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Biomolecules
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Feature Papers in Section "Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates"
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Feature Papers in Section "Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates"

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates".

Deadline for manuscript submissions: 30 September 2026 | Viewed by 1188

Special Issue Editor

Dr. Valentyn Oksenych

E-Mail Website
Guest Editor
Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
Interests: DNA repair; DNA damage response; genetics; primary immunodeficiency; B lymphocyte development; mouse models
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue aims to showcase high-quality feature papers that advance our understanding of the structure, function, dynamics, and biological roles of major biomacromolecules. We welcome contributions that provide significant conceptual advances, innovative methodologies, and comprehensive perspectives on proteins, nucleic acids, and carbohydrates across molecular, cellular, and translational contexts. Submissions may include original research articles, methodological papers, or review articles that highlight emerging trends and address fundamental questions in biochemistry, molecular biology, structural biology, and chemical biology.

Topics of interest include, but are not limited to, the following: protein folding, stability, and interactions; nucleic acid biology and genome maintenance; RNA structure and function; enzymatic mechanisms; carbohydrate chemistry and glycobiology; biomolecular assemblies; computational modeling and biophysical characterization; and applications of biomacromolecules in biotechnology, immunology, and medicine.

This Special Issue provides an opportunity to present impactful work to a broad interdisciplinary audience and to contribute to a curated collection representing the latest progress in biomacromolecular research. We look forward to receiving high-quality manuscripts that reflect the diversity and innovation of this rapidly evolving field.

Dr. Valentyn Oksenych
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-blind 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

  • biomacromolecules
  • proteins
  • DNA
  • RNA
  • chromatin
  • epigenetics
  • gene regulation
  • genomics
  • proteomics
  • metabolomics
  • computational approaches
  • molecular biotechnology
  • molecular therapeutics

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

Published Papers (3 papers)

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Research

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20 pages, 3048 KB  
Article
A Simplified Strategy for Nanobody Production and Use Based on Functional GST-Nanobody Fusion Proteins
by Agustín A. Burgos, Andrés Rivera-Dictter, Pablo Mendoza-Soto, Tammy P. Pástor, José Munizaga, Guillermo Valenzuela-Nieto and Gonzalo A. Mardones
Biomolecules 2026, 16(2), 306; https://doi.org/10.3390/biom16020306 - 14 Feb 2026
Viewed by 539
Abstract
Nanobodies (VHHs or single-domain antibodies) are powerful affinity reagents, but their routine use is often limited by production constraints and by the lack of a conserved Fc region for secondary detection. We describe a simplified strategy in which functional GST–nanobody fusion proteins are [...] Read more.
Nanobodies (VHHs or single-domain antibodies) are powerful affinity reagents, but their routine use is often limited by production constraints and by the lack of a conserved Fc region for secondary detection. We describe a simplified strategy in which functional GST–nanobody fusion proteins are expressed directly in the cytoplasm of Escherichia coli OrigamiTM 2 (DE3), a strain that supports disulfide bond formation through trxB/gor mutations. Using well-characterized nanobodies against GFP (Lag2) and mCherry (C11), we designed N-terminal GST fusions and confirmed by AlphaFold3-based modeling that both constructs preserve the GST fold and the VHH (Variable domain of the Heavy-chain antibody of Heavy-chain-only antibodies) β-sandwich with defined CDR loops and a predicted intradomain disulfide bond. Following IPTG induction and purification by glutathione affinity and size-exclusion chromatography, we obtained soluble GST-nb-GFP and GST-nb-mCherry at ~8–12 mg/L. Isothermal titration calorimetry showed nanomolar binding to their antigens (Kd ~123 nM for GFP and ~199 nM for mCherry). Consistent with conformational epitope recognition, GST-nanobodies were reactive in native-state dot blots but not in denaturing Western blots under the conditions tested. The GST moiety enabled indirect immunofluorescence via anti-GST antibodies, yielding specific labeling of GFP- or mCherry-tagged TGN38 in HeLa and H4 cells. Finally, we demonstrate “GST-nanobody pulldown” as a robust method for affinity capture from cell lysates. Together, this platform provides a low-cost, versatile route to functional nanobody reagents without requiring tag removal, and complements other nanobody designs (e.g., VHH-Fc fusions) in an application-dependent manner. Full article
(This article belongs to the Special Issue Feature Papers in Section "Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates")
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Review

