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1.  A spectroscopic investigation of the interaction between c-MYC DNA and tetrapyridinoporphyrazinatozinc(II) 
Journal of Biological Physics  2014;40(3):275-283.
The c-MYC gene plays an important role in the regulation of cell proliferation and growth and it is overexpressed in a wide variety of human cancers. Around 90% of c-MYC transcription is controlled by the nuclease-hypersensitive element III1 (NHE III1), whose 27-nt purine-rich strand has the ability to form a G-quadruplex structure under physiological conditions. Therefore, c-MYC DNA is an attractive target for drug design, especially for cancer chemotherapy. Here, the interaction of water-soluble tetrapyridinoporphyrazinatozinc(II) with 27-nt G-rich strand (G/c-MYC), its equimolar mixture with the complementary sequence (GC/c-MYC) and related C-rich oligonucleotide (C/c-MYC) is investigated. Circular dichroism (CD) measurements of the G-rich 27-mer oligonucleotide in 150 mM KCl, pH 7 demonstrate a spectral signature consistent with parallel G-quadruplex DNA. Furthermore, the CD spectrum of the GC rich oligonucleotide shows characteristics of both duplex and quadruplex structures. Absorption spectroscopy implies that the complex binding of G/c-MYC and GC/c-MYC is a two-step process; in the first step, a very small red shift and hypochromicity and in the second step, a large red shift and hyperchromicity are observed in the Q band. Emission spectra of zinc porphyrazine are quenched upon addition of three types of DNA. According to the results of spectroscopy, it can be concluded the dominant binding mode is probably, outside binding and end stacking.
doi:10.1007/s10867-014-9348-x
PMCID: PMC4059838  PMID: 24824526
Zinc porphyrazine; c-MYC promoter; DNA binding; Spectroscopy
2.  Comment on “Modulating DNA configuration by interfacial traction: an elastic rod model to characterize DNA folding and unfolding” 
Journal of Biological Physics  2014;40(3):259-266.
In this comment, we point out that the tractions induced by interfacial energy, which are referred to as the tractions on the central axis curve of the DNA elastic rod presented by Huang (J. Biol. Phys. 37(1), 79–90, 2011), are incorrect. The correct tractions are provided in this literature. Further, with the use of the correct tractions, we present new numerical results, which for the values given by Zaixing Huang do not give rise to the physical behavior observed for DNA by the author.
doi:10.1007/s10867-014-9345-0
PMCID: PMC4059836  PMID: 24793419
DNA configuration; Interfacial traction; DNA folding and unfolding; Comment
3.  A mathematical model of the unidirectional block caused by the pulmonary veins for anatomically induced atrial reentry 
Journal of Biological Physics  2014;40(3):219-258.
It is widely believed that the pulmonary veins (PVs) of the left atrium play the central role in the generation of anatomically induced atrial reentry but its mechanism has not been analytically explained. To understand this mechanism, a new analytic approach is proposed by adapting the geometric relative acceleration analysis from spacetime physics based on the hypothesis that a large relative acceleration can translate to a dramatic increase in the curvature of a wavefront and subsequently to conduction failure. By verifying the strong dependency of the propagational direction and the magnitude of anisotropy for conduction failure, this analytic method reveals that a unidirectional block can be generated by asymmetric propagation toward the PVs. This model is validated by computational tests in a T-shaped domain, computational simulations for three-dimensional atrial reentry and previous in-silico reports for anatomically induced atrial reentry.
doi:10.1007/s10867-014-9340-5
PMCID: PMC4059837  PMID: 24789612
Atrial reentry; Unidirectional block; Conduction failure; Relative acceleration
4.  Influence of individual cell motility on the 2D front roughness dynamics of tumour cell colonies 
Journal of Biological Physics  2014;40(3):285-308.
