Int. J. Mol. Sci., Volume 10, Issue 5 (May 2009) – 28 articles , Pages 1942-2439

The present study found that ricin toxicity did not only manifest itself as inhibition of protein synthesis, but also induced apoptosis of immune cells and played an extremely significant role in intestinal injury. In this report, we describe a novel method to estimate binding events occurring on intestinal brush border membranes (BBM) based on SPR technology in an attempt to mimic the real intestinal surface capable of interacting physically and/or actively with certain biological molecules. Combined with HPCE-ESI-MS indentification, we obtained 28 kinds of proteins in BBM that interacted with ricin. Full article

The OB-fold is a diverse structure superfamily based on a β-barrel motif that is often supplemented with additional non-conserved secondary structures. Previous deletion mutagenesis and NMR hydrogen exchange studies of three OB-fold proteins showed that the structural stabilities of sites within the conserved β-barrels were larger than sites in non-conserved segments. In this work we examined a database of 80 representative domain structures currently classified as OB-folds, to establish the basis of this effect. Residue-specific values were obtained for the number of Cα-Cα distance contacts, sequence hydrophobicities, crystallographic B-factors, and theoretical B-factors calculated from a Gaussian Network Model. All four parameters point to a larger average flexibility for the non-conserved structures compared to the conserved β-barrels. The theoretical B-factors and contact densities show the highest sensitivity.Our results suggest a model of protein structure evolution in which novel structural features develop at the periphery of conserved motifs. Core residues are more resistant to structural changes during evolution since their substitution would disrupt a larger number of interactions. Similar factors are likely to account for the differences in stability to unfolding between conserved and non-conserved structures. Full article

In this work, attention is mainly focused on those properties of water which are essentially changed in the physiological temperature range of warm-blooded organisms. Studying in detail the half-width of the diffusion peak in the quasi-elastic incoherent neutron scattering, the behavior of the entropy and the kinematic shear viscosity, it is shown that the character of the translational and rotational thermal motions in water radically change near T_H ~ 315 K, which can be interpreted as the temperature of the smeared dynamic phase transition. These results for bulk pure water are completed by the analysis of the isothermic compressibility and the NMR-spectra for water-glycerol solutions. It was noted that the non-monotone temperature dependence of the isothermic compressibility (β_T) takes also place for the water-glycerol solutions until the concentration of glycerol does not exceed 30 mol%. At that, the minimum of β_T shifts at left when the concentration increases. All these facts give us some reasons to assume that the properties of the intracellular and extracellularfluidsare close to ones for pure water. Namely therefore, we suppose that the upper temperature limit for the life of warm-blooded organisms [T_D = (315 ± 3) K] is tightly connected with the temperature of the dynamic phase transition in water. This supposition is equivalent to the assertion that the denaturation of proteins at T ≥ T_H is mainly provoked by the rebuilding of the H-bond network in the intracellular and extracellular fluids, which takes place at T ≥ T_H. A question why the heavy water cannot be a matrix for the intracellular and extracellular fluids is considered. The lower physiological pH limit for the life of warm-blooded organisms is discussed. Full article

Withania somnifera is an important medicinal plant, which is used in traditional medicine to cure many diseases.Flavonoids were determined in the extracts of W. somnifera root (WSREt) and leaf (WSLEt). The amounts of total flavonoids found in WSREt and WSLEt were 530 and 520 mg/100 g dry weight (DW), respectively. Hypoglycaemic and hypolipidaemic effects of WSREt and WSLEt were also investigated in alloxan-induced diabetic rats. WSREt and WSLEt and the standard drug glibenclamide were orally administered daily to diabetic rats for eight weeks. After the treatment period, urine sugar, blood glucose, haemoglobin (Hb), glycosylated haemoglobin (HbA1C), liver glycogen, serum and tissues lipids, serum and tissues proteins, liver glucose-6-phosphatase (G6P) and serum enzymes like aspartate transaminase (AST), alanine transaminase (ALT), acid phosphatase (ACP) and alkaline phosphatase (ALP) levels were determined. The levels of urine sugar, blood glucose, HbA1C, G6P, AST, ALT, ACP, ALP, serum lipids except high density lipoprotein-bound cholesterol (HDL-c) and tissues like liver, kidney and heart lipids were significantly (p < 0.05) increased, however Hb, total protein, albumin, albumin:globulin (A:G) ratio, tissues protein and glycogen were significantly (p < 0.05) decreased in alloxan-induced diabetic rats. Treatment of the diabetic rats with WSREt, WSLEt and glibenclamide restored the changes of the above parameters to their normal level after eight weeks of treatment, indicating that WSREt and WSLEt possess hypoglycaemic and hypolipidaemic activities in alloxan-induced diabetes mellitus (DM) rats. Full article

