title: Loop-sequence features and stability determinants in antibody variable domains by high-throughput experiments.
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.
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan.
authors.forename: Hung-Ju
authors.initials: HJ
authors.lastname: Chang
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan.
authors.forename: Jhih-Wei
authors.initials: JW
authors.lastname: Jian
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.
authors.forename: Hung-Ju
authors.initials: HJ
authors.lastname: Hsu
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.
authors.forename: Yu-Ching
authors.initials: YC
authors.lastname: Lee
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.
authors.forename: Hong-Sen
authors.initials: HS
authors.lastname: Chen
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.
authors.forename: Jhong-Jhe
authors.initials: JJ
authors.lastname: You
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.
authors.forename: Shin-Chen
authors.initials: SC
authors.lastname: Hou
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Zoology, College of Life Sciences, National Taiwan University, Taipei 106, Taiwan.
authors.forename: Chih-Yun
authors.initials: CY
authors.lastname: Shao
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University, Taipei 106, Taiwan.
authors.forename: Yen-Ju
authors.initials: YJ
authors.lastname: Chen
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.
authors.forename: Kuo-Ping
authors.initials: KP
authors.lastname: Chiu
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan.
authors.forename: Hung-Pin
authors.initials: HP
authors.lastname: Peng
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.
authors.forename: Kuo Hao
authors.initials: KH
authors.lastname: Lee
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei 115, Taiwan. Electronic address: yangas@gate.sinica.edu.tw.
authors.forename: An-Suei
authors.initials: AS
authors.lastname: Yang
mesh_terms: D000595:Amino Acid Sequence; D022801:Complementarity Determining Regions / Q000737:chemistry* / Q000276:immunology; D057166:High-Throughput Screening Assays; D006801:Humans; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019151:Peptide Library; D011485:Protein Binding; D017510:Protein Folding; D055550:Protein Stability; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D057127:Single-Chain Antibodies / Q000737:chemistry* / Q000276:immunology; D013205:Staphylococcal Protein A / Q000737:chemistry / Q000276:immunology; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D042461:Vascular Endothelial Growth Factor A / Q000737:chemistry* / Q000276:immunology
chemical_list: D022801:Complementarity Determining Regions; D019151:Peptide Library; D057127:Single-Chain Antibodies; D013205:Staphylococcal Protein A; C467484:VEGFA protein, human; D042461:Vascular Endothelial Growth Factor A