The dynamics of in situ 2D HeLa cell quasi-linear and quasi-radial colony fronts in a standard culture medium is investigated. For quasi-radial colonies, as the cell population increased, a kinetic transition from an exponential to a constant front average velocity regime was observed. Special attention was paid to individual cell motility evolution under constant average colony front velocity looking for its impact on the dynamics of the 2D colony front roughness. From the directionalities and velocity components of cell trajectories in colonies with different cell populations, the influence of both local cell density and cell crowding effects on individual cell motility was determined. The average dynamic behaviour of individual cells in the colony and its dependence on both local spatio-temporal heterogeneities and growth geometry suggested that cell motion undergoes under a concerted cell migration mechanism, in which both a limiting random walk-like and a limiting ballistic-like contribution were involved. These results were interesting to infer how biased cell trajectories influenced both the 2D colony spreading dynamics and the front roughness characteristics by local biased contributions to individual cell motion. These data are consistent with previous experimental and theoretical cell colony spreading data and provide additional evidence of the validity of the Kardar-Parisi-Zhang equation, within a certain range of time and colony front size, for describing the dynamics of 2D colony front roughness.
doi:10.1007/s10867-014-9349-9
PMCID: PMC4059834  PMID: 24893945
Cell population; Colony spatio-temporal heterogeneity; Crowding effects; Biased cell trajectories; Cell migration concerted mechanism
5.  Sharp intense line in the bioluminescence emission of the firefly 
Journal of Biological Physics  2014;40(3):267-274.
Numerous investigations have been carried out on the spectral distribution of the light of different species of fireflies. Here we record the emission spectrum of the Indian species of the firefly Luciola praeusta Kiesenwetter 1874 (Coleoptera : Lampyridae : Luciolinae) on a color film. Green and red color-sectors, with an intense yellow one in between, appear in this spectrum. Intensity profile of this spectrum reveals a hitherto undetected strong narrow yellow line, which lies within the full-width-at-half maximum (FWHM) of the intensity profile. The spectrum recorded in a high-resolution spectrometer confirms the presence of this sharp intense line. This finding lends support to an earlier drawn analogy between the in vivo emission of the firefly and laser light.
doi:10.1007/s10867-014-9346-z
PMCID: PMC4059835  PMID: 24771391
Firefly light; Emission band; Sharp yellow line; Random laser
7.  The role of screening and treatment in the transmission dynamics of HIV/AIDS and tuberculosis co-infection: a mathematical study 
Journal of Biological Physics  2014;40(2):139-166.
In this paper, we present a deterministic non-linear mathematical model for the transmission dynamics of HIV and TB co-infection and analyze it in the presence of screening and treatment. The equilibria of the model are computed and stability of these equilibria is discussed. The basic reproduction numbers corresponding to both HIV and TB are found and we show that the disease-free equilibrium is stable only when the basic reproduction numbers for both the diseases are less than one. When both the reproduction numbers are greater than one, the co-infection equilibrium point may exist. The co-infection equilibrium is found to be locally stable whenever it exists. The TB-only and HIV-only equilibria are locally asymptotically stable under some restriction on parameters. We present numerical simulation results to support the analytical findings. We observe that screening with proper counseling of HIV infectives results in a significant reduction of the number of individuals progressing to HIV. Additionally, the screening of TB reduces the infection prevalence of TB disease. The results reported in this paper clearly indicate that proper screening and counseling can check the spread of HIV and TB diseases and effective control strategies can be formulated around ‘screening with proper counseling’.
doi:10.1007/s10867-014-9342-3
PMCID: PMC4049375  PMID: 24664795
Co-infection; Basic reproduction number; Simulation
9.  An elastic rod model to evaluate effects of ionic concentration on equilibrium configuration of DNA in salt solution 
Journal of Biological Physics  2014;40(2):179-192.
As a coarse-gained model, a super-thin elastic rod subjected to interfacial interactions is used to investigate the condensation of DNA in a multivalent salt solution. The interfacial traction between the rod and the solution environment is determined in terms of the Young–Laplace equation. Kirchhoff’s theory of elastic rod is used to analyze the equilibrium configuration of a DNA chain under the action of the interfacial traction. Two models are established to characterize the change of the interfacial traction and elastic modulus of DNA with the ionic concentration of the salt solution, respectively. The influences of the ionic concentration on the equilibrium configuration of DNA are discussed. The results show that the condensation of DNA is mainly determined by competition between the interfacial energy and elastic strain energy of the DNA itself, and the interfacial traction is one of forces that drive DNA condensation. With the change of concentration, the DNA segments will undergo a series of alteration from the original configuration to the condensed configuration, and the spiral-shape appearing in the condensed configuration of DNA is independent of the original configuration.
doi:10.1007/s10867-014-9344-1
PMCID: PMC4049377  PMID: 24691983
DNA condensation; Interfacial traction; Ionic concentration
10.  Dynamics of lysozyme and its hydration water under an electric field 
Journal of Biological Physics  2014;40(2):167-178.
