Molecular dynamics simulation reveals DNA-specific recognition mechanism via c-Myb in pseudo-palindromic consensus of mim-1 promoter / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

This study aims to gain insight into the DNA-specific recognition mechanism of c-Myb transcription factor during the regulation of cell early differentiation and proliferation. Therefore, we chose the chicken myeloid gene, mitochondrial import protein 1 (mim-1), as a target to study the binding specificity between potential dual-Myb-binding sites. The c-Myb-binding site in mim-1 is a pseudo-palindromic sequence AACGGTT, which contains two AACNG consensuses. Simulation studies in different biological scenarios revealed that c-Myb binding with mim-1 in the forward strand (complex F) ismore stable than that inthereverse strand (complex R). The principal component analysis (PCA) dynamics trajectory analyses suggested an opening motion of the recognition helices of R2 and R3 (R2R3), resulting in the dissociation of DNA from c-Myb in complex R at 330 K, triggered by the reduced electrostatic potential on the surface of R2R3. Furthermore, the DNA confirmation and hydrogen-bond interaction analyses indicated that the major groove width of DNA increased in complex R, which affected on the hydrogen-bond formation ability between R2R3 and DNA, and directly resulted in the dissociation of DNA from R2R3. The steered molecular dynamics (SMD) simulation studies also suggested that the electrostatic potential, major groove width, and hydrogen bonds made major contribution to the DNA‍-specific recognition. In vitro trials confirmed the simulation results that c-Myb specifically bound to mim-1 in the forward strand. This study indicates that the three-dimensional (3D) structure features play an important role in the DNA-specific recognition mechanism by c-Myb besides the AACNG consensuses, which is beneficial to understanding the cell early differentiation and proliferation regulated by c-Myb, as well as the prediction of novel c-Myb-binding motifs in tumorigenesis.

Structure-activity relationship of coptis alkaloid bitterness inhibited by mPEG-PLLA / 中国中药杂志

Inhibition of bitterness is a significant measure to improve the compliance and clinical efficacy of traditional Chinese medicine(TCM) decoction. According to the characteristics of TCM decoction, such as high dispersion of bitterness components, multi-component bitterness superposition and strong instantaneous stimulation, the research group put forward a new strategy to inhibit bitterness in the early stage based on the self-assembly characteristics of amphiphilic substances in aqueous solution, in order to reduce the distribution of bitterness components in real solution and achieve the purpose of bitter-masking. It was found that the bitter-masking effect of amphiphilic substances was different on the bitter compounds of various structures. Therefore, it was speculated that there might be a certain relationship between the bitter inhibition effect and the substrate structure. In this paper, the interaction between mPEG-PLLA and five bitter alkaloids(bamatine, jatrorrhizine, berberine, epiberberine and coptisine) in Coptidis Rhizoma was studied to explore the effect of substrate structure on the inhibition of bitterness. The sensory test of volunteers was used to determine the bitter-masking effect of mPEG-PLLA on the decoction of Coptidis Rhizoma and its main bitter alkaloids. The molecular docking and molecular force field were applied to locate the bitter groups and the bitter-masking parts. The relationship between the bitter strength and the structure was analyzed by the surface electrostatic potential of the bitter alkaloids, and the correlation between the bitter-masking effect and the structural parameters of the bitter components was explored by factor analysis, so as to clarify the structure-activity relationship of mPEG-PLLA in masking the bitterness of coptis alkaloids. It was found that mPEG-PLLA had significant taste masking effect on the decoction of Coptidis Rhizoma and five alkaloids. The masking effect was obviously related to the structure of different alkaloids: the effect increased with the increase of the number of hydrogen donors, rotatable bonds, molecular weight, and hydrophobicity, and decreased with the increase of surface electrostatic potential, electrophilicity and binding energy with bitter receptors. In this study, the influence of alkaloid structure of Coptidis Rhizoma on the butter-masking effect of mPEG-PLLA was preliminarily elucidated, providing a scientific basis for better exerting the bitter-masking effect of amphiphilic block copolymers.

