Unveiling Protein Functions, Dynamics and Interactions in Health and Disease Using Experimental and Theoretical Approaches, 2nd Edition

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

Deadline for manuscript submissions: closed (28 February 2026) | Viewed by 806

Special Issue Editors


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Guest Editor
1. Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
2. New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
Interests: molecular biology; biosensors; peptides; protein-protein interactions; cancer research; Fragile X syndrome (FXS)

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Guest Editor
Department of Earth and Environmental Sciences, University of Milano-Bicocca, 20126 Milan, Italy
Interests: molecular dynamics; molecular dynamics simulations; metadynamics; ligand binding

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Guest Editor Assistant
1. Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
2. New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
Interests: biosensors; nanotechnology; molecular biology; recombinant protein production

Special Issue Information

Dear Colleagues,

Following the successful publication of the first edition of this Special Issue, we are pleased to announce a second edition, entitled “Unveiling Protein Functions, Dynamics and Interactions in Health and Disease Using Experimental and Theoretical Approaches, 2nd Edition”.

In recent years, important scientific results have been obtained thanks to the application of approaches and techniques deriving from the most diverse branches of science, which are sometimes very far from each other. This is particularly true for biological sciences, in which, for example, the use of computational techniques to support experimental data, and vice versa, has been a fruitful strategy in a large number of studies. In this scenario, the study of protein features such as the interplay between their structure/dynamics and function, and their intermolecular interactions, both in health and diseases, plays a key role.

Frequently, experimental results alone, even if combining different disciplines, do not provide a clear understanding of a complex biological problem. In particular, in the study of proteins’ function, some key questions can arise, for instance, concerning the role of mutations or of conformational changes in proteins’ structure associated with a specific cellular function. The use of standard or advanced theoretical approaches (i.e., classical molecular dynamics, molecular docking or enhanced sampling approaches) can help both the comprehension of experimental data and, in turn, better guide the design of future experiments.

The aim of this Special Issue is to bridge the gap that sometimes exists among different approaches that are exploited for a common purpose, i.e., understanding and describing the different functional dynamical features of proteins in specific physiological and pathological conditions. Publishing a multi-disciplinary collection, including molecular biology, structural biology, biophysics, biochemistry, bioinformatics, and computational chemistry, is the aim of this Special Issue.

In this context, this Special Issue aims to report on the current experimental and computational trends in the field of protein functions, interactions, and dynamics. For this Special Issue, original research articles, reviews, and perspectives are welcome to be submitted. Research areas may include, but are not limited to, the following:

(i) Understanding the structural, dynamical, and functional role of point mutations;

(ii) Conformational changes in proteins linked to their function;

(iii) Protein–protein, protein–nucleic acid, and protein–ligand interactions in health and diseases;

(iv) Protein design and engineering for biomedical applications.

We look forward to receiving your contributions.

Dr. Alice Romagnoli
Dr. Stefano Motta
Guest Editors

Dr. Jesmina Rexha
Guest Editor Assistant

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Keywords

  • protein structure and dynamics
  • protein–protein interactions
  • point mutations
  • molecular biology
  • molecular modeling
  • molecular dynamics
  • biochemistry
  • bioinformatics
  • protein–ligand interaction
  • protein–nucleic acid interaction
  • protein conformational changes

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Published Papers (1 paper)

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Research

14 pages, 1768 KB  
Article
A Campomelic Dysplasia A76E Mutation in Sox9 Destabilizes Protein and DNA Binding Dynamics
by Zeyaul Islam and Prasanna R. Kolatkar
Biomolecules 2026, 16(5), 646; https://doi.org/10.3390/biom16050646 - 27 Apr 2026
Viewed by 426
Abstract
Sox9, a pivotal transcription factor belonging to the Sox family, orchestrates critical processes throughout embryonic development, maintenance and differentiation, and exerts a profound influence on organogenesis. Its regulatory versatility stems from precise binding to defined DNA regions, often in collaboration with tissue-specific partners. [...] Read more.
Sox9, a pivotal transcription factor belonging to the Sox family, orchestrates critical processes throughout embryonic development, maintenance and differentiation, and exerts a profound influence on organogenesis. Its regulatory versatility stems from precise binding to defined DNA regions, often in collaboration with tissue-specific partners. The dysregulation of Sox9 during chondrogenesis leads to a skeletal malformation termed campomelic dysplasia and has emerged as a significant factor in various other human diseases, including cancer. A point mutation at position 76 (alanine to glutamic acid, A76E) of Sox9 is recognized as one of the causes of campomelic dysplasia. We have used a combination of biophysical, structural and computational techniques to characterize the Sox9 A76E mutant and compare it with the wild-type (WT) Sox9. WT and A76E Sox9 assemble as homodimers, but form predominantly monomeric complexes in the presence of Sox-specific DNA. A CD analysis shows that the A76E mutant preserves the folding as well as the overall secondary structure of Sox9. Both A76E and WT Sox9 behave similarly in the presence of Sox-specific DNA. Perturbation, with increased temperature, displays a lower melting point for A76E, relative to WT Sox9, indicating decreased stability that may arise due to the long and charged side chain of glutamic acid compared to the small hydrophobic alanine, making unfavorable intra-molecular interactions. The destabilizing effect of the A76E mutant may disturb the formation of a stable higher-order complex that is a prerequisite for normal gene expression. Full article
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