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Protein Structure and Its Interactions

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 January 2026 | Viewed by 940

Special Issue Editor


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Guest Editor
College of Pharmacy and Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul 037601, Republic of Korea
Interests: crystal structure; proteins; protein structure; X-ray diffraction; protein-protein interaction; protein expression; protein characterization

Special Issue Information

Dear Colleagues,

Understanding protein structure and its molecular interactions is fundamental to advancing modern biology and medicine. High-resolution structural techniques such as cryo-electron microscopy, X-ray crystallography, and NMR spectroscopy have enabled unprecedented insights into the dynamic architecture of proteins and their functional assemblies. Recent developments in AI-based protein structure prediction, such as AlphaFold and RoseTTAFold, have further accelerated discovery in structural biology, revealing novel interfaces and previously uncharacterized complexes. This Special Issue welcomes original research and reviews focused on the structural basis of protein–protein, protein–ligand, and protein–nucleic acid interactions. Topics may include structural dynamics, allosteric regulation, computational modeling, drug-target interactions, and mechanisms of molecular recognition. Studies integrating experimental and computational approaches are particularly encouraged. This Special Issue aims to showcase cutting-edge discoveries that deepen our understanding of protein structure-function relationships and their implications for disease mechanisms and therapeutic development.

Prof. Dr. Dong Hae Shin
Guest Editor

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Keywords

  • protein–protein interactions (PPIs)
  • protein–ligand binding
  • molecular recognition
  • binding affinity and specificity
  • molecular interface analysis

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Published Papers (2 papers)

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Research

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21 pages, 3521 KB  
Article
Structural and Functional Analysis of ASFV pI73R Reveals GNB1 Binding and Host Gene Modulation
by Katarzyna Magdalena Dolata, Barbara Bettin, Richard Küchler, Katrin Pannhorst, Dmitry S. Ushakov, Walter Fuchs and Axel Karger
Int. J. Mol. Sci. 2025, 26(24), 11768; https://doi.org/10.3390/ijms262411768 - 5 Dec 2025
Viewed by 208
Abstract
African swine fever virus (ASFV) causes a highly fatal disease in domestic pigs, resulting in substantial economic losses to the global swine industry. Vaccine development continues to be hindered by limited characterization of viral proteins and their functional redundancies. In this study, we [...] Read more.
African swine fever virus (ASFV) causes a highly fatal disease in domestic pigs, resulting in substantial economic losses to the global swine industry. Vaccine development continues to be hindered by limited characterization of viral proteins and their functional redundancies. In this study, we employ combined experimental and computational approaches to characterize the ASFV I73R protein (pI73R), which contains a Z-DNA binding domain and plays a critical role in ASFV virulence and pathogenesis. We demonstrate that pI73R shares significant structural similarity with transcription factors of the forkhead box (FOX) protein family. Overexpression of pI73R results in downregulation of Crooked neck-like protein 1 (CRNKL1), a core spliceosome component, suggesting a potential mechanism by which pI73R modulates host protein synthesis. Using high-resolution mass spectrometry, we map the pI73R interactome and identify the host protein Guanine nucleotide-binding protein subunit beta-1 (GNB1) as a novel direct interactor of pI73R which may facilitate its nuclear transport. Furthermore, we show that pI73R exhibits consistent oligomerization and expression across different ASFV genotypes, highlighting its functional importance. Taken together, these results provide new insights into pI73R function, ASFV–host dynamics, and offer promising directions for antiviral strategy development. Full article
(This article belongs to the Special Issue Protein Structure and Its Interactions)
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Review

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22 pages, 3854 KB  
Review
A Generalized AI View of Tricopeptide Repeats: What’s in a Name
by Sailen Barik
Int. J. Mol. Sci. 2025, 26(23), 11649; https://doi.org/10.3390/ijms262311649 - 1 Dec 2025
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Abstract
Tricopeptide repeats refer to 30 or more amino acid (aa) repeats, of which the best studied ones are 34-aa and 35-aa long, named Tetratricopeptide and Pentatricopeptide repeats, respectively, and abbreviated as TPR and PPR. Recently, 37-aa and 38-aa repeats (Heptatricopeptide, HPR; Octatricopeptide, OPR) [...] Read more.
Tricopeptide repeats refer to 30 or more amino acid (aa) repeats, of which the best studied ones are 34-aa and 35-aa long, named Tetratricopeptide and Pentatricopeptide repeats, respectively, and abbreviated as TPR and PPR. Recently, 37-aa and 38-aa repeats (Heptatricopeptide, HPR; Octatricopeptide, OPR) have been reported, but 36-aa repeats or repeats outside the 34–38 range (such as 33-aa or 39-aa) are apparently missing. This review is an analytical discourse of the structural and functional commonalities as well as differences among all tricopeptide repeats. In structure, the use of Artificial Intelligence (AI)-based prediction and experimental 3D structures revealed that regardless of the number of amino acids, these repeats are all alpha-helical in nature, whereby the tandem helices are joined by relatively flexible linkers or spacers to form a superhelix. In function, many tricopeptide repeats bind specific RNA, thus playing important roles in RNA processing and stability. The specificity is determined by the interaction between specific amino acid residues with the nucleotides in the RNA, while the helices offer a scaffold that holds the interacting residues in position. Detailed analysis of various known TPR and PPR revealed conserved amino acids at specific positions, such that they serve as signature motifs. Moreover, extra helices upstream or downstream of the repeat domains often maintain the continuum of the superhelical vortex. Evidently, the overall helicity and the presence of critical amino acid residues in strategic places are more important for the biological function of the tricopeptide repeats than the exact amino acid length of the repeat. Full article
(This article belongs to the Special Issue Protein Structure and Its Interactions)
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