Aβ_1-40 coated 20 nm gold colloidal nanoparticles exhibit a reversible color change as pH is externally altered between pH 4 and 10. This reversible process may contain important information on the initial reversible step reported for the fibrillogenesis of Aβ (a hallmark of Alzheimer’s disease). We examined this reversible color change by microscopic investigations. AFM images on graphite surfaces revealed the morphology of Aβ aggregates with gold colloids. TEM images clearly demonstrate the correspondence between spectroscopic features and conformational changes of the gold colloid. Full article

The goal of present work was to investigate the use of bioerodible polymeric nanoparticles as carriers of retinoic acid (RA), which is known to induce differentiation of several cell lines into neurons. A novel method, named “Colloidal-Coating”, has been developed for the preparation of nanoparticles based on a copolymer of maleic anhydride and butyl vinyl ether (VAM41) loaded with RA. Nanoparticles with an average diameter size of 70 nm and good morphology were prepared. The activity of the encapsulated RA was evaluated on SK-N-SH human neuroblastoma cells, which are known to undergo inhibition of proliferation and neuronal differentiation upon treatment with RA. The activity of RA was not affected by the encapsulation and purification processes. Full article

The formation of complex organic molecules in a reactor filled with gaseous mixtures possibly reproducing the primitive terrestrial atmosphere and ocean demonstrated more than 50 years ago that inorganic synthesis of prebiotic molecules is possible, provided that some form of energy is provided to the system. After that groundbreaking experiment, gas-phase prebiotic molecules have been observed in a wide variety of extraterrestrial objects (including interstellar clouds, comets and planetary atmospheres) where the physical conditions vary widely. A thorough characterization of the chemical evolution of those objects relies on a multi-disciplinary approach: 1) observations allow us to identify the molecules and their number densities as they are nowadays; 2) the chemistry which lies behind their formation starting from atoms and simple molecules is accounted for by complex reaction networks; 3) for a realistic modeling of such networks, a number of experimental parameters are needed and, therefore, the relevant molecular processes should be fully characterized in laboratory experiments. A survey of the available literature reveals, however, that much information is still lacking if it is true that only a small percentage of the elementary reactions considered in the models have been characterized in laboratory experiments. New experimental approaches to characterize the relevant elementary reactions in laboratory are presented and the implications of the results are discussed. Full article

Mitochondrial dysfunction is a hallmark of almost all diseases. Acquired or inherited mutations of the mitochondrial genome DNA may give rise to mitochondrial diseases. Another class of disorders, in which mitochondrial impairments are initiated by extramitochondrial factors, includes neurodegenerative diseases and syndromes resulting from typical pathological processes, such as hypoxia/ischemia, inflammation, intoxications, and carcinogenesis. Both classes of diseases lead to cellular energetic depression (CED), which is characterized by decreased cytosolic phosphorylation potential that suppresses the cell’s ability to do work and control the intracellular Ca²⁺ homeostasis and its redox state. If progressing, CED leads to cell death, whose type is linked to the functional status of the mitochondria. In the case of limited deterioration, when some amounts of ATP can still be generated due to oxidative phosphorylation (OXPHOS), mitochondria launch the apoptotic cell death program by release of cytochrome c. Following pronounced CED, cytoplasmic ATP levels fall below the thresholds required for processing the ATP-dependent apoptotic cascade and the cell dies from necrosis. Both types of death can be grouped together as a mitochondrial cell death (MCD). However, there exist multiple adaptive reactions aimed at protecting cells against CED. In this context, a metabolic shift characterized by suppression of OXPHOS combined with activation of aerobic glycolysis as the main pathway for ATP synthesis (Warburg effect) is of central importance. Whereas this type of adaptation is sufficiently effective to avoid CED and to control the cellular redox state, thereby ensuring the cell survival, it also favors the avoidance of apoptotic cell death. This scenario may underlie uncontrolled cellular proliferation and growth, eventually resulting in carcinogenesis. Full article