The effects of a static electric field on the dynamics of lysozyme and its hydration water are investigated by means of incoherent quasi-elastic neutron scattering (QENS). Measurements were performed on lysozyme samples, hydrated respectively with heavy water (D 2O) to capture the protein dynamics and with light water (H 2O), to probe the dynamics of the hydration shell, in the temperature range from 210 < T < 260 K. The hydration fraction in both cases was about ∼ 0.38 gram of water per gram of dry protein. The field strengths investigated were respectively 0 kV/mm and 2 kV/mm ( ∼2 × 10 6 V/m) for the protein hydrated with D 2O and 0 kV and 1 kV/mm for the H 2O-hydrated counterpart. While the overall internal protons dynamics of the protein appears to be unaffected by the application of an electric field up to 2 kV/mm, likely due to the stronger intra-molecular interactions, there is also no appreciable quantitative enhancement of the diffusive dynamics of the hydration water, as would be anticipated based on our recent observations in water confined in silica pores under field values of 2.5 kV/mm. This may be due to the difference in surface interactions between water and the two adsorption hosts (silica and protein), or to the existence of a critical threshold field value E c∼2–3 kV/mm for increased molecular diffusion, for which electrical breakdown is a limitation for our sample.
doi:10.1007/s10867-014-9343-2
PMCID: PMC4049378  PMID: 24664796
Quasi-elastic neutron scattering; Protein dynamics; Electric field; Diffusion
11.  Molecular models of the Mojave rattlesnake (Crotalus scutulatus scutulatus) venom metalloproteinases reveal a structural basis for differences in hemorrhagic activities 
Journal of Biological Physics  2014;40(2):193-216.
Rattlesnake venom can differ in composition and in metalloproteinase-associated activities. The molecular basis for this intra-species variation in Crotalus scutulatus scutulatus (Mojave rattlesnake) remains an enigma. To understand the molecular basis for intra-species variation of metalloproteinase-associated activities, we modeled the three-dimensional structures of four metalloproteinases based on the amino acid sequence of four variations of the proteinase domain of the C. s. scutulatus metalloproteinase gene (GP1, GP2, GP3, and GP4). For comparative purposes, we modeled the atrolysin metalloproteinases of C. atrox as well. All molecular models shared the same topology. While the atrolysin metalloproteinase molecular models contained highly conserved substrate binding sites, the Mojave rattlesnake metalloproteinases showed higher structural divergence when superimposed onto each other. The highest structural divergence among the four C. s. scutulatus molecular models was located at the northern cleft wall and the S’1-pocket of the substrate binding site, molecular regions that modulate substrate selectivity. Molecular dynamics and field potential maps for each C. s. scutulatus metalloproteinase model demonstrated that the non-hemorrhagic metalloproteinases (GP2 and GP3) contain highly basic molecular and field potential surfaces while the hemorrhagic metalloproteinases GP1 and atrolysin C showed extensive acidic field potential maps and shallow but less dynamic active site pockets. Hence, differences in the spatial arrangement of the northern cleft wall, the S’1-pocket, and the physico-chemical environment surrounding the catalytic site contribute to differences in metalloproteinase activities in the Mojave rattlesnake. Our results provide a structural basis for variation of metalloproteinase-associated activities in the rattlesnake venom of the Mojave rattlesnake.
Electronic Supplementary Material
The online version of this article (doi:10.1007/s10867-013-9339-3) contains supplementary material, which is available to authorized users.
doi:10.1007/s10867-013-9339-3
PMCID: PMC4049379  PMID: 24522289
Molecular models; Rattlesnake venom metalloproteinases; Structural basis of hemorrhagic activity
12.  Multi-ion versus single-ion conduction mechanisms can yield current rectification in biological ion channels 
Journal of Biological Physics  2014;40(2):109-119.
