Molecular dynamics simulation in vacuo and in solution of [Aib5,6-D-Ala8] cyclolinopeptide A: a conformational and comparative study.

The conformation of a Cyclolinopeptide A analogue, c-(Pro-Pro-Phe-Phe-Aib-Aib-Ile-D-Ala-Val), has been investigated by means of molecular dynamics simulations, in various molecular environments. The molecular dynamics results are compared with that obtained for Cyclolinopeptide A and a detailed analysis of the different behaviour for the two compounds is reported. A complete analysis of hydrogen bonds is presented.     

The multifaceted role of TMEM16A in cancer

The calcium-activated chloride channel TMEM16A is intimately linked to cancers. Over decades, TMEM16A over-expression and contribution to prognosis have been widely studied for multiple cancers strengthening the idea that TMEM16A could be a valuable biomarker and a promising therapeutic target. Surprisingly, from the survey of the literature, it appears that TMEM16A has been involved in multiple cancer-related functions and a large number of molecular targets of TMEM16A have been proposed. Thus, TMEM16A appears to be an ion channel with a multifaceted role in cancers.In this review, we summarize the latest development regarding TMEM16A contribution to cancers. We will survey TMEM16A contribution in cancer prognosis, the origins of its over-expression in cancer cells, the multiple biological functions and molecular pathways regulated by TMEM16A. Then, we will consider the question regarding the molecular mechanism of TMEM16A in cancers and the possible basis for the multifaceted role of TMEM16A in cancers.     

Phosphoproteins in dictyostelium discoideum

The phosphoproteins of Dictyostelium discoideum were compared at different stages of development by polyacrylamide gel electrophoresis. Certain phosphoproteins of vegetative amoebae were conserved while others appeared and disappeared during development. Four major phosphoproteins with apparent subunit molecular weights of 50,000, 47,000, 38,000, and 34,000 disappeared precociously in response to exogenous cAMP. Two membranal phosphoproteins, with apparent subunit molecular weights of 80,000 and 81,000, appeared precociously in response to added cAMP. One of these phosphoproteins, molecular weight of 80,000, has been identified tentatively as the “contact site A” glycoprotein. Another membranal protein, with apparent subunit molecular weight of 42,000, unaffected in its appearance by cAMP, has been identified tentatively as phosphoactin.     

Genetic variation in wheat endosperm proteins: an analysis by two-dimensional electrophoresis using intervarietal chromosomal substitution lines

Summary The major endosperm proteins in a range of genotypes of hexaploid wheat have been fractionated by two-dimensional electrophoresis. The genotypes included nine varieties and forty four intervarietal substitution lines in which chromosomes 1A, 1B, 1D, 6A, 6B or 6D from eight of the varieties have been introduced one at a time into a common genetic background. The appearance of different protein subunits was often correlated with a chromosome substitution. This showed that many of the genes for the high molecular weight protein subunits (molecular weight range 55,000 to 140,000 determined by SDS polyacrylamide gel electrophoresis) are specified by chromosomes 1A, 1B and 1D while many of the lower molecular weight subunits (molecular weight range 30,000 to 45,000) are specified by chromosomes 6A, 6B and 6D. The different protein subunits correlated with chromosome substitution could not always be recognised in the varietal source of the substituted chromosome. The different subunits specified by homologous chromosomes in different wheat varieties may differ in isoelectric point and/or molecular weight.     

超富集植物吸收富集重金属的生理和分子生物学机制

与普通植物相比,超富集植物在地上部富集大量重金属离子的情况下可以正常生长,其富集重金属的机理已经成为当前植物逆境生理研究的热点领域．尤其是近两年,随着分子生物学等现代技术手段的引人,关于重金属离子富集机理的研究取得了一定进展．通过与酵母突变株功能互补克隆到了多条编码微量元素转运蛋白的全长cDNA;也从分子水平上研究了谷胱甘肽、植物螯合素、金属硫蛋白、有机酸或氨基酸等含巯基物质与重金属富集之间的可能关系．本文从植物生理和分子生物学角度简要评述超富集植物对重金属元素的吸收、富集、整合及区室化的机制．     

Differences in conformational behavior of ATA and TAT sequences in single strand DNA trimer.

