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Biomolecules
Special Issues
Recent Molecular Research on Protein Structure and Function
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Recent Molecular Research on Protein Structure and Function

A Special Issue of Biomolecules (ISSN 2218-273X) belonging to the section "Molecular Biology".

Deadline for manuscript submissions: 15 December 2026 | Viewed by 4921

Editor

Dr. Sonani Ravi Raghav

E-Mail Website
Guest Editor
Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
Interests: protein chemistry; biochemistry; structural biology; protein-protein interactions; structrual and functional elucidation of proteins and protiein complexes

Special Issue Information

Dear Colleagues,

We are pleased to invite you to submit your original research and review articles for a Special Issue of Biomolecules titled ‘Recent Molecular Research on Protein Structure and Function’. Proteins are central to virtually all cellular processes, and understanding their structure and function is crucial for advancing our knowledge in molecular biology, biotechnology, and medicine.

This Special Issue aims to bring together the latest research on the molecular mechanisms underlying protein structure, function, and interactions. We encourage submissions that explore the dynamic relationship between protein architecture and its functional roles in diverse biological contexts. This includes both experimental and computational studies that investigate how protein structures contribute to their biological activities, as well as the development of new technologies for probing these relationships.

In this Special Issue, original research articles and reviews are welcome. Research areas may include (but are not limited to) the following:

  • Protein folding and misfolding mechanisms;
  • Protein–protein and protein–ligand interactions ;
  • Computational predictions of protein structure and function;
  • Structure–function relationships in enzymes and other functional proteins;
  • Structural insights into disease-related proteins (e.g., neurodegenerative diseases, cancer);
  • Advances in techniques for structural analysis (X-ray crystallography, NMR, cryo-EM, etc.);
  • Impact of post-translational modifications on protein function and stability.

We look forward to receiving your contributions and to the opportunity to showcase cutting-edge research in the field of protein structure and function.

Dr. Sonani Ravi Raghav
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 250 words) can be sent to the Editorial Office for assessment.

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-anonymized 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

  • protein structure
  • protein function
  • molecular mechanisms
  • protein folding
  • structural biology

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  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (3 papers)

