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Journal of Biological Physics

Željana Bonačić Lošić, Tomislav Donđivić, Davor Juretić
Triosephosphate isomerase (TIM) is often described as a fully evolved housekeeping enzyme with near-maximal possible reaction rate. The assumption that an enzyme is perfectly evolved has not been easy to confirm or refute. In this paper, we use maximization of entropy production within known constraints to examine this assumption by calculating steady-state cyclic flux, corresponding entropy production, and catalytic activity in a reversible four-state scheme of TIM functional states. The maximal entropy production (MaxEP) requirement for any of the first three transitions between TIM functional states leads to decreased total entropy production...
January 3, 2017: Journal of Biological Physics
Ludmila Yakushevich
The creation of mechanical analogues of biological systems is known as a useful instrument that helps to understand better the dynamical mechanisms of the functioning of living organisms. Mechanical analogues of biomolecules are usually constructed for imitation of their internal mobility, which is one of the most important properties of the molecules. Among the different types of internal motions, angular oscillations of nitrous bases are of special interest because they make a substantial contribution to the base pairs opening that in turn is an important element of the process of the DNA-protein recognition...
December 30, 2016: Journal of Biological Physics
Yuri M Yevdokimov, Sergey G Skuridin, Sergey V Semenov, Ljubov A Dadinova, Viktor I Salyanov, Efim I Kats
In this research, we observe and rationalize theoretically the transition from hexagonal to cholesteric packing of double-stranded (ds) DNA in dispersion particles. The samples were obtained by phase exclusion of linear ds DNA molecules from water-salt solutions of poly(ethylene glycol)-PEG-with concentrations ranging from 120 mg ml(-1) to 300 mg ml(-1). In the range of PEG concentrations from 120 mg ml(-1) to 220 mg ml(-1) at room temperature, we find ds DNA molecule packing, typical of classical cholesterics...
December 27, 2016: Journal of Biological Physics
Arkadiusz Bryll, Andrzej Ślęzak
In this paper, the authors investigate the membrane transport of aqueous non-electrolyte solutions in a single-membrane system with the membrane mounted horizontally. The purpose of the research is to analyze the influence of volume flows on the process of forming concentration boundary layers (CBLs). A mathematical model is provided to calculate dependences of a concentration polarization coefficient (ζ s ) on a volume flux (J vm ), an osmotic force (Δπ) and a hydrostatic force (ΔP) of different values...
November 12, 2016: Journal of Biological Physics
Maryam Ghahremani Nasab, Leila Hassani, Sara Mohammadi Nejad, Davood Norouzi
A DNA enzyme with peroxidase activity is a G-quadruplex-based DNAzyme formed by hemin and G-quadruplex DNA. Activity of peroxide DNAzymes can be influenced by the structure of quadruplex DNA. In this investigation, the interaction of hemin with T30695 G-quadruplex DNA is evaluated. Molecular dynamic simulation indicates that the binding mode of hemin to G-quadruplex DNA is end-stacking, which is consistent with absorption spectroscopy. Based on fluorescence spectroscopy, hemin ejects thiazole orange from bases of four-strand DNA...
October 17, 2016: Journal of Biological Physics
Leonor Cruzeiro, Léo Degrève
According to the thermodynamic hypothesis, the native state of proteins is uniquely defined by their amino acid sequence. On the other hand, according to Levinthal, the native state is just a local minimum of the free energy and a given amino acid sequence, in the same thermodynamic conditions, can assume many, very different structures that are as thermodynamically stable as the native state. This is the Levinthal limit explored in this work. Using computer simulations, we compare the interactions that stabilize the native state of four different proteins with those that stabilize three non-native states of each protein and find that the nature of the interactions is very similar for all such 16 conformers...
