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PDBsum entry 3wii
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Immune system
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PDB id
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3wii
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References listed in PDB file
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Key reference
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Title
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Structural features of interfacial tyrosine residue in robo1 fibronectin domain-Antibody complex: crystallographic, Thermodynamic, And molecular dynamic analyses.
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Authors
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T.Nakayama,
E.Mizohata,
T.Yamashita,
S.Nagatoishi,
M.Nakakido,
H.Iwanari,
Y.Mochizuki,
Y.Kado,
Y.Yokota,
R.Satoh,
K.Tsumoto,
H.Fujitani,
T.Kodama,
T.Hamakubo,
T.Inoue.
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Ref.
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Protein Sci, 2015,
24,
328-340.
[DOI no: ]
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PubMed id
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Abstract
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ROBO1, fibronectin Type-III domain (Fn)-containing protein, is a novel
immunotherapeutic target for hepatocellular carcinoma in humans. The crystal
structure of the antigen-binding fragment (Fab) of B2212A, the monoclonal
antibody against the third Fn domain (Fn3) of ROBO1, was determined in pursuit
of antibody drug for hepatocellular carcinoma. This effort was conducted in the
presence or absence of the antigen, with the chemical features being
investigated by determining the affinity of the antibody using molecular
dynamics (MD) and thermodynamics. The structural comparison of B2212A Fab
between the complex and the free form revealed that the interfacial Tyr(L) 50
(superscripts L, H, and F stand for the residues in the light chain, heavy
chain, and Fn3, respectively) played important roles in Fn3 recognition. That
is, the aromatic ring of Tyr(L) 50 pivoted toward Phe(F) 68, forming a CH/π
interaction and a new hydrogen bond with the carbonyl O atom of Phe(F) 68. MD
simulations predicted that the Tyr(L) 50-Phe(F) 68 interaction almost entirely
dominated Fab-Fn3 binding, and Ala-substitution of Tyr(L) 50 led to a reduced
binding of the resultant complex. On the contrary, isothermal titration
calorimetry experiments underscored that Ala-substitution of Tyr(L) 50 caused an
increase of the binding enthalpy between B2212A and Fn3, but importantly, it
induced an increase of the binding entropy, resulting in a suppression of loss
in the Gibbs free energy in total. These results suggest that mutation analysis
considering the binding entropy as well as the binding enthalpy will aid in the
development of novel antibody drugs for hepatocellular carcinoma.
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