupancy within the cavity but is positionally disordered,
making it undetectable by standard crystallographic methods. A theoretically
based crystallographic-phase refinement technique also suggested that there was
the equivalent of two fully occupied water molecules within the apolar cavity.
To resolve these discrepancies we sought to obtain an experimentally phased
electron density map that was free of possible bias caused by mathematical
modeling of the protein or the solvent. By combining native diffraction data
with multiple wavelength anomalous data from a platinum derivative, accurate
phases were obtained. Using these experimental phases, we estimate that
occupancy of the apolar cavity in IL-1beta by solvent is close or equal to zero.
Polar cavities in the protein that contain ordered solvent molecules serve as
internal controls.
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Selected figure(s)
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Figure 1.
Fig. 1. Electron density within cavities in IL-1  . (A)
Cavity 1. (B) Cavity 2. (C) Cavity 3. (D) Cavity 4. (E) Cavity
5. Cavity walls are rendered as translucent cyan surfaces.
Residues surrounding each cavity are displayed in ball-and-stick
format, with atoms that contact the cavity surface shown as
larger spheres. Ordered water molecules are shown as large cyan
spheres, with hydrogen-bonding interactions represented by
dotted lines. Each plot depicts experimental electron density
levels on the plane through the region of highest density (Table
4). Electron density values are represented by colors shown on
the scale, with contours every 0.5 e/Å^3 (black lines).
The cavity walls are indicated by white margins. These images
were created by using MSP (36), MOLSCRIPT (40), RASTER3D (41),
SLICED (M.L.Q., unpublished FORTRAN program), and GRI (42).
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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S.Sekharan,
A.Altun,
and
K.Morokuma
(2010).
Photochemistry of visual pigment in a G(q) protein-coupled receptor (GPCR)--insights from structural and spectral tuning studies on squid rhodopsin.
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Chemistry,
16,
1744-1749.
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E.Jardón-Valadez,
A.N.Bondar,
and
D.J.Tobias
(2009).
Dynamics of the internal water molecules in squid rhodopsin.
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Biophys J,
96,
2572-2576.
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G.G.Dodson,
D.P.Lane,
and
C.S.Verma
(2008).
Molecular simulations of protein dynamics: new windows on mechanisms in biology.
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EMBO Rep,
9,
144-150.
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J.C.Rasaiah,
S.Garde,
and
G.Hummer
(2008).
Water in nonpolar confinement: from nanotubes to proteins and beyond.
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Annu Rev Phys Chem,
59,
713-740.
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J.Qvist,
M.Davidovic,
D.Hamelberg,
and
B.Halle
(2008).
A dry ligand-binding cavity in a solvated protein.
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Proc Natl Acad Sci U S A,
105,
6296-6301.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
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Links
