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Biophysica, Volume 3, Issue 2 (June 2023) – 12 articles

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24 pages, 4160 KiB  
Article
A Two-Species Finite Volume Scalar Model for Modeling the Diffusion of Poly(lactic-co-glycolic acid) into a Coronary Arterial Wall from a Single Half-Embedded Drug Eluting Stent Strut
by Rodward L. Hewlin, Jr., Maegan Edwards and John P. Kizito
Biophysica 2023, 3(2), 385-408; https://doi.org/10.3390/biophysica3020026 - 15 Jun 2023
Viewed by 1233
Abstract
This paper outlines the methodology and results for a two-species finite volume scalar computational drug transport model developed for simulating the mass transport of Poly(lactic-co-glycolic acid (PLGA)) from a half-embedded single strut implanted in a coronary arterial vessel wall. The mathematical drug transport [...] Read more.
This paper outlines the methodology and results for a two-species finite volume scalar computational drug transport model developed for simulating the mass transport of Poly(lactic-co-glycolic acid (PLGA)) from a half-embedded single strut implanted in a coronary arterial vessel wall. The mathematical drug transport model incorporates the convection-diffusion equation in scalar form (dimensionless) with a two-species (free-drug and bound-drug) mass transport setup, including reversible equilibrium reaction source terms for the free and bound-drug states to account for the pharmaco-kinetic reactions in the arterial wall. The relative reaction rates of the added source terms control the interconversion of the drug between the free and bound-drug states. The model is solved by a 2D finite-volume method for discretizing and solving the free and bound drug transport equations with anisotropic vascular drug diffusivities. This model is an improvement over previously developed models using the finite-difference and finite element method. A dimensionless characteristic scaling pre-analysis was conducted a priori to evaluate the significance of implementing the reaction source terms in the transport equations. This paper reports the findings of an investigation of the interstitial flow profile into the arterial wall and the free and bound drug diffusion profiles with a parametric study of varying the polymer drug concentration (low and high), tortuosity, porosity, and Peclet and DamKöhler numbers over the course of 400 h (16.67 days). The results also reveal how a single species drug delivery model that neglects both a reversible binding reaction source term and the porosity and tortuosity of the arterial wall cannot accurately predict the distribution of both the free and bound drug. Full article
(This article belongs to the Special Issue Molecular Structure and Simulation in Biological System)
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12 pages, 4679 KiB  
Article
Computational Modeling of the Neurofibromin-Stimulated Guanosine Triphosphate Hydrolysis by the KRas Protein
by Igor Polyakov and Alexander Nemukhin
Biophysica 2023, 3(2), 373-384; https://doi.org/10.3390/biophysica3020025 - 31 May 2023
Cited by 2 | Viewed by 1264
Abstract
We report the results of computational studies of the guanosine triphosphate (GTP) hydrolysis in the active site of the KRas-NF1 protein complex, where KRas stands for the K-isoform of the Ras (ras sarcoma) protein and NF1 (neurofbromin-1) is the activating protein. The model [...] Read more.
We report the results of computational studies of the guanosine triphosphate (GTP) hydrolysis in the active site of the KRas-NF1 protein complex, where KRas stands for the K-isoform of the Ras (ras sarcoma) protein and NF1 (neurofbromin-1) is the activating protein. The model system was constructed using coordinates of heavy atoms from the crystal structure PDB ID 6OB2 with the GTP analog GMPPNP. Large-scale classical molecular dynamics (MD) calculations were performed to analyze conformations of the enzyme-substrate complexes. The Gibbs energy profiles for the hydrolysis reaction were computed using MD simulations with quantum mechanics/molecular mechanics (QM/MM) interaction potentials. The density functional theory DFT(ωB97X-D3/6-31G**) approach was applied in QM and the CHARMM36 force field parameters in MM. The most likely scenario of the chemical step of the GTP hydrolysis in KRas-NF1 corresponds to the water-assisted mechanism of the formation of the inorganic phosphate coupled with the dissociation of GTP to GDP. Full article
(This article belongs to the Special Issue Molecular Structure and Simulation in Biological System)
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11 pages, 1861 KiB  
Article
Decomposition of Small Molecules for Fragment-Based Drug Design
by Nikita N. Ivanov, Dmitry A. Shulga and Vladimir A. Palyulin
Biophysica 2023, 3(2), 362-372; https://doi.org/10.3390/biophysica3020024 - 24 May 2023
Viewed by 2300
Abstract
In the drug design process, a frequent task is the decomposition of small molecules into fragments. There exist a number of approaches and methods to break molecules into fragments. However, a method that allows the decomposition of molecules into non-overlapping fragments that is [...] Read more.
