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Journal of Biological Physics

R M Sarimov, T A Matveyeva, V N Binhi
Using an original laser interferometer of enhanced sensitivity, an increase in the refractive index of a protein solution was observed during the reaction of proteolysis catalyzed by pepsin. The increase in the refractive index of the protein solution at a concentration of 4 mg/ml was [Formula: see text] for bovine serum albumin and [Formula: see text] for lysozyme. The observed effect disproves the existing idea that the refractive index of protein solutions is determined only by their amino acid composition and concentration...
May 11, 2018: Journal of Biological Physics
Lucia Balejcikova, Katarina Siposova, Peter Kopcansky, Ivo Safarik
The interaction of amyloid β-peptide (Aβ) with the iron-storage protein ferritin was studied in vitro. We have shown that Aβ during fibril formation process is able to reduce Fe(III) from the ferritin core (ferrihydrite) to Fe(II). The Aβ-mediated Fe(III) reduction yielded a two-times-higher concentration of free Fe(II) than the spontaneous formation of Fe(II) by the ferritin itself. We suggest that Aβ can also act as a ferritin-specific metallochaperone-like molecule capturing Fe(III) from the ferritin ferrihydrite core...
May 9, 2018: Journal of Biological Physics
Z V Gagkaeva, E S Zhukova, V Grinenko, A K Grebenko, K V Sidoruk, T A Voeikova, M Dressel, B P Gorshunov
Employing optical spectroscopy we have performed a comparative study of the dielectric response of extracellular matrix and filaments of electrogenic bacteria Shewanella oneidensis MR-1, cytochrome c, and bovine serum albumin. Combining infrared transmission measurements on thin layers with data of the terahertz spectra, we obtain the dielectric permittivity and AC conductivity spectra of the materials in a broad frequency band from a few cm-1 up to 7000 cm-1 in the temperature range from 5 to 300 K. Strong absorption bands are observed in the three materials that cover the range from 10 to 300 cm-1 and mainly determine the terahertz absorption...
May 7, 2018: Journal of Biological Physics
Roya Zandi, Cristian Micheletti, Rudolf Podgornik
No abstract text is available yet for this article.
April 18, 2018: Journal of Biological Physics
Klaus Jaffe
Computer experiments that mirror the evolutionary dynamics of sexual and asexual organisms as they occur in nature were used to test features proposed to explain the evolution of sexual recombination. Results show that this evolution is better described as a network of interactions between possible sexual forms, including diploidy, thelytoky, facultative sex, assortation, bisexuality, and division of labor between the sexes, rather than a simple transition from parthenogenesis to sexual recombination. Diploidy was shown to be fundamental for the evolution of sex; bisexual reproduction emerged only among anisogamic diploids with a synergistic division of reproductive labor; and facultative sex was more likely to evolve among haploids practicing assortative mating...
April 16, 2018: Journal of Biological Physics
Julien Bernaud, Axel Rossi, Anny Fis, Lara Gardette, Ludovic Aillot, Hildegard Büning, Martin Castelnovo, Anna Salvetti, Cendrine Faivre-Moskalenko
Virus families have evolved different strategies for genome uncoating, which are also followed by recombinant vectors. Vectors derived from adeno-associated viruses (AAV) are considered as leading delivery tools for in vivo gene transfer, and in particular gene therapy. Using a combination of atomic force microscopy (AFM), biochemical experiments, and physical modeling, we investigated here the physical properties and stability of AAV vector particles. We first compared the morphological properties of AAV vectors derived from two different serotypes (AAV8 and AAV9)...
April 14, 2018: Journal of Biological Physics
Pedro J de Pablo, Mercedes Hernando-Pérez, Carolina Carrasco, José L Carrascosa
We use the nano-dissection capabilities of atomic force microscopy to induce structural alterations on individual virus capsids in liquid milieu. We fracture the protein shells either with single nanoindentations or by increasing the tip-sample interaction force in amplitude modulation dynamic mode. The normal behavior is that these cracks persist in time. However, in very rare occasions they self-recuperate to retrieve apparently unaltered virus particles. In this work, we show the topographical evolution of three of these exceptional events occurring in T7 bacteriophage capsids...
