{"doi":"10.1016/j.csbj.2025.08.008","title":"Characterization of the KRas G12D-inhibitor interactions by differential HDX-MS and molecular dynamics simulations","abstract":"Hydrogen-deuterium exchange (HDX) combined with mass spectrometry (MS) is a powerful technique for studying changes in protein structure and dynamics upon ligand binding. Protein-ligand complexes can result in increased protection of peptide-bond amides in HDX indicating protein structure stabilization. We have characterized the interaction of small-molecule inhibitors towards the KRas G12D oncoprotein by intact-protein and bottom-up HDX-MS, in combination with molecular dynamics (MD) simulations. Significant differences in HDX protection were detected upon inhibitor binding in the flexible switch-II pocket of the protein. MD simulations of the free and inhibitor-bound KRas G12D proteins also revealed changes in the hydrogen bond network of backbone amides in the switch-II region upon inhibitor binding, explaining the observed HDX protection changes. We have proposed simple semi-empirical metrics which relate changes in HDX-MS experimental values and observed in MD simulations changes in individual backbone hydrogen-bonds between free- and ligand-bound protein states. This combined HDX-MS and MD approach provides an atomistic picture of changes in the KRas G12D secondary structure upon ligand binding and may be a useful tool for future drug design efforts.","journal":"Computational and Structural Biotechnology Journal","year":2025,"id":534440,"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":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9536,"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":985794,"name":"Brandon Novy","orcid":"0000-0001-5304-2640","position":1,"is_corresponding":false},{"id":1417052,"name":"E Nagy","orcid":"0000-0002-9940-3218","position":2,"is_corresponding":false},{"id":466069,"name":"Konstantin I. Popov","orcid":"0000-0002-9394-972X","position":3,"is_corresponding":false},{"id":616160,"name":"Jason B. Cross","orcid":"0000-0002-0919-2833","position":4,"is_corresponding":false},{"id":329596,"name":"Roopa Thapar","orcid":"0000-0002-9786-6980","position":5,"is_corresponding":false},{"id":360584,"name":"Christoph H. Borchers","orcid":"0000-0003-2394-6512","position":6,"is_corresponding":false},{"id":592049,"name":"Evgeniy V. Petrotchenko","orcid":"0000-0003-3612-9546","position":0,"is_corresponding":true}],"reference_count":29,"raw_metadata":null,"created_at":"2026-07-19T02:51:47.434742Z","pmid":"40837237","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":[]}