This review is variously a presentation, reflection, synthesis and report with reference to more recent developments of an article – in a journal which has ceased publication – entitled “Some Electrode Theorems with Experimental Corroboration, Inclusive of the Ag/AgCl System” Internet Journal of Chemistry, (http://www.ijc.com), Special Issues: Vol. 2 Article 24 (1999). The results from new lemmas relating charge densities and capacitance in a metallic electrode in equilibrium with an ionic solution are used to explain the data and observed effects due to Esin, Markov, Grahame, Lang and Kohn. Size effects that vary the measured e.m.f. of electrodes due to changes in the electronic chemical potential are demonstrated in experiment and theory implying the need for standardization of electrodes with respect to geometry and size. The widely used Stern modification of the Gouy-Chapman theory is shown to be mostly inapplicable for many of the problems where it is employed. Practical consequences of the current development include the possibility of determining the elusive single-ion activity coefficients of solution ions directly from the expression given by a simplified capacitance theorem, the potential of zero charge and the determination of single ion concentrations of active species in the electrode reactions from cell e.m.f. measurements. Full article

Identification of protein-protein interface residues is crucial for structural biology. This paper proposes a covering algorithm for predicting protein-protein interface residues with features including protein sequence profile and residue accessible area. This method adequately utilizes the characters of a covering algorithm which have simple, lower complexity and high accuracy for high dimension data. The covering algorithm can achieve a comparable performance (69.62%, Complete dataset; 60.86%, Trim dataset with overall accuracy) to a support vector machine and maximum entropy on our dataset, a correlation coefficient (CC) of 0.2893, 58.83% specificity, 56.12% sensitivity on the Complete dataset and 0.2144 (CC), 53.34% (specificity), 65.59% (sensitivity) on the Trim dataset in identifying interface residues by 5-fold cross-validation on 61 protein chains. This result indicates that the covering algorithm is a powerful and robust protein-protein interaction site prediction method that can guide biologists to make specific experiments on proteins. Examination of the predictions in the context of the 3-dimensional structures of proteins demonstrates the effectiveness of this method. Full article

We demonstrate that the temperature-dependent phase behaviors of parallel and perpendicular cylinder-forming block copolymers are governed by domain-domain segregation forces inherently present in block copolymer material itself. With increasing temperature, a parallel cylinder-forming block copolymer experienced a parallel cylinder straightening process before the order-disorder transition (ODT) and did not show long-range composition fluctuations near the ODT temperature due to the weak segregation forces between the block domains. A perpendicular cylinder-forming block copolymer with a strong segregation force between the block domains displayed cylinder orientation transition from perpendicular to parallel below the ODT temperature. On the other hand, a perpendicular cylinder-forming block copolymer material with an exceptionally strong segregation force between the block domains maintained its initial perpendicular cylinder orientation up to near the ODT temperature. In both cases of perpendicular cylinder-forming block copolymers, submicrometer-scale long-range composition fluctuations were observed well above the ODT temperature due to their intrinsically strong segregation forces between the block domains. Full article

Recently, artificial microRNA (amiRNA) has become a promising RNA interference (RNAi) technology. Here, we describe a flexible and reliable method for constructing both single- and multi-amiRNA expression vectors. Two universal primers, together with two specific primers carrying the encoding sequence of amiRNA were designed and utilized to synthesize the functional amiRNA cassette through a one-step PCR. With appropriate restriction sites, the synthesized amiRNA cassettes can be cloned into any site of different destination vectors. Using the method, we constructed both single- and multi-amiRNA expression vectors to target three reporter genes, which code firefly luciferase (Fluc), enhanced green fluorescent protein (EGFP) and β-galactosidase (LacZ), respectively. The expressions of three genes were all specifically inhibited by either the corresponding single- or the multi-amiRNA expression vector in 293T cells. And the RNAi efficiency of each amiRNA produced by both single- and multi-amiRNA expression vectors was comparable. Full article