In the drug design process, a frequent task is the decomposition of small molecules into fragments. There exist a number of approaches and methods to break molecules into fragments. However, a method that allows the decomposition of molecules into non-overlapping fragments that is meaningful in terms of medicinal chemistry is absent, and in this work, we present a new simple approach for the decomposition of molecules—MedChemFrag. It aims to break drug-like molecules into a set of rings and linkers, which are close to the perception of “fragments” by medicinal chemists. In contrast to most previous efforts aimed at breaking molecules using retrosynthetic feasible rules, our approach strives to preserve the functional groups, which may reveal the specific interaction pattern, e.g., the amide groups. Full article
(This article belongs to the Special Issue Molecular Structure and Simulation in Biological System)
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14 pages, 2990 KiB  
Article
Phenotypic and Biomechanical Characteristics of Human Fetal Neural Progenitor Cells Exposed to Pesticide Compounds
by Marissa C. Sarsfield, Jennifer Vasu, Sabreen M. Abuoun, Nischal Allena and Chandrasekhar R. Kothapalli
Biophysica 2023, 3(2), 348-361; https://doi.org/10.3390/biophysica3020023 - 18 May 2023
Viewed by 1154
Abstract
Various forms of pesticides have been reported to be among the environmental toxicants, which are detrimental to human health. The active ingredients of these formulations can enter the human body through air, food, or water. Epidemiological studies suggest that these compounds strongly affect [...] Read more.
Various forms of pesticides have been reported to be among the environmental toxicants, which are detrimental to human health. The active ingredients of these formulations can enter the human body through air, food, or water. Epidemiological studies suggest that these compounds strongly affect the developing brain in fetal and infant stages due to their ability to breach the underdeveloped blood–brain barrier. Since neural progenitor stem cells (NPCs) in the developing brain are the most vulnerable to these compounds, the mechanisms by which NPCs experience toxicity upon exposure to these chemicals must be investigated. Here, we assessed the viability of human fetal NPCs in 2D cultures in the presence of the active ingredients of six widely used pesticides using Live/Dead® and Hoechst staining. The IC50 values ranged from 4.1–201 μM. A significant drop in cell viability with increasing toxicant concentration (p < 0.01) was noted, with the order of toxicity being malathion < 4-aminopyridine < methoprene < prallethrin < temephos < pyriproxyfen. Changes in cellular biomechanical characteristics (Young’s modulus, tether force, membrane tension, and tether radius) were quantified using atomic force microscopy, whereas cell migration was elucidated over 48 h using a customized wound-healing assay. The Young’s modulus of fetal NPCs exposed to IC50/2 doses of these compounds was reduced by 38–70% and that of those exposed to IC50 doses was reduced by 71–80% (p < 0.001 vs. controls for both; p < 0.01 for IC50 vs. IC50/2 for each compound). Similar patterns were noted for tether forces and membrane tension in fetal NPCs. NPC migration was found to be compound type- and dose-dependent. These results attest to the significant detrimental effects of these compounds on various aspects of the human fetal NPC phenotype, and the utility of cell mechanics as a marker to assess developmental neurotoxicity. Full article
(This article belongs to the Collection Feature Papers in Biophysics)
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13 pages, 8969 KiB  
Review
Developmental Pattern Formation: Spanish Contributions from a Biophysical Perspective
by Javier Buceta and Léna Guitou
Biophysica 2023, 3(2), 335-347; https://doi.org/10.3390/biophysica3020022 - 06 May 2023
Viewed by 1814
Abstract
During the last few decades, developmental pattern formation has evolved from being a descriptive discipline to a quantitative one. That process has been possible due to the implementation of multidisciplinary approaches where biophysicists and mathematicians have played a key role. In this review, [...] Read more.
