Lateral mobility of phospholipid molecules in thin liquid films

The Fluorescence Recovery After Photobleaching (FRAP) method was applied to measure the lateral mobility of the fluorescent lipid analog, dioctadecylindocarbocyanine perchlorate (Dil-C18), in microscopic thin liquid films (Foam Films (FFs)). The foam film structures were comprised of two phosphatidylcholine monolayers adsorbed at air/water interfaces which sandwiched a thin liquid core. Lateral diffusion of the DiI molecules in the plane of the monolayers was determined as a function of the thickness of the thin liquid core of the film between the FF monolayers. The results obtained indicated that the diffusion coefficient was strongly dependent both on the distance between the FF monolayers in the range 4 nm to 85 nm (corresponding to the FF thickness) and on the film type. The applicability of the FRAP method for studying the molecular mobility in phospholipid FFs was demonstrated. Considerable differences in the surface diffusion coefficient of Dil were observed, ranging between 2 × 10^–8 cm²/s and 22 × 10^–8 cm²/s in so called yellow, gray, common black and Newton black FFs. The effect of the presence of polyethylene glycol (PEG-400) in the liquid core of lecithin FFs on surface diffusion was also studied. The surface diffusion results from the FF studies were compared with data from black lipid membranes (BLMs). These structures are related in thickness terms but the molecular orientation in FFs is the reverse of that in BLMs. Correspondence to: Z. Lalchev     

Fine morphology of frontal filaments in nauplii of cirriped crustaceans

Fine morphology of the frontal filaments (FFs) at all nauplius stages of two barnacle species (Verruca stroemia and Hesperibalanus hesperius) has been investigated by scanning electron microscopy. FFs have been detected at the second nauplius stage and persist during all stages. FFs contain a wide proximal and a fine distal parts, but they are not actually separated as segments of the limbs, and the area between them looks like a single cuticular crease. Apical and subapical pores have been found at the top of each FF in the larvae of both species, which may indicate the chemoreceptor function of these organs.     

Chemical and molecular mechanisms of antioxidants: experimental approaches and model systems

Free radicals derived from oxygen, nitrogen and sulphur molecules in the biological system are highly active to react with other molecules due to their unpaired electrons. These radicals are important part of groups of molecules called reactive oxygen/nitrogen species (ROS/RNS), which are produced during cellular metabolism and functional activities and have important roles in cell signalling, apoptosis, gene expression and ion transportation. However, excessive ROS attack bases in nucleic acids, amino acid side chains in proteins and double bonds in unsaturated fatty acids, and cause oxidative stress, which can damage DNA, RNA, proteins and lipids resulting in an increased risk for cardiovascular disease, cancer, autism and other diseases. Intracellular antioxidant enzymes and intake of dietary antioxidants may help to maintain an adequate antioxidant status in the body. In the past decades, new molecular techniques, cell cultures and animal models have been established to study the effects and mechanisms of antioxidants on ROS. The chemical and molecular approaches have been used to study the mechanism and kinetics of antioxidants and to identify new potent antioxidants. Antioxidants can decrease the oxidative damage directly via reacting with free radicals or indirectly by inhibiting the activity or expression of free radical generating enzymes or enhancing the activity or expression of intracellular antioxidant enzymes. The new chemical and cell-free biological system has been applied in dissecting the molecular action of antioxidants. This review focuses on the research approaches that have been used to study oxidative stress and antioxidants in lipid peroxidation, DNA damage, protein modification as well as enzyme activity, with emphasis on the chemical and cell-free biological system.     

Three-dimensional quantitative structure (3-D QSAR) activity relationship studies on imidazolyl and N-pyrrolyl heptenoates as 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) inhibitors by comparative molecular similarity indices analysis (CoMSIA)

A comparative molecular similarity indices analysis (CoMSIA) of a set of 29 imidazolyl and N-pyrrolyl heptenoates have been performed to find out the structural requirements for 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) inhibitory activity. The HMG like side chain, a common moiety of statins, was used to align the molecules. The results guide to design new chemical entities with high potency.     

Chemical genetics: exploring and controlling cellular processes with chemical probes.

The new field of chemical biology brings together chemists and biologists who are seeking to understand and mimic the natural world. One research strategy in this new field is the development of biologically active small molecules as molecular probes. This approach, which has been called 'chemical' genetics, has allowed elucidation of several pathways that have been difficult to study using traditional genetic approaches.     

