Loop-sequence features and stability determinants in antibody variable domains by high-throughput experiments

Hung Ju Chang, Jhih Wei Jian, Hung Ju Hsu, Yu Ching Lee, Hong Sen Chen, Jhong Jhe You, Shin Chen Hou, Chih Yun Shao, Yen Ju Chen, Kuo Ping Chiu, Hung Pin Peng, Kuo Hao Lee, An Suei Yang

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

Protein loops are frequently considered as critical determinants in protein structure and function. Recent advances in high-throughput methods for DNA sequencing and thermal stability measurement have enabled effective exploration of sequence-structure-function relationships in local protein regions. Using these data-intensive technologies, we investigated the sequence-structure- function relationships of six complementarity-determining regions (CDRs) and ten non-CDR loops in the variable domains of a model vascular endothelial growth factor (VEGF)-binding single-chain antibody variable fragment (scFv) whose sequence had been optimized via a consensus-sequence approach. The results show that only a handful of residues involving long-range tertiary interactions distant from the antigen-binding site are strongly coupled with antigen binding. This implies that the loops are passive regions in protein folding; the essential sequences of these regions are dictated by conserved tertiary interactions and the consensus local loop-sequence features contribute little to protein stability and function.

Original languageEnglish
Pages (from-to)9-21
Number of pages13
JournalStructure
Volume22
Issue number1
DOIs
Publication statusPublished - Jan 7 2014
Externally publishedYes

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Antibodies
Complementarity Determining Regions
Antigens
High-Throughput Nucleotide Sequencing
Single-Chain Antibodies
Proteins
Protein Stability
Protein Folding
Consensus Sequence
Vascular Endothelial Growth Factor A
Hot Temperature
Binding Sites
Technology

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology

Cite this

Loop-sequence features and stability determinants in antibody variable domains by high-throughput experiments. / Chang, Hung Ju; Jian, Jhih Wei; Hsu, Hung Ju; Lee, Yu Ching; Chen, Hong Sen; You, Jhong Jhe; Hou, Shin Chen; Shao, Chih Yun; Chen, Yen Ju; Chiu, Kuo Ping; Peng, Hung Pin; Lee, Kuo Hao; Yang, An Suei.

In: Structure, Vol. 22, No. 1, 07.01.2014, p. 9-21.

Research output: Contribution to journalArticle

Chang, HJ, Jian, JW, Hsu, HJ, Lee, YC, Chen, HS, You, JJ, Hou, SC, Shao, CY, Chen, YJ, Chiu, KP, Peng, HP, Lee, KH & Yang, AS 2014, 'Loop-sequence features and stability determinants in antibody variable domains by high-throughput experiments', Structure, vol. 22, no. 1, pp. 9-21. https://doi.org/10.1016/j.str.2013.10.005
Chang, Hung Ju ; Jian, Jhih Wei ; Hsu, Hung Ju ; Lee, Yu Ching ; Chen, Hong Sen ; You, Jhong Jhe ; Hou, Shin Chen ; Shao, Chih Yun ; Chen, Yen Ju ; Chiu, Kuo Ping ; Peng, Hung Pin ; Lee, Kuo Hao ; Yang, An Suei. / Loop-sequence features and stability determinants in antibody variable domains by high-throughput experiments. In: Structure. 2014 ; Vol. 22, No. 1. pp. 9-21.
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