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Biomolecular Structure, Function and Interactions: 2nd Edition
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Biomolecular Structure, Function and Interactions: 2nd Edition

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

Deadline for manuscript submissions: 20 July 2026 | Viewed by 6677

Special Issue Editor

Dr. Ivo Crnolatac

E-Mail Website1 Website2
Guest Editor
Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
Interests: biomolecular interactions; DNA/RNA; protein structure; protein function; drug discovery
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues, 

Biophysical chemistry is a truly interdisciplinary endeavour combining the principles of physics, biology, and chemistry to explore the processes in biological systems and their underlying physical and chemical properties. The focus is on understanding how biological molecules, such as proteins, nucleic acids, and lipids, interact with each other and with their environment at a molecular level. Thus, biomolecular interactions are a fundamental part of biophysical chemistry. We aim to publish important and exciting studies on protein–protein, protein–DNA, protein–ligand, and receptor–ligand interactions in this Special Issue. Furthermore, manuscripts on biomolecular structure and function, protein folding, and stability are welcome. Publications on innovations in biophysical techniques facilitating further progress in this prominent field of research would, likewise, be appreciated.

This Special Issue is supervised by Dr. Ivo Crnolatac and assisted by our Topical Advisory Panel Member Dr. Rajendra Rohokale  (University of Florida).

Dr. Ivo Crnolatac
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • biophysical chemistry
  • protein–protein interactions
  • protein–DNA interactions
  • protein–ligand interactions
  • receptor–ligand interactions
  • biomolecular structure and function
  • protein folding and stability

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Related Special Issue

Published Papers (6 papers)