The conformational behavior of single strand (ss) TAT and ATA trimers of DNA have been studied by computational chemistry tools including CICADA software interfaced with AMBER molecular mechanics and dynamics. The Single-Coordinate-Driving (SCD) method has been used in conjunction with molecular dynamics simulated annealing. It has been revealed that the conformational flexibility of each sequence differs substantially from the other one. Four common conformational families have been found for both trimers. These are: helical, reverse-stacked (base 3), half-stacked (base 3), reverse-stacked (base 1). However, the energies of conformers representing the families are different for both the studied systems. An additional conformational family, bulged, has been found for ss(ATA), while ss(TAT) has been found also in half-stacked (base 1) conformation. In general, ss(TAT) exhibits a higher number of low energy conformations while ss(ATA) shows one interesting low energy conformational interconversion between reverse-stacked (A3) family and half-stacked (A3) family. The high conformational variability of the trimers has been confirmed by flexibility analysis and by molecular dynamics simulations, which have also shown the conformational stability of single conformational families. It has been concluded that the methodology used is able to provide a very detailed picture of the conformational space of these molecules.     

Quantum-classical simulation methods for hydrogen transfer in enzymes: a case study of dihydrofolate reductase

A variety of theoretical approaches have been used to investigate hydrogen transfer in enzymatic reactions. The free energy barriers for hydrogen transfer in enzymes have been calculated using classical molecular dynamics simulations in conjunction with quantum mechanical/molecular mechanical and empirical valence bond potentials. Nuclear quantum effects have been included with several different approaches. Applications of these approaches to hydride transfer in dihydrofolate reductase are consistent with experimental measurements and provide significant insight into the protein conformational changes that facilitate the hydride transfer reaction.     

Differences in Conformational Behavior of ATA and TAT Sequences in Single Strand DNA Trimer

Abstract

The conformational behavior of single strand (ss) TAT and ATA trimers of DNA have been studied by computational chemistry tools including CICADA software interfaced with AMBER molecular mechanics and dynamics. The Single-Coordinate-Driving (SCD) method has been used in conjunction with molecular dynamics simulated annealing. It has been revealed that the conformational flexibility of each sequence differs substantially from the other one. Four common conformational families have been found for both trimers. These are: helical, reverse-stacked (base 3), half-stacked (base 3), reverse-stacked (base 1). However, the energies of conformers representing the families are different for both the studied systems. An additional conformational family, bulged, has been found for ss(ATA), while ss(TAT) has been found also in half-stacked (base 1) conformation. In general, ss(TAT) exhibits a higher number of low energy conformations while ss(ATA) shows one interesting low energy conformational interconversion between reverse-stacked (A3) family and half-stacked (A3) family. The high conformational variability of the trimers has been confirmed by flexibility analysis and by molecular dynamics simulations, which have also shown the conformational stability of single conformational families. It has been concluded that the methodology used is able to provide a very detailed picture of the conformational space of these molecules.     

Human chromokinesin KIF4A functions in chromosome condensation and segregation

Accurate chromosome alignment at metaphase and subsequent segregation of condensed chromosomes is a complex process involving elaborate and only partially characterized molecular machinery. Although several spindle associated molecular motors have been shown to be essential for mitotic function, only a few chromosome arm--associated motors have been described. Here, we show that human chromokinesin human HKIF4A (HKIF4A) is an essential chromosome-associated molecular motor involved in faithful chromosome segregation. HKIF4A localizes in the nucleoplasm during interphase and on condensed chromosome arms during mitosis. It accumulates in the mid-zone from late anaphase and localizes to the cytokinetic ring during cytokinesis. RNA interference--mediated depletion of HKIF4A in human cells results in defective prometaphase organization, chromosome mis-alignment at metaphase, spindle defects, and chromosome mis-segregation. HKIF4A interacts with the condensin I and II complexes and HKIF4A depletion results in chromosome hypercondensation, suggesting that HKIF4A is required for maintaining normal chromosome architecture. Our results provide functional evidence that human KIF4A is a novel component of the chromosome condensation and segregation machinery functioning in multiple steps of mitotic division.     

