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Biophysica, Volume 5, Issue 3 (September 2025) – 9 articles

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14 pages, 1386 KiB  
Article
Probing the Interaction Between Icariin and Proteinase K: A Combined Spectroscopic and Molecular Modeling Study
by Zhongbao Han, Huizi Zheng, Yimeng Qi, Dilshadbek T. Usmanov, Liyan Liu and Zhan Yu
Biophysica 2025, 5(3), 32; https://doi.org/10.3390/biophysica5030032 - 28 Jul 2025
Viewed by 114
Abstract
Icariin (ICA) is widely recognized for its health benefits. In this work, we examined the intermolecular interactions between ICA and proteinase K (PK) via multi-spectroscopic techniques and molecular simulations. The experimental findings revealed that ICA quenched the fluorescence emission of PK by forming [...] Read more.
Icariin (ICA) is widely recognized for its health benefits. In this work, we examined the intermolecular interactions between ICA and proteinase K (PK) via multi-spectroscopic techniques and molecular simulations. The experimental findings revealed that ICA quenched the fluorescence emission of PK by forming a noncovalent complex. Both hydrogen bonding and van der Waals interactions are essential for the complex’s formation. Then Förster resonance energy transfer (FRET), competitive experiments, and synchronous fluorescence spectroscopy were adopted to verify the formation of the complex. Molecular docking studies demonstrated that ICA could spontaneously bind to PK by hydrogen bonding and hydrophobic interactions, which is consistent with the spectroscopic results. The PK-ICA complex’s dynamic stability was evaluated using a 50 ns molecular dynamics (MD) simulation. The simulation results revealed no significant structural deformation or positional changes throughout the entire simulation period. The complex appears to be rather stable, as seen by the average root-mean-square deviation (RMSD) fluctuations for the host protein in the PK-ICA complex of 1.08 Å and 3.09 Å. These outcomes of molecular simulations suggest that ICA interacts spontaneously and tightly with PK, consistent with the spectroscopic findings. The approach employed in this research presents a pragmatic and advantageous method for examining protein–ligand interactions, as evidenced by the concordance between empirical and theoretical findings. Full article
(This article belongs to the Special Issue Biomedical Optics: 3rd Edition)
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16 pages, 8409 KiB  
Article
Imaging of Laser-Induced Thermal Convection and Conduction in Artificial Vitreous Humor
by Jack Pelzel, Reese Anderson, Darin J. Ulness and Krys Strand
Biophysica 2025, 5(3), 31; https://doi.org/10.3390/biophysica5030031 - 27 Jul 2025
Viewed by 141
Abstract
This study extends the application of photothermal spectroscopy to explore heat transfer dynamics in biological fluids, focusing on the examination of artificial vitreous humor (VH) models of human VH and an endogenous sample of cervine (deer) VH. The research integrates previously established methods [...] Read more.
This study extends the application of photothermal spectroscopy to explore heat transfer dynamics in biological fluids, focusing on the examination of artificial vitreous humor (VH) models of human VH and an endogenous sample of cervine (deer) VH. The research integrates previously established methods for analyzing thermal lensing through photothermal deflection. By visualizing convective and conductive heat transfer processes in the artificial components of human VH, one gains insights into the dynamic behavior of heat transfer in the VH. Relevance extends to clinical cases where pathology requires replacement of endogenous VH with an artificial VH substitute. Several VH substitutes identified in the literature were chosen for this study based on their physical properties and relative abundance in the VH. Individual component fluids, and mixtures of these components, were analyzed at various concentrations based on their physiological concentration ranges in the human VH as they varied with age, sex, and certain disease states. By way of comparison to endogenous biological VH, a sample of VH obtained from a female white-tailed deer eye was analyzed, enhancing the understanding of heat transfer in artificial components of the VH compared to endogenous VH. There is a vast array of ophthalmological procedures that utilize an external heat source interacting with endogenous or artificial VH. The data found in this study will progress the understanding of heat transfer within artificial VH components in comparison to endogenous VH and contribute to the advancement of certain ophthalmological procedures. Full article
(This article belongs to the Special Issue Biomedical Optics: 3rd Edition)
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17 pages, 8708 KiB  
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 158
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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17 pages, 931 KiB  
Article
How to Improve the Repeatability, Reproducibility and Accuracy in the Dynamic Structuration of Water by Electromagnetic Waves?
by Marie-Valérie Moreno, Sid Ahmed Ben Mansour and Frédéric Roscop
Biophysica 2025, 5(3), 29; https://doi.org/10.3390/biophysica5030029 - 21 Jul 2025
Viewed by 182
Abstract
This study represents a first step toward improving the repeatability, reproducibility, and accuracy of a process designed to enhance dynamic water structuring. We aim is to investigate the optical reflectivity of a watery magnesium chloride solution treated with electromagnetic waves, we employ a [...] Read more.
