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PDBsum entry 3ev3
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References listed in PDB file
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Key reference
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Title
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Multiple solvent crystal structures of ribonuclease a: an assessment of the method.
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Authors
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M.Dechene,
G.Wink,
M.Smith,
P.Swartz,
C.Mattos.
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Ref.
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Proteins, 2009,
76,
861-881.
[DOI no: ]
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PubMed id
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Abstract
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The multiple solvent crystal structures (MSCS) method uses organic solvents to
map the surfaces of proteins. It identifies binding sites and allows for a more
thorough examination of protein plasticity and hydration than could be achieved
by a single structure. The crystal structures of bovine pancreatic ribonuclease
A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane,
50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6-hexanediol, 70%
isopropanol, 50% R,S,R-bisfuran alcohol, 70% t-butanol, 50% trifluoroethanol, or
1.0M trimethylamine-N-oxide. This set of structures is compared with four sets
of crystal structures of RNAse A from the protein data bank (PDB) and with the
solution NMR structure to assess the validity of previously untested assumptions
associated with MSCS analysis. Plasticity from MSCS is the same as from PDB
structures obtained in the same crystal form and deviates only at crystal
contacts when compared to structures from a diverse set of crystal environments.
Furthermore, there is a good correlation between plasticity as observed by MSCS
and the dynamic regions seen by NMR. Conserved water binding sites are
identified by MSCS to be those that are conserved in the sets of structures
taken from the PDB. Comparison of the MSCS structures with inhibitor-bound
crystal structures of RNAse A reveals that the organic solvent molecules
identify key interactions made by inhibitor molecules, highlighting ligand
binding hot-spots in the active site. The present work firmly establishes the
relevance of information obtained by MSCS. Proteins 2009. (c) 2009 Wiley-Liss,
Inc.
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Figure 3.
Figure 3. Crystallographic water molecules on the surface of
RNAse A shown as red spheres. Water molecules from one
representative MSCS model are shown on the left. Water molecules
superimposed from all 20 MSCS models are shown on the right.
This figure was prepared using Pymol (Delano Scientific).
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Figure 6.
Figure 6. Organic solvent binding sites on the surface of RNAse
A. Ribbon diagram of RNAse A showing the binding sites for
organic solvent molecules. The  -strands
are shown in dark gray and the  -helices
are shown in purple. Residues 16-22 are colored in salmon. The
organic solvent molecules are colored as follows: DIO, red; DMF,
purple; DMS, green; HEZ, orange; IPA, blue; RSF, yellow; TBU,
cyan; ETF, brown; and TMO, black. Organic solvent binding sites
are numbered as in Supporting Information Table sII. The RNAse
active site pockets are labeled. This figure was prepared using
Pymol (Delano Scientific).
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2009,
76,
861-881)
copyright 2009.
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