NDLI: Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses.

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Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Yokota, Yuki Yamashita, Takefumi Satoh, Reiko Nagatoishi, Satoru Kado, Yuji Tsumoto, Kouhei Inoue, Tsuyoshi Nakayama, Taisuke Mizohata, Eiichi Mochizuki, Yasuhiro Iwanari, Hiroko Kodama, Tatsuhiko Nakakido, Makoto Fujitani, Hideaki Hamakubo, Takao
Description	Country affiliation: Japan Author Affiliation: Nakayama T ( Structural Physical Chemistry, Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Osaka, Japan.)
Abstract	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.
ISSN	09618368
e-ISSN	1469896X
DOI	10.1002/pro.2619
Journal	Protein Science
Issue Number	3
Volume Number	24
Language	English
Publisher	Wiley-Blackwell (on behalf of The Protein Society)
Publisher Date	2015-03-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Fibronectins Chemistry Nerve Tissue Proteins Receptors, Immunologic Tyrosine Metabolism Molecular Dynamics Simulation Protein Structure, Tertiary Recombinant Proteins Thermodynamics Research Support, Non-u.s. Gov't Discipline Biochemistry
Content Type	Text
Resource Type	Article
Subject	Medicine Molecular Biology Biochemistry

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