There is clear evidence that the net magnitude of negative charge at the intracellular end of inwardly rectifying potassium channels helps to generate an asymmetry in the magnitude of the current that will pass in each direction. However, a complete understanding of the physical mechanism that links these charges to current rectification has yet to be obtained. Using Brownian dynamics, we compare the conduction mechanism and binding sites in rectifying and non-rectifying channel models. We find that in our models, rectification is a consequence of asymmetry in the hydrophobicity and charge of the pore lining. As a consequence, inward conduction can occur by a multi-ion conduction mechanism. However, outward conduction is restricted, since there are fewer ions at the intracellular entrance and outwardly moving ions must cross the pore on their own. We pose the question as to whether the same mechanism could be at play in inwardly rectifying potassium channels.
Electronic Supplementary Material
The online version of this article (doi:10.1007/s10867-013-9338-4) contains supplementary material, which is available to authorized users.
doi:10.1007/s10867-013-9338-4
PMCID: PMC4049380  PMID: 24463792
Kir channels; Transmembrane domain; Binding sites; Brownian dynamics; Rectification mechanism
13.  THz time scale structural rearrangements and binding modes in lysozyme-ligand interactions 
Journal of Biological Physics  2014;40(2):121-137.
Predicting the conformational changes in proteins that are relevant for substrate binding is an ongoing challenge in the aim of elucidating the functional states of proteins. The motions that are induced by protein-ligand interactions are governed by the protein global modes. Our measurements indicate that the detected changes in the global backbone motion of the enzyme upon binding reflect a shift from the large-scale collective dominant mode in the unbound state towards a functional twisting deformation that assists in closing the binding cleft. Correlated motion in lysozyme has been implicated in enzyme function in previous studies, but detailed characterization of the internal fluctuations that enable the protein to explore the ensemble of conformations that ultimately foster large-scale conformational change is yet unknown. For this reason, we use THz spectroscopy to investigate the picosecond time scale binding modes and collective structural rearrangements that take place in hen egg white lysozyme (HEWL) when bound by the inhibitor (NAG) 3. These protein thermal motions correspond to fluctuations that have a role in both selecting and sampling from the available protein intrinsic conformations that communicate function. Hence, investigation of these fast, collective modes may provide knowledge about the mechanism leading to the preferred binding process in HEWL-(NAG) 3. Specifically, in this work we find that the picosecond time scale hydrogen-bonding rearrangements taking place in the protein hydration shell with binding modify the packing density within the hydrophobic core on a local level. These localized, intramolecular contact variations within the protein core appear to facilitate the large cooperative movements within the interfacial region separating the α- and β- domain that mediate binding. The THz time-scale fluctuations identified in the protein-ligand system may also reveal a molecular mechanism for substrate recognition.
Electronic Supplementary Material
The online version of this article (doi:10.1007/s10867-014-9341-4) contains supplementary material, which is available to authorized users.
doi:10.1007/s10867-014-9341-4
PMCID: PMC4049381  PMID: 24682643
Ligand-binding; THz time-scale fluctuations
14.  The stabilizing role of the Sabbath in pre-monarchic Israel:a mathematical model 
Journal of Biological Physics  2015;41(2):203-221.
The three monotheistic cultures have many common institutions and some of them germinated in pre-monarchic Israel. Reasonably, the essential institutions were in place at that starting point; this work explores the possibility that the Sabbath is one of these institutions. Our mathematical examination points to the potential cultural, civic, and social role of the weekly Sabbath, that is, the Sabbath institution, in controlling deviation from social norms. It begins with an analogy between spread of transgression (defined as lack of conformity with social norms) and of biological infection. Borrowing well-known mathematical methods, we derive solution sets of social equilibrium and study their social stability. The work shows how a weekly Sabbath could in theory enhance social resilience in comparison with a similar assembly with a more natural and longer period, say between New Moon and Full Moon. The examination reveals that an efficient Sabbath institution has the potential to ensure a stable organization and suppress occasional appearances of transgression from cultural norms and boundaries. The work suggests the existence of a sharp threshold governed by the “Basic Sabbath Number ש0”—a critical observance of the Sabbath, or large enough ש0, is required to ensure suppression of transgression. Subsequently, the model is used to explore an interesting question: how old is the Sabbath? The work is interdisciplinary, combining anthropological concepts with mathematical analysis and with archaeological parallels in regards to the findings.
Electronic supplementary material
The online version of this article (doi:10.1007/s10867-014-9373-9) contains supplementary material, which is available to authorized users.
doi:10.1007/s10867-014-9373-9
PMCID: PMC4366438  PMID: 25596025
SIRS epidemic model; Periodic forcing; Social dynamics; Nonlinear dynamics; Sabbath; Cultural anthropology
15.  Modeling anterograde and retrograde transport of short mobile microtubules from the site of axonal branch formation 
Journal of Biological Physics  2013;40(1):41-53.
