{"doi":"10.1016/j.bpj.2009.08.012","title":"Common Structural Transitions in Explicit-Solvent Simulations of Villin Headpiece Folding","abstract":null,"journal":"Biophysical Journal","year":2009,"id":625907,"datarank":0.7465100613630863,"base_score":4.976733742420574,"endowment":4.976733742420574,"self_citation_contribution":0.7465100613630863,"citation_network_contribution":0.0,"self_endowment_contribution":0.7465100613630863,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":144,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":19751,"name":"Klaus Schulten","orcid":"0000-0001-7192-9632","position":1,"is_corresponding":false},{"id":506370,"name":"Lydia Freddolino","orcid":"0000-0002-5821-4226","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Common Structural Transitions in Explicit-Solvent Simulations of Villin Headpiece Folding","abstract":"Molecular dynamics simulations of protein folding can provide very high-resolution data on the folding process; however, due to computational challenges most studies of protein folding have been limited to small peptides, or made use of approximations such as Gō potentials or implicit solvent models. We have performed a set of molecular dynamics simulations totaling >50 micros on the villin headpiece subdomain, one of the most stable and fastest-folding naturally occurring proteins, in explicit solvent. We find that the wild-type villin headpiece reliably folds to a native conformation on timescales similar to experimentally observed folding, but that a fast folding double-norleucine mutant shows significantly more heterogeneous behavior. Along with other recent simulation studies, we note the occurrence of nonnative structures intermediates, which may yield a nativelike signal in the fluorescence measurements typically used to study villin folding. Based on the wild-type simulations, we propose alternative approaches to measure the formation of the native state.","is_dataset_classified":null,"base_score":4.976733742420574,"endowment":4.976733742420574,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"19843466","pmcid":"PMC2764099","openalex_id":"https://openalex.org/W2113991454","authors":[],"funders":[{"funder_name":"National Institutes of Health","grant_id":"P41-RR05969","title":null},{"funder_name":"National Centre for Supercomputing Applications","grant_id":"MCA93S028","title":null},{"funder_name":"National Science Foundation","grant_id":"PHY0822613","title":null},{"funder_name":"NCRR NIH HHS","grant_id":"P41 RR005969","title":null},{"funder_name":"National Science Foundation","grant_id":"0822613","title":"PFC: Center for the Physics of Living Cells"}],"total_grants":5,"fwci":8.1888,"citation_percentile":0.9840591,"influential_citations":0,"citation_trend":[{"year":2012,"count":22},{"year":2013,"count":17},{"year":2014,"count":12},{"year":2015,"count":7},{"year":2016,"count":8},{"year":2017,"count":7},{"year":2018,"count":4},{"year":2019,"count":4},{"year":2020,"count":6},{"year":2021,"count":4},{"year":2022,"count":2},{"year":2023,"count":1},{"year":2024,"count":5},{"year":2025,"count":1}],"oa_status":"bronze","license":"Elsevier Non-Commercial","oa_locations":[{"url":"http://www.cell.com/article/S0006349509013599/pdf","host_type":"journal"},{"url":"http://www.cell.com/article/S0006349509013599/pdf","host_type":"publisher"},{"url":"https://api.elsevier.com/content/article/PII:S0006349509013599?httpAccept=text/xml","host_type":"publisher"},{"url":"https://api.elsevier.com/content/article/PII:S0006349509013599?httpAccept=text/plain","host_type":"publisher"},{"url":"https://doi.org/10.1016/j.bpj.2009.08.012","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/19843466","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2764099","host_type":"repository"},{"url":"http://dx.doi.org/10.1016/j.bpj.2009.08.012","host_type":""},{"url":"https://dx.doi.org/10.1016/j.bpj.2009.08.012","host_type":""}],"fields_of_study":["Protein Structure and Dynamics","Enzyme Structure and Function","RNA and protein synthesis mechanisms","0301 basic medicine","0303 health sciences","03 medical and health sciences"],"mesh_terms":["Fluorescence","Kinetics","Microfilament Proteins","Models, Molecular","Mutation","Norleucine","Protein Conformation","Solvents","Video Recording","Protein Folding","Molecular Dynamics Simulation"],"keywords":["Villin","Protein folding","Molecular dynamics","Downhill folding","Folding (DSP implementation)","Phi value analysis","Chemistry","Native state","Contact order","Crystallography","Folding funnel","Chemical physics","Computational chemistry","Actin","Biochemistry","Models, Molecular","Protein Conformation","Microfilament Proteins","Biophysics","Video Recording","Molecular Dynamics Simulation","Fluorescence","Kinetics","Mutation","Norleucine","Solvents"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life in Land"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"pdb"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-04T11:30:41.662322Z","pmid":null,"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":[]}