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Editorial Board Members’ Collection Series: “Molecular Dynamics”

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

Deadline for manuscript submissions: 31 October 2024 | Viewed by 1240

Special Issue Editors


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Guest Editor
Department of Chemistry & Biochemistry, Benton Hall 221, University of Missouri-St. Louis, One University Blvd., St. Louis, MO 63121, USA
Interests: antiviral strategies; DNA-binding molecules; DNA-binding polyamides; small DNA tumor viruses; negative strand RNA viruses; HPV; bioorganic; biomimetic; organic chemistry; NextGen sequencing; green chemistry; biochemistry; biophysical; synthetic; analytical chemistry; bioinorganic chemistry

Special Issue Information

Dear Colleagues,

The molecular dynamics simulation of macromolecule motion enables the computational study of proteins, carbohydrates, nucleic acids, lipids, solvents, ions, and metabolites at temporal and spatial scales, which is not accessible by other methods.

In addition, computational drug design relies on knowing the active sites or allosteric sites of enzymes to find chemical compounds that can stably bind to the amino acids present in them, thus inhibiting or modulating their activity.

The present collection will comprise contributions that discuss the following topics related to the computational simulation of macromolecules (though this list is not exhaustive):

  • Quantum Mechanics;
  • Classical mechanics;
  • Hybrid QM/MM;
  • Molecular dynamics at the atomic level;
  • Steered molecular dynamics;
  • Coarse-graining;
  • Docking(Protein–protein, protein–ligand);
  • The molecular dynamics of protein–ligand interactions;
  • Drug design;
  • Virtual screening.

Manuscripts in which computational simulation is used to propose physically realistic and novel models of biological processes, as well as their potential for use in the study of disease, are welcome.

Dr. Paulino Gómez-Puertas
Prof. Dr. James K. Bashkin
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • quantum mechanics
  • classical mechanics
  • hybrid QM/MM
  • molecular dynamics at the atomic level
  • steered molecular dynamics
  • coarse-graining
  • docking(protein–protein, protein–ligand)
  • the molecular dynamics of protein–ligand interactions
  • drug design
  • virtual screening

Published Papers (1 paper)

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Research

17 pages, 10262 KiB  
Article
STAG2: Computational Analysis of Missense Variants Involved in Disease
by David Ros-Pardo, Paulino Gómez-Puertas and Íñigo Marcos-Alcalde
Int. J. Mol. Sci. 2024, 25(2), 1280; https://doi.org/10.3390/ijms25021280 - 20 Jan 2024
Viewed by 938
Abstract
The human STAG2 protein is an essential component of the cohesin complex involved in cellular processes of gene expression, DNA repair, and genomic integrity. Somatic mutations in the STAG2 sequence have been associated with various types of cancer, while congenital variants have been [...] Read more.
The human STAG2 protein is an essential component of the cohesin complex involved in cellular processes of gene expression, DNA repair, and genomic integrity. Somatic mutations in the STAG2 sequence have been associated with various types of cancer, while congenital variants have been linked to developmental disorders such as Mullegama–Klein–Martinez syndrome, X-linked holoprosencephaly-13, and Cornelia de Lange syndrome. In the cohesin complex, the direct interaction of STAG2 with DNA and with NIPBL, RAD21, and CTCF proteins has been described. The function of STAG2 within the complex is still unknown, but it is related to its DNA binding capacity and is modulated by its binding to the other three proteins. Every missense variant described for STAG2 is located in regions involved in one of these interactions. In the present work, we model the structure of 12 missense variants described for STAG2, as well as two other variants of NIPBl and two of RAD21 located at STAG2 interaction zone, and then analyze their behavior through molecular dynamic simulations, comparing them with the same simulation of the wild-type protein. This will allow the effects of variants to be rationalized at the atomic level and provide clues as to how STAG2 functions in the cohesin complex. Full article
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