Exploring Structures and Dynamics of Protamine Molecules through Molecular Dynamics Simulations

Hossain Shadman, Caleb Edward Gallops, Jesse D. Ziebarth, Jason E. Derouchey, Yongmei Wang

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


Protamines are arginine-rich proteins that condense DNA in sperm. Despite their importance in reproduction, information on protamine structure is scarce. We, therefore, used molecular dynamics to examine the structures of salmon, bull P1, and human P1 protamines. The sizes and shapes of each protamine varied widely, indicating that they were disordered with structures covering a broad conformational landscape, from hairpin loop structures to extended coils. Despite their general disorder, the protamines did form secondary structures, including helices and hairpin loops. In eutherians, hairpins may promote disulfide bonding that facilitates protamine-DNA condensation, but the specifics of this bonding is not well established. We examined inter-residue distances in the simulations to predict residue pairs likely to form intramolecular bonds, leading to the identification of bonding pairs consistent with previous results in bull and human. These results support a model for eutherian protamine structures where a highly charged center is surrounded by disulfide-bond-stabilized loops.

Original languageEnglish
Pages (from-to)42083-42095
Number of pages13
JournalACS Omega
Issue number46
StatePublished - Nov 22 2022

Bibliographical note

Publisher Copyright:
© 2022 American Chemical Society. All rights reserved.

ASJC Scopus subject areas

  • General Chemistry
  • General Chemical Engineering


Dive into the research topics of 'Exploring Structures and Dynamics of Protamine Molecules through Molecular Dynamics Simulations'. Together they form a unique fingerprint.

Cite this