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Biophysica, Volume 3, Issue 1 (March 2023) – 14 articles

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17 pages, 10180 KiB  
Article
Comparison of Empirical Zn2+ Models in Protein–DNA Complexes
by Senta Volkenandt and Petra Imhof
Biophysica 2023, 3(1), 214-230; https://doi.org/10.3390/biophysica3010014 - 20 Mar 2023
Viewed by 1861
Abstract
Zinc ions are the second most abundant ions found in humans. Their role in proteins can be merely structural but also catalytic, owing to their transition metal character. Modelling their geometric–coordination versatility by empirical force fields is, thus, a challenging task. In this [...] Read more.
Zinc ions are the second most abundant ions found in humans. Their role in proteins can be merely structural but also catalytic, owing to their transition metal character. Modelling their geometric–coordination versatility by empirical force fields is, thus, a challenging task. In this work, we evaluated three popular models, specifically designed to represent zinc ions with regard to their capability of preserving structural integrity. To this end, we performed molecular dynamics simulations of two zinc-containing protein–DNA complexes, which differed in their zinc coordination, i.e., four cysteines or two cysteines and two histidines. The most flexible non-bonded 12-6-4 Lennard–Jones-type model shows a preference for six-fold coordination of the Zn2+-ions in contradiction to the crystal structure. The cationic dummy atom model favours tetrahedral geometry, whereas the bonded extended zinc AMBER force field model, by construction, best preserves the initial geometry of a regular or slightly distorted tetrahedron. Our data renders the extended zinc AMBER force field the best model for structural zinc ions in a given geometry. In more complicated cases, though, more flexible models may be advantageous. Full article
(This article belongs to the Collection Feature Papers in Biophysics)
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11 pages, 3709 KiB  
Article
Structural Analysis of Interactions between Epidermal Growth Factor Receptor (EGFR) Mutants and Their Inhibitors
by Yingzhe Guo, Zeqian Du and Ting Shi
Biophysica 2023, 3(1), 203-213; https://doi.org/10.3390/biophysica3010013 - 14 Mar 2023
Cited by 3 | Viewed by 1943
Abstract
People’s lives and health are gravely threatened by non-small-cell lung cancer (NSCLC). Mutations in epidermal growth factor receptor (EGFR), a transmembrane receptor tyrosine kinase, are considered one of the causes of NSCLC. Tyrosine kinase inhibitors (TKIs) are typically used to treat patients with [...] Read more.
People’s lives and health are gravely threatened by non-small-cell lung cancer (NSCLC). Mutations in epidermal growth factor receptor (EGFR), a transmembrane receptor tyrosine kinase, are considered one of the causes of NSCLC. Tyrosine kinase inhibitors (TKIs) are typically used to treat patients with EGFR mutations. In this study, Gefitinib, a member of the first generation of TKIs, was used to treat an EGFR single-point mutation (single mutant, SM). Patients harboring additional T790M mutations in the kinase domain of the EGFR were resistant to Gefitinib. Then, the L858R/T790M double mutation (double mutant, DM) was treated with the second generation of TKIs, such as Afatinib. Here, we constructed four computational models to uncover the structural basis between EGFR mutants (SM and DM) and corresponding inhibitors (Gefitinib and Afatinib). The binding energy in the G-SM (representing Gefitinib in complex with SM) system was larger than that in the G-DM (Representing Gefitinib in complex with DM) system. Gefitinib’s affinity with L792 and M793 was drastically reduced by the longer side chain of M790 in the G-DM system, which pushed Gefitinib outside of the pocket. Additionally, the A-DM system’s binding energy was higher than the G-DM system’s. Afatinib, unlike Gefitinib, induced the P-loop region to move downwards to decrease the pocket entrance size to accommodate Afatinib properly and stably in the A-DM (Afatinib in complex with DM) system. These results uncover the details of interactions between EGFR and its inhibitors and shed light on the design of new tyrosine kinase inhibitors. Full article
(This article belongs to the Special Issue Molecular Structure and Simulation in Biological System)
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22 pages, 8519 KiB  
Article
Neuronal Cultures: Exploring Biophysics, Complex Systems, and Medicine in a Dish
by Jordi Soriano
Biophysica 2023, 3(1), 181-202; https://doi.org/10.3390/biophysica3010012 - 10 Mar 2023
Cited by 6 | Viewed by 2726
Abstract
Neuronal cultures are one of the most important experimental models in modern interdisciplinary neuroscience, allowing to investigate in a control environment the emergence of complex behavior from an ensemble of interconnected neurons. Here, I review the research that we have conducted at the [...] Read more.
