{"doi":"10.1063/5.0177437","title":"Toward determining amyloid fibril structures using experimental constraints from Raman spectroscopy","abstract":"We present structural models for three different amyloid fibril polymorphs prepared from amylin20-29 (sequence SNNFGAILSS) and amyloid-β25-35 (Aβ25-35) (sequence GSNKGAIIGLM) peptides. These models are based on the amide C=O bond and Ramachandran ψ-dihedral angle data from Raman spectroscopy, which were used as structural constraints to guide molecular dynamics (MD) simulations. The resulting structural models indicate that the basic structural motif of amylin20-29 and Aβ25-35 fibrils is extended β-strands. Our data indicate that amylin20-29 forms both antiparallel and parallel β-sheet fibril polymorphs, while Aβ25-35 forms a parallel β-sheet fibril structure. Overall, our work lays the foundation for using Raman spectroscopy in conjunction with MD simulations to determine detailed molecular-level structural models of amyloid fibrils in a manner that complements gold-standard techniques, such as solid-state nuclear magnetic resonance and cryogenic electron microscopy.","journal":"The Journal of Chemical Physics","year":2023,"id":353418,"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":8,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8378,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1010567,"name":"Uma Nudurupati","orcid":"0000-0003-4166-384X","position":1,"is_corresponding":false},{"id":711362,"name":"Riley J. Workman","orcid":"0009-0002-8784-9949","position":2,"is_corresponding":false},{"id":1010568,"name":"Taras I. Lakoba","orcid":"0000-0002-1873-004X","position":3,"is_corresponding":false},{"id":1099673,"name":"Nicholas Perez","orcid":"0009-0005-3625-0858","position":4,"is_corresponding":false},{"id":1099674,"name":"Delaney Nelson","orcid":"0000-0003-4947-5691","position":5,"is_corresponding":false},{"id":812101,"name":"Yangguang Ou","orcid":"0000-0002-6902-3978","position":6,"is_corresponding":false},{"id":467117,"name":"David Punihaole","orcid":"0000-0002-4637-9672","position":7,"is_corresponding":false},{"id":1010566,"name":"Madeline Harper","orcid":"0009-0008-9894-1875","position":0,"is_corresponding":true}],"reference_count":104,"raw_metadata":null,"created_at":"2026-07-19T01:12:58.542950Z","pmid":"38078532","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":[]}