Kernel energy method: application to DNA

The kernel energy method (KEM) has been used in three recent papers (1-3) to calculate the quantum mechanical ab inito molecular energy of peptides and the protein insulin. It was found to have good accuracy. The computational difficulty of representing a molecule increases only modestly with the number of atoms. The calculations are simplified by adopting the approximation that a full biological molecule can be represented by smaller "kernels" of atoms. In this paper, the accuracy of the KEM is tested in the application to DNA, whose basic kernels, chemical bonding, and overall molecular structure are quite different from peptides and proteins. The basic kernel in the case of peptides and proteins is an amino acid. The basic kernel in the case of DNA is a nucleotide consisting of a phosphate-sugar-base. The molecular energy is calculated for all three basic types of DNA, i.e., B, A, and Z configurations of DNA. The results give an accuracy that is comparable to that achieved with peptides and proteins. Thus, the KEM is found to be applicable to major types of biological molecules.     

Enhanced development of porcine embryos cloned from bone marrow mesenchymal stem cells

In the present study, we have characterized an isolated population of porcine bone marrow mesenchymal stem cells (MSCs) for multilineage commitment and compared the developmental potential of cloned embryos with porcine MSCs and fetal fibroblasts (FFs). MSCs exhibited robust alkaline phosphatase activity and later transformed into mineralized nodules following osteoinduction. Furthermore, MSCs underwent adipogenic and chondrogenic differentiation by producing lipid droplets and proteoglycans, respectively. Primary cultures of FFs from a female fetus at ~30 day of gestation were established. Donor cells at 3-4 passage were employed for nuclear transfer (NT). Cell cycle analysis showed that the majority of MSCs in confluence were in the G0/G1 stage. Cumulus-oocyte complexes were matured and fertilized in vitro (IVF) as control. The cleavage rate was significantly (P<0.05) higher in IVF than in NT embryos with MSCs and FFs (84.54.6% vs. 52.25.4% and 50.85.2%, respectively). However, blastocyst rates in IVF and NT embryos derived from MSCs (20.62.5% and 18.43.0%) did not differ, but were significantly (P<0.05) higher than NT derived from FFs (9.52.1%). Total cell number and the ratio of ICM to total cells among blastocysts cloned from MSCs (34.45.2 and 0.380.08, respectively) were significantly (P<0.05) higher than those from FFs (22.65.5 and 0.180.12, respectively). Proportions of TUNEL positive cells in NT embryos from FFs (7.31.8%) were significantly (P<0.05) higher than in MSCs (4.61.3%) and IVF (2.50.9%). The results clearly demonstrate that multipotent bone marrow MSCs have a greater potential as donor cells than FFs in achieving enhanced production of cloned porcine embryos.     

Novel forms of chemical protein diversity -- in nature and in the laboratory

Novel chemical variants of proteins have been found in nature, including potent 'microprotein' natural products and folded protein molecules that contain a cyclic polypeptide chain. Researchers have used chemical synthesis and genetic methods to make these proteins and more: protein catenanes, neoglycoproteins, and artificial protein molecules with novel architectures or made from novel building blocks. De novo design has taken a big step forward with the accurate design and construction of proteins with complex molecular structure. A variety of non-coded amino acids and other building blocks has been used to make increasingly sophisticated protein molecular devices for use as biosensors and for the study of signal transduction inside living cells.     

Do night and around-the-clock firefighters’ shift schedules induce deviation in tau from 24 hours of systolic and diastolic blood pressure circadian rhythms?