Neuronal cultures are one of the most important experimental models in modern interdisciplinary neuroscience, allowing to investigate in a control environment the emergence of complex behavior from an ensemble of interconnected neurons. Here, I review the research that we have conducted at the neurophysics laboratory at the University of Barcelona over the last 15 years, describing first the neuronal cultures that we prepare and the associated tools to acquire and analyze data, to next delve into the different research projects in which we actively participated to progress in the understanding of open questions, extend neuroscience research on new paradigms, and advance the treatment of neurological disorders. I finish the review by discussing the drawbacks and limitations of neuronal cultures, particularly in the context of brain-like models and biomedicine. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain)
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23 pages, 4140 KiB  
Review
A Brief Review of FT-IR Spectroscopy Studies of Sphingolipids in Human Cells
by Bahar Faramarzi, Martina Moggio, Nadia Diano, Marianna Portaccio and Maria Lepore
Biophysica 2023, 3(1), 158-180; https://doi.org/10.3390/biophysica3010011 - 2 Mar 2023
Cited by 4 | Viewed by 4586
Abstract
In recent years, sphingolipids have attracted significant attention due to their pivotal role in cellular functions and physiological diseases. A valuable tool for investigating the characteristics of sphingolipids can be represented via FT-IR spectroscopy, generally recognized as a very powerful technique that provides [...] Read more.
In recent years, sphingolipids have attracted significant attention due to their pivotal role in cellular functions and physiological diseases. A valuable tool for investigating the characteristics of sphingolipids can be represented via FT-IR spectroscopy, generally recognized as a very powerful technique that provides detailed biochemical information on the examined sample with the unique properties of sensitivity and accuracy. In the present paper, some fundamental aspects of sphingolipid components of human cells are summarized, and the most relevant articles devoted to the FT-IR spectroscopic studies of sphingolipids are revised. A short description of different FT-IR experimental approaches adopted for investigating sphingolipids is also given, with details about the most commonly used data analysis procedures. The present overview of FT-IR investigations, although not exhaustive, attests to the relevant role this vibrational technique has played in giving significant insight into many aspects of this fascinating class of lipids. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Italy)
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19 pages, 5071 KiB  
Article
Insights into the Substrate Uptake Mechanism of Mycobacterium Tuberculosis Ribose 5-Phosphate Isomerase and Perspectives on Drug Development
by Leonardo Bartkevihi, Ícaro P. Caruso, Bruna Martins, José R. M. Pires, Danielle M. P. Oliveira, Cristiane Dinis Anobom and Fabio C. L. Almeida
Biophysica 2023, 3(1), 139-157; https://doi.org/10.3390/biophysica3010010 - 1 Mar 2023
Viewed by 1445
Abstract
The active site of the dimeric ribose 5-phosphate isomerase B (RpiB) contains a solvent-exposed barrier formed by residues H12, R113, R137, and R141, which is closed upon the complexation of phosphate. The substrate ribose 5-phosphate (R5P) has to overcome the surface barrier to [...] Read more.
The active site of the dimeric ribose 5-phosphate isomerase B (RpiB) contains a solvent-exposed barrier formed by residues H12, R113, R137, and R141, which is closed upon the complexation of phosphate. The substrate ribose 5-phosphate (R5P) has to overcome the surface barrier to reach an internal cavity and then bind in the linear configuration of ribose to the interface between the two subunits. NMR and molecular dynamics simulation are suitable methods to describe the transient nature of the RpiB active site and help our understanding of the mechanism of substrate entrance. In this study, we show that the entrance of the nucleotides AMP/ADP into the internal cavity of mycobacterium tuberculosis RpiB (MtRpiB) does not involve a canonical open/close-lid conformational transition usually observed in many enzymes. Instead, a flipping mechanism in which the nucleotide phosphate interacts with the surface barrier followed by the flip of the nitrogenous base and ribose is responsible for changing the substrate/ligand orientation from a solvent-exposed to a buried state. Based on these results, we propose a substrate/inhibitor uptake mechanism that could provide a basis for rational drug design using MtRpiB, which is an essential enzyme and a good target for drug development. Full article
(This article belongs to the Special Issue Molecular Structure and Simulation in Biological System)
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18 pages, 5761 KiB  
Article
Investigation of the Impact of Lipid Acyl Chain Saturation on Fusion Peptide Interactions with Lipid Bilayers
by William T. Heller and Piotr A. Zolnierczuk
Biophysica 2023, 3(1), 121-138; https://doi.org/10.3390/biophysica3010009 - 28 Feb 2023
Cited by 2 | Viewed by 2160
Abstract
The interaction of many peptides with lipid bilayer membranes strongly depends on the lipid composition. Here, a study of the impact of unsaturated lipid acyl chains on the interaction of a derivative of the HIV-1 fusion peptide with lipid bilayer vesicles is presented. [...] Read more.