A newLondon-Eyring-Polanyi-Sato (LEPS) potential energy surface (PES) is used in the O + CH₄ → OH + CH₃ reaction via the quasiclassical trajectory method (QCT). Comparing with the experiments and the former ab initio calculations, the new LEPS PES describes the actual potential energy surface of the O + CH₄ reaction successfully. The four polarization dependent “generalized” differential cross sections (PDDCS) are presented in the center of mass frame. In the meantime, the distribution of dihedral angle [P(φ_r), the distribution of angle between k and j' (P(θ_r)] and the angular distribution of product rotational vectors in the form of polar plots in θ_r andφ_r (P(θ_r, φ_r) are calculated. The isotope effect for the reactions O + CD₄ is also calculated. These results are in good agreement with the experiments. Full article

Nanofiber scaffolds formed by self-assembling peptide RADA16-I have been used for the study of cell proliferation to mimic an extracellular matrix. In this study, we investigated the effect of RADA16-I on the growth of human leukemia cells in vitro and in nude mice. Self-assembly assessment showed that RADA16-I molecules have excellent self-assembling ability to form stable nanofibers. MTT assay displayed that RADA16-I has no cytotoxicity for leukemia cells and human umbilical vein endothelial cells (HUVECs) in vitro. However, RADA16-I inhibited the growth of K562 tumors in nude mice. Furthermore, we found RADA16-I inhibited vascular tube-formation by HUVECs in vitro. Our data suggested that nanofiber scaffolds formed by RADA16-I could change tumor microenvironments, and inhibit the growth of tumors. The study helps to encourage further design of self-assembling systems for cancer therapy. Full article

Quantum dots (QDs) are useful novel luminescent markers, but their embryonic toxicity is yet to be fully established, particularly in oocyte maturation and sperm fertilization. Earlier experiments by our group show that CdSe-core QDs have cytotoxic effects on mouse blastocysts and are associated with defects in subsequent development. Here, we further investigate the influence of CdSe-core QDs on oocyte maturation, fertilization, and subsequent pre- and postimplantation development. CdSe-core QDs induced a significant reduction in the rates of oocyte maturation, fertilization, and in vitro embryo development, but not ZnS-coated CdSe QDs. Treatment of oocytes with 500 nM CdSe-core QDs during in vitro maturation (IVM) led to increased resorption of postimplantation embryos and decreased placental and fetal weights. To our knowledge, this is the first study to report the negative impact of CdSe-core QDs on mouse oocyte development. Moreover, surface modification of CdSe-core QDs with ZnS effectively prevented this cytotoxicity. Full article

The Particle Swarm Optimization (PSO) and Support Vector Machines (SVMs) approaches are used for predicting the thermodynamic parameters for the 1:1 inclusion complexation of chiral guests with β-cyclodextrin. A PSO is adopted for descriptor selection in the quantitative structure-property relationships (QSPR) of a dataset of 74 chiral guests due to its simplicity, speed, and consistency. The modified PSO is then combined with SVMs for its good approximating properties, to generate a QSPR model with the selected features. Linear, polynomial, and Gaussian radial basis functions are used as kernels in SVMs. All models have demonstrated an impressive performance with R² higher than 0.8. Full article

A new possible scenario for the origin of the molecular collective behaviour associated with the emergence of living matter is presented. We propose that the transition from a non-living to a living cell could be mapped to a quantum transition to a coherent entanglement of condensates, like in a multigap BCS superconductor. Here the decoherence-evading qualities at high temperature are based on the Feshbach resonance that has been recently proposed as the driving mechanism for high T_c superconductors. Finally we discuss how the proximity to a particular critical point is relevant to the emergence of coherence in the living cell. Full article