This study represents a first step toward improving the repeatability, reproducibility, and accuracy of a process designed to enhance dynamic water structuring. We aim is to investigate the optical reflectivity of a watery magnesium chloride solution treated with electromagnetic waves, we employ a novel methodology derived from human plethysmography (PPG) with three wavelengths spanning the visible and infrared spectra. We measured the reflectance of 17 flasks at 536 nm, 660 nm, and 940 nm before and after treatment, first using the succussion method (control) and second using a 50 Hz signal. The observed variability was acceptable, with repeatability errors below 0.15% and reproducibility errors below 3.5% across all wavelengths before and after treatment. Out of 51 samples dynamically structured using the succussion method, we obtained two false negatives, while one false negative was recorded out of 51 samples dynamically structured using the electromagnetic (EM) method. PPG appears to be a relevant sensor, as it correctly detected dynamically structured water in 99 out of 102 cases, using either the succussion or electromagnetic method. Our results show significant differences in reflectance (supposedly correlated with water’s structured status) at 536 nm between dynamically structured and dynamic non-structured samples (p < 0.001). Future improvements will include a validation protocol against gold-standard spectrophotometry with a larger sample size. Full article
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12 pages, 2650 KiB  
Article
Calibration and Detection of Phosphine Using a Corrosion-Resistant Ion Trap Mass Spectrometer
by Dragan Nikolić and Xu Zhang
Biophysica 2025, 5(3), 28; https://doi.org/10.3390/biophysica5030028 - 17 Jul 2025
Viewed by 183
Abstract
We present a corrosion-resistant quadrupole ion trap mass spectrometer (QIT-MS) designed for trace detection of volatiles in sulfuric acid aerosols, with a specific focus on phosphine (PH3). Here, we detail the gas calibration methodology using permeation tube technology for generating certified [...] Read more.
We present a corrosion-resistant quadrupole ion trap mass spectrometer (QIT-MS) designed for trace detection of volatiles in sulfuric acid aerosols, with a specific focus on phosphine (PH3). Here, we detail the gas calibration methodology using permeation tube technology for generating certified ppb-level PH3/H2S/CO2 mixtures, and report results from mass spectra with sufficient resolution to distinguish isotopic envelopes that validate the detection of PH3 at a concentration of 62 ppb. Fragmentation patterns for PH3 and H2S agree with NIST data, and signal-to-noise performance confirms ppb sensitivity over 2.6 h acquisition periods. We further assess spectral interferences from oxygen isotopes and propose a detection scheme based on isolated phosphorus ions (P+) to enable specific and interference-resistant identification of PH3 and other reduced phosphorus species of astrobiological interest in Venus-like environments. This work extends the capabilities of QIT-MS for trace gas analysis in chemically aggressive atmospheric conditions. Full article
(This article belongs to the Special Issue Mass Spectrometry Applications in Biology Research)
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16 pages, 3376 KiB  
Article
Evidence of the Differences Between Human and Bovine Serum Albumin Through the Interaction with Coumarin-343: Experimental (ICD) and Theoretical Studies (DFT and Molecular Docking)
by Carmen Regina de Souza, Maurício Ikeda Yoguim, Nathalia Mariana Pavan, Nelson Henrique Morgon, Valdecir Farias Ximenes and Aguinaldo Robinson de Souza
Biophysica 2025, 5(3), 27; https://doi.org/10.3390/biophysica5030027 - 15 Jul 2025
Viewed by 214
Abstract
Coumarins are known for interacting with proteins and exhibiting diverse biological activities. This study investigates the interaction between coumarin-343 (C343) and human (HSA) and bovine (BSA) serum albumins. Fluorescence spectroscopy and theoretical simulations, including density functional theory (DFT) and molecular docking, were used [...] Read more.