The interaction of many peptides with lipid bilayer membranes strongly depends on the lipid composition. Here, a study of the impact of unsaturated lipid acyl chains on the interaction of a derivative of the HIV-1 fusion peptide with lipid bilayer vesicles is presented. Lipid bilayer vesicles composed of mixtures of lipids with two saturated acyl chains and lipids and one saturated and one unsaturated acyl chain, but identical head groups, were studied. The dependence of the peptide conformation on the unsaturated lipid content was probed by circular dichroism spectroscopy, while the impact of the peptide on the bilayer structure was determined by small-angle neutron scattering. The impact of the peptide on the lipid bilayer vesicle dynamics was investigated using neutron spin echo spectroscopy. Molecular dynamics simulations were used to characterize the behavior of the systems studied to determine if there were clear differences in their physical properties. The results reveal that the peptide–bilayer interaction is not a simple function of the unsaturated lipid acyl chain content of the bilayer. Instead, the peptide behavior is more consistent with that seen for the bilayer containing only unsaturated lipids, which is supported by lipid-specific interactions revealed by the simulations. Full article
(This article belongs to the Special Issue Molecular Structure and Simulation in Biological System)
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12 pages, 3383 KiB  
Article
The Effectiveness of Suffruticosol B in Treating Lung Cancer by the Laser Trapping Technique
by Mulugeta S. Goangul, Rance M. Solomon, Daniel L. Devito, Charles A. Brown, James Coopper, Daniel B. Erenso, Ying Gao, Aline Pellizzaro, Jennifer M. Revalee and Horace T. Crogman
Biophysica 2023, 3(1), 109-120; https://doi.org/10.3390/biophysica3010008 - 13 Feb 2023
Cited by 1 | Viewed by 1594
Abstract
We used laser trapping to study the effects of suffruticosol B on lung cancer cells. Physical and mechanical changes were found to be statistically significant, with a 63.97% increase over untreated cells and a 79.57% increase over untreated cells after treatment for 3 [...] Read more.
We used laser trapping to study the effects of suffruticosol B on lung cancer cells. Physical and mechanical changes were found to be statistically significant, with a 63.97% increase over untreated cells and a 79.57% increase over untreated cells after treatment for 3 or 6 h, respectively. The treatment affected the internal structure of the cells, with changes in their elastic properties. The cellular responses showed that treatment with suffruticosol B resulted in the decreased proliferation and invasion of cancer cells. These results suggest that the treatment may be useful in preventing or treating lung cancer. Full article
(This article belongs to the Special Issue Biological Effects of Ionizing Radiation)
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16 pages, 1855 KiB  
Review
Contribution of smFRET to Chromatin Research
by Bhaswati Sengupta and Mai Huynh
Biophysica 2023, 3(1), 93-108; https://doi.org/10.3390/biophysica3010007 - 8 Feb 2023
Viewed by 1901
Abstract
Chromatins are structural components of chromosomes and consist of DNA and histone proteins. The structure, dynamics, and function of chromatins are important in regulating genetic processes. Several different experimental and theoretical tools have been employed to understand chromatins better. In this review, we [...] Read more.