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32 pages, 10527 KB  
Review
Single-Molecule Conductance of Non-Redox Proteins: Mechanisms, Measurements, and Applications
by Zhimin Fan, Miao Chen, Jie Xiang and Bintian Zhang
Biomolecules 2026, 16(4), 495; https://doi.org/10.3390/biom16040495 - 25 Mar 2026
Abstract
Charge transport underpins essential biological processes, including cellular respiration, photosynthesis, and enzymatic catalysis. Advances in molecular electronics have enabled single-molecule measurements that unequivocally establish redox-active proteins as efficient electron conductors, with their metal cofactors serving as intrinsic redox relays. By contrast, ubiquitous non-redox [...] Read more.
Charge transport underpins essential biological processes, including cellular respiration, photosynthesis, and enzymatic catalysis. Advances in molecular electronics have enabled single-molecule measurements that unequivocally establish redox-active proteins as efficient electron conductors, with their metal cofactors serving as intrinsic redox relays. By contrast, ubiquitous non-redox proteins lacking such redox centers have long been considered poor conductors. However, recent research has challenged this view, demonstrating that efficient charge transport in non-redox proteins can be mediated through polypeptide backbones, aromatic side-chain arrays, and hydrogen bond networks. This review surveys progress in understanding the single-molecule conductance of non-redox proteins. Firstly, we elucidate the fundamental transport mechanisms, highlighting the interplay between coherent tunneling and thermally activated hopping. We then provide an overview of state-of-the-art experimental techniques for single-molecule characterization. Through analysis of diverse systems spanning short peptides to large enzymes, we illustrate how aromatic amino acid networks and dynamic conformational fluctuations govern conductance, enabling emerging applications in label-free biosensing and single-molecule protein/DNA sequencing. Finally, we discuss persistent challenges and outline future opportunities for integrating protein-based conductors into bioelectronic devices. This review aims to stimulate further research and pave the way for novel applications harnessing protein conductance. Full article
(This article belongs to the Special Issue Feature Papers in Section "Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates")
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19 pages, 939 KB  
Review
Navigating Challenges in Mass Spectrometry Analysis of Endogenous and Synthetic Protein Modifications
by Caroline M. Hanson, Dina L. Bai and Jarrod A. Marto
Biomolecules 2026, 16(3), 367; https://doi.org/10.3390/biom16030367 - 28 Feb 2026
Viewed by 408
Abstract
Mass spectrometry-based analysis of post-translational modifications (PTMs) is a key strategy for characterizing protein regulation and identifying disease-associated targets, with endogenous PTMs serving as biomarkers for disease diagnosis and therapeutic response. More recently, chemical proteomic strategies have adapted PTM-focused workflows to measure engagement [...] Read more.
Mass spectrometry-based analysis of post-translational modifications (PTMs) is a key strategy for characterizing protein regulation and identifying disease-associated targets, with endogenous PTMs serving as biomarkers for disease diagnosis and therapeutic response. More recently, chemical proteomic strategies have adapted PTM-focused workflows to measure engagement of covalent and photoactivatable small-molecule probes, expanding the scope of ligand discovery for these disease-associated targets. This review provides an overview of mass spectrometry-based PTM analysis workflows, including LC–MS/MS acquisition and post-acquisition data processing, with an emphasis on how modification-specific physicochemical properties influence PTM detection and identification. Common analytical challenges that limit PTM identification, including variable MS/MS fragmentation behavior and modification site localization, are discussed using modifications such as phosphorylation and photoaffinity labeling probe adducts as representative examples. Recent advances in acquisition strategies and computational tools that improve spectral quality and confidence in PTM assignment are also summarized. Additionally, approaches for the analytical validation of modification events, such as metabolic labeling strategies, are described. Together, this review outlines key considerations, capabilities, and limitations of MS-based PTM profiling and provides a framework for interpreting PTM datasets to support their effective integration into downstream biochemical and disease target validation studies. Full article
(This article belongs to the Special Issue Feature Papers in Section "Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates")
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