三种致病疫霉交配型分子检测方法的比较

致病疫霉Phytophthora infestans属于异宗配合卵菌,当A1、A2两种交配型同时存在时,可以进行有性生殖,产生卵孢子。检测疫霉菌交配型的传统方法是采用对峙培养,这种方法耗时长并且需要标准的A1、A2交配型菌株作为参照。因此,人们希望开发出更加简便和快捷的可直接基于核苷酸序列差异的分子检测方法。目前,已报道了3个与致病疫霉交配型紧密连锁的分子标记可用于交配型的检测。本研究用64株致病疫霉菌比较了3种基于交配型分子标记的检测方法与传统方法检测的结果。结果显示,依据分子标记的3种分子检测方法与传统对峙培养方法测定的交配型结果一致率为61%-73%,而且3种分子检测方法都不能检测出自育菌株。因此,致病疫霉交配型的分子检测方法还有待进一步研究。     

Febrile seizures: traffic slows in the heat

Febrile seizures, which occur in young children, have long been known to have a major inherited component. Mutations in some genes that encode sodium channel and GABA(A) receptor subunits have been found in a few families affected by febrile seizures. These mutations account only for a minority of cases, and much remains to be learnt about the molecular architecture of febrile seizures. A rare inherited cause--a mutation in the GABA(A) receptor subunit GABRG2 gene--has been recently shown to cause a temperature-dependent intracellular trafficking defect. This is an important step in unravelling the molecular pathogenesis of this common childhood disorder.     

Purification, immunological and biochemical characterization of Ap4A binding protein from Xenopus laevis oocytes.

Diadenosine 5',5'-P1,P4-tetraphosphate (Ap4A) binding protein specifically binds Ap4A. The protein has been purified from Xenopus laevis oocytes and presents an estimated molecular weight of 100,000 by gel filtration. In the first stages of the purification, the Ap4A binding activity is found associated to DNA polymerase alpha-DNA primase, forming heterogeneous high molecular weight complexes. A monoclonal antibody has been prepared against the purified Ap4A binding protein. The antibody partially neutralizes the Ap4A binding activity. Using the immunoblot technique, it has been shown that the antibody is able to recognize either native or SDS-denatured Ap4A binding protein. The monoclonal antibody immunoreacted with a polypeptide of 90,000 which coincides with the molecular weight obtained by gel chromatography and indicates that the native Ap4A binding protein from Xenopus oocytes is probably a monomeric protein.     

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.     

Molecules and morphologies: the perpetuation of pattern in the ciliated protozoa.

Three apparently conflicting generalizations concerning the relationships between molecules and cell structure may be derived from studies on cellular patterning in the ciliates. (A) Cells with identical genes and molecular composition may have different hereditary patterns. (B) Genes, through their prescribed molecular derivatives, constrain the modes of pattern permutation and define the states of greatest stability. (C) Cells with identical hereditary patterns may have entirely different genes and molecular compostitons. These priniciples may be reconciled through the recognition that they are characteristically applicable over different time intervals. Hereditary differences within a clone and without related molecular differences (principle A) may persist for hundreds of cell generations, but they are resolved eventually within a constant environment (principle B) as the configuration of minimal free energy is approached. On an even longer time scale, molecular substitutions have occurred for many or most components of the cell, but these have been constrained by selective pressures on an ancient design (principle C) that disallow substitutions affecting certain form-function relations which have been elevated to an adaptive peak.     

Molecular and cellular aspects of development of arbuscular mycorrhizal symbiosis and its role in plant life

Development of arbuscular mycorrhizal (AM) symbiosis with plant root system in term of molecular and cellular events have been analysed. A role of AM symbiosis in plant life has been discussed. Molecular methods for analysis of arbuscular mycorrhizal fungi have been described.     