Chromatins are structural components of chromosomes and consist of DNA and histone proteins. The structure, dynamics, and function of chromatins are important in regulating genetic processes. Several different experimental and theoretical tools have been employed to understand chromatins better. In this review, we will focus on the literatures engrossed in understanding of chromatins using single-molecule Förster resonance energy transfer (smFRET). smFRET is a single-molecule fluorescence microscopic technique that can furnish information regarding the distance between two points in space. This has been utilized to efficiently unveil the structural details of chromatins. Full article
(This article belongs to the Collection Feature Papers in Biophysics)
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22 pages, 10971 KiB  
Article
Structural Insights into Plasticity and Discovery of Flavonoid Allosteric Inhibitors of Flavivirus NS2B–NS3 Protease
by Marielena Vogel Saivish, Gabriela de Lima Menezes, Vivaldo Gomes da Costa, Liliane Nebo, Gislaine Celestino Dutra da Silva, Carolina Colombelli Pacca, Rafael Elias Marques, Maurício Lacerda Nogueira and Roosevelt Alves Da Silva
Biophysica 2023, 3(1), 71-92; https://doi.org/10.3390/biophysica3010006 - 1 Feb 2023
Cited by 1 | Viewed by 2348
Abstract
Flaviviruses are among the most critical pathogens in tropical regions; they cause various severe diseases in developing countries but are not restricted to these countries. The development of antiviral therapeutics is crucial for managing flavivirus outbreaks. Ten proteins are encoded in the flavivirus [...] Read more.
Flaviviruses are among the most critical pathogens in tropical regions; they cause various severe diseases in developing countries but are not restricted to these countries. The development of antiviral therapeutics is crucial for managing flavivirus outbreaks. Ten proteins are encoded in the flavivirus RNA. The N2B–NS3pro protein complex plays a fundamental role in flavivirus replication and is a promising drug target; however, no flavivirus protease inhibitors have progressed to the preclinical stage. This study analyzed the structural models and plasticity of the NS2B–NS3pro protein complex of five medically important non-dengue flaviviruses (West Nile, Rocio, Ilhéus, yellow fever, and Saint Louis encephalitis). The flavonoids amentoflavone, tetrahydrorobustaflavone, and quercetin were selected for their exceptional binding energies as potential inhibitors of the NS2B–NS3pro protein complex. AutoDock Vina results ranged from −7.0 kcal/mol to −11.5 kcal/mol and the compounds preferentially acted non-competitively. Additionally, the first structural model for the NS2B–NS3pro protein complex was proposed for Ilhéus and Rocio viruses. The NS2B–NS3pro protease is an attractive molecular target for drug development. The three identified natural flavonoids showed great inhibitory potential against the viral species. Nevertheless, further in silico and in vitro studies are required to obtain more information regarding NS2B–NS3pro inhibition by these flavonoids and their therapeutic potential. Full article
(This article belongs to the Special Issue Molecular Structure and Simulation in Biological System)
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2 pages, 148 KiB  
Editorial
Acknowledgment to the Reviewers of Biophysica in 2022
by Biophysica Editorial Office
Biophysica 2023, 3(1), 69-70; https://doi.org/10.3390/biophysica3010005 - 28 Jan 2023
Viewed by 917
Abstract
High-quality academic publishing is built on rigorous peer review [...] Full article
23 pages, 3505 KiB  
Article
Effect of the Neck Linker on Processive Stepping of Kinesin Motor
by Ping Xie
Biophysica 2023, 3(1), 46-68; https://doi.org/10.3390/biophysica3010004 - 28 Jan 2023
Cited by 3 | Viewed by 2277
Abstract
Kinesin motor protein, which is composed of two catalytic domains connected together by a long coiled-coil stalk via two flexible neck linkers (NLs), can step processively on a microtubule towards the plus end by hydrolyzing adenosine triphosphate (ATP) molecules. To understand what the [...] Read more.
Kinesin motor protein, which is composed of two catalytic domains connected together by a long coiled-coil stalk via two flexible neck linkers (NLs), can step processively on a microtubule towards the plus end by hydrolyzing adenosine triphosphate (ATP) molecules. To understand what the role is that the NL plays in the processive stepping, the dynamics of the kinesin motor are studied theoretically here by considering the mutation or deletion of an N-terminal cover strand that contributes to the docking of the NL in kinesin-1, the extension of the NL in kinesin-1, the mutation of the NL in kinesin-1, the swapping of the NL of kinesin-2 with that of kinesin-1, the joining of the stalk and neck of Ncd that moves towards the minus end of MT to the catalytic domain of kinesin-1, the replacement of catalytic domain of kinesin-1 with that of Ncd, and so on. The theoretical results give a consistent and quantitative explanation of various available experimental results about the effects of these mutations on motor dynamics and, moreover, provide predicted results. Additionally, the processive motility of kinesin-6 MKLP2 without NL docking is also explained. The available experimental data about the effect of NL mutations on the dynamics of the bi-directional kinesin-5 Cin8 are also explained. The studies are critically implicative to the mechanism of the stepping of the kinesin motor. Full article
(This article belongs to the Collection Feature Papers in Biophysics)
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11 pages, 1843 KiB  
Article
Emergence of Gloomy Eyelet inside DNA
by Jean-Marc Sabatier and Farzan Amini
Biophysica 2023, 3(1), 35-45; https://doi.org/10.3390/biophysica3010003 - 20 Jan 2023
Viewed by 6109
Abstract
The purpose of this article is to study gloomy eyelet (GE) inside the cell nucleus by using models of warp drive hydro (WDH), swinging spring, Rankine, co-moving reference frame, and Poincare. The beat wave frequency (ω) of blood pressure on the vessel and [...] Read more.