During the last few decades, developmental pattern formation has evolved from being a descriptive discipline to a quantitative one. That process has been possible due to the implementation of multidisciplinary approaches where biophysicists and mathematicians have played a key role. In this review, we highlight relevant Spanish contributions and stress their biophysical approaches, as well as provide some historical context. Finally, this work also aimed at bridging the concepts from biology to physics/math (and back) and at shedding light on some directions for future research. Full article
(This article belongs to the Special Issue State-of-the-Art Biophysics in Spain 2.0)
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17 pages, 3197 KiB  
Article
Insights into Chemical Interactions and Related Toxicities of Deep Eutectic Solvents with Mammalian Cells Observed Using Synchrotron Macro–ATR–FTIR Microspectroscopy
by Saffron J. Bryant, Zo L. Shaw, Louisa Z. Y. Huang, Aaron Elbourne, Amanda N. Abraham, Jitraporn Vongsvivut, Stephen A. Holt, Tamar L. Greaves and Gary Bryant
Biophysica 2023, 3(2), 318-334; https://doi.org/10.3390/biophysica3020021 - 04 May 2023
Cited by 3 | Viewed by 1498
Abstract
Deep eutectic solvents (DESs) and ionic liquids (ILs) are highly tailorable solvents that have shown a lot of promise for a variety of applications including cryopreservation, drug delivery, and protein stabilisation. However, to date, there is very limited information on the detailed interactions [...] Read more.
Deep eutectic solvents (DESs) and ionic liquids (ILs) are highly tailorable solvents that have shown a lot of promise for a variety of applications including cryopreservation, drug delivery, and protein stabilisation. However, to date, there is very limited information on the detailed interactions of these solvents with mammalian cells. In this work, we studied six DESs and one IL that show promise as cryoprotective agents, applying synchrotron macro–ATR–FTIR to examine their effects on key biochemical components of HaCat mammalian cells. These data were paired with resazurin metabolic assays and neutron reflectivity experiments to correlate cellular interactions with cellular toxicity. Stark differences were observed even between solvents that shared similar components. In particular, it was found that solvents that are effective cryoprotective agents consistently showed interactions with cellular membranes, while high toxicity correlated with strong interactions of the DES/IL with nucleic acids and proteins. This work sheds new light on the interactions between novel solvents and cells that may underpin future biomedical applications. Full article
(This article belongs to the Collection Feature Papers in Biophysics)
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11 pages, 2213 KiB  
Article
Comparative Investigation of XPS Spectra of Oxidated Carbon Nanotubes and Graphene
by Viktor P. Afanas’ev, Grigorii S. Bocharov, Alexander V. Eletskii, Lidiya G. Lobanova, Konstantin I. Maslakov and Serguei V. Savilov
Biophysica 2023, 3(2), 307-317; https://doi.org/10.3390/biophysica3020020 - 13 Apr 2023
Cited by 2 | Viewed by 1598
Abstract
X-ray photoelectron emission spectra of thermally reduced graphene oxide samples and carbon nanotubes (CNTs) with various oxidation degrees are presented in this paper. A method for the reconstruction of differential electron inelastic scattering cross sections from the energy loss spectra of photoelectrons is [...] Read more.
