{
  "abstract": "In this work, we evaluate whether computed conformational ensembles of seven tripeptides─the six C-terminal amidated D/Y/F sequence isomers and the closely related sequence FFD─are informative of their self-assembly propensity. Using all-atom molecular dynamics (AA-MD) simulations and intramolecular side-chain dihedral angles as a collective variable, we calculate conformational free-energy landscapes (FELs) for these sequences. We then introduce a novel method to numerically characterize the computed FELs and find a correlation between thermal conformational accessibility and a sequence's tendency to self-assemble or remain in solution. In addition, we evaluate and rationalize the impact of water model selection on conformational ensembles in terms of peptide-water interaction strengths, and also investigate the influence of ionization state on conformation. The presented methodology implicitly accounts for amino acid sequence context, which is a major determinant of divergent properties for sequence isomers. It also has a low associated computational cost, making use of single-molecule simulations to predict supramolecular assembly outcomes. These features are an important advancement toward a general scheme for the theory-informed design of peptide materials.",
  "abstract_shown": true,
  "affiliations": [
    "Advanced Science Research Center (ASRC) at the Graduate Center of the City University of New York , 85 St Nicholas Terrace, New York, New York10031, United States.",
    "Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, New York, New York10065, United States.",
    "Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York10016, United States."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 3,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Zhuojun Li"
    },
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Rein V Ulijn",
      "orcid": "0000-0002-7138-1213"
    },
    {
      "affs": [
        0
      ],
      "name": "Hamish W A Swanson",
      "orcid": "0000-0002-3075-3199"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/9q1dwf2c35b1z.bib",
  "cited_by": 0,
  "doi": "10.1021/acs.jpcb.6c03754",
  "fulltext_url": "https://europepmc.org/articles/PMC13700000",
  "id": "9q1dwf2c35b1z",
  "issns": [
    "1520-6106",
    "1520-5207"
  ],
  "landing_url": "https://europepmc.org/article/MED/42910877",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Article"
    ],
    [
      "heading",
      "B: Biomaterials and Membranes"
    ],
    [
      "openalex",
      "2502|Supramolecular Self-Assembly in Materials"
    ]
  ],
  "openalex": "W7221538411",
  "pdf_url": "https://europepmc.org/articles/PMC13700000?pdf=render",
  "pmcid": "PMC13700000",
  "pmid": "42910877",
  "published": "2026-10-01",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/9q1dwf2c35b1z.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:20:14Z",
      "native_id": "MED:42910877",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42910877"
    },
    {
      "first_seen": "2026-10-30T12:20:31Z",
      "native_id": "PMC13700000",
      "source": "pmc",
      "url": "https://doi.org/10.1021/acs.jpcb.6c03754"
    }
  ],
  "subjects": [
    {
      "field": "chemistry",
      "origin": "openalex:2502|Supramolecular Self-Assembly in Materials",
      "subfield": "materials-polymers"
    }
  ],
  "title": "Molecular Conformation as a Determinant of Self-Assembly in Sequence-Isomeric Tripeptides.",
  "title_text": "Molecular Conformation as a Determinant of Self-Assembly in Sequence-Isomeric Tripeptides.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:36:29Z",
  "url": "https://research.draconitic.com/paper/9q1dwf2c35b1z",
  "venue": "The journal of physical chemistry. B",
  "versions": []
}