Funciones de cottorno para árboles como medida e similitud entre campos escalaares moleculares. un estudo de similitud molecular / Contour tree fucctions over molcular scalar fields representations. a moleculaar similarity study / Funções de conorrno de árvore em representaçõe de campos escalares molecularees. um estudo de similaridade molecular

En este trabajo se implementó una función de contorno de un árbol para establecer medidas de similitud molecular. El estudio se realizó con 73 moléculas orgánicas divididas en 8 grupos funcionales optimizadas con un nivel de teoría DFT//B3LYP/6-31G(d,p) a las cuales se les calculó el Potencial Electrostático Molecular y el Laplaciano de la Densidad Electrónica en una rejilla tridimensional. A partir de los valores de estas propiedades, caracterizando y codificando según su topología, se generaron grafos (árboles) que se compararon a través de la función propuesta. La caracterización y clasificación de las moléculas orgánicas con el Potencial Electrostático Molecular muestra una separación correspondiente a moléculas que en su estructura poseen heteroátomos con funciones químicas por lo menos estructuralmente similares, y con el Laplaciano de la Densidad Electrónica se obtuvo como resultado una clasificación acorde con el número de pares de electrones libres asociados a los heteroátomos en las moléculas y a la naturaleza de los átomos que los aportan. Lo anterior evidencia que las funciones de contorno de árbol propuestas en el estudio son una alternativa rápida para clasificar a grosso modo moléculas orgánicas.

In this job, Contour Tree Functions were implemented to establish molecular similarity measures. The study was carried by using 73 organic molecules, divided in 8 functional groups and optimized at theory level DFT//B3LYP/6-31G(d,p). The molecular electrostatic potential and the Laplacian of the electron density in a 3D grid for each one were calculated. From the values of these properties, characterizing and encoding the topology, we generated graphs (trees) that are compared with the proposed function. The characterization and classification of the organic molecules with the molecular electrostatic potential show a separation corresponding to molecules that have heteroatoms in their structure with at least similar chemical functions; with the Laplacian of the electron density we achieved a classification according to the number of free pairs of electrons associated to the heteroatoms in the molecules and to the nature provided by the heteroatoms. This is evidence that Contour Tree Functions proposed in this study are a quick alternative to broadly classify organic molecules.

Neste trabalho, funções de contorno de árvore foram implementadas para estabelecer medidas de similaridade molecular. O estudo foi conduzido com 73 moléculas orgânicas, divididas em 8 grupos funcionais, otimizadas com nível de teoria DFT//B3LYP/6-31G (d,p) para que eles calculassem o potencial eletrostático molecular e o Laplaciano da densidade de elétrons em uma grade tridimensional. A partir dos valores dessas propriedades, caracterização e codificação da topologia, geramos gráficos (árvores) que são comparados com a função proposta. A caracterização e classificação de moléculas orgânicas com potencial eletrostático molecular mostra uma separação correspondente ás moléculas que possuem heteroátomos em sua estrutura com funções químicas, pelo menos, estruturalmente semelhantes. Com o Laplaciano da densidade de elétrons foi obtido como resultado consistente com a classificação do número de pares de elétrons livres associados com heteroátomos nas moléculas e a natureza dos átomos que contribuem. Essa é uma evidência de que as funções de contorno de árvore proposto no estudo são uma alternativa rápida para classificar, grosso modo, moléculas orgânicas.

Alginate Microencapsulation of Islet Cells Using Electrostatic Droplet Generator / 대한이식학회지

BACKGROUND: Microencapsulation of islet cells has been studied for the treatment of type I diabetes to protect islets from immune attack by recipient cells during islet transplantation. In this study, we established optimal preparation conditions for islet microcapsules with good morphology and cell viability by employing an electrostatic droplet generator. METHODS: To obtain good quality islet microcapsules, various parameters such as the inner diameter of the electrostatic droplet generator nozzle, concentrations and infusion rates of alginate, electrostatic strength, and calcium chloride concentrations were tested. The size and shape of the capsules and cell viability were examined by light microscopy, and insulin secretion from the cells was determined by an ELISA analysis. RESULTS: The optimal preparation conditions for microencapsulation were a 0.35 mm inner nozzle diameter, a 1.75% alginate concentration, a 20 mL/hr alginate infusion rate, a 5 kV electrostatic potential, and a 75 mM calcium chloride. Under these conditions, over 90% of the capsules had a proper size (300~350 micrometer) and shape, and cell viability was 91%. Cell viability was maintained at greater than 80% even after the capsules were cultured for 2 weeks. However, glucose-induced insulin secretion of encapsulated islet cells was reduced by 85% compared to that of nonencapsulated cells. CONCLUSIONS: The results showed that an encapsulation technique using an electrostatic droplet generator is useful for making islet microcapsules with good morphology and cell viability. This technique is necessary to study microencapsulation using primary islets, enhancing glucose-induced insulin secretion, and to perform a functional evaluation of encapsulated islets in vivo in the near future.

