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Modifications of Molecular Structure and Interactions in Epigenome, 3rd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: 20 June 2025 | Viewed by 2131

Special Issue Editors

Special Issue Information

Dear Colleagues,

Beyond the regulatory mechanisms of classical genetics, epigenetics offers new answers to fundamental questions of life in regard to fertility, embryo development, and aging. The molecular machinery of epigenetic regulation has been correlated with various aspects of environmental pollution, psychological stress, physical activity, and nutrition. Public health issues, such as tobacco smoking or alcoholism, have also been investigated in the context of epigenetics. In the past few decades, the identification of epigenetic drug targets has become an emerging field. Beyond the classical genetic background of cancer, epigenetic abnormalities have been detected during the initiation and propagation of the disease. The pathophysiology of autoimmune and inflammatory diseases has also been associated with epigenetic alterations in immune and other cells.

Epigenetic regulation involves heritable changes in gene expression that occur independent of changes in the primary DNA sequence. Such changes in gene expression are coupled to the chromatin structure. Modifications of its components, such as DNA methylation, covalent histone modifications, nucleosome positioning, histone variants, and miRNAs, add up to combinatorial patterns collectively termed as the epigenome. The regulatory machinery also involves numerous enzymes and other proteins interacting with chromatin components. The understanding and precise description of such molecular interactions is key to the mapping of the epigenome and to the design of new molecules interfering with epigenetic diseases. The present Special Issue welcomes manuscripts on molecular interactions of epigenetic regulation, including new methodological approaches and applications of established techniques.

Dr. Uko Maran
Dr. Csaba Hetényi
Guest Editors

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Keywords

  • molecular epigenetics
  • chemical epigenetics
  • cryo-electron microscopy
  • crystallography
  • NMR
  • structural bioinformatics
  • cheminformatics
  • molecular modeling
  • molecular dynamics
  • docking target selection
  • target validation
  • post-translational modification
  • PTM
  • covalent modification
  • methylation
  • acetylation
  • histone code
  • reader
  • writer
  • transferase
  • PHD finger
  • bromodomain
  • free energy
  • binding
  • isothermal titration calorimetry
  • surface plasmon resonance spectroscopy
  • peptide

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Published Papers (1 paper)

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Research

17 pages, 3308 KiB  
Article
Construction of Histone–Protein Complex Structures by Peptide Growing
by Balázs Zoltán Zsidó, Bayartsetseg Bayarsaikhan, Rita Börzsei and Csaba Hetényi
Int. J. Mol. Sci. 2023, 24(18), 13831; https://doi.org/10.3390/ijms241813831 - 7 Sep 2023
Cited by 1 | Viewed by 1731
Abstract
The structures of histone complexes are master keys to epigenetics. Linear histone peptide tails often bind to shallow pockets of reader proteins via weak interactions, rendering their structure determination challenging. In the present study, a new protocol, PepGrow, is introduced. PepGrow uses docked [...] Read more.
The structures of histone complexes are master keys to epigenetics. Linear histone peptide tails often bind to shallow pockets of reader proteins via weak interactions, rendering their structure determination challenging. In the present study, a new protocol, PepGrow, is introduced. PepGrow uses docked histone fragments as seeds and grows the full peptide tails in the reader-binding pocket, producing atomic-resolution structures of histone–reader complexes. PepGrow is able to handle the flexibility of histone peptides, and it is demonstrated to be more efficient than linking pre-docked peptide fragments. The new protocol combines the advantages of popular program packages and allows fast generation of solution structures. AutoDock, a force-field-based program, is used to supply the docked peptide fragments used as structural seeds, and the building algorithm of Modeller is adopted and tested as a peptide growing engine. The performance of PepGrow is compared to ten other docking methods, and it is concluded that in situ growing of a ligand from a seed is a viable strategy for the production of complex structures of histone peptides at atomic resolution. Full article
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