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Structure. 2014 Jan 7;22(1):22-34. doi: 10.1016/j.str.2013.10.006. Epub 2013 Nov 21.

Antibody variable domain interface and framework sequence requirements for stability and function by high-throughput experiments.

Author information

1
Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan; Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.
2
Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.
3
Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan.
4
Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Science, National Taiwan University, Taipei 106, Taiwan; Chemical Biology and Molecular Biophysics program, Taiwan International Graduate Program at Academia Sinica, Taipei 115, Taiwan.
5
Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Zoology, College of Life Sciences, National Taiwan University, Taipei 106, Taiwan.
6
Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan; Genomics Research Center, Academia Sinica, Taipei 115, Taiwan. Electronic address: yangas@gate.sinica.edu.tw.

Abstract

Protein structural stability and biological functionality are dictated by the formation of intradomain cores and interdomain interfaces, but the intricate sequence-structure-function interrelationships in the packing of protein cores and interfaces remain difficult to elucidate due to the intractability of enumerating all packing possibilities and assessing the consequences of all the variations. In this work, groups of β strand residues of model antibody variable domains were randomized with saturated mutagenesis and the functional variants were selected for high-throughput sequencing and high-throughput thermal stability measurements. The results show that the sequence preferences of the intradomain hydrophobic core residues are strikingly flexible among hydrophobic residues, implying that these residues are coupled indirectly with antigen binding through energetic stabilization of the protein structures. By contrast, the interdomain interface residues are directly coupled with antigen binding. The interdomain interface should be treated as an integral part of the antigen-binding site.

PMID:
24268647
DOI:
10.1016/j.str.2013.10.006
[Indexed for MEDLINE]
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