Systolic (S) and diastolic (D) blood pressures (BP) [SBP and DBP] are circadian rhythmic with period (τ) in healthy persons assumed to be maintained at 24.0h. We tested this assumption in a sample of 30 healthy career (mean >12 yrs) 30-to-46 yr-old male Caucasian French firefighters (FFs) categorized into three groups according to work schedule and duties: Group A – 12 FFs working 12h day, 12h night, and occasionally 24h shifts and whose primary duties are firefighting plus paramedical and road rescue services; Group B – 9 FFs working mostly 12h day and 12h night shifts and whose duties are answering incoming emergency calls and coordinating service vehicle dispatch from fire stations with Group A personnel; Group C – 9 day shift (09:00–17:00h) FFs charged with administrative tasks. SBP and DBP, both in winter and in summer studies of the same FFs, were sampled by ambulatory BP monitoring every 1h between 06:00–23:00h and every 2h between 23:01–05:59h, respectively, their approximate off-duty wake and sleep spans, for 7 consecutive days. Activity (wrist actigraphy) was also sampled at 1-min intervals. Prominent τ of each variable was derived by a power spectrum program written for unequal-interval time series data, and between-group differences in incidence of τ≠24h of FFs were assessed by chi square test. Circadian rhythm disruption (τ≠24h) of either the SBP or DBP rhythm occurred almost exclusively in night and 24h shift FFs of Group A and B, but almost never in day shift FFs of Group C, and it was not associated with altered τ from 24.0h of the circadian activity rhythm. In summer, occurrence of τ≠24 for FFs of Group A and B differed from that for FFs of Group C in SBP (p=0.042) and DBP (p=0.015); no such differences were found in winter (p>0.10). Overall, manifestation of prominent τ≠24h of SBP or DBP time series was greater in summer than winter, 27.6% versus 16.7%, when workload of Group B FFs, i.e. number of incoming emergency telephone calls, and of Group A FFs, i.e. number of dispatches for provision of emergency services, was, respectively, two and fourfold greater and number of 12h night shifts worked by Group B FFs and number of 24h shifts worked by Group A FFs was, respectively, 92% and 25% greater. FFs of the three groups exhibited no winter-summer difference in τ≠24h of SBP or SDP; however, τ≠24h of DBP in Group B FFs was more frequent in summer than winter (p=0.046). Sleep/wake cycle disruption, sleep deprivation, emotional and physical stress, artificial light-at-night, and altered nutrient timings are hypothesized causes of τ≠24h for BP rhythms of affected Groups A and B FFs, but with unknown future health effects.     

High-throughput assays for promiscuous inhibitors

High-throughput screening (HTS) searches large libraries of chemical compounds for those that can modulate the activity of a particular biological target; it is the dominant technique used in early-stage drug discovery. A key problem in HTS is the prevalence of nonspecific or 'promiscuous' inhibitors. These molecules have peculiar properties, act on unrelated targets and can dominate the results from screening campaigns. Several explanations have been proposed to account for promiscuous inhibitors, including chemical reactivity, interference in assay read-out, high molecular flexibility and hydrophobicity. The diversity of these models reflects the apparently unrelated molecules whose behaviors they seek to explain. However, a single mechanism may explain the effects of many promiscuous inhibitors: some organic molecules form large colloid-like aggregates that sequester and thereby inhibit enzymes. Hits from HTS, leads for drug discovery and even several drugs appear to act through this mechanism at micromolar concentrations. Here, we report two rapid assays for detecting promiscuous aggregates that we tested against 1,030 'drug-like' molecules. The results from these assays were used to test two preliminary computational models of this phenomenon and as benchmarks to develop new models.     

Molecular chirality and the origin of life

In the living systems L-amino acids and D-sugars are found with almost no exceptions. Although all the molecular chirality must have been established prior to the emergence of life, the origin of the asymmetry of molecules is still an unsolved problem. The time of appearance of the asymmetry of molecules, therefore, was quite problematic during chemical evolution.Since Pasteur's discovery in 1848, a large number of works for solving this problem have been carried out on the basis of mathematics, physics or chemistry. All the proposals which put forth for breaking the symmetry are still considered to be too weak to explain the cause of obtaining the chiral purity as a result of the symmetry breaking of molecules. In order to expand our scope, new sources of the symmetry breaking of molecules should be considered.In this article, some approaches to the achiral-chiral transition are reviewed, which will give an idea for the origin of asymmetry of molecules.     

Chemical approaches to the lysophospholipid receptors

Both ligand-based and GPCR privileged scaffold chemical tools have recently emerged to provide new insights into the function and physiology of the GPCR lysophospholipid receptors both in vitro and in vivo. Both rational, design-based approaches as well as hybrid approaches where high throughput screening has been coupled to an understanding of critical molecular interactions have been productive in advancing understanding of physiology and potential therapeutics in this field. It is now feasible to identify reasonably potent and selective small molecules that provide chemical proof-of-concept in vivo directly from high throughput screening. These developments, coupled with the availability of receptor knock-out mice, presage rapid progress in the field.     

