Use of the Ising model for doubly ordered macromolecules

We developed a statistical model, based on a one-dimensional Ising model, for a recently studied polypeptide which displays an endothermic helix-to-coil transition with an “anomalous” behavior in the heat of solution. The model supports the assumption of an ordering of the chains due to a specific hydrogen bond interaction among them, beside the helical ordering of the backbone; this double ordering of the macromolecule produces the “anomalous” experimental behavior. With the hypothesis of a highly coopertive interaction among amide groups and side chains, we find that the backbone cooperation increases the chains cooperation, but not vice versa; this influence when the cooperation in the backbone increases.     

Long-range interactions between macromolecules in ordered media

The results of theoretical calculations of interactions between macromolecules dissolved in ordered media such as liquid crystals and biological membranes (lipid bilayers) are reviewed. Expressions for the potentials of interactions between macromolecules of different shape incorporated into nematic liquid crystals, thin films, and lipid mono- and bilayers were derived. In addition to exact expressions, simple evaluating formulae are given. The two-dimensional "gas" of macromolecules swimming on the membrane was considered, and the expression of state for this "gas" was derived. It was shown that in the "gas", phase transitions accompanied by the formation of two-dimensional clusters may occur. The estimates of critical density at which these transitions occur are given.     

Antibacterial activity of singly and doubly modified salinomycin derivatives

The increasing challenge of antibiotic resistance stimulates the search for novel antibacterial agents, especially such that would be effective against multi-drug resistant bacterial strains. Fortunately, natural compounds are excellent sources of potentially new drug leads. Particularly interesting in this context are polyether antibiotic salinomycin (SAL) and its semi-synthetic derivatives, as they exhibit large spectrum of bioactivity. We synthesized and evaluated the antibacterial activity of a series of SAL analogs; four singly (2–3, 15, 17) and two doubly modified (16, 18) derivatives were found to show excellent inhibitory activity not only against planktonic Gram(+) bacterial cells, but also towards select strains of methicillin-resistant staphylococci with the MIC values of 1–4 µg mL⁻¹. Of note, the most promising candidates were more effective in preventing bacterial biofilm formation than unmodified SAL and a commonly used antibiotic – ciprofloxacin. Furthermore, we proved that rational modification of C20 hydroxyl of SAL may reduce genotoxic properties of the obtained analogs. Mechanistically, the structure-activity relationship studies suggested that electroneutral transport mechanism could be beneficial in terms of ensuring high antibacterial activity of SAL derivatives.     

Optical activity and evolution

It is noted that the chemical reactions occurring in rarefied cosmic clouds (molecular concentration 10² cm^–3) differ from similar laboratory reactions by the much greater effect on the outcome of external force fields. In this light it is hypothesized that the synthesis of optically active substances may occur in the outer space under the conjoint stereospecific effect of a magnetic and other molecule-orienting field. It is further conjectured that the optically active substances of the Solar System had been produced in the course of its formation out of the primal rarefied cloud.     

Optical activity and evolution

Dissymmetric combinations of weak natural fields exert a stereospecific effect, which may result under some conditions characteristic of outer space in the formation of appreciable amounts of optically active compounds. Synthesis of optically active matter could occur in the early stages of the formation of the Solar System.     

Optical activity of octopus metarhodopsins.

The optical activity of octopus rhodopsin, acid metarhodopsin and alkaline metarhodopsin was studied by a sensitive and rapid CD apparatus. For sometime it has been thought that cephalopod metarhodopsins do not have any optical activity associated with their main absorption band. However, the present work shows that acid metarhodopsin in digitonin has a positive CD band at 498 nm and a negative CD band at 436 nm and alkaline metarhodopsin has a negative CD band at 381 nm. Detergent affected the wavelength of the CD peak of the visual pigments though the pattern of the spectrum was similar. From these results it is concluded that the conformation of all-trans retinal in octopus metarhodopsin is influenced by the asymmetric conformation of the protein near the retinal and therefore inducing optical activity.     

Optical activity of polypeptides and proteins

Using methods described in a previous publication the optical activity of a number of polypeptides and proteins has been calculated. The systems included the α-helix, the two β-structures, polyproline I, polyproline II, collagen and collagen models, and poly-N-methylalanine. In addition to these orderded structures, calculations were also performed on the α, β and nonperiodic regions of myoglobin, lysozyme, ribonuclease-S and β-chymotrypsin. The α and β structures in prteins differ from the polypeptide models by being very short and partially disordered. It is concluded that the 222-nm band of the α-helix is a good method for detecting helices in proteins but that the 207-and 191-nm bands of the helix will not fit a linear superposition model. The circular dichroism of the so-called β regions of proteins differs markedly from that for ideal β structure because of breakdownin symmetry. As a result estimates of β-structure in proteins based on polypeptide models are not likely to be quantitative. The theoretical methods give an adequate account of the optical activity of all the ordered polypeptides except polyproline II and collagen and (by inference) the nonperiodic chains in the various proteins. This difficulty is the remaining barrier to a complete theory of the optical activity of the polypeptide backbone in globular proteins.     

