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Biophysica
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Investigations into Protein Structure
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Investigations into Protein Structure

A special issue of Biophysica (ISSN 2673-4125).

Deadline for manuscript submissions: 28 February 2026 | Viewed by 5323

Special Issue Editor

Dr. Salvatore Giovanni De Simone

E-Mail Website
Guest Editor
Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Diseases Populations (INCT-IDPN), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
Interests: vaccines; infectious diseases; molecular immunology; epitopes; neglected diseases; biochemistry; molecular biology; proteins; structure; cell biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Proteins, the fundamental components of life, are not just essential to the complex interplay of cellular, physiological, and immunological processes. They are, in fact, the ultimate expression of genetic information, meticulously decoded from DNA. Within the dynamic environment of the cell, proteins perform a wide range of functions, acting as both structural frameworks and catalysts that power biological reactions. A sophisticated code embedded in the four-letter DNA alphabet is central to their versatility. This genetic code, through sequences of amino acids, determines the folding and configuration of proteins into an astounding variety of structures, each uniquely suited to a specific role. From the resilient collagen fibers that provide tissue support to the dynamic molecular motors enabling cellular motion, proteins exemplify the diversity encoded in the genome.

Additionally, proteins orchestrate biochemical reactions and can serve as antigens, sparking targeted immune responses and therapeutic innovations. Their amino acid sequences and specific regions act as catalysts, mediate protein-protein interactions, and drive numerous biological processes that would otherwise proceed sluggishly. Whether functioning as enzymes facilitating nutrient breakdown for energy or as signaling molecules regulating cellular communication, proteins are not just important; they are central to all biological activity. Despite their complexity, proteins arise from a relatively simple genetic blueprint, which can produce an almost limitless array of structures, each optimized for its function. This simplicity amidst complexity highlights the elegance of life’s molecular machinery, driven by proteins’ hierarchical structures. Proteins, from providing structural support to ensuring catalytic efficiency, embody biological systems' adaptability and precision, highlighting life's extraordinary intricacies. This Special Issue aims to gather studies that push the boundaries of our understanding of protein structures, including enzymes, structural proteins, membranes, and other components of living organisms. Contributions related to bioinformatics, methodologies for examining the four structural levels of proteins, SAXS, cryoelectron microscopy, and the interactions between these levels and biochemical and immunological properties, and drug development studies are particularly encouraged. With the wealth of knowledge accumulated over the years, a comprehensive collection of expert articles on this special issue would provide significant value to researchers worldwide.

Dr. Salvatore Giovanni De Simone
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. Biophysica is an international peer-reviewed open access quarterly 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 1200 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
  • enzymes
  • structural proteins
  • membranes

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Published Papers (6 papers)

