A CFF 91-based Continuum Solvation Model: Solvation Free Energies of Small Organic Molecules and Conformations of the Alanine Dipeptide in Solution

Abstract

For molecular mechanics simulations of solvated molecules, it is important to use a consistent approach for calculating both the force field energy and the solvation free energy. A continuum solvation model based upon the atomic charges provided with the CFF91 force field is derived. The electrostatic component of the solvation free energy is described by the Poisson-Bolzmann equation while the nonpolar comonent of the solvation energy is assumed to be proportional to the solvent accessible surface area of the solute. Solute atomic radii used to describe the interface between the solute and solvent are fitted to reproduce the energies of small organic molecules. Data for 140 compounds are presented and compared to experiment and to the results from the well-characterized quantum mechanical solvation model AM1-SM2. In particular, accurate results are obtained for amino acid neutral analogues (mean unsigned error of 0.3 kcal/mol). The conformational energetics of the solvated alanine dipeptide is discussed.     

崇测冰帽不同的冰川样品可培养细菌群落结构差异北大核心CSCD

【目的】研究细菌群落组成在西昆仑崇测冰帽冰川雪样、冰碛物和土样中的差异。【方法】通过传统的纯培养和菌株16S r RNA基因序列鉴定,分析菌株在门水平和属水平的群落结构。【结果】冰川细菌由Actinobacteria、Firmicutes、Proteobacteria和Bacteroidetes 4个门组成。雪样以Proteobacteria为优势,而土样和冰碛物则以Actinobacteria为优势。在属的水平上,冰川土样中的优势属仅有Arthrobacter,雪样中的优势属主要有Methylobacterium、Modestobacter、Hymenobacter、Brevundimonas、Bacillus这5种。雪环境的细菌群落结构与冰碛物和土样的差异性较大,而冰碛物和土样之间的差异性不大。Skermanella可能为崇测冰帽所特有的细菌。【结论】初步说明了在冰川退缩的气候环境下,冰川雪样细菌多样性的脆弱性,以及冰川雪环境细菌资源保护的重要性。     

Ice Nucleus Production of Fusarium moniliforme var. subglutinans in Relation to Its Growth Characteristics

The effects of culture conditions on the ice nucleus production of Fusarium moniliforme var. subglutinans isolated from the gut of larvae of the rice stem borer (Chilo suppressalis Walker) were examined. The ice nucleus production was only affected by cultivation temperature and pH: the optimum temperature and pH were 15°C to 20°C and 4.0 to 6.0, respectively.     

Relationship between Recrystallization Rate of Ice Crystals in Sugar Solutions and Water Mobility in Freeze-Concentrated Matrix

To better understand the relation between recrystallization rate and water mobility in freeze-concentrated matrix, isothermal ice recrystallization rates in several sugar aqueous solutions and self-diffusion coefficients of water component in corresponding freeze-concentrated matrix were measured. The sugars used were fructose, glucose, maltose, and sucrose. The sugar concentrations and temperature were varied so that ice contents for all samples were almost equal. Neither recrystallization rates nor diffusion coefficients depended uniformly on temperature. The recrystallization rates increased with increasing the diffusion coefficients, and a direct relationship was found between recrystallization rate and diffusion coefficient. This indicated that self-diffusion coefficient of water component in freeze-concentrated matrix is a useful parameter for predicting and controlling recrystallization rate in sugar solutions relevant to frozen desserts.     

Hydration of lysozyme as observed by infrared spectrometry

Infrared spectra of a film of lysozyme 3 mum thick, immersed in an atmosphere displaying a relative humidity, or hygrometry, which spans the whole range from 0 to 1 at room temperature, are recorded. The evolution of the spectra with this relative humidity is quantitatively analyzed on the basis of a newly proposed method. It allows the precise measurement of the quantity of water that remains embedded inside the dried sample at each stage of hydration, and the definition, in terms of chemical reactions of the three hydration mechanisms that correspond to the three hydration spectra on which all experimental spectra can be decomposed. With respect to preceding similar studies, some refinements are introduced that allow improvement of the interpretation, but that also raise some new questions, which mainly concern the structure of the hydrogen-bond network around the carbonyl peptide groups.     

