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Advances in Protein–Ligand Interactions
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Advances in Protein–Ligand Interactions

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

Deadline for manuscript submissions: 20 February 2025 | Viewed by 7092

Special Issue Editor

Prof. Dr. Dong-Jun Yu

E-Mail Website1 Website2
Guest Editor
School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
Interests: pattern recognition; machine learning; neural networks and fuzzy systems; protein structure and function analysis; protein–protein interaction network; large-scale protein data mining; DNA/RNA functionality analysis

Special Issue Information

Dear Colleagues,

Protein–ligand interactions are fundamental molecular phenomena in organisms. Proteins, which play important roles in various biological functions, depend on highly specific interactions with ligands to carry out their activities.

Protein–ligand interactions can exhibit remarkable specificity and efficiency, involving diverse types of ligands such as proteins, nucleic acids, lipids, small molecules, substrates, allosteric modulators, inhibitors, and drugs. These interactions play crucial roles in regulating signal transduction within cells, controlling metabolic pathways, facilitating physiological processes, and contributing to pathophysiological conditions. Therefore, comprehending the mechanisms underlying protein–ligand interactions, including their atomic-level binding modalities, conformational flexibility, and mutational effects, holds immense significance for drug design and advancements in biotechnology.

This Special Issue of IJMS aims to provide a platform to showcase cutting-edge research, encompassing diverse forms of investigation, including experimental and computational studies. The objective is to provide a comprehensive landscape of protein–ligand interactions. Contributions are invited that shed light on the importance of these interactions in biomedicine and molecular pathology, as well as their applications in biotechnology and the food industry.

Prof. Dr. Dong-Jun Yu
Guest Editor

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.

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Keywords

  • drug design
  • binding specificity
  • molecular docking
  • ligand screening
  • structural biology
  • protein–protein interactions
  • protein–ligand interactions
  • protein–lipid complexes
  • protein–nucleic acid interactions

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Published Papers (4 papers)