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Research

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23 pages, 12042 KB  
Article
AI-Assisted Computed Structure Models for Pre-Ubiquitylation Complexes Assembled by Respiratory Syncytial Viral Suppressors of Cellular Interferon Response
by Sailen Barik
Int. J. Mol. Sci. 2026, 27(5), 2437; https://doi.org/10.3390/ijms27052437 - 6 Mar 2026
Viewed by 511
Abstract
Multiple viruses suppress the antiviral defense system of the host for optimal growth and pathogenesis by co-opting the ubiquitin-mediated proteasomal system (UPS) that promotes the degradation of cellular substrates belonging to the interferon pathway. In the Orthopneumovirus genus, respiratory syncytial virus (RSV), a [...] Read more.
Multiple viruses suppress the antiviral defense system of the host for optimal growth and pathogenesis by co-opting the ubiquitin-mediated proteasomal system (UPS) that promotes the degradation of cellular substrates belonging to the interferon pathway. In the Orthopneumovirus genus, respiratory syncytial virus (RSV), a significant pathogen in human and other animals, employs a pair of viral nonstructural proteins (NS1, NS2) to assemble the UPS. The lack of experimental three-dimensional structures of the substrate proteins and the NS-assembled UPS has impeded progress in our understanding of the mechanism of this assembly process. In an effort to remedy this deficiency, I have taken advantage of the burgeoning field of AI (artificial intelligence) and machine learning programs, such as AlphaFold3, to model the pre-ubiquitylation cores in various combination of the subunits to construct three-dimensional structures, named ‘computed structure models’ (CSMs). The UPS core universally comprises an adapter protein connected to the “substrate” that is to be degraded by the “substrate receptor”. The NS proteins are believed to act as receptors, and cellular Elongin BC as an adapter. These CSMs lend support to the biochemical results where known while also suggesting that the complete core of three proteins is energetically more stable than a complex of only the NS protein and the substrate. In the absence of experimental structures, these results offer, for the first time, a mechanistic insight into RSV-triggered assembly of the UPS, which should allow for a better design of future experiments, and eventually new antiviral regimens. Full article
(This article belongs to the Special Issue Biomolecular Structure, Function and Interactions: 2nd Edition)
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25 pages, 63422 KB  
Article
Molecular Modeling and Gene Ontology Implicate SLC35F4 and SLC35F5 as Golgi-Associated Importers of Flavin-Adenine-Dinucleotide
by Zheyun Niu, Dongming Jiang and Daniel M. Hardy
Int. J. Mol. Sci. 2026, 27(1), 512; https://doi.org/10.3390/ijms27010512 - 4 Jan 2026
Viewed by 988
Abstract
Solute carriers (SLCs) mediate cell- and organelle-specific import and export of nutrients and metabolites required for every biochemical process that occurs in a cell. Functional studies have ascribed activities to many human genes annotated as SLCs, but more than 100 SLCs remain orphans. [...] Read more.
Solute carriers (SLCs) mediate cell- and organelle-specific import and export of nutrients and metabolites required for every biochemical process that occurs in a cell. Functional studies have ascribed activities to many human genes annotated as SLCs, but more than 100 SLCs remain orphans. Here, we applied a set of computational tools to characterize the orphan carriers SLC35F4 and SLC35F5. Phylogenetic analysis grouped SLC35F4 sister to SLC35F3, a suspected thiamine transporter, in a clade with SLC35F5, and distinct from an SLC35F6/2/1 clade. Transcriptome datasets revealed a restricted function for SLC35F4 in the cerebellum, in contrast to the more widespread distribution of SLC35F5. Gene ontology identified the Golgi apparatus as the likely residence of both transporters. Conceptual docking of 71 candidate substrates predicted high affinities of SLC35F4 (10–40 nM) and SLC35F5 (0.1–0.4 nM) for flavin adenine dinucleotide (FAD), straddling that of the known FAD transporter SLC25A32 (2–4 nM), while returning much lower affinities (by 30–fold or more) for all other tested substrates. Docking to SLC35F3 returned low affinity for both FAD and thiamine as candidate substrates. Thus, SLC35F4 and SLC35F5 but not closely related SLC35F3 likely import FAD into the Golgi apparatus, where the cofactor serves as the oxidant for disulfide-bond formation during tissue-specific, post-translational modification of secretory proteins. These findings provide strong direction for the definitive experiments yet needed to confirm the carriers’ subcellular localization, transport activities, and contributions to protein maturation and trafficking. Full article
(This article belongs to the Special Issue Biomolecular Structure, Function and Interactions: 2nd Edition)
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20 pages, 5425 KB  
Article
Structure, Function and Dynamics of mCoral, a pH-Responsive Engineered Variant of the mCherry Fluorescent Protein with Improved Hydrogen Peroxide Tolerance
by Athena Zitti, Ozan Aksakal, Danoo Vitsupakorn, Pierre J. Rizkallah, Halina Mikolajek, James A. Platts, Georgina E. Menzies and D. Dafydd Jones
Int. J. Mol. Sci. 2026, 27(1), 154; https://doi.org/10.3390/ijms27010154 - 23 Dec 2025
Viewed by 1032
Abstract
The red fluorescent protein mCherry is one of the most widely used fluorescent proteins in biology. Here, we have changed the chromophore chemistry by converting the thioether group of M66 to a thiol group through mutation to cysteine. The new variant, termed mCoral [...] Read more.
The red fluorescent protein mCherry is one of the most widely used fluorescent proteins in biology. Here, we have changed the chromophore chemistry by converting the thioether group of M66 to a thiol group through mutation to cysteine. The new variant, termed mCoral (due to its orange fluorescence hue), has similar brightness to mCherry but improved resistance to hydrogen peroxide. The variant is also responsive to pH with low and high pKa forms that have distinct spectral properties, which DFT analysis suggests is due to protonation state changes in the newly introduced thiol group, as well as the phenol group. The structure of mCoral reveals that the M66C mutation creates a space within the β-barrel structure that is filled by a water molecule, which makes new polar interactions, including the backbone carbonyl group of F65. Molecular dynamics simulations suggest that this additional water molecule, together with local solvation around the chromophore, could play a role in promoting planarity of the full conjugated system comprising the chromophore. The mCoral chromophore makes slightly more H-bonds with water than mCherry. The main water exit point for mCherry is also narrower in mCoral, providing a potential explanation for increased resistance to hydrogen peroxide. Overall, a small structural change to mCherry has resulted in a new fluorescent protein with potentially useful characteristics and an insight into the role of dynamics and water in defining the structure–function relationship in red fluorescent proteins. Full article
(This article belongs to the Special Issue Biomolecular Structure, Function and Interactions: 2nd Edition)
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11 pages, 1236 KB  
Article
Structure-Based Engineering of a PTPsigma Ectodomain for Enhanced Solubility and Productivity
by Sung Ho Park, Woochan Lim, Jian Kang, Sumin Jo, Hye Hyeon Jang, Heejin Yang, Suk Hyun Yoo, Myeongbin Kim and Seong Eon Ryu
Int. J. Mol. Sci. 2025, 26(17), 8345; https://doi.org/10.3390/ijms26178345 - 28 Aug 2025
Viewed by 941
Abstract
Protein tyrosine phosphatase receptor sigma (PTPRS) regulates cellular signals involved in hematopoietic stem cell development, synaptic plasticity, and synovium differentiation. The soluble extracellular Ig-like domains of PTPRS have therapeutic potential by binding to a ligand, inhibiting the ligand-binding of endogenous PTPRS. However, the [...] Read more.
Protein tyrosine phosphatase receptor sigma (PTPRS) regulates cellular signals involved in hematopoietic stem cell development, synaptic plasticity, and synovium differentiation. The soluble extracellular Ig-like domains of PTPRS have therapeutic potential by binding to a ligand, inhibiting the ligand-binding of endogenous PTPRS. However, the wild-type Ig-like domains have poor solubility, which limits their therapeutic use. In this study, we identified solvent-exposed hydrophobic residues on the surface of PTPRS and mutated the residues to hydrophilic residues for solubility-enhancing engineering. The mutagenesis screening increased its solubility up to five-fold. In addition, the expression yields were also increased by up to 14-fold. The biochemical and functional analysis of the engineered PTPRS showed that the mutant protein had comparable properties to the wild type. Thus, the engineered PTPRS has potential for therapeutic applications where modulation of PTPRS is critical. Full article
(This article belongs to the Special Issue Biomolecular Structure, Function and Interactions: 2nd Edition)
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14 pages, 3713 KB  
Article
Titin’s Intrinsically Disordered PEVK Domain Modulates Actin Polymerization
by Áron Gellért Altorjay, Hedvig Tordai, Ádám Zolcsák, Nikoletta Kósa, Tamás Hegedűs and Miklós Kellermayer
Int. J. Mol. Sci. 2025, 26(14), 7004; https://doi.org/10.3390/ijms26147004 - 21 Jul 2025
Viewed by 1625
Abstract
The multi-domain muscle protein titin provides elasticity and mechanosensing functions to the sarcomere. Titin’s PEVK domain is intrinsically disordered due to the presence of a large number of prolines and highly charged residues. Although PEVK does not have canonical actin-binding motifs, it has [...] Read more.
The multi-domain muscle protein titin provides elasticity and mechanosensing functions to the sarcomere. Titin’s PEVK domain is intrinsically disordered due to the presence of a large number of prolines and highly charged residues. Although PEVK does not have canonical actin-binding motifs, it has been shown to bind F-actin. Here, we explored whether the PEVK domain may also affect actin assembly. We cloned the middle, 733-residue-long segment (called PEVKII) of the full-length PEVK domain, expressed in E. coli and purified by using His- and Avi-tags engineered to the N- and C-termini, respectively. Actin assembly was monitored by the pyrene assay in the presence of varying PEVKII concentrations. The structural features of PEVKII-associated F-actin were studied with atomic force microscopy. The added PEVKII enhanced the initial and log-phase rates of actin assembly and the peak F-actin quantity in a concentration-dependent way. However, the critical concentration of actin polymerization was unaltered. Thus, PEVK accelerates actin polymerization by facilitating its nucleation. This effect was highlighted in the AFM images of F-actin–PEVKII adsorbed to the supported lipid bilayer. The sample was dominated by radially symmetric complexes of short actin filaments. PEVK’s actin polymerization-modulating effect may, in principle, have a function in regulating sarcomeric actin length and turnover. Altogether, titin’s PEVK domain is not only a non-canonical actin-binding protein that regulates sarcomeric shortening, but one that may modulate actin polymerization as well. Full article
(This article belongs to the Special Issue Biomolecular Structure, Function and Interactions: 2nd Edition)
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Review

