Journal
STRUCTURE
Volume 22, Issue 1, Pages 9-21Publisher
CELL PRESS
DOI: 10.1016/j.str.2013.10.005
Keywords
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Funding
- National Science Council [NSC 100IDP006-3, NSC 99-2311-B-001-014-MY3]
- Genomics Research Center at Academia Sinica [AS-100-TP2-B01]
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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.
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