Coumarins are known for interacting with proteins and exhibiting diverse biological activities. This study investigates the interaction between coumarin-343 (C343) and human (HSA) and bovine (BSA) serum albumins. Fluorescence spectroscopy and theoretical simulations, including density functional theory (DFT) and molecular docking, were used to analyze the ligand–protein complex formation. The fluorescence quenching data revealed that C343 binds to both proteins, with binding constants of 2.1 × 105 mol·L−1 (HSA) and 6.5 × 105 mol·L−1 (BSA), following a 1:1 stoichiometry. Binding site markers identified drug site I (DS1), located in subdomain IIA, as the preferential binding region for both proteins. Computational results supported these findings, showing high affinity for DS1, with binding energies of −69.02 kcal·mol−1 (HSA) and −67.22 kcal·mol−1 (BSA). While complex formation was confirmed for both proteins, differences emerged in the induced circular dichroism (ICD) signals. HSA displayed a distinct ICD profile compared to BSA in both intensity and absorption maximum. Molecular Docking revealed that the C343 conformation differed between HSA and BSA, explaining the variation in ICD signals. These results highlight the importance of protein structure in modulating ligand interactions and spectral responses. Full article
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10 pages, 693 KiB  
Article
An Engineered Cargo-Transport Molecular Motor Composed of a Kinesin Monomer and a Diffusing Microtubule-Associated Protein
by Ping Xie
Biophysica 2025, 5(3), 26; https://doi.org/10.3390/biophysica5030026 - 2 Jul 2025
Viewed by 254
Abstract
An engineered molecular motor composed of an ATP-dependent kinesin-1 monomer and an ATP-independent diffusing microtubule-associated protein is proposed, and its dynamics are studied theoretically. It is shown that the engineered motor can move directionally on microtubules towards the plus end, bearing great potential [...] Read more.
An engineered molecular motor composed of an ATP-dependent kinesin-1 monomer and an ATP-independent diffusing microtubule-associated protein is proposed, and its dynamics are studied theoretically. It is shown that the engineered motor can move directionally on microtubules towards the plus end, bearing great potential for applications in therapeutics or nanorobotics. The engineered motor can have an unloaded velocity similar to the wild-type kinesin-1 dimer, can take a mechanical (either forward or backward) step by hydrolyzing an ATP molecule under any load, and can generate the maximum force that is about half of that generated by the wild-type kinesin-1 dimer. Full article
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20 pages, 3040 KiB  
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 299
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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16 pages, 2830 KiB  
Article
Detecting Early Changes in Cartilage Collagen and Proteoglycans Distribution Gradients in Mice Harboring the R992C Collagen II Mutant Using 2D Correlation Infrared Spectroscopy
by Jolanta Fertala, Andrzej Steplewski and Andrzej Fertala
Biophysica 2025, 5(3), 24; https://doi.org/10.3390/biophysica5030024 - 22 Jun 2025
Viewed by 261
Abstract
Collagen II is a vital structural component in developing bones and mature cartilage. Mutations in this protein cause spondyloepiphyseal dysplasia, a disease characterized primarily by altered skeletal growth and manifesting with a range of phenotypes, from lethal to mild. This study examined transgenic [...] Read more.
Collagen II is a vital structural component in developing bones and mature cartilage. Mutations in this protein cause spondyloepiphyseal dysplasia, a disease characterized primarily by altered skeletal growth and manifesting with a range of phenotypes, from lethal to mild. This study examined transgenic mice harboring the R992C (p.R1124C) substitution in collagen II. Previous research demonstrated significant growth abnormalities and disorganized growth plate structure in these mice, and histological signs of osteoarthritic changes in the knee joints of 9-month-old mice with the R992C mutation. Our study focuses on detecting early structural changes in the articular cartilage that occur before histological signs become apparent. Through microscopic and spectroscopic analyses, we observed significant alterations in the distribution gradients of collagenous proteins and proteoglycans in the cartilage of R992C mutant mice. We propose that these early changes, eventually leading to articular cartilage degeneration in older mice, underscore the progressive nature of osteoarthritic changes linked to collagen II mutations. By identifying these early structural aberrations, our findings emphasize the importance of early detection of osteoarthritic changes, potentially facilitating timely, non-surgical interventions. Full article
(This article belongs to the Collection Feature Papers in Biophysics)
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