State-of-the-Art Molecular Structure and Dynamics and Biophysics in Asia

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 847

Special Issue Editors


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Guest Editor
Institute of Quantitative Biology and Medicine, Soochow University, Suzhou 215123, China
Interests: molecular dynamics simulation; molecular docking; ion channels
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Institute of Quantitative Biology, Zhejiang University, Hangzhou 310027, China
Interests: molecular dynamics; protein folding; protein-protein interaction; machine learning
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Modern biophysics, biochemistry, and molecular biology emerged since the discovery of the double-helical structure model of DNA using X-ray crystallography in the 1950s. Decoding the mystery of life from a microscopic point of view used to be very challenging but has recently come of age. Over the decades, progress in technologies such as single-particle cryo-electron microscopy, single-molecule fluorescence experiments, and molecular modeling has enabled the studies of biomolecules covering small organic molecules/drugs to proteins, DNA, RNA, and cell membranes at biomolecular or even atomic levels. Particularly, the introduction of novel machine learning algorithms to the field of structural and computational biology helps scientists to better characterize the interactions between biomolecules while revealing the mechanisms behind dynamic biological processes. The combination of lab experiments and in silico approaches is reshaping many aspects of today’s biophysics, biochemistry, and molecular biology.

In this Special Issue, we encourage scientists in Asia from diverse backgrounds to contribute original research or review articles, including but not limited to studies of protein/DNA/RNA/lipid interactions, bio-nano interfaces, functional biomolecule design, and molecular machines, etc.

We look forward to receiving your contributions.

Dr. Xuanyu Meng
Prof. Dr. Ruhong Zhou
Guest Editors

Manuscript Submission Information

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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. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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

  • molecular modeling
  • molecular dynamics simulation
  • protein–protein interaction
  • protein folding
  • bioinformatics
  • molecular docking
  • drug design
  • machine learning

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Related Special Issue

Published Papers (2 papers)

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Research

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15 pages, 3567 KB  
Article
Role of Charge Density of Polycations in DNA Complexation and Condensation
by Jianxiang Huang, Yangwei Jiang, Dong Zhang, Jingyuan Li, Youqing Shen and Ruhong Zhou
Biomolecules 2025, 15(7), 983; https://doi.org/10.3390/biom15070983 - 10 Jul 2025
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Abstract
Polycationic gene vectors have been studied extensively for gene delivery, and the charge density of polycations plays a pivotal role in condensing nucleic acids. Recently, we have synthesized two kinds of polycations with varied charge densities: poly(2-(dimethylamino)ethyl methacrylate) (denoted as A100) and a [...] Read more.
Polycationic gene vectors have been studied extensively for gene delivery, and the charge density of polycations plays a pivotal role in condensing nucleic acids. Recently, we have synthesized two kinds of polycations with varied charge densities: poly(2-(dimethylamino)ethyl methacrylate) (denoted as A100) and a copolymer of 2-(tetramethyleneimino)ethyl methacrylate and 2-(diisopropyl-amino)ethyl methacrylate with a 3:1 feed ratio (denoted as B75D25). Despite its lower charge density, B75D25-based vectors exhibit higher transfection efficiency than A100-based vectors, prompting the hypothesis that hydrophobic interactions, rather than solely high charge density, enhance DNA complexation and gene delivery. This study aims to investigate the molecular mechanisms underlying these differences using molecular dynamics (MD) simulations to study the complexation of DNA with B75D25s and A100s. Our simulations reveal that DNA is quite uniformly covered by B75D25s, and the complexation is not only driven by the electrostatic attraction with DNA but more importantly by the hydrophobic interactions among B75D25s. In contrast, only a small fraction of A100s bind to DNA, which is due to the strong electrostatic repulsion among A100s. Our results reveal the contribution of hydrophobic interactions to the complexation of low-charge-density B75D25s with DNA. These results suggest that high charge density may not be essential for DNA condensation and efficient gene delivery. Full article
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Review

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20 pages, 2585 KB  
Review
An Overview of Contrasting Experimental Results on Dynamics of Kinesin-1 Molecular Motors: Insight into the Underlying Mechanism
by Ping Xie
Biomolecules 2025, 15(10), 1453; https://doi.org/10.3390/biom15101453 - 14 Oct 2025
Abstract
The conventional kinesin (kinesin-1) molecular motor is a prototypical member of the kinesin superfamily. It can processively step on microtubules toward the plus end by hydrolyzing ATP molecules, performing the biological function of shuttling cargos in cells. Its dynamics have been thoroughly studied [...] Read more.
The conventional kinesin (kinesin-1) molecular motor is a prototypical member of the kinesin superfamily. It can processively step on microtubules toward the plus end by hydrolyzing ATP molecules, performing the biological function of shuttling cargos in cells. Its dynamics have been thoroughly studied using various methods including biochemical measurement, single molecule imaging, single molecule optical trapping, and so on. While most of the experiments yielded consistent results on the dynamics of the motor, a lot of conflicting experimental results have also been presented. Here, a brief review is given of the diverse conflicting experimental results. Furthermore, a model for the chemomechanical coupling of the motor is briefly reviewed, which can consistently and quantitatively explain these conflicting experimental results in addition to the other experimental results. A consistent explanation of the diverse conflicting experimental results with the same model is an essential criterion for determining the correctness of the model. Full article
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