Effect of HPr phosphorylation on structure,dynamics, and interactions in the course of transcriptional control

The serine46-phosphorylated form of the bacterial protein HPr fulfils an essential function in carbon catabolite repression (CCR). Using molecular dynamics (MD) we studied the effect of Ser46 phosphorylation on the molecular properties of HPr and its capability to act as the co-repressor of carbon catabolite protein A (CcpA). The calculated pK (a) values for a representative set of HPr(Ser46P) structures indicate that the phosphate group of HPr(Ser46P) exists predominantly in the unprotonated form under neutral conditions. A hydrogen bond detected in HPr(Ser46P) between one phosphate-group oxygen and a side-chain hydrogen of Asn43-an amino acid conserved in all HPr proteins of Gram-positive bacteria that regulate their carbon consumption by CCR-might fulfil an important role in CcpA-HPr(Ser46P) complex formation. MD simulations show that the Ser46P-Asn43 hydrogen bond present in the unbound structure is replaced by intermolecular interactions upon complex formation. The degree to which amino acids in the CcpA-HPr(Ser46P) interface contribute to cofactor binding was analyzed by in silico alanine scanning. Lys307, Arg303, Asp296, Val300, and Tyr295 of CcpA were identified as important amino acids for the CcpA-HPr(Ser46P) interaction. Three of these residues are directly involved in sensing the correct phosphorylation state at His15(HPr) and Ser46(HPr). A substitution of interface residues Val319, Val314, Ser316, Leu321 and Gln320 by alanine showed that these amino acids, which contact helix alpha2 of HPr(Ser46P), play a less prominent role for complex formation.     

小麦冰重结晶抑制蛋白基因TaIRI5的克隆及分析

为了明确小麦冰重结晶抑制蛋白基因(TaIRI5)在小麦生长发育过程中的作用,该研究以小麦品种‘北京841’为材料,利用RT-PCR方法克隆TaIRI5基因,并对该基因进行生物信息学分析、组织特异性表达分析、启动子活性分析以及亚细胞定位分析。结果显示:(1)成功克隆到TaIRI5基因,该基因全长1203 bp,开放阅读框为858 bp,编码285个氨基酸,蛋白质分子量为70.7 kD,等电点为5.07,属于疏水性蛋白。(2)实时荧光定量PCR结果显示,TaIRI5基因在小麦的根、茎、叶片、雌蕊、雄蕊、护颖、种子中均有表达,其中根部的相对表达量最高,在雌蕊中表达量最低,表明该基因在小麦的生长发育过程中起重要作用。(3)TaIRI5基因的启动子分析表明,该区域除CAAT-box和TATA-box启动子核心元件外,该序列还包含9个光响应元件和6个激素应答元件及其他元件;利用TaIRI5基因不同长度(498 bp、999 bp、1500 bp)的3个候选启动子,构建了含有GUS基因的pCAMBIA1301融合表达载体;烟草转化实验表明,3个候选启动子都能启动该基因的表达,但表达模式略有差异。(4)成功构建含有GFP基因的融合载体pCAMBIA1300-TaIRI5-GFP,亚细胞定位结果显示,TaIRI5定位于细胞膜上。该研究结果为进一步研究小麦TaIRI5基因功能奠定了基础。     

Partial Reversion by 5-Aminouracil of the Inhibition of Coleoptile Growth in Hordeum vulgare by Large Volumes of Water

Barley seedlings show a differential response to an increasein the volume of water on which they are grown. On 20 ml, ascompared with 9 ml of water, germination of some seeds is delayedand growth of some coleoptiles is inhibited at 45 h. Both effectsincrease progressively from 9 to 20 ml. Treatment with 5-aminouracilcan reverse, in part, the effects of high volumes of water.With 12, 17, and 20 ml of solution 5-AU increases the frequencyof germination and coleoptile growth. Its effect is most markedon 20 ml of solution, i.e. the volume that produces the greatestover-all inhibition of growth when seeds are on water is theone at which 5-AU is most effective in stimulating growth. Ofthe three concentrations tested, 10^–4 M was most effectivewhen used at a volume of 20 ml.     