Histidine-15 and lytic activity of lysozyme.

The literature data on the activity of histidine-15 modified hen egg white lysozyme are conflicting: the modified enzyme is reported to have more activity, similar activity or less activity by different authors. Amino acid analysis had shown modification of the single His-15. Detailed activity studies on His-15-modified (by iodoacetic acid or diethyl pyrocarbonate) lysozyme have shown that the contradicting reports are due to the specific choices of ionic strengths and cell wall substrate concentrations and can be attributed to the substrate being negatively charged. Our analysis suggests that even though histidine-15 is far removed from the active site of lysozyme, its chemical modification or binding of the negatively-charged substrate near it, changes the conformation around the active site. However, the change in the optimum activity on chemically modifying His-15 is small.

Molecular mechanism of facilitated transport by carrier ionophores:A study of energetics.

The mechanism of ion transport by carrier ionophores is investigated. The electrostatic potential is used as index of the binding energy of a cation with valinomycin and enniatin B. The ion binding capacities of these ionophores are studied as functions of conformation and of distance of an approaching ion-complex. The energetics of dirnerisation and the binding energy profile of an ion in dimers of valinomycin and enniatin B are examined. The binding energy profiles and the electrostatic potential surfaces of valinomycin and enniatin B are compared in relation to their biological activities.

Specificity in the interaction of non intercalative groove binding ligands with nucleic acids.

This paper presents results of theoretical computations on the interaction energies and geometries for the binding to nucleic acids of a number of representative groove binding non intercalating drugs: netropsin, distamycin A, SN 18071, etc. The computations account for the specificity of binding in all cases and demonstrate that the formation of hydrogen bonds is not necessary neither for binding nor for the preference for the minor groove of AT sequences of B-DNA. It appears that if a relatively good steric fit can be obtained in the minor groove, the interaction will be preferentially stabilized there by the favorable electrostatic potential generated in this groove by the AT sequences. The computation of the interaction energies in free space does not reproduce, however, the order of affinities of the ligands studied and yields too great values of the binding energies. The introduction of the solvent effect, through the computation of the hydration and cavitation effects, confirms the specificity, improves the ordering and brings the values of the energies close to the experimental ones. The theoretical account of the "surprising" effect of netrospin binding to the major groove of the TψC stem of tRNAPhe confirms the decisive significance of the distribution of the molecular electrostatic potential for the selection of the binding site. The inclusion in the computations of the flexibility of DNA enables to predict correctly the main features of the macromolecular deformation upon the binding of the ligand.

Simple theoretical models for biochemical systems, with applications to DNA.

A set oflogically connected models, to study chemical systems ofbiological interest, is presented. The sequence in the set is dictated by a progressive reduction of details with a corresponding enlargement of the field of application. The exposition starts with models suitable for interactions among a finite number of molecules, passes then to models considering also solvent effects and ends with models specialized for DNA containing systems.

Studies involving the electrostatic potential of valinomycin.

The electrostatic potential of valinomycin in various conformations as obtained by the crystal structures (uncomplexed, complexed) and theoretical considerations have been evaluated and compared. The potential energy profiles along the Ζ axis of the bracelet-like structures show a systematic variation from the uncomplexed to the complexed structure. This type of conformational change and the potential variation are probably associated with different states of ion transport, like the capture and release of ions by the ionophore. Also, the asymmetry of the molecule due to D-HyIV on one side and L-Lac on the other side is reflected in the potential values along the Z-axis, the magnitude of which, is considerable in the uncomplexed structure. The evaluation of the potential at the ab-initio level on smaller fragments indicate that the order of liganding capacity of oxygen is amide > ether > ester. Also, the inductive effects due to alkyl substitution is negligible as evidenced by the potential studies on the substituted amides and esters.