April 13, 2018: Journal of Biological Physics
Shivangi Nangia, Jason G Pattis, Eric R May
Flock House virus (FHV) is a well-characterized model system to study infection mechanisms in non-enveloped viruses. A key stage of the infection cycle is the disruption of the endosomal membrane by a component of the FHV capsid, the membrane active γ peptide. In this study, we perform all-atom molecular dynamics simulations of the 21 N-terminal residues of the γ peptide interacting with membranes of differing compositions. We carry out umbrella sampling calculations to study the folding of the peptide to a helical state in homogenous and heterogeneous membranes consisting of neutral and anionic lipids...
April 11, 2018: Journal of Biological Physics
Ravi Kant, Vamseedhar Rayaprolu, Kaitlyn McDonald, Brian Bothner
The beauty, symmetry, and functionality of icosahedral virus capsids has attracted the attention of biologists, physicists, and mathematicians ever since they were first observed. Viruses and protein cages assemble into functional architectures in a range of sizes, shapes, and symmetries. To fulfill their biological roles, these structures must self-assemble, resist stress, and are often dynamic. The increasing use of icosahedral capsids and cages in materials science has driven the need to quantify them in terms of structural properties such as rigidity, stiffness, and viscoelasticity...
April 10, 2018: Journal of Biological Physics
Bart van der Holst, Willem K Kegel, Roya Zandi, Paul van der Schoot
The spontaneous encapsulation of genomic and non-genomic polyanions by coat proteins of simple icosahedral viruses is driven, in the first instance, by electrostatic interactions with polycationic RNA binding domains on these proteins. The efficiency with which the polyanions can be encapsulated in vitro, and presumably also in vivo, must in addition be governed by the loss of translational and mixing entropy associated with co-assembly, at least if this co-assembly constitutes a reversible process. These forms of entropy counteract the impact of attractive interactions between the constituents and hence they counteract complexation...
April 3, 2018: Journal of Biological Physics
Guo-Hua Li
The P2X receptor is a trimeric transmembrane protein that acts as an ATP-gated ion channel. Its transmembrane domain (TMD) contains only six helices and three of them, the M2 helices, line the ion conduction pathway. Here, using molecular dynamics simulation, I identify four conformational states of the TMD that are associated with four types of packing between M2 helices. Packing in the extracellular half of the M2 helix produces closed conformations, while packing in the intracellular half produces both open and closed conformations...
April 2, 2018: Journal of Biological Physics
D C Rapaport
Molecular dynamics simulation is used to model the self-assembly of polyhedral shells containing 180 trapezoidal particles that correspond to the T = 3 virus capsid. Three kinds of particle, differing only slightly in shape, are used to account for the effect of quasi-equivalence. Bond formation between particles is reversible and an explicit atomistic solvent is included. Under suitable conditions the simulations are able to produce complete shells, with the majority of unused particles remaining as monomers, and practically no other clusters...
April 2, 2018: Journal of Biological Physics
B Velmurugan, P Senthilkumaar, S Karthikeyan
The use of pesticides in agriculture can make their way into the earth and wash into the amphibian system causing ecological stress. This study aims to understand the changes occurring in gill tissues as a result of fenvalerate exposure using Fourier-transform infrared spectroscopy. The intensity ratio of the selected bands I1545 /I1657, I2924 /I2853 , and I1045 /I1545 measures changes in proteins, lipids, and carbohydrates. Curve-fitting analysis was performed in the selected band region to analyze the quantitative changes of proteins, lipids, and carbohydrates...
March 15, 2018: Journal of Biological Physics
Ágata Paim, Isabel C Tessaro, Nilo S M Cardozo, Patricia Pranke
Tissue engineering is a multidisciplinary field of research in which the cells, biomaterials, and processes can be optimized to develop a tissue substitute. Three-dimensional (3D) architectural features from electrospun scaffolds, such as porosity, tortuosity, fiber diameter, pore size, and interconnectivity have a great impact on cell behavior. Regarding tissue development in vitro, culture conditions such as pH, osmolality, temperature, nutrient, and metabolite concentrations dictate cell viability inside the constructs...