Optical oxygen-sensing properties of porphyrin derivatives anchored on ordered porous aluminium oxide plates.

An optical oxygen-sensing activity of anchored porphyrin derivatives on ordered porous aluminium oxide plates was studied in relevance to development of new oxygen-sensing systems. Porphyrin derivatives, 5,10,15,20-tetrakis(4-carboxylundecane-1-oxy)porphyrin, 5-[4-(11-carboxylundecane-1-oxy)-10,15,20-triphenyl]porphyrin, 5-(4-carboxylphenyl)-10,15,20-triphenylporphyrin, and their platinum complexes, 5,10,15,20-tetrakis(4-carboxylundecane-1-oxy)porphyrinatoplatinum(II), 5-[4-(11-carboxylundecane-1-oxy)-10,15,20-triphenyl]porphyrinatoplatinum(II), 5-(4-carboxylphenyl)-10,15,20-triphenylporphyrinatoplatinum(II), were synthesized and anchored by an equilibrium adsorption method on aluminium oxide plates, which were prepared by an anodic oxidation. The excitation spectra of the porphyrin-anchored layers showed a broadened and blue-shifted Soret band compared with the corresponding porphyrins in DMSO. The luminescence intensity decreased with increasing oxygen concentrations. The oxygen-sensing ability estimated from I(0)/I(100) (I(0) and I(100) denote the luminescence intensity in 0 and 100% oxygen) was 9.08, 6.78, 8.71, 81.9, 35.5, and 39.1, which are greater than those of corresponding porphyrin derivatives in DMSO under the measured conditions, and indicates the remarkable enhancement effect of platinum(II). Non-linear Stern-Volmer plots were well fitted by the two component system to give the oxygen-sensitive constant (K(SV1)/%(-1)), the oxygen-insensitive constant (K(SV2)/%(-1)), and the former contribution (f(1)): 0.232, 3.32 x 10(-2), and 0.642; 0.141, 2.05 x 10(-2), and 0.687; 0.143, 1.05 x 10(-2), and 0.882; 17.3, 7.04 x 10(-3), and 0.980; 10.2, 1.43 x 10(-2), and 0.935; 16.3, 8.35 x 10(-3), and 0.954. The response time for the change of the atmospheric gas from argon to oxygen was 9.4 s, 12.5 s, 9.6 s, 5.0 s, 8.9 s, and 4.6 s, indicating the shortening effect of platinum. The reverse effect of platinum was observed in the change from oxygen to argon: 15.5 s, 17.0 s, 20.8 s, 667.4 s, 590.1 s, and 580.4 s, indicating the specific interaction of oxygen to the platinum(II) center.     

Physical activity assessment with accelerometers: an evaluation against doubly labeled water

This review focuses on the ability of different accelerometers to assess daily physical activity as compared with the doubly labeled water (DLW) technique, which is considered the gold standard for measuring energy expenditure under free-living conditions. The PubMed Central database (U.S. NIH free digital archive of biomedical and life sciences journal literature) was searched using the following key words: doubly or double labeled or labeled water in combination with accelerometer, accelerometry, motion sensor, or activity monitor. In total, 41 articles were identified, and screening the articles' references resulted in one extra article. Of these, 28 contained sufficient and new data. Eight different accelerometers were identified: 3 uniaxial (the Lifecorder, the Caltrac, and the CSA/MTI/Actigraph), one biaxial (the Actiwatch AW16), 2 triaxial (the Tritrac-R3D and the Tracmor), one device based on two position sensors and two motion sensors (ActiReg), and the foot-ground contact pedometer. Many studies showed poor results. Only a few mentioned partial correlations for accelerometer counts or the increase in R(2) caused by the accelerometer. The correlation between the two methods was often driven by subject characteristics such as body weight. In addition, standard errors or limits of agreement were often large or not presented. The CSA/MTI/Actigraph and the Tracmor were the two most extensively validated accelerometers. The best results were found for the Tracmor; however, this accelerometer is not yet commercially available. Of those commercially available, only the CSA/MTI/Actigraph has been proven to correlate reasonably with DLW-derived energy expenditure.     

Effects of acidic and basic macromolecules on the activity of protein phosphatase-1

The dephosphorylation of phosphorylase a by the catalytic subunit of protein phosphatase-1 obtained from rabbit skeletal muscle is inhibited by heparin in a noncompetitive manner with respect to phosphorylase a (Ki = 8 micrograms/ml). The inhibitory effect of heparin is also observed in the presence of effectors (e.g., glucose and AMP) modifying the dephosphorylation of phosphorylase a. Heat-stable protein inhibitors of protein phosphatase-1 can develop their inhibitory effect of the activity of protein phosphatase-1 even in the presence of heparin. The inhibitory effect of heparin and the heat-stable inhibitor-2 of phosphatase is additive. Polybrene, a heparin antagonist, prevented phosphatase-1 from the inhibition caused by heparin or the inhibitors. Proteins with basic character, histone fractions (H1, H3) and protamine sulfate, can counteract with the inhibitory effect of heparin, but they cannot intercept the actions of inhibitor-1 or -2.     