October 14, 2016: Journal of Biological Physics
Chongming Jiang, Chunyan Cui, Weirong Zhong, Gang Li, Li Li, Yuanzhi Shao
We study in silico the influence of host tissue inhomogeneity on tumor cell proliferation and diffusion by simulating the mobility of a tumor on percolation clusters with different homogeneities of surrounding tissues. The proliferation and diffusion of a tumor in an inhomogeneous tissue could be characterized in the framework of the percolation theory, which displays similar thresholds (0.54, 0.44, and 0.37, respectively) for tumor proliferation and diffusion in three kinds of lattices with 4, 6, and 8 connecting near neighbors...
October 2016: Journal of Biological Physics
S M Saberi Fathi
Knowledge regarding the 3D structure of a protein provides useful information about the protein's functional properties. Particularly, structural similarity between proteins can be used as a good predictor of functional similarity. One method that uses the 3D geometrical structure of proteins in order to compare them is the similarity value (SV). In this paper, we introduce a new definition of the SV measure for comparing two proteins. To this end, we consider the mass of the protein's atoms and concentrate on the number of protein's atoms to be compared...
October 2016: Journal of Biological Physics
Parvaneh Sayyad-Amin, Mohammad-Reza Jahansooz, Azam Borzouei, Fatemeh Ajili
Water shortage leads to a low quality of water, especially saline water in most parts of agricultural regions. This experiment was designed to determine the effects of saline irrigation on sorghum as a moderately salt-tolerant crop. To study salinity effects on photosynthetic pigment attributes including the chlorophyll content and chlorophyll fluorescence, an experiment was performed in a climate-controlled greenhouse at two vegetative and reproductive stages. The experimental design was factorial based on a completely randomized design with five NaCl concentrations (control, 50, 100, 150, and 200 mM), two grain and sweet-forage sorghum cultivars (Kimia and Pegah, respectively) and four replications...
October 2016: Journal of Biological Physics
I Nedkov, L Slavov, R Angelova, B Blagoev, D Kovacheva, M V Abrashev, M Iliev, V Groudeva
A detailed investigation of nanostructured iron oxides/(oxy)hydroxides gathered after cultivation of bacteria from the genus Leptothrix as iron (II) oxidizers is presented. A specific type of medium is selected for the cultivation of the bacteria. Results for sediment powder and bio-film on glass substrate samples from the same media are discussed. XRD, Raman spectroscopy, SEM, and TEM images and PPMS measurements are used to prove the exact composition of the biogenic products and to interpret the oxidation process...
October 2016: Journal of Biological Physics
Rudolf Podgornik
No abstract text is available yet for this article.
October 2016: Journal of Biological Physics
Mi Li, Lianqing Liu, Xiubin Xiao, Ning Xi, Yuechao Wang
Methotrexate is a commonly used anti-cancer chemotherapy drug. Cellular mechanical properties are fundamental parameters that reflect the physiological state of a cell. However, so far the role of cellular mechanical properties in the actions of methotrexate is still unclear. In recent years, probing the behaviors of single cells with the use of atomic force microscopy (AFM) has contributed much to the field of cell biomechanics. In this work, with the use of AFM, the effects of methotrexate on the viscoelastic properties of four types of cells were quantitatively investigated...
October 2016: Journal of Biological Physics
Ziad Khattari
The present work utilizes the Langmuir monolayer technique to detect the adsorption kinetics of native low-density lipoproteins and their oxidized form with the lipid monolayer. We found that low-density lipoproteins and oxidized low-density lipoproteins are able to penetrate the LM up to pressure π = 9.9 and 11.6 mN/m. Also, the adsorption constants of both particles were found to depend strongly on the monolayer initial pressure. It is found that less compressed lipid monolayers could accommodate more native low-density lipoproteins than the oxidized ones due their higher binding affinity toward monolayers...