March 5, 2018: Journal of Biological Physics
Alexander Y Grosberg, Robijn Bruinsma
The Lifshitz equation for the confinement of a linear polymer in a spherical cavity of radius R has the form of the Schrödinger equation for a quantum particle trapped in a potential well with flat bottom and infinite walls at radius R. We show that the Lifshitz equation of a confined annealed branched polymer has the form of the Schrödinger equation for a quantum harmonic oscillator. The resulting confinement energy has a 1/R4 dependence on the confinement radius R, in contrast to the case of confined linear polymers, which have a 1/R2 dependence...
June 2018: Journal of Biological Physics
V V Boiko, V R Romanyuk, O P Gnatyuk, O O Ilchenko, S O Karakhim, A V Korovin, G I Dovbeshko
The impact of confinement of DNA molecules in a limited volume of the cavity of photonic crystals (PC) on the vibrational properties of the DNA molecule and its conformation is studied. According to our preliminary study, the aqueous shell is removed when the DNA molecules are infiltrated into the PC cavities. Raman scattering (RS) DNA marker lines showed a dramatic conformational change of DNA in the PC cavities and the appearance of new unknown conformational states. We observed the enhancement of vibrational modes of DNA in the PC in comparison with free DNA of about tenfold and the absence of vibrational modes in DNA bases in a region of 1450-1700 cm-1 ...
March 2018: Journal of Biological Physics
Fernando Maia de Oliveira, João Benhur Mokochinski, Yohandra Reyes Torres, Herta Stutz Dalla Santa, Pedro Pablo González-Borrero
This paper describes the application of the photoacoustic spectroscopic (PAS) for detection of bioactive compounds in Agaricus brasiliensis mycelium. The mycelium was cultivated by solid-state fermentation and by submerged fermentation. Vegetal residues from food industry were used as substrates for fermentation: apple pomace (Malus domestica), wheat (Triticum aestivum), peel and pomace of pineapple (Ananas comosus), malt (Hordeum vulgare) and grape pomace (Vitis vinifera). Dry and ground samples of biomass were directly put into the PA cell...
March 2018: Journal of Biological Physics
A J da Silva, S Floquet, D O C Santos
The authors apologize for the following errors published in the article. However, these errors do not modify the main assumptions in our work nor affects the discussion (interpretation) of the results.
March 2018: Journal of Biological Physics
Ying Wang, Xuguang Shi
In general, the geometric structure of DNA is characterized using an elastic rod model. The Landau model provides us a new theory to study the geometric structure of DNA. By using the decomposition of the arc unit in the helical axis of DNA, we find that the free-energy density of DNA is similar to the free-energy density of a two-condensate superconductor. By using the φ-mapping topological current theory, the torus knot soliton hidden in DNA is demonstrated. We show the relation between the geometric structure and free-energy density of DNA and the Frenet equations in differential geometry theory are considered...
March 2018: Journal of Biological Physics
Vlado A Buljan, Manuel B Graeber, R M Damian Holsinger, Daniel Brown, Brett D Hambly, Edward J Delikatny, Vladimira R Vuletic, Xavier N Krebs, Ilijan B Tomas, John J Bohorquez-Florez, Guo Jun Liu, Richard B Banati
We have used cell culture of astrocytes aligned within microchannels to investigate calcium effects on primary cilia morphology. In the absence of calcium and in the presence of flow of media (10 μL.s-1 ) the majority (90%) of primary cilia showed reversible bending with an average curvature of 2.1 ± 0.9 × 10-4  nm-1 . When 1.0 mM calcium was present, 90% of cilia underwent bending. Forty percent of these cilia demonstrated strong irreversible bending, resulting in a final average curvature of 3.9 ± 1 × 10-4  nm-1 , while 50% of cilia underwent bending similar to that observed during calcium-free flow...
March 2018: Journal of Biological Physics
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