Inhibition of branching and spine maturation by repulsive guidance molecule in cultured cortical neurons

Repulsive guidance molecule (RGM) is a membrane-bound protein that was originally identified as an axon guidance molecule in the visual system. Functional studies in Xenopus and chick embryos revealed the roles of RGM in axon guidance and laminar patterning, while those in mouse embryos demonstrated its function in regulating cephalic neural tube closure. Moreover, RGM inhibition enhanced the growth of injured axons and promoted functional recovery after spinal cord injury in rats. Here, we demonstrate in vitro that RGMa, an RGM homolog, inhibits neurite growth and cortical neuron branching on mouse embryonic day 16. Further, exposure of cultured neurons to RGMa significantly reduced the number of colocalized immunoreactive clusters of synapsin 1 and PSD-95 in the spines. This RGMa-mediated inhibition of the assembly of presynaptic and postsynaptic components suggests a role of RGMa in inhibiting mature synapse formation. Thus, RGMa may negatively regulate neuronal network formation in cortical neurons.     

Inhibition of Ribonuclease A by polyphenols present in green tea

We report the effect of the natural polyphenolic compounds from green tea on the catalytic activity of Ribonuclease A (RNase A). The compounds behave as noncompetitive inhibitors of the protein with inhibition constants ranging from 80-1300 microM. The dissociation constants range from 50-150 microM for the RNase A-polyphenol complexes as determined by ultraviolet (UV) and circular dichroism (CD) studies. We have also investigated the changes in the secondary structure of RNase A on complex formation by CD and Fourier transformed infrared (FTIR) spectroscopy. The presence of the gallate moiety has been shown to be important for the inhibition of enzymatic activity. Docking studies for these compounds indicate that the preferred site of binding is the region encompassing residues 34-39 with possible hydrogen bonding with Lys 7 and Arg 10. Finally we have also looked at changes in the accessible surface area of the interacting residues on complex formation for an insight into the residues involved in the interaction.     

Altered secretary efficiency of Streptomyces hygroscopicus transglutaminase in Escherichia coli by the pro-peptide modification

Streptomyces transglutaminase (TGase) is naturally synthesized as a zymogen (pro-TGase), which is then processed to produce the active enzyme through removal of its pro-peptide. In this study, we investigated the effect of the pro-peptide on the secretion of Streptomyces hygroscopicus TGase in Escherichia coli by modifying its pro-peptide. Four N-terminal amino acid residues (Tyr12, Asn27, Asn30, and Arg32) in the pro-peptide predicted to interact with TGase region through hydrogen bonds. When the four amino acid residues were mutated into Ala, the secretion of TGase was partially or completely inhibited. Furthermore, deletion of the C-terminal α-helix^37–42 in the pro-peptide concomitantly decreased the secretion of TGase. However, deletion of the C-terminal loop^43–52 of the pro-peptide, resulted in increased secretion of TGase by approximately 70% as compared with the control native pro-peptide. These findings indicate that modification of the pro-peptide has a significant impact on the secretory efficiency of TGase in E. coli.     

A Multisubstrate Kinetic Mechanism of Dopamine Transport in the Nucleus Accumbens and Its Inhibition by Cocaine

Abstract: Kinetic studies of dopamine transport into suspensions of nucleus accumbens (NAcc) and effects of Na⁺ and Cl^? as cosubstrates were performed using rotating disk electrode voltammetry. To mimic chemical neurotransmission, dopamine was added as a rapid pulse, and transporter-mediated clearance of dopamine was evaluated kinetically. This paradigm was shown to approximate a zero trans entry transport experiment. Dopamine was taken up with apparent K_m and V_max values of 1.3 µM and 375 pmol/s/g wet weight, respectively. Transport exhibited apparent trans acceleration. Substitution of Na⁺ with choline or Cl^? with isethionate reduced dopamine transport with reaction orders of two and unity, respectively, accompanied by reductions in V_max with no changes in K_m. Apparent K_Na and K_Cl values were 70.0 and 92.1 mM, respectively. Dopamine transport in NAcc was found to follow a partially random, sequential mechanism in which dopamine and Na⁺ bind randomly to the transporter followed by binding of Cl^? before transport. Cocaine inhibited dopamine transport and the influences of the other substrates allosterically with an overall K_i of 0.30 µM. Thus, the general kinetic mechanism of the transport of dopamine in the NAcc is identical to that previously reported by this laboratory for dopamine transport in the striatum. However, the dopamine transporter in the NAcc is more tightly regulated by Na⁺, possesses a higher kinetic turnover rate, is four times more sensitive to cocaine than the striatal transporter, and exhibits cocaine inhibition independent of [substrate]. These findings suggest that cocaine modulates chemical signaling in NAcc differently than in striatum, providing down-regulation of function irrespective of [substrate], thereby enhancing dopaminergic signaling more robustly in the NAcc than in the striatum.     

