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PDBsum entry 2pw7
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References listed in PDB file
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Key reference
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Title
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Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups.
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Authors
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J.L.Schlessman,
C.Abe,
A.Gittis,
D.A.Karp,
M.A.Dolan,
B.García-Moreno e.
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Ref.
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Biophys J, 2008,
94,
3208-3216.
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PubMed id
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Abstract
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Although internal water molecules are essential for the structure and function
of many proteins, the structural and physical factors that govern internal
hydration are poorly understood. We have examined the molecular determinants of
internal hydration systematically, by solving the crystal structures of variants
of staphylococcal nuclease with Gln-66, Asn-66, and Tyr-66 at cryo (100 K) and
room (298 K) temperatures, and comparing them with existing cryo and room
temperature structures of variants with Glu-66, Asp-66, Lys-66, Glu-92 or Lys-92
obtained under conditions of pH where the internal ionizable groups are in the
neutral state. At cryogenic temperatures the polar moieties of all these
internal side chains are hydrated except in the cases of Lys-66 and Lys-92. At
room temperature the internal water molecules were observed only in variants
with Glu-66 and Tyr-66; water molecules in the other variants are probably
present but they are disordered and therefore undetectable crystallographically.
Each internal water molecule establishes between 3 and 5 hydrogen bonds with the
protein or with other internal water molecules. The strength of interactions
between internal polar side chains and water molecules seems to decrease from
carboxylic acids to amides to amines. Low temperature, low cavity volume, and
the presence of oxygen atoms in the cavity increase the positional stability of
internal water molecules. This set of structures and the physical insight they
contribute into internal hydration will be useful for the development and
benchmarking of computational methods for artificial hydration of pockets,
cavities, and active sites in proteins.
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