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PDBsum entry 1kip
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Complex (immunoglobulin/hydrolase)
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PDB id
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1kip
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Contents |
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107 a.a.
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116 a.a.
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129 a.a.
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Hydrogen bonding and solvent structure in an antigen-Antibody interface. Crystal structures and thermodynamic characterization of three fv mutants complexed with lysozyme.
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Authors
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B.A.Fields,
F.A.Goldbaum,
W.Dall'Acqua,
E.L.Malchiodi,
A.Cauerhff,
F.P.Schwarz,
X.Ysern,
R.J.Poljak,
R.A.Mariuzza.
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Ref.
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Biochemistry, 1996,
35,
15494-15503.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
perfect match.
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Abstract
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Using site-directed mutagenesis, X-ray crystallography, and titration
calorimetry, we have examined the structural and thermodynamic consequences of
removing specific hydrogen bonds in an antigen-antibody interface. Crystal
structures of three antibody FvD1.3 mutants, VLTyr50Ser (VLY50S), VHTyr32Ala
(VHY32A), and VHTyr101Phe (VHY101F), bound to hen egg white lysozyme (HEL) have
been determined at resolutions ranging from 1.85 to 2.10 A. In the wild-type
(WT) FvD1.3-HEL complex, the hydroxyl groups of VLTyr50, VHTyr32, and VHTyr101
each form at least one hydrogen bond with the lysozyme antigen. Thermodynamic
parameters for antibody-antigen association have been measured using isothermal
titration calorimetry, giving equilibrium binding constants Kb (M-1) of 2.6 x
10(7) (VLY50S), 7.0 x 10(7) (VHY32A), and 4.0 x 10(6) (VHY101F). For the WT
complex, Kb is 2.7 x 10(8) M-1; thus, the affinities of the mutant Fv fragments
for HEL are 10-, 4-, and 70-fold lower than that of the original antibody,
respectively. In all three cases entropy compensation results in an affinity
loss that would otherwise be larger. Comparison of the three mutant crystal
structures with the WT structure demonstrates that the removal of direct
antigen-antibody hydrogen bonds results in minimal shifts in the positions of
the remaining protein atoms. These observations show that this complex is
considerably tolerant, both structurally and thermodynamically, to the
truncation of antibody side chains that form hydrogen bonds with the antigen.
Alterations in interface solvent structure for two of the mutant complexes
(VLY50S and VHY32A) appear to compensate for the unfavorable enthalpy changes
when protein-protein interactions are removed. These changes in solvent
structure, along with the increased mobility of side chains near the mutation
site, probably contribute to the observed entropy compensation. For the VHY101F
complex, the nature of the large entropy compensation is not evident from a
structural comparison of the WT and mutant complexes. Differences in the local
structure and dynamics of the uncomplexed Fv molecules may account for the
entropic discrepancy in this case.
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Secondary reference #1
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Title
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Bound water molecules and conformational stabilization help mediate an antigen-Antibody association.
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Authors
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T.N.Bhat,
G.A.Bentley,
G.Boulot,
M.I.Greene,
D.Tello,
W.Dall'Acqua,
H.Souchon,
F.P.Schwarz,
R.A.Mariuzza,
R.J.Poljak.
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Ref.
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Proc Natl Acad Sci U S A, 1994,
91,
1089-1093.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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Solvent rearrangement in an antigen-Antibody interface introduced by site-Directed mutagenesis of the antibody combining site.
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Authors
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X.Ysern,
B.A.Fields,
T.N.Bhat,
F.A.Goldbaum,
W.Dall'Acqua,
F.P.Schwarz,
R.J.Poljak,
R.A.Mariuzza.
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Ref.
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J Mol Biol, 1994,
238,
496-500.
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PubMed id
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