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28 pages, 4887 KB  
Review
Structure and Function of Ocular Proteoglycans: Essential Proteins for Vision
by James Melrose
Int. J. Mol. Sci. 2026, 27(4), 1943; https://doi.org/10.3390/ijms27041943 - 18 Feb 2026
Viewed by 935
Abstract
This narrative review outlines the structure and essential functions of ocular proteoglycans (PGs) in visual processing as documented in the extensive literature on this subject matter. The eye, as one of the most complex sensory organs, relies on the coordinated activity of various [...] Read more.
This narrative review outlines the structure and essential functions of ocular proteoglycans (PGs) in visual processing as documented in the extensive literature on this subject matter. The eye, as one of the most complex sensory organs, relies on the coordinated activity of various tissues and cell types, with PGs playing a central role in facilitating communication and maintaining tissue function. These molecules stabilise ocular tissues; for example, SPACRCAN (IMPG2) and hyaluronan aggregates in the interphotoreceptor matrix protect photoreceptors from oxidative stress. Specialised heparan sulfate PGs, such as pikachurin, eyes-shut, and the neurexin family, stabilise synapses and ensure synaptic specificity and plasticity. Pikachurin is particularly important for the rapid transmission of visual signals at the bipolar ribbon synapse. A diverse array of chondroitin sulfate (aggrecan, versican, neurocan, brevican, phosphacan, NG2), keratan sulfate (SV2), and heparan sulfate (perlecan, agrin, collagen XVIII) PGs are differentially expressed in ocular tissues, contributing to tissue stability and homeostasis. In the cornea, sclera, and choroid, small leucine-rich repeat PGs (SLRPs) maintain three-dimensional structure, corneal transparency, and tissue function through interactions with cytokines and growth factors. The vitreous humour contains opticin and nyctalopin, which support the nutrition of avascular regions and facilitate bipolar ribbon synapse signalling. Ultimately, the effectiveness of the eye as a visual organ depends significantly on the functional roles of its constituent PGs. Full article
(This article belongs to the Special Issue Biomolecular Structure, Function and Interactions: 2nd Edition)
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