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Biomolecules
Special Issues
Innovative Biomolecular Structure Analysis Techniques
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Innovative Biomolecular Structure Analysis Techniques

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Biophysics: Structure, Dynamics, and Function".

Deadline for manuscript submissions: 30 June 2025 | Viewed by 2648

Special Issue Editor

Dr. Tzanko I. Doukov

E-Mail Website
Guest Editor
Macromolecular Crystallographic Group, Stanford Synchrotron Radiation Lightsource, National Accelerator Laboratory, Stanford University, Stanford, CA 94309, USA
Interests: macromolecular crystallography; metalloproteins; room and physiological temperature crystallography; structural dynamics

Special Issue Information

Dear Colleagues,

We are pleased to invite you to submit your original research articles for a Special Issue of the journal Biomolecules on Innovative Biomolecular Structure Analysis Techniques.

The field of biomolecular structure analysis is rapidly evolving, with new techniques constantly being developed. This Special Issue will provide a forum for researchers to present their latest work on innovative biomolecular structure analysis techniques.

We are particularly interested in articles that report on the use of new techniques to:

  • Determine the three-dimensional structure of biomolecules;
  • Study the dynamics of biomolecules;
  • Investigate the interactions between biomolecules;
  • Derive the energy landscapes of enzymes.

All articles will be subject to the journal's standard peer-review process.

If you have any questions, please do not hesitate to contact the editor.

Dr. Tzanko I. Doukov
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. 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

  • macromolecular crystallography
  • room temperature crystallography
  • protein ensembles
  • NMR
  • MD simulations

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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.
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  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

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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16 pages, 4451 KiB  
Article
Phi-Value and NMR Structural Analysis of a Coupled Native-State Prolyl Isomerization and Conformational Protein Folding Process
by Ulrich Weininger, Maximilian von Delbrück, Franz X. Schmid and Roman P. Jakob
Biomolecules 2025, 15(2), 259; https://doi.org/10.3390/biom15020259 - 10 Feb 2025
Viewed by 607
Abstract
Prolyl cis/trans isomerization is a rate-limiting step in protein folding, often coupling directly to the acquisition of native structure. Here, we investigated the interplay between folding and prolyl isomerization in the N2 domain of the gene-3-protein from filamentous phage fd, which [...] Read more.
Prolyl cis/trans isomerization is a rate-limiting step in protein folding, often coupling directly to the acquisition of native structure. Here, we investigated the interplay between folding and prolyl isomerization in the N2 domain of the gene-3-protein from filamentous phage fd, which adopts a native-state cis/trans equilibrium at Pro161. Using mutational and Φ-value analysis, we identified a discrete folding nucleus encompassing the β-strands surrounding Pro161. These native-like interactions form early in the folding pathway and provide the energy to shift the cis/trans equilibrium toward the cis form. Variations distant from the Pro161-loop have minimal impact on the cis/trans ratio, underscoring the spatial specificity and localized control of the isomerization process. Using NMR spectroscopy, we determined the structures for both native N2 forms. The cis- and trans-Pro161 conformations are overall identical and exhibit only slight differences around the Pro161-loop. The cis-conformation adopts a more compact structure with improved backbone hydrogen bonding, explaining the approximately 10 kJ·mol−1 stability increase of the cis state. Our findings highlight that prolyl isomerization in the N2 domain is governed by a localized folding nucleus rather than global stability changes. This localized energetic coupling ensures that proline isomerization is not simply a passive, slow step but an integral component of the folding landscape, optimizing both the formation of native structure and the establishment of the cis-conformation. Full article
(This article belongs to the Special Issue Innovative Biomolecular Structure Analysis Techniques)
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13 pages, 3383 KiB  
Article
Exploring the Gating Mechanism of the Human Copper Transporter, hCtr1, Using EPR Spectroscopy
by Shahaf Peleg, Shelly Meron, Yulia Shenberger, Lukas Hofmann, Lada Gevorkyan-Airapetov and Sharon Ruthstein
Biomolecules 2025, 15(1), 127; https://doi.org/10.3390/biom15010127 - 14 Jan 2025
Viewed by 951
Abstract
Ctr1 is a membrane-spanning homotrimer that facilitates copper uptake in eukaryotic cells with high affinity. While structural details of the transmembrane domain of human Ctr1 have been elucidated using X-ray crystallography and cryo-EM, the transfer mechanisms of copper and the conformational changes that [...] Read more.
Ctr1 is a membrane-spanning homotrimer that facilitates copper uptake in eukaryotic cells with high affinity. While structural details of the transmembrane domain of human Ctr1 have been elucidated using X-ray crystallography and cryo-EM, the transfer mechanisms of copper and the conformational changes that control the gating mechanism remain poorly understood. The role of the extracellular N-terminal domains is particularly unclear due to the absence of a high-resolution structure of the full-length hCtr1 protein and limited biochemical and biophysical characterization of the transporter in solution and in cell. In this study, we employed distance electron paramagnetic resonance to investigate the conformational changes of the extracellular N-terminal domain of full-length hCtr1, both in vitro and in cells, as a function of Cu(I) binding. Our results demonstrate that at specific Cu(I) concentrations, the extracellular chains move closer to the lumen to facilitate copper transfer. Additionally, while at these concentrations the intracellular part is penetrating the lumen, suggesting a ball-and-chain gating mechanism. Moreover, this phenomenon was observed for both reconstituted protein in micelles and in native cell membranes. However, the measured distance values were slightly different, suggesting that the membrane’s characteristics and therefore its lipid composition also impact and even regulate the gating mechanism of hCtr1. Full article
(This article belongs to the Special Issue Innovative Biomolecular Structure Analysis Techniques)
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Review

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19 pages, 3318 KiB  
Review
AFM for Studying the Functional Activity of Enzymes
by Irina A. Ivanova, Anastasia A. Valueva, Maria O. Ershova and Tatiana O. Pleshakova
Biomolecules 2025, 15(4), 574; https://doi.org/10.3390/biom15040574 - 12 Apr 2025
Viewed by 309
Abstract
The conventional approach to investigating enzyme systems involves the simultaneous investigation of a large number of molecules and observing ensemble-averaged properties. However, modern science allows us to study the properties of single molecules and to obtain data on biochemical systems at a fundamentally [...] Read more.
The conventional approach to investigating enzyme systems involves the simultaneous investigation of a large number of molecules and observing ensemble-averaged properties. However, modern science allows us to study the properties of single molecules and to obtain data on biochemical systems at a fundamentally new level, significantly expanding our understanding of the mechanisms of biochemical processes. Imaging of single biomolecules with high spatial and temporal resolution is among such modern research tools. To effectively image the individual steps or intermediates of biochemical reactions in single-molecule experiments, we need to develop a methodology for data acquisition and analysis. Its development will make it possible to solve the problem of separating the static and dynamic disorder present in the parameters identified by traditional proteomic methods. Such a methodology may be based on AFM imaging, the high-resolution microscopic visualization of enzymes. This review focuses on this direction of research, including the relevant methodological and practical solutions related to the potential of developing a single-molecule approach to the study of enzyme systems using AFM-based techniques. We focus on the results of enzyme reaction studies, as there are still few such studies, as opposed to the AFM studies of the mechanical properties of individual enzyme molecules. Full article
(This article belongs to the Special Issue Innovative Biomolecular Structure Analysis Techniques)
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