Applications of Molecular Dynamics to Biological Systems

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Biochemistry, Biophysics and Computational Biology".

Deadline for manuscript submissions: 26 August 2025 | Viewed by 1077

Special Issue Editor

Oden Institute, The University of Texas at Austin, Austin, TX 78712, USA
Interests: computer simulations; computational biophysics; membranes; membrane permeation; conformational transitions of proteins; molecular dynamics; reaction pathways; long time dynamics; RNA folding
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Special Issue Information

Dear Colleagues,

Molecular Dynamics (MD) simulations have become a standard tool in investigating biomolecular systems. While experiments are indispensable and simulations must be verified by experiments, atomistic information supplants wet laboratory data with highly detailed spatial and temporal molecular information. The atomically detailed mechanisms revealed by computer simulations lead to a better understanding of fundamental processes. The simulations are synergetic with experiments and suggest new measurements and directions of investigation. While significant challenges in using MD continue to attract considerable research attention (achieving long-time dynamics, efficient sampling of confirmational space, the accuracy of force fields, etc.), the field is sufficiently mature such that meaningful experiment-guiding predictions are made by simulating the corresponding systems. Biological systems investigated by physics-based computer simulations are highly diverse in size, time scale, and general complexity. Computational investigations vary from relatively small molecules, such as peptides and nucleotides, to large assemblies, such as chromatin and biological membranes. Different spatial and temporal scales are necessary to understand the biological behavior of signaling, reactions, structure formation, and flexibility. Processes of individual biological molecules are simulated with high accuracy (e.g., peptide and protein folding in aqueous solutions). Conformational transitions and activations of proteins and protein complexes have long been a focus of simulations and experimental interactions, and the two provide an invaluable exchange of complementing views. Complex assemblies with multiple phases are also of significant interest and include phospholipid membranes, their interactions with embedded proteins, and peptide permeation. Another field that MD significantly impacts is chromatin modeling, with extremely large length scales at the molecular scale. In summary, molecular biophysics structures and events with exceptionally long time scales (from femtoseconds to hours) and spatial scales (from angstrom to micrometers) are revealed by the tools of MD.

Dr. Ron Elber
Guest Editor

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Keywords

  • computer simulation
  • biophysical modeling
  • molecular dynamics

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Published Papers (1 paper)

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Research

22 pages, 23356 KiB  
Article
Conformational Dynamics of Mitochondrial Inorganic Pyrophosphatase hPPA2 and Its Changes Caused by Pathogenic Mutations
by Ekaterina Bezpalaya, Svetlana Kurilova, Nataliya Vorobyeva and Elena Rodina
Life 2025, 15(1), 100; https://doi.org/10.3390/life15010100 - 15 Jan 2025
Viewed by 721
Abstract
Inorganic pyrophosphatases, or PPases, are ubiquitous enzymes whose activity is necessary for a large number of biosynthetic reactions. The catalytic function of PPases is dependent on certain conformational changes that have been previously characterized based on the comparison of the crystal structures of [...] Read more.
Inorganic pyrophosphatases, or PPases, are ubiquitous enzymes whose activity is necessary for a large number of biosynthetic reactions. The catalytic function of PPases is dependent on certain conformational changes that have been previously characterized based on the comparison of the crystal structures of various complexes. The current work describes the conformational dynamics of a structural model of human mitochondrial pyrophosphatase hPPA2 using molecular dynamics simulation, all-atom principal component analysis, and coarse-grained normal mode analysis. In addition to the wild-type enzyme, four mutant variants of hPPA2 were characterized that correspond to the natural pathogenic variants causing severe mitochondrial dysfunction and cardio pathologies. As a result, we identified the global type of flexible motion that seems to be shared by other dimeric PPases. This motion is discussed in terms of the allosteric behavior of the protein. Analysis of the observed conformational dynamics revealed the formation of a binding site for anionic ligands in the active site that could be relevant to enzyme catalysis. Based on the comparison of the wild-type and mutant PPases dynamics, we suggest the possible molecular mechanisms of the functional incompetence of hPPA2 caused by mutations. The results of this work allow for deeper insight into the structural basis of PPase function and the possible effects of pathogenic mutations on the protein structure and function. Full article
(This article belongs to the Special Issue Applications of Molecular Dynamics to Biological Systems)
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