The folding of protein molecules in the GroEL inner cavity under the co-chaperonin GroES lid is widely accepted as a crucial event of GroEL-assisted protein folding. This review is focused on the data showing that GroEL-assisted protein folding may proceed out of the complex with the chaperonin. The models of GroEL-assisted protein folding assuming ligand-controlled dissociation of nonnative proteins from the GroEL surface and their folding in the bulk solution are also discussed. Full article

We recently described Rolly Protein (ROLP), a small protein synthesized by substrate-adherent cells in a broad range of tissues. In a first set of experiments performed taking advantage of bone forming tibial cartilage as an experimental model we showed that ROLP transcription is associated to cells in an active proliferation state, whereas its downregulation is observed when cell proliferation decreases. Taking advantage of siRNA technology we also documented the expression modulation of some apoptosis-related genes in ROLP-silenced cells. In this work we search for the possible molecular interactors of ROLP by using both the antibody array approach as well as the co-immunoprecipitation approach. Results suggest the occurrence of an interaction of ROLP with Erythrocyte membrane Protein Band 4.1/3(Epb4.1/3), an oncosuppressor downregulated in tumor development and in metastatic tissues; in addition we report experimental results that keep in line also with a potential interaction of ROLP with other PDZ-containing proteins. We also present experimental evidences supporting a role played by ROLP in cell adhesion thus supporting the existence of a biologically relevant link between ROLP and Epb4.1/3. We here suggest that ROLP might exert its biological role cooperating with Epb4.1/3, a protein that is involved in biological pathways that are often inhibited in tumor metastasis. Given the role of Epb4.1/3 in contrasting cancerogenesis we think that its cooperation with ROLP might be relevant in cancer studies and deserves further investigation. Full article

Most of our knowledge regarding the process of protein import into mitochondria has come from research employing Saccharomyces cerevisiae as a model system. Recently, several mammalian homologues of the mitochondrial motor proteins were identified. Of particular interest for us is the human Tim14/Pam18-Tim16/Pam16 complex. We chose a structural approach in order to examine the evolutionary conservation between yeast Tim14/Pam18-Tim16/Pam16 proteins and their human homologues. For this purpose, we examined the structural properties of the purified human proteins and their interaction with their yeast homologues, in vitro. Our results show that the soluble domains of the human Tim14/Pam18 and Tim16/Pam16 proteins interact with their yeast counterparts, forming heterodimeric complexes and that these complexes interact with yeast mtHsp70. Full article

The objective of this study was to elucidate the effects of hydroxylpropyl-β-cyclodextrin (HP-β-CD) on the in vitro stability of insulin. It was found that HP-β-CD had positive effects on the stability of insulin in acid and base and under high temperature conditions. Furthermore, use of HP-β-CD could also increase the stability of disulfide bonds which are important to the conformation of insulin. Through ¹H-NMR experiments it was found that the protective effect of HP-β-CD was due to complexation with insulin. The results suggest that the presence of HP-β-CD could improve the stability of insulin in different environments. Full article

This paper shows that the steadystate of a system of conjugated reactions, which are characterized by disproportionation of entropy and proceed in the domain of linear interactions, is an attractor of ordering. Such systems are primed to produce ordering, and life is a specific manifestation of the sustained ordering inherent to the chemistry of carbon. The adenosine triphospate (ATP) molecule has properties which makes ATP hydrolysis to be most appropriate to form such a system in primitive world. Hence, ATP is suggested to play a key role in prebiological evolution. Principles of the origin and evolution of life following from the concept of ordering are stated. Full article