This theoretical research is motivated by a recent model of microtubule (MT) transport put forward by Baas and Mozgova (Cytoskeleton 69:416–425, 2012). According to their model, in an axon all plus-end-distal mobile MTs move anterogradely while all minus-end-distal mobile MTs move retrogradely. Retrograde MT transport thus represents a mechanism by which minus-end-distal MTs are removed from the axon. We suggested equations that implement Baas and Mozgova’s model. We employed these equations to simulate transport of short mobile MTs from a region (such as the site of axonal branch formation) where MT severing activity results in generation of a large number of short MTs of both orientations. We obtained the exact and approximate transient solutions of these equations utilizing the Laplace transform technique. We applied the obtained solutions to calculate the average rates of anterograde and retrograde transport of short MTs.
doi:10.1007/s10867-013-9334-8
PMCID: PMC3923956  PMID: 24271236
Microtubule transport; Neurons; Molecular motors; Exact solution
16.  Papaverine increases human serum albumin glycation 
Journal of Biological Physics  2014;40(1):97-107.
Glycation is a non-enzymatic reaction that is initiated by the primary addition of sugars to amino groups of proteins. In the early phase of glycation, the synthesis of intermediates leads to formation of Amadori compounds. In the last phase, advanced glycation end products (AGE) are irreversibly formed following a complex cascade of reactions. It has recently been shown that glycation also affects diabetes-related complications and Alzheimer’s disease. In this study, human serum albumin at a concentration of 10 mg/ml was incubated in PBS with 40 mM of glucose and in different concentrations of papaverine (25, 100, 250, 500 μM) for 42 days at 37 °C. HSA with no additives as well as with glucose 40 mM were incubated as a control and as a glycated sample, respectively. Following the incubation, the samples were prepared for circular dichroism, fluorescence and absorbance techniques. The results showed that in presence of papaverine and glucose, the glycation of HSA increased notably compared with the glycated sample. In conclusion, in this work, we showed that papaverine affects HSA and increases its glycation level.
doi:10.1007/s10867-013-9337-5
PMCID: PMC3923957  PMID: 24414229
Glycation; Human serum albumin; Papaverine; Glucose
17.  Simultaneous identification of growth law and estimation of its rate parameter for biological growth data: a new approach 
Journal of Biological Physics  2014;40(1):71-95.
Scientific formalizations of the notion of growth and measurement of the rate of growth in living organisms are age-old problems. The most frequently used metric, “Average Relative Growth Rate” is invariant under the choice of the underlying growth model. Theoretically, the estimated rate parameter and relative growth rate remain constant for all mutually exclusive and exhaustive time intervals if the underlying law is exponential but not for other common growth laws (e.g., logistic, Gompertz, power, general logistic). We propose a new growth metric specific to a particular growth law and show that it is capable of identifying the underlying growth model. The metric remains constant over different time intervals if the underlying law is true, while the extent of its variation reflects the departure of the assumed model from the true one. We propose a new estimator of the relative growth rate, which is more sensitive to the true underlying model than the existing one. The advantage of using this is that it can detect crucial intervals where the growth process is erratic and unusual. It may help experimental scientists to study more closely the effect of the parameters responsible for the growth of the organism/population under study.
doi:10.1007/s10867-013-9336-6
PMCID: PMC3923958  PMID: 24402566
Growth curve models; Average relative growth rate; Interval specific rate parameter; Overall rate parameter; Model selection
18.  Changes of protein stiffness during folding detect protein folding intermediates 
Journal of Biological Physics  2013;40(1):15-23.
Single-molecule force-quench atomic force microscopy (FQ-AFM) is used to detect folding intermediates of a simple protein by detecting changes of molecular stiffness of the protein during its folding process. Those stiffness changes are obtained from shape and peaks of an autocorrelation of fluctuations in end-to-end length of the folding molecule. The results are supported by predictions of the equipartition theorem and agree with existing Langevin dynamics simulations of a simplified model of a protein folding. In the light of the Langevin simulations the experimental data probe an ensemble of random-coiled collapsed states of the protein, which are present both in the force-quench and thermal-quench folding pathways.
