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Interaction between the antigen and antibody is controlled by the constant domains: Normal mode dynamics of the HEL–HyHEL‐10 complex
Author(s) -
Adachi Masaaki,
Kurihara Youji,
Nojima Hiroyuki,
TakedaShitaka Mayuko,
Kamiya Kenshu,
Umeyama Hideaki
Publication year - 2003
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.03100803
Subject(s) - dissociation constant , chemistry , antigen , complementarity determining region , biophysics , antibody , molecule , immunoglobulin fab fragments , molecular dynamics , monoclonal antibody , biology , biochemistry , receptor , immunology , computational chemistry , organic chemistry
Abstract The antigen binding fragment (Fab) of a monoclonal antibody (HyHEL‐10) consists of variable domains (Fv) and constant domains (CL–CH1). Normal modes have been calculated from the three‐dimensional structures of hen egg lysozyme (HEL) with Fab, those of HEL with Fv, and so on. Only a small structural change was found between HEL–Fab and HEL–Fv complexes. However, HEL–Fv had a one order of magnitude lower dissociation constant than HEL–Fab. The Cα fluctuations of HEL–Fab differed from those of HEL–Fv with normal mode calculation, and the dynamics can be thought to be related to the protein–protein interactions. CL–CH1 may have influence not only around local interfaces between CL–CH1 and Fv, but also around the interacting regions between HEL and Fv, which are longitudinally distant. Eighteen water molecules were found in HEL–Fv around the interface between HEL and Fv compared with one water molecule in HEL–Fab. These solvent molecules may occupy the holes and channels, which may occur due to imperfect complementarity of the complex. Therefore, the suppression of atomic vibration around the interface between Fv and HEL can be thought to be related to favorable and compact interface formation by complete desolvation. It is suggested that the ability to control the antigen–antibody affinity is obtained from modifying the CL–CH1. The second upper loop in the constant domain of the light chain (UL2–CL), which is a conserved gene in several light chains, showed the most remarkable fluctuation changes. UL2–CL could play an important role and could be attractive for modification in protein engineering.