Skip to content
DraconiticResearch
Search Sources API
197,768 studies31 sourcesUpdated 29 min ago
Peer-reviewedCC BYThe journal of physical chemistry. B

Molecular Conformation as a Determinant of Self-Assembly in Sequence-Isomeric Tripeptides.

  • Zhuojun Li1,2
  • Rein V Ulijn1,2,3
  • Hamish W A Swanson1
  1. 1Advanced 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.
  2. 2Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, New York, New York10065, United States.
  3. 3Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York10016, United States.
Read full textPDFDOICite

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.

Related

  1. Molecular ground-state conformation prediction based on the Mamba state space model
    Yuxin Gou, Aming Wu, Richang Hong +1
    Communications ChemistryPeer-reviewedCC BY-NC-ND 4.0Full textGeneral chemistryPMC
  2. Conformational Soft Hash (CSH): A Rotation-Invariant Molecular Fingerprint for Conformation-Sensitive Similarity Search and Blockchain-Based Conformational Registry
    Jakub Hryc
    ChemRxivPreprintCC BYFull textGeneral chemistryChemRxiv
  3. Many Electrons, One Determinant: Hartree--Fock Theory, Basis Sets, and Molecular Integrals
    Pierre-François Loos
    arXivPreprintarXiv licenceFull textPhysical chemistryCondensed matterarXiv
  4. Sliding Window Attention with Auditable Chemical Sinks for Long-Sequence Molecular Transformation Modeling
    Dina Khalil, Mariam Tawfik, Sarah Farouk +2
    ChemRxivPreprintLicence not statedGeneral chemistryChemRxiv
  5. Sequence order controls silver(I) coordination in aqueous His–Met–Pro tripeptide–nitrate mixtures: an ab initio molecular dynamics study
    Fu Wei, Xu Wu, Yongjian Huang +1
    ChemRxivPreprintLicence not statedGeneral chemistryChemRxiv

Cite

BibTeXRIS
BibTeX
@article{li2026molecular,
  title = {{Molecular Conformation as a Determinant of Self-Assembly in Sequence-Isomeric Tripeptides.}},
  author = {Zhuojun Li and Rein V Ulijn and Hamish W A Swanson},
  journal = {The journal of physical chemistry. B},
  year = {2026},
  month = oct,
  doi = {10.1021/acs.jpcb.6c03754},
  url = {https://europepmc.org/article/MED/42910877},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Molecular Conformation as a Determinant of Self-Assembly in Sequence-Isomeric Tripeptides.
AU  - Zhuojun Li
AU  - Rein V Ulijn
AU  - Hamish W A Swanson
PY  - 2026
DA  - 2026/10/01
JO  - The journal of physical chemistry. B
DO  - 10.1021/acs.jpcb.6c03754
UR  - https://europepmc.org/article/MED/42910877
AB  - 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.
SN  - 1520-6106
SN  - 1520-5207
ER  -