重组人内皮抑素对食管癌细胞生长抑制作用的体外研究

目的:探讨重组人内皮抑素(rhES)对食管鳞癌系KYSE-150及TE1细胞生长的影响。方法:应用四甲基偶氮唑盐(MTT)法,以大鼠成纤维细胞L929为对照细胞,检测rhES不同浓度(0、12.5、25、50、100、200、400、600μg/ml)和作用时间(24h、48h)对食管鳞癌系KYSE-150、TE1和L929细胞的生长抑制作用。结果:大鼠L929细胞经rhES处理后,吸光度A值轻微降低,差异不具有统计学意义(P>0.05),食管鳞癌系KYSE-150、TE1经rhES处理后,吸光度A值明星降低,差异具有统计学意义(P<0.05)。结论:rhES明显抑制食管鳞癌系KYSE-150及TE1细胞增殖,且呈时间-剂量依赖性。     

Inhibition of Tumor Cell Growth in vitro by Damavaricin C Derivatives

Damavaricin C, a degradative derivative of streptovaricin C, has a new active hydroxyl group at the C–19 position of the naphthoquinone moiety where various groups can be substituted by ether linkage. The biological activities of these ethers were compared against animal cells, including normal, virus transformed, and human cancer cells in vitro. Some of derivatives showed preferential lethal activity on virus transformed cells in vitro.     

Functional aberration of myofibrils by cardiomyopathy-causing mutations in the coiled-coil region of the troponin-core domain

Two cardiomyopathy-causing mutations, E244D and K247R, in human cardiac troponin T (TnT) are located in the coiled-coil region of the Tn-core domain. To elucidate effects of mutations in this region on the regulatory function of Tn, we measured Ca²⁺-dependent ATPase activity of myofibrils containing various mutants of TnT at these residues. The results confirmed that the mutant E244D increases the maximum ATPase activity without changing the Ca²⁺-sensitivity. The mutant K247R was shown for the first time to have the effect similar to the mutant E244D. Furthermore, various TnT mutants (E244D, E244M, E244A, E244K, K247R, K247E, and K247A) showed various effects on the maximum ATPase activity while the Ca²⁺-sensitivity was unchanged. Molecular dynamics simulations of the Tn-core containing these TnT mutants suggested that the hydrogen-bond network formed by the side chains of neighboring residues around residues 244 and 247 is important for Tn to function properly.     

Four of the Most Common Mutations in Primary Hyperoxaluria Type 1 Unmask the Cryptic Mitochondrial Targeting Sequence of Alanine:glyoxylate Aminotransferase Encoded by the Polymorphic Minor Allele

The gene encoding the liver-specific peroxisomal enzyme alanine:glyoxylate aminotransferase (AGT, EC. 2.6.1.44) exists as two common polymorphic variants termed the “major” and “minor” alleles. The P11L amino acid replacement encoded by the minor allele creates a hidden N-terminal mitochondrial targeting sequence, the unmasking of which occurs in the hereditary calcium oxalate kidney stone disease primary hyperoxaluria type 1 (PH1). This unmasking is due to the additional presence of a common disease-specific G170R mutation, which is encoded by about one third of PH1 alleles. The P11L and G170R replacements interact synergistically to reroute AGT to the mitochondria where it cannot fulfill its metabolic role (i.e. glyoxylate detoxification) effectively. In the present study, we have reinvestigated the consequences of the interaction between P11L and G170R in stably transformed CHO cells and have studied for the first time whether a similar synergism exists between P11L and three other mutations that segregate with the minor allele (i.e. I244T, F152I, and G41R). Our investigations show that the latter three mutants are all able to unmask the cryptic P11L-generated mitochondrial targeting sequence and, as a result, all are mistargeted to the mitochondria. However, whereas the G170R, I244T, and F152I mutants are able to form dimers and are catalytically active, the G41R mutant aggregates and is inactive. These studies open up the possibility that all PH1 mutations, which segregate with the minor allele, might also lead to the peroxisome-to-mitochondrion mistargeting of AGT, a suggestion that has important implications for the development of treatment strategies for PH1.     