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Research

17 pages, 6063 KiB  
Article
PRITrans: A Transformer-Based Approach for the Prediction of the Effects of Missense Mutation on Protein–RNA Interactions
by Fang Ge, Cui-Feng Li, Chao-Ming Zhang, Ming Zhang and Dong-Jun Yu
Int. J. Mol. Sci. 2024, 25(22), 12348; https://doi.org/10.3390/ijms252212348 - 17 Nov 2024
Viewed by 1180
Abstract
Protein–RNA interactions are essential to many cellular functions, and missense mutations in RNA-binding proteins can disrupt these interactions, often leading to disease. To address this, we developed PRITrans, a specialized computational method aimed at predicting the effects of missense mutations on protein–RNA interactions, [...] Read more.
Protein–RNA interactions are essential to many cellular functions, and missense mutations in RNA-binding proteins can disrupt these interactions, often leading to disease. To address this, we developed PRITrans, a specialized computational method aimed at predicting the effects of missense mutations on protein–RNA interactions, which is vital for understanding disease mechanisms and advancing molecular biology research. PRITrans is a novel deep learning model designed to predict the effects of missense mutations on protein–RNA interactions, which employs a Transformer architecture enhanced with multiscale convolution modules for comprehensive feature extraction. Its primary innovation lies in integrating protein language model embeddings with a deep feature fusion strategy, effectively handling high-dimensional feature representations. By utilizing multi-layer self-attention mechanisms, PRITrans captures nuanced, high-level sequence information, while multiscale convolutions extract features across various depths, thereby enhancing predictive accuracy. Consequently, this architecture enables significant improvements in ΔΔG prediction compared to traditional approaches. We validated PRITrans using three different cross-validation strategies on two newly reconstructed mutation datasets, S315 and S630 (containing 315 forward and 315 reverse mutations). The results consistently demonstrated PRITrans’s strong performance on both datasets. PRITrans demonstrated strong predictive capability, achieving a Pearson correlation coefficient of 0.741 and a root mean square error (RMSE) of 1.168 kcal/mol on the S630 dataset. Moreover, its robust performance extended to independent test sets, achieving a Pearson correlation of 0.699 and an RMSE of 1.592 kcal/mol. These results underscore PRITrans’s potential as a powerful tool for protein-RNA interaction studies. Moreover, when tested against existing prediction methods on an independent dataset, PRITrans showed improved predictive accuracy and robustness. Full article
(This article belongs to the Special Issue Advances in Protein–Ligand Interactions)
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27 pages, 17523 KiB  
Article
Anti-Inflammatory and Antioxidant Pyrrolo[3,4-d]pyridazinone Derivatives Interact with DNA and Bind to Plasma Proteins—Spectroscopic and In Silico Studies
by Aleksandra Kotynia, Edward Krzyżak, Julia Żądło, Maja Witczak, Łukasz Szczukowski, Jakub Mucha, Piotr Świątek and Aleksandra Marciniak
Int. J. Mol. Sci. 2024, 25(3), 1784; https://doi.org/10.3390/ijms25031784 - 1 Feb 2024
Cited by 3 | Viewed by 1219
Abstract
From the point of view of the search for new pharmaceuticals, pyridazinone derivatives are a very promising group of compounds. In our previous works, we have proved that newly synthesized ligands from this group have desirable biological and pharmacokinetic properties. Therefore, we decided [...] Read more.
From the point of view of the search for new pharmaceuticals, pyridazinone derivatives are a very promising group of compounds. In our previous works, we have proved that newly synthesized ligands from this group have desirable biological and pharmacokinetic properties. Therefore, we decided to continue the research evaluating the activity of pyrrolo[3,4-dpyridazinone derivatives. In this work, we focused on the interactions of five pyridazinone derivatives with the following biomolecules: DNA and two plasma proteins: orosomucoid and gamma globulin. Using several of spectroscopic methods, such as UV-Vis, CD, and fluorescence spectroscopy, we proved that the tested compounds form stable complexes with all biomacromolecules selected for analysis. These findings were also confirmed by the results obtained by molecular modeling. All tested pyridazinone derivatives bind to the ctDNA molecule via groove binding mechanisms. All these molecules can also be bound and transported by the tested plasma proteins; however, the stability of the complexes formed is lower than those formed with serum albumin. Full article
(This article belongs to the Special Issue Advances in Protein–Ligand Interactions)
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13 pages, 2956 KiB  
Article
The Amyloid Assembly of the Bacterial Hfq Is Lipid-Driven and Lipid-Specific
by Florian Turbant, Quentin Machiels, Jehan Waeytens, Frank Wien and Véronique Arluison
Int. J. Mol. Sci. 2024, 25(3), 1434; https://doi.org/10.3390/ijms25031434 - 24 Jan 2024
Viewed by 1475
Abstract
Under specific conditions, some proteins can self-assemble into fibrillar structures called amyloids. Initially, these proteins were associated with neurodegenerative diseases in eucaryotes. Nevertheless, they have now been identified in the three domains of life. In bacteria, they are involved in diverse biological processes [...] Read more.
Under specific conditions, some proteins can self-assemble into fibrillar structures called amyloids. Initially, these proteins were associated with neurodegenerative diseases in eucaryotes. Nevertheless, they have now been identified in the three domains of life. In bacteria, they are involved in diverse biological processes and are usually useful for the cell. For this reason, they are classified as “functional amyloids”. In this work, we focus our analysis on a bacterial functional amyloid called Hfq. Hfq is a pleiotropic regulator that mediates several aspects of genetic expression, mainly via the use of small noncoding RNAs. Our previous work showed that Hfq amyloid-fibrils interact with membranes. This interaction influences Hfq amyloid structure formation and stability, but the specifics of the lipid on the dynamics of this process is unknown. Here, we show, using spectroscopic methods, how lipids specifically drive and modulate Hfq amyloid assembly or, conversely, its disassembly. The reported effects are discussed in light of the consequences for bacterial cell life. Full article
(This article belongs to the Special Issue Advances in Protein–Ligand Interactions)
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15 pages, 3672 KiB  
Article
Mimicking Protein Kinase C Phosphorylation Inhibits Arc/Arg3.1 Palmitoylation and Its Interaction with Nucleic Acids
by Barbara Barylko, Clinton A. Taylor 4th, Jason Wang, Svetlana Earnest, Steve Stippec, Derk D. Binns, Chad A. Brautigam, David M. Jameson, George N. DeMartino, Melanie H. Cobb and Joseph P. Albanesi
Int. J. Mol. Sci. 2024, 25(2), 780; https://doi.org/10.3390/ijms25020780 - 8 Jan 2024
Cited by 1 | Viewed by 1840
Abstract
Activity-regulated cytoskeleton-associated protein (Arc) plays essential roles in diverse forms of synaptic plasticity, including long-term potentiation (LTP), long-term depression (LTD), and homeostatic plasticity. In addition, it assembles into virus-like particles that may deliver mRNAs and/or other cargo between neurons and neighboring cells. Considering [...] Read more.
Activity-regulated cytoskeleton-associated protein (Arc) plays essential roles in diverse forms of synaptic plasticity, including long-term potentiation (LTP), long-term depression (LTD), and homeostatic plasticity. In addition, it assembles into virus-like particles that may deliver mRNAs and/or other cargo between neurons and neighboring cells. Considering this broad range of activities, it is not surprising that Arc is subject to regulation by multiple types of post-translational modification, including phosphorylation, palmitoylation, SUMOylation, ubiquitylation, and acetylation. Here we explore the potential regulatory role of Arc phosphorylation by protein kinase C (PKC), which occurs on serines 84 and 90 within an α-helical segment in the N-terminal domain. To mimic the effect of PKC phosphorylation, we mutated the two serines to negatively charged glutamic acid. A consequence of introducing these phosphomimetic mutations is the almost complete inhibition of Arc palmitoylation, which occurs on nearby cysteines and contributes to synaptic weakening. The mutations also inhibit the binding of nucleic acids and destabilize high-order Arc oligomers. Thus, PKC phosphorylation of Arc may limit the full expression of LTD and may suppress the interneuronal transport of mRNAs. Full article
(This article belongs to the Special Issue Advances in Protein–Ligand Interactions)
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