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Research

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14 pages, 1540 KB  
Article
Distinct Thermal Response of SARS-CoV-2 Spike Proteins S1 and S2 by Coarse-Grained Simulations
by Pornthep Sompornpisut, Linh Truong Hoai, Panisak Boonamnaj, Brian G. Olson and Ras B. Pandey
Biophysica 2025, 5(4), 50; https://doi.org/10.3390/biophysica5040050 - 31 Oct 2025
Viewed by 135
Abstract
Large-scale computer simulations were employed to investigate the conformational response of the spike protein components S1 and S2 using a coarse-grained model. Temperature was systematically varied to assess the balance between stabilizing residue–residue interactions and thermal fluctuations. The resulting contact profiles reveal distinct [...] Read more.
Large-scale computer simulations were employed to investigate the conformational response of the spike protein components S1 and S2 using a coarse-grained model. Temperature was systematically varied to assess the balance between stabilizing residue–residue interactions and thermal fluctuations. The resulting contact profiles reveal distinct segmental reorganization and self-assembly behaviors between S1 and S2. At lower, thermoresponsive temperatures, pronounced segmental globularization occurs in the N-terminal domain (NTD; M153–K202) and receptor-binding domain (RBD; E406–E471) of S1, whereas S2 exhibits alternating regions of high and low contact density. Increasing temperature reduces this segmental globularization, leaving only minor persistence at elevated temperatures. The temperature dependence of the radius of gyration (Rg) further demonstrates the contrasting thermal behaviors of S1 and S2. For S1, Rg increases continuously and monotonically with temperature, reaching a steady-state value approximately 50% higher than that at low temperature. In contrast, S2 displays a non-monotonic response: Rg initially rises to a maximum nearly sevenfold higher than its low-temperature value, then decreases with further temperature increase. Scaling analysis of the structure factor reveals that the globularity of S1 diminishes significantly upon heating, while S2 becomes modestly more compact yet retains its predominantly fibrous character. Full article
(This article belongs to the Special Issue Investigations into Protein Structure)
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14 pages, 632 KB  
Article
Protein Polarimetry, Perfected: Specific Rotation Measurement for the Refracto-Polarimetric Detection of Cryptic Protein Denaturation
by Lisa Riedlsperger, Heinz Anderle, Andreas Schwaighofer and Martin Lemmerer
Biophysica 2025, 5(3), 34; https://doi.org/10.3390/biophysica5030034 - 7 Aug 2025
Cited by 1 | Viewed by 1413
Abstract
Protein polarimetry has been evaluated as a simple and straightforward technique to detect the cryptic denaturation of exemplary proteins. The general rules of rotation vs. amino acid and structural composition and the respective knowledge gaps were reviewed, and the specific rotation of cystine [...] Read more.
Protein polarimetry has been evaluated as a simple and straightforward technique to detect the cryptic denaturation of exemplary proteins. The general rules of rotation vs. amino acid and structural composition and the respective knowledge gaps were reviewed, and the specific rotation of cystine was determined in 4 M NaCl solution as [α]D20 = –302.5°. The specific rotations at 589 nm and 436 nm and the ratio were measured for several model proteins, some purified plasma-derived proteins and for three monoclonal antibodies. The immunoglobulin G concentrates all showed a narrow ratio range likely characteristic for this protein class. Heat denaturation experiments were conducted at temperatures between 50 and 85 °C both for short-time (10 min) and for prolonged periods of heat exposure (up to 210 min). Denaturation by heat resulted not only in the known levorotatory shift, but also in a shift in the specific rotation ratio. The stabilizing effect of fatty acids in bovine serum could be demonstrated by this parameter. Polarimetry thus appears to be a particularly sensitive and simple method for the characterization of the identity and the thermal stability of proteins and should therefore be added again as a complimentary method to the toolbox of protein chemistry. Full article
(This article belongs to the Special Issue Investigations into Protein Structure)
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17 pages, 8708 KB  
Article
Optimizing Single-Particle Analysis Workflow: Comparative Analysis of the Symmetry Parameter and Particle Quantity upon Reconstruction of the Molecular Complex
by Myeong Seon Jeong, Han-ul Kim, Mi Young An, Yoon Ho Park, Sun Hee Park, Sang J. Chung, Yoon-Sun Yi, Sangmi Jun, Young Kwan Kim and Hyun Suk Jung
Biophysica 2025, 5(3), 30; https://doi.org/10.3390/biophysica5030030 - 22 Jul 2025
Viewed by 691
Abstract
Recent major advancements in cryo-electron microscopy (cryo-EM) have enabled high-resolution structural analysis, accompanied by developments in image processing software packages for single-particle analysis (SPA). SPA facilitates the 3D reconstruction of proteins and macromolecular complexes from numerous individual particles. In this study, we systematically [...] Read more.
Recent major advancements in cryo-electron microscopy (cryo-EM) have enabled high-resolution structural analysis, accompanied by developments in image processing software packages for single-particle analysis (SPA). SPA facilitates the 3D reconstruction of proteins and macromolecular complexes from numerous individual particles. In this study, we systematically evaluated the impact of symmetry parameters and particle quantity on the 3D reconstruction efficiency using the dihydrolipoyl acetyltransferase (E2) inner core of the pyruvate dehydrogenase complex (PDC). We specifically examined how inappropriate symmetry constraints can introduce structural artifacts and distortions, underscoring the necessity for accurate symmetry determination through rigorous validation methods such as directional Fourier shell correlation (FSC) and local-resolution mapping. Additionally, our analysis demonstrates that efficient reconstructions can be achieved with a moderate particle number, significantly reducing computational costs without compromising structural accuracy. We further contextualize these results by discussing recent developments in SPA workflows and hardware optimization, highlighting their roles in enhancing reconstruction accuracy and computational efficiency. Overall, our comprehensive benchmarking provides strategic insights that will facilitate the optimization of SPA experiments, particularly in resource-limited settings, and offers practical guidelines for accurately determining symmetry and particle quantity during cryo-EM data processing. Full article
(This article belongs to the Special Issue Investigations into Protein Structure)
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14 pages, 2559 KB  
Article
Insights into Cysteine Protease Complexes with Grafted Chitosan–Poly(N-vinylpyrrolidone) Copolymers: Catalytic Activity and Storage Stability
by Maria S. Lavlinskaya, Andrey V. Sorokin, Anastasia N. Dubovitskaya, Anastasia I. Yutkina, Maxim S. Kondratyev, Marina G. Holyavka, Yuriy F. Zuev and Valeriy G. Artyukhov
Biophysica 2025, 5(2), 18; https://doi.org/10.3390/biophysica5020018 - 8 May 2025
Cited by 1 | Viewed by 796
Abstract
The investigation of structure–function relationships in enzyme polysaccharide complexes provides a theoretical foundation for modulating enzyme properties and expanding their industrial applications. In this study, the interaction of cysteine proteases—bromelain, ficin, and papain—with a grafted chitosan–poly(N-vinylpyrrolidone) copolymers, Cs-g-PVP, was [...] Read more.
The investigation of structure–function relationships in enzyme polysaccharide complexes provides a theoretical foundation for modulating enzyme properties and expanding their industrial applications. In this study, the interaction of cysteine proteases—bromelain, ficin, and papain—with a grafted chitosan–poly(N-vinylpyrrolidone) copolymers, Cs-g-PVP, was examined, and its effect on the catalytic and stability properties of the enzymes was assessed. Molecular docking and Fourier-transform infrared spectroscopy were used to analyze the topology of the resulting complexes and identify macromolecular fragments involved in binding. Based on the obtained results, it was hypothesized that complex formation would lead to a slight reduction in the catalytic activity of cysteine proteases. In vitro studies of the complexes confirmed this hypothesis, showing that the enzymes retained more than 63% of their proteolytic activity while their half-inactivation time during storage increased by up to ~12-fold. The investigated Cs-g-PVP copolymers demonstrated high efficiency as supports for the studied enzymes, capable of retaining up to 100% of the added enzymes. Full article
(This article belongs to the Special Issue Investigations into Protein Structure)
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Review

