Amicyanin metal-site structure and interaction with MADH: PAC and NMR spectroscopy of Ag-, Cd-, and Cu-amicyanin

To investigate the structural control mechanisms in the metal site of amicyanin when interacting with MADH, redox-inactive Ag⁺- and Cd²⁺-substituted amicyanins were studied with perturbed angular correlations of -rays (PAC) spectroscopy. PAC experiments on ^111mCd-substituted amicyanin revealed two different metal-site structures, which are very likely in dynamic exchange on a ~5 ns timescale. Only one structure binds to MADH. The dissociation constants, K _d, are 9±2 M with MADH^red and 38±11 M with MADH^ox, indicating that the Cd-amicyanin binding affinity is regulated by the MADH redox state. PAC experiments on ¹¹¹Ag-substituted amicyanin also showed two different forms of Ag-amicyanin, probably reflecting relaxation from Ag to Cd geometry. No binding of Ag-amicyanin to MADH could be observed with PAC, suggesting that the K _d is larger than 43 M, based on the 95% confidence limit. NMR revealed large chemical shift differences between native copper amicyanin and both metal-substituted forms. Affected residues are found up to 15 Å away from the metal ion. The Ag⁺- and Cd²⁺-substituted amicyanins demonstrate no change in coordination as a function of pH, contrary to Cu⁺-amicyanin which shows protonation of the copper ligand His96 with pK _a=6.8. It is concluded that, contrary to other blue copper proteins, Ag⁺-amicyanin is not a close mimic of Cu⁺-amicyanin, and that structural changes in the metal site have large effects on the affinity for the redox partner.Electronic Supplementary Material Supplementary material is available in the online version of this article at Abbreviations AOM angular overlap model - HSQC heteronuclear single-quantum coherence - MADH methylamine dehydrogenase - MADH^ox oxidized MADH - MADH^red reduced MADH - NOESY nuclear Overhauser effect spectroscopy - NQI nuclear quadrupole interaction - PAC perturbed angular correlations of -rays - TOCSY total correlation spectroscopy     

Efficient minimization of angle-dependent potentials for polypeptides in internal coordinates

Angular potentials play an important role in the refinement of protein structures through angle-dependent restraints (e.g., those determined by cross-correlated relaxations, residual dipolar couplings, and hydrogen bonds). Analytic derivatives of such angular potentials with respect to the dihedral angles of proteins would be useful for optimizing such restraints and other types of angular potentials (i.e., such as we are now introducing into protein structure prediction) but have not been described. In this article, analytic derivatives are calculated for four types of angular potentials and integrated with the efficient recursive derivative calculation methods of Gō and coworkers. The formulas are implemented in publicly available software and illustrated by refining a low-resolution protein structure with idealized vector-angle, dipolar-coupling, and hydrogen-bond restraints. The method is now being used routinely to optimize hydrogen-bonding potentials in ROSETTA.     

祁连山高寒草原主要植物种群格局对冬季放牧的响应

以肃南裕固族自治县鹿场冬季牧场为研究对象,采用偏离系数及t检验方法结合Ripley''s K函数及蒙特卡罗随机模拟对紫花针茅种群与醉马草种群进行格局分析,进一步采用计盒维数与信息维数对紫花针茅种群与醉马草种群进行分形分析,揭示在放牧系统中优势植物的种群变化。格局分析结果表明：牧场植物的种群格局出现5种变化规律。紫花针茅种群的偏离系数在放牧率3.64 AUM/hm²时^#,出现最小值。醉马草种群的偏离系数在放牧率4.16AUM/hm²时,出现最大值。在0-1 m的研究尺度内,紫花针茅种群与醉马草种群的Ripley''s K函数结果均在蒙特卡洛随机模拟区间内,呈随机分布格局。分形分析结果表明：伴随放牧率增大,紫花针茅种群的计盒维数区间为[1.596,1.962],醉马草种群的计盒维数区间为[1.831,1.945];紫花针茅种群的信息维数区间为[1.590,1.899],醉马草种群的信息维数区间为[1.633,1.913]。在放牧率4.34 AUM/hm²时,紫花针茅种群与醉马草种群空间占据差值达到最大,信息维数相对较低,种群分布相对均匀,格局变化相对缓慢,经济效益与生态效益相平衡,最适合管理牧场。     

Fractal root system of Melica przewalskyi along different aspect in degraded grassland