October 2016: Journal of Biological Physics
Tianyi Zhou, Yixuan Ming, Susan F Perry, Svetlana Tatic-Lucic
We successfully determine the ranges of dielectric permittivity, cytoplasm conductivity, and specific membrane capacitance of mouse hippocampal neuronal and glial cells using dielectrophoresis (DEP) crossover frequency (CF). This methodology is based on the simulation of CF directly from the governing equation of a dielectric model of mammalian cells, as well as the measurements of DEP CFs of mammalian cells in different suspension media with different conductivities, based on a simple experimental setup. Relationships between the properties of cells and DEP CF, as demonstrated by theoretical analysis, enable the simultaneous estimation of three properties by a straightforward fitting procedure based on experimentally measured CFs...
October 2016: Journal of Biological Physics
Jan Trnka, Šárka Nedomová, Vojtěch Kumbár, Michal Šustr, Jaroslav Buchar
The mechanical behavior of eggshell was determined in terms of average rupture force and corresponding deformation. For the experiment, we selected goose eggs (Anser anser f. domestica). Samples of eggs were compressed along their x-axis and z-axis. The effect of the loading orientation can be described in terms of the eggshell contour curvature. Two different experimental methods were used: compression between two plates (loading rates up to 5 mm/s) and the Hopkinson split pressure bar technique. This second method enables achieving loading rates up to about 17 m/s...
October 2016: Journal of Biological Physics
Ghanim Ullah, Aman Ullah
The inositol 1,4,5-trisphosphate (InsP3) receptor (InsP3R) channel is crucial for the generation and modulation of highly specific intracellular Ca(2+) signals performing numerous functions in animal cells. However, the single channel behavior during Ca(2+) signals of different spatiotemporal scales is not well understood. To elucidate the correlation between the gating dynamics of single InsP3Rs and spatiotemporal Ca(2+) patterns, we simulate a cluster of InsP3Rs under varying ligand concentrations and extract comprehensive gating statistics of all channels during events of different sizes and durations...
October 2016: Journal of Biological Physics
Elif Kubat Öktem, Karen Mruk, Joshua Chang, Ata Akin, William R Kobertz, Robert H Brown
No abstract text is available yet for this article.
June 7, 2016: Journal of Biological Physics
N E Muzzio, M A Pasquale, M A C Huergo, A E Bolzán, P H González, A J Arvia
To deal with complex systems, microscopic and global approaches become of particular interest. Our previous results from the dynamics of large cell colonies indicated that their 2D front roughness dynamics is compatible with the standard Kardar-Parisi-Zhang (KPZ) or the quenched KPZ equations either in plain or methylcellulose (MC)-containing gel culture media, respectively. In both cases, the influence of a non-uniform distribution of the colony constituents was significant. These results encouraged us to investigate the overall dynamics of those systems considering the morphology and size, the duplication rate, and the motility of single cells...
June 2016: Journal of Biological Physics
Matjaž Žganec, Nicholas Kruczek, Brigita Urbanc
Amyloid β-protein (A β) assembles into oligomers that play a seminal role in Alzheimer's disease (AD), a leading cause of dementia among the elderly. Despite undisputed importance of A β oligomers, their structure and the basis of their toxicity remain elusive. Previous experimental studies revealed that the [K16A] substitution strongly inhibits toxicity of the two predominant A β alloforms in the brain, A β 40 and A β 42, whereas the [K28A] substitution exerts only a moderate effect. Here, folding and oligomerization of [A16]A β 40, [A28]A β 40, [A16]A β 42, and [A28]A β 42 are examined by discrete molecular dynamics (DMD) combined with a four-bead implicit solvent force field, DMD4B-HYDRA, and compared to A β 40 and A β 42 oligomer formation...
June 2016: Journal of Biological Physics
Vladas Skakauskas, Pranas Katauskis
A mathematical model for Shiga 2 toxin neutralization by A-and B-subunit-specific human monoclonal antibodies initially delivered in the extracellular domain is presented, taking into account toxin and antibodies interaction in the extracellular domain, diffusion of toxin, antibodies, and their reaction products toward the cell, the receptor-mediated toxin and complex composed of toxin and antibody to A-subunit internalization from the extracellular into the intracellular medium and excretion of this complex back to the extracellular environment via recycling endosomal carriers...
June 2016: Journal of Biological Physics
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