Electronic supplementary material
The online version of this article (doi:10.1007/s10867-013-9331-y) contains supplementary material, which is available to authorized users.
doi:10.1007/s10867-013-9331-y
PMCID: PMC3923959  PMID: 23975672
STM and AFM manipulations of a single molecule; Folding: thermodynamics, statistical mechanics, models, and pathways;  Mechanical properties of molecules
19.  An effective mesoscopic model of double-stranded DNA 
Journal of Biological Physics  2013;40(1):1-14.
Watson and Crick’s epochal presentation of the double helix structure in 1953 has paved the way to intense exploration of DNA’s vital functions in cells. Also, recent advances of single molecule techniques have made it possible to probe structures and mechanics of constrained DNA at length scales ranging from nanometers to microns. There have been a number of atomistic scale quantum chemical calculations or molecular level simulations, but they are too computationally demanding or analytically unfeasible to describe the DNA conformation and mechanics at mesoscopic levels. At micron scales, on the other hand, the wormlike chain model has been very instrumental in describing analytically the DNA mechanics but lacks certain molecular details that are essential in describing the hybridization, nano-scale confinement, and local denaturation. To fill this fundamental gap, we present a workable and predictive mesoscopic model of double-stranded DNA where the nucleotides beads constitute the basic degrees of freedom. With the inter-strand stacking given by an interaction between diagonally opposed monomers, the model explains with analytical simplicity the helix formation and produces a generalized wormlike chain model with the concomitant large bending modulus given in terms of the helical structure and stiffness. It also explains how the helical conformation undergoes overstretch transition to the ladder-like conformation at a force plateau, in agreement with the experiment.
doi:10.1007/s10867-013-9333-9
PMCID: PMC3923960  PMID: 24306264
DNA helical structure; DNA elasticity; generalized wormlike chain model
20.  Biophysical characterization of a recombinant aminopeptidase II from the thermophilic bacterium Bacillus stearothermophilus 
Journal of Biological Physics  2013;40(1):25-40.
In the present study, the biophysical properties of His6-tagged Bacillus stearothermophilus aminopeptidase II (His6-tagged BsAmpII) are characterized in detail by gel-filtration, analytical ultracentrifugation, and various spectroscopic techniques. Using size-exclusion chromatography and analytical ultracentrifugation, we demonstrate that His6-tagged BsAmpII exists predominantly as a dimer in solution. The enzyme is active and stable at pHs ranging from 6.5 to 8.5. Far-UV circular dichroism analysis reveals that the secondary structures of His6-tagged BsAmpII are significantly altered in the presence of SDS, whereas the presence of 5–10% acetone and ethanol was harmless to the folding of the enzyme. Thermal unfolding of His6-tagged BsAmpII was found to be irreversible and led to the formation of aggregates. The native enzyme started to unfold beyond 0.6 M guanidine hydrochloride and had a midpoint of denaturation at 1.34 M. This protein remained active at concentrations of urea below 2.7 M but experienced an irreversible unfolding by >5 M denaturant. Taken together, this work lays a foundation for potential biotechnological applications of His6-tagged BsAmpII.
doi:10.1007/s10867-013-9332-x
PMCID: PMC3923962  PMID: 24165863
Aminopeptidase; Bacillus stearothermophilus; Thermal denaturation; Guanidine hydrochloride; Urea
21.  Influence of C-H...O interactions on the structural stability of β-lactamases 
Journal of Biological Physics  2013;39(4):649-663.
β-Lactamases produced by pathogenic bacteria cleave β-lactam antibiotics and render them ineffective. Understanding the principles that govern the structural stability of β-lactamases requires elucidation of the nature of the interactions that are involved in stabilization. In the present study, we systematically analyze the influence of CH...O interactions on determining the specificity and stability of β-lactamases in relation to environmental preferences. It is interesting to note that all the residues located in the active site of β-lactamases are involved in CH...O interactions. A significant percentage of CH...O interactions have a higher conservation score and short-range interactions are the predominant type of interactions in β-lactamases. These results will be useful in understanding the stability patterns of β-lactamases.
doi:10.1007/s10867-013-9324-x
PMCID: PMC3758823  PMID: 23996409
β-lactamases; CH...O interactions; Stabilization centers; Conservation; Solvent accessibility; Secondary structure
22.  Network model of a protein globule 
Journal of Biological Physics  2013;39(4):673-685.