High resolution crystal structure of rat long chain hydroxy acid oxidase in complex with the inhibitor 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1, 2, 3-thiadiazole. Implications for inhibitor specificity and drug design

Long chain hydroxy acid oxidase (LCHAO) is responsible for the formation of methylguanidine, a toxic compound with elevated serum levels in patients with chronic renal failure. Its isozyme glycolate oxidase (GOX), has a role in the formation of oxalate, which can lead to pathological deposits of calcium oxalate, in particular in the disease primary hyperoxaluria. Inhibitors of these two enzymes may have therapeutic value. These enzymes are the only human members of the family of FMN-dependent l-2-hydroxy acid-oxidizing enzymes, with yeast flavocytochrome b₂ (Fcb2) among its well studied members. We screened a chemical library for inhibitors, using in parallel rat LCHAO, human GOX and the Fcb2 flavodehydrogenase domain (FDH). Among the hits was an inhibitor, CCPST, with an IC₅₀ in the micromolar range for all three enzymes. We report here the crystal structure of a complex between this compound and LCHAO at 1.3 Å resolution. In comparison with a lower resolution structure of this enzyme, binding of the inhibitor induces a conformational change in part of the TIM barrel loop 4, as well as protonation of the active site histidine. The CCPST interactions are compared with those it forms with human GOX and those formed by two other inhibitors with human GOX and spinach GOX. These compounds differ from CCPST in having the sulfur replaced with a nitrogen in the five-membered ring as well as different hydrophobic substituents. The possible reason for the ∼100-fold difference in affinity between these two series of inhibitors is discussed. The present results indicate that specificity is an issue in the quest for therapeutic inhibitors of either LCHAO or GOX, but they may give leads for this quest.     

乌梁素海冰封期浮游植物分布特征及其与水质指标的关系北大核心CSCD

为揭示寒旱区冰封期富营养化湖泊水体中浮游植物群落结构及其与水质指标的响应关系,该研究以乌梁素海为对象,于2019年1月在湖区设立12个采样点采集水样及浮游植物,通过对浮游植物定性定量检测和水体理化性质测定分析,以明确冰封期乌梁素海浮游植物群落结构空间变化特征及主要水质指标的分布规律;结合RDA分析和Pearson相关性分析揭示了浮游植物与水质指标的响应关系,为水体富营养化程度评估及防控提供理论依据。结果显示:(1)冰封期乌梁素海12个样点的水质指标特征差异明显,各水质指标从北到南具有不同的变化趋势。(2)冰封期乌梁素海共检出浮游植物61种,其中隐藻门的丰度最高(4.76×10^(6)个·L^(-1)),甲藻门的生物量最高(18.09 mg·L^(-1)),但湖区不同位置的优势浮游植物类群有所差异,北湖区蓝隐藻和伪鱼腥藻丰度明显高于南湖区。(3)不同种类的浮游植物在空间分布上存在明显的差异,且在P3样点的多样性最低,P8样点的多样性最高,并发现中、下湖区物种类型多且组成较为均匀。(4)浮游植物的丰度与TP呈显著正相关关系,生物量与TP呈极显著正相关关系,多样性指数与TP呈正相关关系。研究表明,冰封期乌梁素海水体处于中等营养水平,水体中总磷(TP)含量是影响浮游植物物种丰度和生物量的主要影响因子;寒旱区冰封期富营养化湖泊浮游植物分布特征为北湖区隐藻门、蓝藻门和甲藻门占优势;南湖区中绿藻门丰度最高。     

Complete Growth Inhibition of Bacillus subtilis by Nisin-Producing Lactococci in Fermented Soybeans

The growth inhibition by nisin-producing lactococci against Bacillus subtilis and its application to soybean miso fermentation were investigated. Lactococcus lactis subsp. lactis IFO12007 (nisin-producing, salt-intolerant) rapidly proliferated to more than 10⁹ cells/g in cooked soybeans without any excessive pH decrease. In spite of the mild decrease in pH, the growth of B. subtilis was completely inhibited; no living cells were detected in a soybean sample inoculated with 10⁶ cells/g and incubated for 24 to 72 h. This Lc. lactis was applied to soybean miso fermentation as a starter culture. It produced high nisin activity (1.28×10⁵ AU/g) in cooked soybean, resulting in the complete growth inhibition of B. subtilis, which had been inoculated at the beginning of the koji fermentation, throughout the process of miso production. Over-acidification, which is undesirable for miso quality, was successfully prevented simply by adding salt which killed the salt-intolerant Lc. lactis. Furthermore, the nisin activity in miso disappeared with aging.