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28 pages, 7928 KB  
Article
Beyond Small Molecules: Orchestrating Cell Fate with Engineered Water-Soluble Membrane Proteins
by Sebastian Valencia-Amores, Israel Davila Aleman, Timothy G. Jenkins and Dario Mizrachi
Biomolecules 2026, 16(4), 546; https://doi.org/10.3390/biom16040546 - 8 Apr 2026
Viewed by 1359
Abstract
The potential of water-soluble membrane proteins (wsMPs) has not been fully realized. In this article, we exploit the nearly identical functionality of wsMPs with their membrane-bound counterparts and show that we can create water-soluble membrane proteins that incorporate into the plasma membranes of [...] Read more.
The potential of water-soluble membrane proteins (wsMPs) has not been fully realized. In this article, we exploit the nearly identical functionality of wsMPs with their membrane-bound counterparts and show that we can create water-soluble membrane proteins that incorporate into the plasma membranes of cells and alter their fate. As a proof of concept, we demonstrate the functional properties of water-soluble engineered pore-forming proteins, K+ ionic channels (MthK), and constitutively active GPCRs—among them frizzled receptors—both in vitro and in vivo. We call this method in vivo deployment of recombinant viable MPs, iDRIVE. Furthermore, we demonstrate that our strategy mediates the unidirectional insertion of MPs into the plasma membrane, and through constitutively active receptors, we present evidence for similar signaling pathway activation between small molecules and our water-soluble proteins using model phenotypes and molecular signaling assays. We present three examples where wsMPs are functional in dictating cellular fate, both in vitro and in vivo. Lastly, we show the induction of similar differential methylation via the activation of the Wnt signaling pathway using the conventional small molecule agonist, CHIR99021, or our wsFrizzled receptors (iDRIVE-FZD) in human embryonic kidney (HEK 293) embryoid spheroids (ESs). Additionally, we show that Wnt activation via wsFrizzled receptors results in even more biologically relevant epigenetic changes than via the small molecule CHIR99021. Future work will employ iDRIVE to differentiate stem cells in the production of research and clinically relevant organoids. Full article
(This article belongs to the Special Issue Recent Molecular Research on Protein Structure and Function)
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24 pages, 19064 KB  
Article
Structural and Computational Analysis of Pseudomonas aeruginosa DNA Gyrase Reveals Molecular Characteristics That May Contribute to Ciprofloxacin Resistance
by Lalith Perera, Libertad García-Villada, Andrea M. Kaminski, Natalya Degtyareva, Lars C. Pedersen and Paul W. Doetsch
Biomolecules 2026, 16(2), 318; https://doi.org/10.3390/biom16020318 - 18 Feb 2026
Cited by 1 | Viewed by 1075
Abstract
Pseudomonas aeruginosa is considered a priority pathogen by the World Health Organization due to its resistance to antibiotics. Isolates resistant to ciprofloxacin (CPFX), a bactericide commonly used against P. aeruginosa, usually carry the mutations T83I or D87N in the GyrA subunit of [...] Read more.
Pseudomonas aeruginosa is considered a priority pathogen by the World Health Organization due to its resistance to antibiotics. Isolates resistant to ciprofloxacin (CPFX), a bactericide commonly used against P. aeruginosa, usually carry the mutations T83I or D87N in the GyrA subunit of the DNA gyrase. Yet, the molecular mechanisms by which these mutations confer CPFX-resistance to P. aeruginosa are unknown. Here we solved the crystal structure of the P. aeruginosa gyrase catalytic cleavage core and used it to carry out molecular dynamic (MD) simulations of CPFX-gyrase binding in the wild-type as well as the T83I and the D87N mutant systems. Our results show that DNA plays the most prominent stabilizing role once CPFX is bound, with relatively minor contributions from Thr83 or Asp87. Interestingly, we found a solvent cavity adjacent to these residues that may provide CPFX access to the active site. Interaction energy analysis using Umbrella Sampling indicates that Thr83 and Asp87 may influence CPFX trajectory during binding. In the mutant systems, the repulsive potential increases at the cavity site, which may hinder CPFX accessing the binding site. These results shed light on P. aeruginosa resistance to CPFX and may help provide a methodology to identify new therapeutic agents to target fluoroquinolone resistant bacteria. Full article
(This article belongs to the Special Issue Recent Molecular Research on Protein Structure and Function)
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19 pages, 1525 KB  
Article
Screening and Validation of Functional Residues of the Antimicrobial Peptide PpRcys1
by Ming Tao, Zixun Fei, Aobo Sun, Guangming Yu, Huaiyuan Ye, Huishao Shi, Wei Zhang and Junjian Wang
Biomolecules 2025, 15(11), 1617; https://doi.org/10.3390/biom15111617 - 18 Nov 2025
Viewed by 1156
Abstract
The excessive use of conventional antibiotics in aquaculture has created significant challenges, making it essential to explore and develop effective alternatives. Antimicrobial peptides (AMPs) have gained attention as potential therapeutic agents owing to their wide-ranging antibacterial effects and their ability to address pathogens [...] Read more.
The excessive use of conventional antibiotics in aquaculture has created significant challenges, making it essential to explore and develop effective alternatives. Antimicrobial peptides (AMPs) have gained attention as potential therapeutic agents owing to their wide-ranging antibacterial effects and their ability to address pathogens resistant to conventional drugs. PpRcys1 is an antimicrobial peptide that mainly targets bacterial cell membranes, exhibiting a minimum inhibitory concentration of 8–32 μM. Its antibacterial activity should be further optimized. Before such optimization, however, it is crucial to identify the key amino acid residues that determine its functional activity. In this study, molecular dynamics simulations indicated that arginine 40 (ARG40), lysine 55 (LYS55), lysine 90 (LYS90), and lysine 93 (LYS93) play critical roles in the interaction between PpRcys1 and bacterial membranes. To investigate this further, these residues were mutated to serine, producing the mutant peptide PpRcys1_RMRK. Compared with PpRcys1, the mutant peptide PpRcys1_RMRK showed a significant reduction in antibacterial activity. Results from molecular dynamics simulations, Western blot, and ELISA demonstrated a marked decrease in its ability to bind to bacterial cell membranes. Membrane permeation assays, cell membrane depolarization experiments, and scanning electron microscopy revealed that PpRcys1 could not compromise the integrity of the bacterial membrane after losing ARG40, LYS55, LYS90 and LYS93. These findings highlight the critical roles of ARG40, LYS55, LYS90, and LYS93 in sustaining the antibacterial activity of PpRcys1. This study provides important initial insights into the structure–activity relationship of PpRcys1 and establishes a theoretical foundation for its future optimization. Full article
(This article belongs to the Special Issue Recent Molecular Research on Protein Structure and Function)
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