Phase transition of a protein globule is considered in the frameworks of (i) the generalized mean-field theory for the order parameter, characterizing the extent of the deviation of a protein three-dimensional structure from its native state and (ii) the network model that treats a protein globule as a small-world network with a significant percent of long-range links between amino acid residues. Temperature dependencies of the introduced order parameter are defined and phase-transition temperatures are found on the basis of the function defining the distribution of links’ numbers for protein residues. An important role of long-range links, promoting considerable rise of thermal protein stability, is demonstrated by the example of a correlation between protein melting temperature and a fraction of disulfide bonds.
doi:10.1007/s10867-013-9326-8
PMCID: PMC3758824  PMID: 23897064
Protein globule; Network model; Small-world network; Phase transition; Order parameter; Mean-field theory; Long-range links
23.  Gamma radiation effects on seed germination, growth and pigment content, and ESR study of induced free radicals in maize (Zea mays) 
Journal of Biological Physics  2013;39(4):625-634.
The effects of gamma radiation are investigated by studying plant germination, growth and development, and biochemical characteristics of maize. Maize dry seeds are exposed to a gamma source at doses ranging from 0.1 to 1 kGy. Our results show that the germination potential, expressed through the final germination percentage and the germination index, as well as the physiological parameters of maize seedlings (root and shoot lengths) decreased by increasing the irradiation dose. Moreover, plants derived from seeds exposed at higher doses (≤0.5 kGy) did not survive more than 10 days. Biochemical differences based on photosynthetic pigment (chlorophyll a, chlorophyll b, carotenoids) content revealed an inversely proportional relationship to doses of exposure. Furthermore, the concentration of chlorophyll a was higher than chlorophyll b in both irradiated and non-irradiated seedlings. Electron spin resonance spectroscopy used to evaluate the amount of free radicals induced by gamma ray treatment demonstrates that the relative concentration of radiation-induced free radicals depends linearly on the absorbed doses.
doi:10.1007/s10867-013-9322-z
PMCID: PMC3758825  PMID: 23996407
Gamma ray; Maize hybrid; Germination potential; Growth parameters; Photosynthetic pigments ; Electron spin resonance spectroscopy
24.  Theoretical electrical conductivity of hydrogen-bonded benzamide-derived molecules and single DNA bases 
Journal of Biological Physics  2013;39(4):607-624.
A benzamide molecule is used as a “reader” molecule to form hydrogen bonds with five single DNA bases, i.e., four normal single DNA bases A,T,C,G and one for 5methylC. The whole molecule is then attached to the gold surface so that a meta-molecule junction is formed. We calculate the transmission function and conductance for the five metal–molecule systems, with the implementation of density functional theory-based non-equilibrium Green function method. Our results show that each DNA base exhibits a unique conductance and most of them are on the pS level. The distinguishable conductance of each DNA base provides a way for the fast sequencing of DNA. We also investigate the dependence of conductivity of such a metal–molecule system on the hydrogen bond length between the “reader” molecule and DNA base, which shows that conductance follows an exponential decay as the hydrogen bond length increases, i.e., the conductivity is highly sensitive to the change in hydrogen bond length.
doi:10.1007/s10867-013-9321-0
PMCID: PMC3758826  PMID: 23996406
Hydrogen-bonded; Benzamide; Conductance; DNA sequencing
25.  Dynamical behaviour of a two-predator model with prey refuge 
Journal of Biological Physics  2013;39(4):701-722.
A three-component model consisting on one-prey and two-predator populations is considered with a Holling type II response function incorporating a constant proportion of prey refuge. We also consider the competition among predators for their food (prey) and shelter. The essential mathematical features of the model have been analyzed thoroughly in terms of stability and bifurcations arising in some selected situations. Threshold values for some parameters indicating the feasibility and stability conditions of some equilibria are determined. The range of significant parameters under which the system admits different types of bifurcations is investigated. Numerical illustrations are performed in order to validate the applicability of the model under consideration.
doi:10.1007/s10867-013-9327-7
PMCID: PMC3758827  PMID: 23975670
Population models; Prey refuge; Persistence; Local stability; Global stability; Limit cycles; Switching of periodic solutions; 92D25; 92D30; 92D40

Results 1-25 (626)