The purpose of this article is to study gloomy eyelet (GE) inside the cell nucleus by using models of warp drive hydro (WDH), swinging spring, Rankine, co-moving reference frame, and Poincare. The beat wave frequency (ω) of blood pressure on the vessel and the swinging spring frequency (Ω) of DNA coincide together on the Rankine model. In this case, it leads to appearing as a sudden pressure drop and an accelerated cavity in the medium of the warp drive hydro (WDH) model. In transient conditions, the vortex flow inside WDH can generate gloomy eyelet (GE), and the tiny distortion of nano space–time revealed inside the gloomy eyelet (GE) inside DNA and the tiny distortion of nano space–time revealed inside the co-moving reference frame (CMRF) model of the gloomy eyelet (GE). The space–time distortion can act as a hidden potential for the cell nucleus and some behaviors of gloomy eyelet can be traced by the frequency responses of human body organs. The interactions between two adjacent different mediums such as the normal cells and abnormal cells, earth’s gravitational effects can lead to changes in the distortion of space–time inside the cell nucleus. Transient bonds between particles can be expected to appear in the gloomy eyelet inside DNA. Identifying the range of changes in the frequency responses and the transient bonds inside the cell nucleus can be introduced as one of the health indicators. Full article
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14 pages, 2020 KiB  
Review
Biological Calorimetry: Old Friend, New Insights
by Olga Abian, Sonia Vega and Adrian Velazquez-Campoy
Biophysica 2023, 3(1), 21-34; https://doi.org/10.3390/biophysica3010002 - 20 Jan 2023
Cited by 2 | Viewed by 2078
Abstract
Calorimetry is an old experimental technique (first instrument developed in S. XVIII), but it is broadly used and still provides key information for understanding biological processes at the molecular level, particularly, cooperative phenomena in protein interactions. Here, we review and highlight some key [...] Read more.
Calorimetry is an old experimental technique (first instrument developed in S. XVIII), but it is broadly used and still provides key information for understanding biological processes at the molecular level, particularly, cooperative phenomena in protein interactions. Here, we review and highlight some key aspects of biological calorimetry. Several biological systems will be described in which calorimetry was instrumental for modeling the behavior of the protein and obtaining further biological insight. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain)
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20 pages, 3772 KiB  
Review
A Review of Fifteen Years Developing Computational Tools to Study Protein Aggregation
by Carlos Pintado-Grima, Oriol Bárcenas, Andrea Bartolomé-Nafría, Marc Fornt-Suñé, Valentín Iglesias, Javier Garcia-Pardo and Salvador Ventura
Biophysica 2023, 3(1), 1-20; https://doi.org/10.3390/biophysica3010001 - 18 Jan 2023
Cited by 4 | Viewed by 3309
Abstract
The presence of insoluble protein deposits in tissues and organs is a hallmark of many human pathologies. In addition, the formation of protein aggregates is considered one of the main bottlenecks to producing protein-based therapeutics. Thus, there is a high interest in rationalizing [...] Read more.
The presence of insoluble protein deposits in tissues and organs is a hallmark of many human pathologies. In addition, the formation of protein aggregates is considered one of the main bottlenecks to producing protein-based therapeutics. Thus, there is a high interest in rationalizing and predicting protein aggregation. For almost two decades, our laboratory has been working to provide solutions for these needs. We have traditionally combined the core tenets of both bioinformatics and wet lab biophysics to develop algorithms and databases to study protein aggregation and its functional implications. Here, we review the computational toolbox developed by our lab, including programs for identifying sequential or structural aggregation-prone regions at the individual protein and proteome levels, engineering protein solubility, finding and evaluating prion-like domains, studying disorder-to-order protein transitions, or categorizing non-conventional amyloid regions of polar nature, among others. In perspective, the succession of the tools we describe illustrates how our understanding of the protein aggregation phenomenon has evolved over the last fifteen years. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain)
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