Developing hybrid molecule therapeutics for diverse enzyme inhibitory action: Active role of coumarin-based structural leads in drug discovery

Hybrid drugs featuring two or more potentially bioactive pharmacophores have been recognized as advanced and superior chemical entities to simultaneously modulate multiple drug targets of multifactorial diseases, thus overcoming the severe side effects associated with a single drug molecule. The selection of these chemical moieties to produce hybrid structures with druggable properties is generally facilitated by the observed and/or anticipated synergistic pharmacological activities of the individual molecules. In this perspective, coumarin template has extensively been studied in pursuit of structurally diverse leads for drug development due to high affinity and specificity to different molecular targets. This review highlights the most commonly exploited approaches conceptualizing the design and construction of hybrid molecules by coupling two or more individual fragments with or without an appropriate linker. In addition to the design strategies, this review also summarizes and reflects on the therapeutic potential of these hybrid molecules for diverse enzyme inhibitory action as well as their observed structure-activity relationship (SAR). Several key features of the synthesized hybrid structures that assert a profound impact on the inhibitory function have also been discussed alongside computational investigations, inhibitor molecular diversity and selectivity toward multiple drug targets. Finally, these drug discovery and development efforts should serve as a handy reference aiming to provide a useful platform for the exploration of new coumarin-based compounds with enhanced enzyme inhibitory profile.     

Interaction between aromatic antibiotics and vitamins: 1H NMR analysis of the heteroassociation of nicotinamide and anthracycline antitumor antibiotics

The interaction between anthracycline antitumor antibiotics daunomycin and novatrone and the vitamin nicotinamide has been investigated by one- and two-dimensional 1H NMR spectroscopy (500 MHz). Due to significant differences in structures of the chromophores of interacting molecules, a two-site heteroassociation model has been developed, allowing the arrangement of one and two nicotinamide molecules on the chromophore of the antibiotic. The equilibrium association constant, thermodynamical parameters (deltaH, deltaS) of the heteroassociation of nicotinamide with daunomycin and novatrone and the induced proton chemical shifts in the heterocomplexes have been determined from the concentration and temperature dependences of proton chemical shifts of interacting molecules. The most favorable structures of 1:1 nicotinamide--daunomycin and nicotinamide-novatrone heteroassociation complexes have been determined using both the molecular mechanics methods (X-PLOR software) and the calculated values of induced proton chemical shifts. Analysis of the results obtained allows one to conclude that two nicotinamide molecules cannot simultaneously bind on one side of the chromophore of antibiotic. Heterocomplexes of the vitamin with the antibiotics with a stoichiometry 1:1 are mainly stabilized by the stacking of aromatic chromophores.     

Robustness and modularity properties of a non-covalent DNA catalytic reaction

The biophysics of nucleic acid hybridization and strand displacement have been used for the rational design of a number of nanoscale structures and functions. Recently, molecular amplification methods have been developed in the form of non-covalent DNA catalytic reactions, in which single-stranded DNA (ssDNA) molecules catalyze the release of ssDNA product molecules from multi-stranded complexes. Here, we characterize the robustness and specificity of one such strand displacement-based catalytic reaction. We show that the designed reaction is simultaneously sensitive to sequence mutations in the catalyst and robust to a variety of impurities and molecular noise. These properties facilitate the incorporation of strand displacement-based DNA components in synthetic chemical and biological reaction networks.     

Symmetry and information content of chemical structures

A method, based on symmetry, is suggested for determining the information content of systems. A comparison has been made between the information for symmetry, topology, and chemical composition. The new information measure increases when the asymmetry of the molecules and the number of atoms in the latter increases. It can distinguish between different molecular conformations, and give a linear correlation with the absolute entropy for homologous series of chemical compounds.     

Free energy of helical transmembrane peptide dimerization in OPLS-AA/Berger force field simulations: inaccuracy and implications for partner-specific Lennard-Jones parameters between peptides and lipids

Interactions between transmembrane (TM) peptides are important in biophysical chemistry, but there are few studies assessing atomistic simulation parameters concerning the energetics of interactions of TM helical peptides. Our potential of mean force analysis using OPLS-AA protein/Berger lipid force fields (FFs) shows that the dimerisation energy of (AALALAA)₃ helical peptides in the dioleoylphosphatidylcholine bilayer is ?4.4 kJ/mol, which was much smaller than the reported experimental value (?12.7 kJ/mol), thus calling for improvement of parameters of the combined FFs. As each of the FFs has been independently developed, we then tested the effects of downscaling the Lennard-Jones (LJ) energy terms between the OPLS-AA atoms and Berger lipid atoms, preserving the parameters within each FF. A 0.9-fold rescaling of the LJ energies was found to render the dimerisation energy close to the experimental value. Solvation of backbone atoms as well as side chain atoms in lipids is crucial for the TM helix interaction. In similar analyses, GROMOS 53A6 FF exhibited as weak dimerisation propensity (~?5.2 kJ/mol) as OPLS-AA/Berger, but CHARMM36 showed relatively accurate propensity (~?9.9 kJ/mol). Challenges and strategies in rendering the TM interaction energy realistic within the framework of current FFs are discussed.