X-ray photoelectron emission spectra of thermally reduced graphene oxide samples and carbon nanotubes (CNTs) with various oxidation degrees are presented in this paper. A method for the reconstruction of differential electron inelastic scattering cross sections from the energy loss spectra of photoelectrons is described and discussed. The analysis of the part of the characteristic photoelectron energy loss spectrum adjacent to the C1 peak indicated a considerable influence of the thermal reduction of graphene oxide on the electron properties of the samples obtained. On the contrary, the oxidation of CNTs by refluxing in a concentrated HNO3 solution does not change the free electron excitation spectrum. Full article
(This article belongs to the Special Issue Biomedical Optics)
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19 pages, 4108 KiB  
Article
Discovery of the Universal tRNA Binding Mode for the TsaD-like Components of the t6A tRNA Modification Pathway
by Boguslaw Stec
Biophysica 2023, 3(2), 288-306; https://doi.org/10.3390/biophysica3020019 - 12 Apr 2023
Viewed by 1188
Abstract
Covalent addition of the threonylcarbamoyl group to N(6) of adenosine 37 (t6A modification) within the anticodon loop of several tRNAs is central to the translational fidelity in all known organisms. Structures for each of the enzyme components in the Tsa (t [...] Read more.
Covalent addition of the threonylcarbamoyl group to N(6) of adenosine 37 (t6A modification) within the anticodon loop of several tRNAs is central to the translational fidelity in all known organisms. Structures for each of the enzyme components in the Tsa (t6A) pathway from all three kingdoms of life have been determined previously. In order to shed light on the poorly defined final step of t6A tRNA modification by TsaD-like components, we performed modeling studies. By docking a tRNA substrate molecule onto reanalyzed complete models of three TsaD-like proteins—TsaD from T. maritima, Qri7 from bacteria, and Kae1 from yeast—we identified a binding site that is common to all of them. An apparently universal binding mode has perfectly oriented tRNA for catalysis by TsaD. Furthermore, it suggests how the conformational changes in TsaD, in response to the binding of the additional regulatory subunits, control enzymatic activity. Re-refinement of the X-ray structure of the TsaBDE complex from T. maritima tentatively suggests that the moiety bound at the active site of the TsaD component is threonylcarbamoyl-AMP (TC-AMP). These findings suggest a detailed model for the mechanism of the catalytic reaction carried out by the TsaD-like components that explains the transfer of unstable TC-AMP from TsaC to TsaD proteins in the t6A modification pathway. Full article
(This article belongs to the Collection Feature Papers in Biophysics)
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12 pages, 6749 KiB  
Article
Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
by Giovanni Novi Inverardi, Francesco Carnovale, Lorenzo Petrolli, Simone Taioli and Gianluca Lattanzi
Biophysica 2023, 3(2), 276-287; https://doi.org/10.3390/biophysica3020018 - 11 Apr 2023
Cited by 1 | Viewed by 1439
Abstract
A novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that [...] Read more.
A novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like coating. In this work, we propose a molecular dynamics protocol, aimed at depicting and characterizing the earliest stages of the embedding process of small biomolecules in a solution of water and orthosilicic acid, here, taken as a precursor of the silica matrix. Overall, we observe a negligible influence of orthosilicic acid on the behavior of stable folded systems (such as ubiquitin). Conversely, intrinsically disordered and unstable peptides are affected by the coating, the latter seemingly inhibiting the fluctuations of flexible moieties. While further scrutiny is in order, our assessment offers a first mechanistic insight of the effects of orthosilicic acid, thereby validating its use in the proposed innovative application of APT to the structural resolution of protein molecules. Full article
(This article belongs to the Collection Feature Papers in Biophysics)
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13 pages, 9534 KiB  
Article
Coarse-Grained MD Simulations of Opioid Interactions with the μ-Opioid Receptor and the Surrounding Lipid Membrane
by Sourav Ray, Konstantin Fackeldey, Christoph Stein and Marcus Weber
Biophysica 2023, 3(2), 263-275; https://doi.org/10.3390/biophysica3020017 - 06 Apr 2023
Viewed by 1204
Abstract
In our previous studies, a new opioid (NFEPP) was developed to only selectively bind to the μ-opoid receptor (MOR) in inflamed tissue and thus avoid the severe side effects of fentanyl. We know that NFEPP has a reduced binding affinity to MOR [...] Read more.