The tumor necrosis factor-alpha (TNF-α) cytokine receptor system modulates apoptosis in many cell types, so we have investigated the role of sTNFR1 in bacterial lipopolysaccharide (LPS)-induced cell death in cultured human decidual stromal cells, hypothesizing that sTNFR1 might play a central role in this action. In this work we characterized in vitro decidual stromal cell viability with LPS treatment and LPS and sTNFR1 co-treatment. We found that LPS treatment induced decidual stromal cell death in a dose-dependent manner and that sTNFR1 blocked the effect of the LPS treatment. There was a significant proliferation among cells co-incubated with LPS at 10 μg/mL and sTNFR1 at 0.1 μg/mL compared with LPS and sTNFR1 at 0.01, 0.05, 0.2 and 0.5 μg/mL (p < 0.01). This study demonstrated that LPS led to decidual stromal cell death in vitro but sTNFR1 down-regulates the cell death due to LPS under the same conditions. Taken together, these results suggested that sTNFR1 could participate in a protective mechanism against endotoxin. Full article

Prior to the emergence of life, it is believed that only L-amino acids were selected for formation of protein and that D-amino acids were eliminated on the primitive Earth. Whilst homochirality is essential for life, the occurrence of proteins containing D-β-aspartyl (Asp) residues in various tissues from elderly subjects has been reported recently. Here, we demonstrate the presence of a D-β-Asp-containing protein in the cardiac muscle of heart, blood vessels of the lung, chief cells of the stomach, longitudinal and circular muscle of the stomach, small intestine and large intestine. Since the D-β-Asp residue occurs through a succinimide intermediate, this isomer may potentially be generated in proteins more easily than initially thought. Formation of the D-β-Asp residue in proteins may be related to stress. Full article

This paper gives an overview of the mathematical methods currently used in quantitative structure-activity/property relationship (QASR/QSPR) studies. Recently, the mathematical methods applied to the regression of QASR/QSPR models are developing very fast, and new methods, such as Gene Expression Programming (GEP), Project Pursuit Regression (PPR) and Local Lazy Regression (LLR) have appeared on the QASR/QSPR stage. At the same time, the earlier methods, including Multiple Linear Regression (MLR), Partial Least Squares (PLS), Neural Networks (NN), Support Vector Machine (SVM) and so on, are being upgraded to improve their performance in QASR/QSPR studies. These new and upgraded methods and algorithms are described in detail, and their advantages and disadvantages are evaluated and discussed, to show their application potential in QASR/QSPR studies in the future. Full article

Jcl:WistarTGN(ARGHGEN)1Nts rat (Mini rat) is a growth hormone (GH)-deficient transgenic rat. The hair cycle in the dorsal skin of male Mini rats enters a long-lasting telogen phase after eights weeks of age, but depilation can induce a transient hair cycle again. In this study, a time-course profiling of genes expression was done on the dorsal skin of male Mini rats along the progression of depilation-induced hair cycle using DNA microarray analysis. As a result, 1,215 probe sets including 1,171 hair cycle-related ones showed more than 3-fold changes in expression compared with that in before-depilation telogen phase. The present data will contribute to elucidating the mechanisms of hair cycle regulation and should lead to the identification of novel molecular targets for hair growth and/or depilation agents. Full article

Fabrication of nano-sized objects is one of the most important issues in nanoscience and nanotechnology. Soft nanomaterials with flexible properties have been given much attention and can be obtained through bottom-up processing from functional molecules, where self-assembly based on supramolecular chemistry and designed assembly have become crucial processes and techniques. Among the various functional molecules, dyes have become important materials in certain areas of nanotechnology and their self-assembling behaviors have been actively researched. In this short review, we briefly introduce recent progress in self-assembly of optical molecules and dyes, based mainly on supramolecular concepts. The introduced examples are classified into four categories: self-assembly of (i) low-molecular-weight dyes and (ii) polymeric dyes and dye self-assembly (iii) in nanoscale architectures and (iv) at surfaces. Full article

Fluoroaromatic compounds are used as agrochemicals and released into environment as pollutants. Glycosylation of 2-, 3-, and 4-fluorophenols using plant cell cultures of Nicotiana tabacum was investigated to elucidate their potential to metabolize these compounds. Cultured N. tabacum cells converted 2-fluorophenol into its β-glucoside (60%) and β-gentiobioside (10%). 4-Fluorophenol was also glycosylated to its β-glucoside (32%) and β-gentiobioside (6%) by N. tabacum cells. On the other hand, N. tabacum glycosylated 3-fluorophenol to β-glucoside (17%). Full article