{"doi":"10.1021/jp900947f","title":"A Statistical Model for Translocation of Structured Polypeptide Chains through Nanopores","abstract":null,"journal":"The Journal of Physical Chemistry B","year":2009,"id":668391,"datarank":0.5926865577872142,"base_score":3.9512437185814275,"endowment":3.9512437185814275,"self_citation_contribution":0.5926865577872142,"citation_network_contribution":0.0,"self_endowment_contribution":0.5926865577872142,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":51,"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":875095,"name":"Fabio Cecconi","orcid":"0000-0001-8351-248X","position":1,"is_corresponding":false},{"id":1745399,"name":"Umberto Marini Bettolo Marconi","orcid":null,"position":2,"is_corresponding":false},{"id":1745400,"name":"Angelo Vulpiani","orcid":null,"position":3,"is_corresponding":false},{"id":1745398,"name":"Alessandro Ammenti","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"A Statistical Model for Translocation of Structured Polypeptide Chains through Nanopores","abstract":"The translocation process of a globular protein (ubiquitin) across a cylindrical nanopore is studied via molecular dynamics simulations. The ubiquitin is described by a native-centric model on a Calpha carbon backbone to investigate the influence of protein-like structural properties on the translocation mechanism. A thermodynamical and kinetic characterization of the process is obtained by studying the statistics of blockage times, the mobility, and the translocation probability as a function of the pulling force F acting in the pore. The transport dynamics occurs when the force exceeds a threshold Fc depending on a free-energy barrier that ubiquitin has to overcome in order to slide along the channel. Such a barrier results from competition of the unfolding energy and the entropy associated with the confinement effects of the pore. We implement appropriate umbrella sampling simulations to compute the free-energy profile as a function of the position of the ubiquitin center of mass inside of the channel (reaction coordinate). This free energy is then used to construct a phenomenological drift-diffusion model in the reaction coordinate which explains and reproduces the behavior of the observables during the translocation.","is_dataset_classified":null,"base_score":3.9512437185814275,"endowment":3.9512437185814275,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"19572676","pmcid":null,"openalex_id":"https://openalex.org/W1972126875","authors":[],"funders":[],"total_grants":0,"fwci":3.5976,"citation_percentile":0.92228253,"influential_citations":0,"citation_trend":[{"year":2012,"count":5},{"year":2013,"count":4},{"year":2014,"count":4},{"year":2015,"count":5},{"year":2016,"count":1},{"year":2017,"count":2},{"year":2018,"count":4},{"year":2019,"count":3},{"year":2020,"count":5},{"year":2021,"count":1},{"year":2022,"count":2},{"year":2023,"count":3},{"year":2024,"count":1}],"oa_status":"closed","license":null,"oa_locations":[{"url":"https://pubs.acs.org/doi/pdf/10.1021/jp900947f","host_type":"publisher"},{"url":"https://doi.org/10.1021/jp900947f","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/19572676","host_type":"repository"},{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.549.2818","host_type":""},{"url":"http://hdl.handle.net/11573/85732","host_type":"repository"},{"url":"http://hdl.handle.net/11581/102618","host_type":"repository"}],"fields_of_study":["Nanopore and Nanochannel Transport Studies","Ion-surface interactions and analysis","Carbon Nanotubes in Composites","Cell Membrane","Models, Molecular","Movement","Nanotechnology","Peptides","Porosity","Protein Conformation","Protein Folding","Protein Transport","Temperature","Thermodynamics","Time Factors","Ubiquitin"],"mesh_terms":["Cell Membrane","Models, Molecular","Movement","Peptides","Protein Conformation","Temperature","Thermodynamics","Time Factors","Porosity","Protein Folding","Protein Transport","Ubiquitin","Nanotechnology"],"keywords":["Reaction coordinate","Nanopore","Umbrella sampling","Potential of mean force","Molecular dynamics","Chromosomal translocation","Chemical physics","Ubiquitin","Biophysics","Energy landscape","Kinetic energy","Chemistry","Nanotechnology","Physics","Materials science","Computational chemistry","Thermodynamics","Classical mechanics","Biology","Biochemistry"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Affordable and clean energy"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-13T21:38:00.862450Z","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":[]}