Molecules and Morphologies: The Perpetuation of Pattern in the Ciliated Protozoa*†

SYNOPSIS. Three apparently conflicting generalizations concerning the relationships between molecules and cell structure may be derived from studies on cellular patterning in the ciliates. (A) Cells with identical genes and molecular composition may have different hereditary patterns. (B) Genes, through their prescribed molecular derivatives, constrain the modes of pattern permutation and define the states of greatest stability. (C) Cells with identical hereditary patterns may have entirely different genes and molecular compositions. These principles may be reconciled through the recognition that they are characteristically applicable over different time intervals. Hereditary differences within a clone and without related molecular differences (principle A) may persist for hundreds of cell generations, but they are resolved eventually within a constant environment (principle B) as the configuration of minimal free energy is approached. On an even longer time scale, molecular substitutions have occurred for many or most components of the cell, but these have been constrained by selective pressures on an ancient design (principle C) that disallow substitutions affecting certain form-function relations which have been elevated to an adaptive peak.     

Detection of Infectious Astroviruses in Water

A method based on the infection of CaCo-2 cells and molecular hybridization with a specific cDNA probe has been developed for the detection of infectious astroviruses in environmental samples. By this procedure wild-type astroviruses have been detected in water from an area where a concurrent gastroenteritis outbreak was reported.     

Cytogenetic and molecular abnormalities in myelodysplastic syndrome

Myelodysplastic syndrome (MDS) is a heterogeneous group of clonal hematological disorders characterized by ineffective hematopoiesis which causes peripheral cytopenias and a risk of progression to acute myeloid leukemia. Although various forms of chromosomal abnormalities have been detected in approximately 50-60% of patients with de novo MDS and in up to 80% of patients with therapy-related MDS, their molecular significance for pathogenesis and disease progression is not yet fully understood. Recent technical advances in molecular biology have disclosed more accurately details of pathological chromosomal and molecular aberrations in MDS. Such details could not be identified with conventional cytogenetical techniques, including G-banding. In particular, with recent technical advances in comparative genome hybridization or single nucleotide polymorphism array technology, several candidate genes for the pathogenesis of MDS have been identified, which are located in minimally deleted or uniparental disomy segments. Moreover, epigenetic deregulation of gene expression is also likely to be involved in the pathogenesis of MDS. Accordingly, in addition to classical oncogenic abnormalities, such as p53 abnormalities, or NRAS mutation, various molecular abnormalities, such as TET2, RPS14, or c-CBL, have been identified and/or proposed as the novel candidates for molecular basis of the development and progression of MDS. A better understanding of the causative molecular events underlying MDS pathogenesis is essential for the development and establishment of a more effective treatment resulting in a complete cure for MDS. We here review current knowledge regarding the molecular significance of chromosomal and genetic aberrations in MDS and the proposed molecular mechanisms of action of new agents for MDS, such as lenalidomide or azacitidine.     

Subunit structures of AMP deaminase isozymes in rat

AMP deaminases A and B have been purified to apparent homogeneity from rat muscle and liver, respectively. The molecular weights of 286,000 and 351,000 were obtained for the native muscle and liver enzymes, respectively, by sedimentation equilibrium studies. On polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate, the muscle preparation exhibited a single polypeptide band with a molecular weight of 72,000; the liver preparation, a molecular weight of 85,000. The data indicate that each enzyme has a tetrameric structure.     

Molecular clocks in reptiles: life history influences rate of molecular evolution

Life history has been implicated as a determinant of variation in rate of molecular evolution amongst vertebrate species because of a negative correlation between body size and substitution rate for many molecular data sets. Both the generality and the cause of the negative body size trend have been debated, and the validity of key studies has been questioned (particularly concerning the failure to account for phylogenetic bias). In this study, a comparative method has been used to test for an association between a range of life-history variables-such as body size, age at maturity, and clutch size-and DNA substitution rate for three genes (NADH4, cytochrome b, and c-mos). A negative relationship between body size and rate of molecular evolution was found for phylogenetically independent pairs of reptile species spanning turtles, lizards, snakes, crocodile, and tuatara. Although this study was limited by the number of comparisons for which both sequence and life-history data were available, the results suggest that a negative body size trend in rate of molecular evolution may be a general feature of reptile molecular evolution, consistent with similar studies of mammals and birds. This observation has important implications for uncovering the mechanisms of molecular evolution and warns against assuming that related lineages will share the same substitution rate (a local molecular clock) in order to date evolutionary divergences from DNA sequences.