{"doi":"10.64898/2025.12.08.692973","title":"Full-Length Context Disrupts Folding of IgG-Binding Domains of Protein A","abstract":"Multidomain proteins are often thought to fold as collections of independently stable domains, a modularity that underpins many assumptions in structural biology and design. Here, we challenge this view by examining the folding behavior of full-length Staphylococcal protein A (SpA), a 516-residue multidomain protein containing five immunoglobulin (Ig)-binding domains. Although each of the five Ig-binding domains of SpA folds stably in isolation (as it is already known experimentally and also confidently predicted by AI models), here, we show that the full-length construct and the individual Ig-binding domains in the full-length construct fail to adopt a stable three-dimensional structure in solution (despite being predicted to be folded by AI models). Instead, full-length SpA populates a compact yet predominantly disordered ensemble with residual secondary structure, where the folded state of each Ig-binding domain is thermodynamically unfavorable. These findings not only challenge long-held assumptions about the modular architecture and stability of SpA but also underscore the limitations of AI-based predictors when decoupled from the thermodynamic context. This work has implications for validating structure predictions, understanding multidomain architecture, and designing modular proteins for biotechnology and medicine.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":584720,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9564,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1498241,"name":"Albert Halbing","orcid":null,"position":1,"is_corresponding":false},{"id":1497849,"name":"Minh Ngoc Nguyen","orcid":"0000-0002-2026-2310","position":2,"is_corresponding":false},{"id":981582,"name":"Mehmet Şen","orcid":"0000-0002-9882-5590","position":3,"is_corresponding":false},{"id":529944,"name":"Richard C. Willson","orcid":"0000-0002-0900-6148","position":4,"is_corresponding":false},{"id":1441569,"name":"Gül H. Zerze","orcid":"0000-0002-3074-3521","position":5,"is_corresponding":false},{"id":1498240,"name":"Kosar Rahimi","orcid":null,"position":0,"is_corresponding":true}],"reference_count":81,"raw_metadata":null,"created_at":"2026-07-19T02:59:16.166424Z","pmid":"41415459","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}