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44 pages, 4680 KB  
Review
Resistance of Nitric Oxide Dioxygenase and Cytochrome c Oxidase to Inhibition by Nitric Oxide and Other Indications of the Spintronic Control of Electron Transfer
by Paul R. Gardner
Biophysica 2025, 5(3), 41; https://doi.org/10.3390/biophysica5030041 - 9 Sep 2025
Viewed by 966
Abstract
Heme enzymes that bind and reduce O2 are susceptible to poisoning by NO. The high reactivity and affinity of NO for ferrous heme produces stable ferrous-NO complexes, which in theory should preclude O2 binding and turnover. However, NO inhibition is often [...] Read more.
Heme enzymes that bind and reduce O2 are susceptible to poisoning by NO. The high reactivity and affinity of NO for ferrous heme produces stable ferrous-NO complexes, which in theory should preclude O2 binding and turnover. However, NO inhibition is often competitive with respect to O2 and rapidly reversible, thus providing cellular and organismal survival advantages. This kinetic paradox has prompted a search for mechanisms for reversal and hence resistance. Here, I critically review proposed resistance mechanisms for NO dioxygenase (NOD) and cytochrome c oxidase (CcO), which substantiate reduction or oxidation of the tightly bound NO but nevertheless fail to provide kinetically viable solutions. A ferrous heme intermediate is clearly not available during rapid steady-state turnover. Reversible inhibition can be attributed to NO competing with O2 in transient low-affinity interactions with either the ferric heme in NOD or the ferric heme-cupric center in CcO. Toward resolution, I review the underlying principles and evidence for kinetic control of ferric heme reduction via an O2-triggered ferric heme spin crossover and an electronically-forced motion of the heme and structurally-linked protein side chains that elicit electron transfer and activate O2 in the flavohemoglobin-type NOD. For CcO, kinetics, structures, and density functional theory point to the existence of an analogous O2 and reduced oxygen intermediate-controlled electron-transfer gate with a linked proton pump function. A catalytic cycle and mechanism for CcO is finally at hand that links each of the four O2-reducing electrons to each of the four pumped protons in time and space. A novel proton-conducting tunnel and channel, electron path, and pump mechanism, most notably first hypothesized by Mårten Wikström in 1977 and pursued since, are laid out for further scrutiny. In both models, low-energy spin-orbit couplings or ‘spintronic’ interactions with O2 and NO or copper trigger the electronic motions within heme that activate electron transfer to O2, and the exergonic reactions of transient reactive oxygen intermediates ultimately drive all enzyme, electron, and proton motions. Full article
(This article belongs to the Special Issue Investigations into Protein Structure)
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20 pages, 3040 KB  
Review
Quantitative Characterization of Nonspecific Interactions Between Macromolecules in Complex Media: Comparison of Experiment, Theory, and Simulation
by Allen P. Minton
Biophysica 2025, 5(3), 25; https://doi.org/10.3390/biophysica5030025 - 24 Jun 2025
Viewed by 642
Abstract
A brief summary of the effect of nonspecific interactions upon chemical equilibria in solutions containing a high total concentration of macromolecular solutes comparable to that found in biological fluid media is presented. Analyses of experimental measurements permitting relatively direct quantitation of the free [...] Read more.
A brief summary of the effect of nonspecific interactions upon chemical equilibria in solutions containing a high total concentration of macromolecular solutes comparable to that found in biological fluid media is presented. Analyses of experimental measurements permitting relatively direct quantitation of the free energy of nonspecific intermolecular interaction in solutions of one or two macrosolutes are described, and a table listing published experimental studies of both homo- and hetero-interactions is provided. Methods for calculating the free energy of nonspecific interaction via theory and computer simulation are described. Recommendations for further progress in both measurement and calculation of interaction free energies are presented. Full article
(This article belongs to the Special Issue Investigations into Protein Structure)
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