Dielectrophoresis of macromolecules

Dilute solutions of rigid helical macromolecules with permanent dipole moments have been studied with dielectrophoresis. The polymers used were poly-γ-benzyl-L -glutmate and poly-n-butyl isocyanate, both fractions of average molecular weight 120,000. In this phenomenon dipolar molecules migrate in an inhomogeneous electric field towards the region of maximum field strength. The field gradient is produced by a 10-μm diameter Pt wire serving as the inner electrode of a cell, and a 2.5-mm diameter cylinder as the outer electrode. An equilibrium exponential concentration gradient is achieved within a few wire radii of the inner electrode in a matter of minutes, making both kinetic and equilibrium measurements feasible. The concentration gradient is monitored by measuring the change in capacitance ΔC of the cell from its value for a uniform solute concentration. The time dependences of ΔC for the build-up of the concentration gradient towards the equilibrium value, and the decay to a uniform concentration after the field is removed have been calculated, using a frictional coefficient and a Boltzmann factor, β₁, as the sole adjustable parameters. For low voltages (β₁ small), the measured build-up and decay are completely symmetrical, in agreement with theory, and yield the same frictional coefficient. For larger β₁, the build-up is faster, reflecting a reduced frictional coefficient due to partial alignment of the long axes of the polymers in the direction of migration. In either case, the decay determines a diffusion constant of randomly aligned molecules, identical to classical diffusion measurement. The value of ΔC at equilibrium, for β₁ small, determines μ²F², where μ is the dipole moment and F is the internal field at the polymer. Combined with a classical dielectric constant measurement, which gives μ²F, both μ and F may be determined, independent of assumptions about cavity shapes. Dielectrophoresis works in alternating as well as constant fields, provided the dipolar orientation can follow the field reversals. The dispersion of dielectrophoresis with frequency is a sensitive measure of the molecular-weight distribution of a given sample.     

Optical excitation and detection of neuronal activity

Optogenetics has emerged as an exciting tool for manipulating neural activity, which in turn, can modulate behavior in live organisms. However, detecting the response to the optical stimulation requires electrophysiology with physical contact or fluorescent imaging at target locations, which is often limited by photobleaching and phototoxicity. In this paper, we show that phase imaging can report the intracellular transport induced by optogenetic stimulation. We developed a multimodal instrument that can both stimulate cells with subcellular spatial resolution and detect optical pathlength (OPL) changes with nanometer scale sensitivity. We found that OPL fluctuations following stimulation are consistent with active organelle transport. Furthermore, the results indicate a broadening in the transport velocity distribution, which is significantly higher in stimulated cells compared to optogenetically inactive cells. It is likely that this label‐free, contactless measurement of optogenetic response will provide an enabling approach to neuroscience.      

Assessment of physical activity in older individuals: a doubly labeled water study.

We compared the accuracy of two physical activity recall questionnaires and a motion detector in 45- to 84-yr-old women (n = 35) and men (n = 32), using doubly labeled water (DLW) in conjunction with indirect calorimetry as the criterion measure. Subjects were administered the Yale Physical Activity Survey (YPAS) and Minnesota Leisure Time Physical Activity Questionnaire (LTA). Physical activity energy expenditure was determined over a 10-day period by using a Caltrac uniaxial accelerometer and DLW in conjunction with indirect calorimetry. In older women, Minnesota LTA (386 +/- 228 kcal/day) and Caltrac (379 +/- 162 kcal/day) underestimated physical activity by approximately 55% compared with DLW (873 +/- 244 kcal/day). No difference was observed between daily physical activity measured by the YPAS (863 +/- 447 kcal/day) and DLW in older women. In older men, Minnesota LTA (459 +/- 288 kcal/day) and Caltrac (554 +/- 242 kcal/day) underestimated daily physical activity by approximately 50-60% compared with DLW (1,211 +/- 429 kcal/day). No difference was found between physical activity measured by the YPAS (1,107 +/- 612 kcal/day) and DLW in older men. Despite no difference in mean physical activity levels between YPAS and DLW in women and men, Bland and Altman (Lancet 1: 307-310, 1986) analyses demonstrated poor concordance between DLW and YPAS (i.e., limits of agreement = -1,310-1,518 kcal/day). Our data suggest that the Minnesota LTA recall and Caltrac uniaxial accelerometer may significantly underestimate free-living daily physical activity energy expenditure in older women and men. Although the YPAS compares favorably with DLW on a group basis, its use as a proxy measure of individual daily physical activity energy expenditure may be limited in older women and men.