DNA groove preference shift upon phosphorylation of a protamine-like cationic peptide

Chhetri, KB and Jang, YH and Lansac, Y and Maiti, PK (2023) DNA groove preference shift upon phosphorylation of a protamine-like cationic peptide. In: Physical Chemistry Chemical Physics .

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Abstract

Protamines, arginine-rich DNA-binding proteins, are responsible for chromatin compaction in sperm cells, but their DNA groove preference, major or minor, is not clearly identified. We herein study the DNA groove preference of a short protamine-like cationic peptide before and after phosphorylation, using all-atom molecular dynamics and umbrella sampling simulations. According to various thermodynamic and structural analyses, a peptide in its non-phosphorylated native state prefers the minor groove over the major groove, but phosphorylation of the peptide bound to the minor groove not only reduces its binding affinity but also brings a serious deformation of the minor groove, eliminating the minor-groove preference. As protamines are heavily phosphorylated before binding to DNA, we expect that the structurally disordered phosphorylated protamines would prefer major grooves to enter into DNA during spermatogenesis. © 2023 The Royal Society of Chemistry.

Item Type:	Journal Article
Publication:	Physical Chemistry Chemical Physics
Publisher:	Royal Society of Chemistry
Additional Information:	The copyright for this article belongs to Royal Society of Chemistry.
Keywords:	Amino acids; Binding energy; Bioinformatics; Molecular dynamics; Peptides; Phosphorylation, Binding affinities; Cationic peptides; Chromatin compaction; DNA-binding protein; Dynamic sampling; Minor grooves; Native state; Sampling simulation; Sperm cells; Umbrella sampling, DNA
Department/Centre:	Division of Physical & Mathematical Sciences > Physics
Date Deposited:	04 Mar 2024 09:12
Last Modified:	04 Mar 2024 09:12
URI:	https://eprints.iisc.ac.in/id/eprint/84320

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