In our previous studies, a new opioid (NFEPP) was developed to only selectively bind to the μ-opoid receptor (MOR) in inflamed tissue and thus avoid the severe side effects of fentanyl. We know that NFEPP has a reduced binding affinity to MOR in healthy tissue. Inspired by the modelling and simulations performed by Sutcliffe et al., we present our own results of coarse-grained molecular dynamics simulations of fentanyl and NFEPP with regards to their interaction with the μ-opioid receptor embedded within the lipid cell membrane. For technical reasons, we have slightly modified Sutcliffe’s parametrisation of opioids. The pH-dependent opioid simulations are of interest because while fentanyl is protonated at the physiological pH, NFEPP is deprotonated due to its lower pKa value than that of fentanyl. Here, we analyse for the first time whether pH changes have an effect on the dynamical behaviour of NFEPP when it is inside the cell membrane. Besides these changes, our analysis shows a possible alternative interaction of NFEPP at pH 7.4 outside the binding region of the MOR. The interaction potential of NFEPP with MOR is also depicted by analysing the provided statistical molecular dynamics simulations with the aid of an eigenvector analysis of a transition rate matrix. In our modelling, we see differences in the XY-diffusion profiles of NFEPP compared with fentanyl in the cell membrane. Full article
(This article belongs to the Special Issue Molecular Structure and Simulation in Biological System)
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11 pages, 3386 KiB  
Article
Computational Modeling of the Interaction of Molecular Oxygen with the miniSOG Protein—A Light Induced Source of Singlet Oxygen
by Igor Polyakov, Anna Kulakova and Alexander Nemukhin
Biophysica 2023, 3(2), 252-262; https://doi.org/10.3390/biophysica3020016 - 02 Apr 2023
Viewed by 1248
Abstract
Interaction of molecular oxygen 3O2 with the flavin-dependent protein miniSOG after light illumination results in creation of singlet oxygen 1O2 and superoxide O2●−. Despite the recently resolved crystal structures of miniSOG variants, oxygen-binding sites near the [...] Read more.
Interaction of molecular oxygen 3O2 with the flavin-dependent protein miniSOG after light illumination results in creation of singlet oxygen 1O2 and superoxide O2●−. Despite the recently resolved crystal structures of miniSOG variants, oxygen-binding sites near the flavin chromophore are poorly characterized. We report the results of computational studies of the protein−oxygen systems using molecular dynamics (MD) simulations with force-field interaction potentials and quantum mechanics/molecular mechanics (QM/MM) potentials for the original miniSOG and the mutated protein. We found several oxygen-binding pockets and pointed out possible tunnels bridging the bulk solvent and the isoalloxazine ring of the chromophore. These findings provide an essential step toward understanding photophysical properties of miniSOG—an important singlet oxygen photosensitizer. Full article
(This article belongs to the Collection Feature Papers in Biophysics)
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21 pages, 3101 KiB  
Article
Complex Physical Properties of an Adaptive, Self-Organizing Biological System
by József Prechl
Biophysica 2023, 3(2), 231-251; https://doi.org/10.3390/biophysica3020015 - 31 Mar 2023
Viewed by 1136
Abstract
Physical modeling of the functioning of the adaptive immune system, which has been thoroughly characterized on genetic and molecular levels, provides a unique opportunity to define an adaptive, self-organizing biological system in its entirety. This paper describes a configuration space model of immune [...] Read more.
Physical modeling of the functioning of the adaptive immune system, which has been thoroughly characterized on genetic and molecular levels, provides a unique opportunity to define an adaptive, self-organizing biological system in its entirety. This paper describes a configuration space model of immune function, where directed chemical potentials of the system constitute a space of interactions. A mathematical approach is used to define the system that couples the variance of Gaussian distributed interaction energies in its interaction space to the exponentially distributed chemical potentials of its effector molecules to maintain its steady state. The model is validated by identifying the thermodynamic and network variables analogous to the mathematical parameters and by applying the model to the humoral immune system. Overall, this statistical thermodynamics model of adaptive immunity describes how adaptive biological self-organization arises from the maintenance of a scale-free, directed molecular interaction network with fractal topology. Full article
(This article belongs to the Collection Feature Papers in Biophysics)
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