Aims Fractal root system is phenotypic plasticity result of plant root architecture to respond to environmental heterogeneity, may reflect the growth strategy of plants to adapt to environmental conditions. Our objective was to explore the relationship between root fractal dimension and fractal abundance of fractal root system of Melica przewalskyi population in response to aspect variation in the northwest of China. Methods The study site was located in a degraded alpine grassland on the northern slope in Qilian Mountains, Gansu Province, China. Survey and sampling were carried out at 40 plots which were set up along four slope aspects transects with 20 m distance between adjacent plots. Handheld GPS was used to determine the elevation, longitude and latitude of each plot. ArcGIS was used to set up digital elevation model (DEM). Community traits were investigated and six individuals roots of M. przewalskyi were collected randomly at each plot. The samples were cleaned and divided into different organs, then scanning the root with the Win-RHIZO for measurements of fractal dimension and fractal abundance in laboratory, and their biomass were then measured after being dried at 80 °C in an oven. Important findings With the slope aspect turned from north to east, west, and south, the density, height and soil moisture content of the plant community displayed a pattern of initial decline, the height, density, root fractal abundance of M. przewalskyi increased and the root fractal dimension decreased. The root fractal dimension was negatively associated with the fractal abundance in all aspects, but the relationship varied along the slope aspects gradient; there was a highly significant negative correlation (p < 0.01) between the root fractal dimension and fractal abundance at north slope and south slope aspect, whereas the correlation only reached a significant level (p < 0.05) at the east slope aspect and west slope aspect; indicating that there is a trade-off between the root fractal dimension and fractal abundance. In addition, when the slope aspect changed from north to east, west and south, the standardized major axis (SMA) slope of the regression equation in the scaling relationships between root fractal dimension and fractal abundance increased (p < 0.05), indicating that the roots of M. przewalskyi at the droughty southern slope have less branch and more sparse in the same soil volume of root exploitation and utilization. Consequently, the resource allocation pattern on reasonable trade-off between root fractal dimension and fractal abundance in different slope aspect of M. przewalskyi, reflects the relationship between the income and the cost of construction of plant root architecture.     

遗传密码格式的组合编码数分析

用N个密码子对m个编码对象进行编码的编码格式是m元N维空间中的一个顶点。64个密码子对20种氨基酸和终止密码子进行编码格式的组合编码数是一个十分巨大的数字。对多元高维编码空间的拓扑特性进行了分析和研究 ,并由此推导出m -N空间的特性三角的排列方式以及给出特性三角公式的数学证明。指出 ,目前的遗传密码的编码格式是21元64维编码空间的一个顶点。应用组合数学分析的方法 ,计算了遗传密码格式的最大组合编码数CM =4.19×1084 ,基因组遗传密码的组合编码数CG =1.13×1080 以及线粒体遗传密码的组合编码数CT =1.38×1079 等。分析结果表明 ,遗传密码的指定是一个小概率事件 ,可能来源于λ简并后的偶数三联密码配对的组合编码的对称破缺     

Prediction analysis for microbiome sequencing data

One goal of human microbiome studies is to relate host traits with human microbiome compositions. The analysis of microbial community sequencing data presents great statistical challenges, especially when the samples have different library sizes and the data are overdispersed with many zeros. To address these challenges, we introduce a new statistical framework, called predictive analysis in metagenomics via inverse regression (PAMIR), to analyze microbiome sequencing data. Within this framework, an inverse regression model is developed for overdispersed microbiota counts given the trait, and then a prediction rule is constructed by taking advantage of the dimension‐reduction structure in the model. An efficient Monte Carlo expectation‐maximization algorithm is proposed for maximum likelihood estimation. The method is further generalized to accommodate other types of covariates. We demonstrate the advantages of PAMIR through simulations and two real data examples.     

黄土高原南麓县域耕地土壤速效养分时空变异

在生态脆弱的黄土高原南麓合阳县,以1983、2006年耕地土壤速效氮、磷、钾含量为对象,利用空间自相关、变异函数及分形维数等方法,研究县域土壤速效养分时空变异特征及主要影响因素.结果表明,从1983到2006年,除土壤速效钾外,耕地速效氮、磷的平均含量分别提高73.98％和92.69％;土壤速效养分全局Moran's I指数和空间相关距均呈递减变化、分维数增加,预示其空间结构减弱,随机变异性增强.土壤速效氮、磷含量在绝大部分研究区域内呈现不同程度累积,而速效钾含量则在59.65％的耕地上减少;导致其不同变化的因素有耕地利用方式、施肥管理、灌溉、土壤类型等,其中以土地利用方式和施肥管理措施的影响最大.     

Galectin-1 attenuates cardiomyocyte hypertrophy through splice-variant specific modulation of CaV1.2 calcium channel

Pressure overload-induced cardiac hypertrophy occurs in response to chronic blood pressure increase, and dysfunction of Ca_V1.2 calcium channel involves in cardiac hypertrophic processes by perturbing intracellular calcium concentration ([Ca²⁺]_i) and calcium-dependent signaling. As a carbohydrate-binding protein, galectin-1 (Gal-1) is found to bind with Ca_V1.2 channel, which regulates vascular Ca_V1.2 channel functions and blood pressure. However, the potential roles of Gal-1 in cardiac Ca_V1.2 channel (Ca_V1.2_CM) and cardiomyocyte hypertrophy remain elusive. By whole-cell patch clamp, we find Gal-1 decreases the I_Ca,L with or without isoproterenol (ISO) application by reducing the channel membrane expression in neonatal rat ventricular myocytes (NRVMs). Moreover, Gal-1 could inhibit the current densities of Ca_V1.2_CM by an alternative exon 9*-dependent manner in heterologously expressed HEK293 cells. Of significance, overexpression of Gal-1 diminishes ISO or KCl-induced [Ca²⁺]_i elevation and attenuates ISO-induced hypertrophy in NRVMs. Mechanistically, Gal-1 decreases the ISO or Bay K8644-induced phosphorylation of intracellular calcium-dependent signaling proteins δCaMKII and HDAC4, and inhibits ISO-triggered translocation of HDAC4 in NRVMs. Pathologically, we observe that the expressions of Gal-1 and Ca_V1.2_E9* channels are synchronously increased in rat hypertrophic cardiomyocytes and hearts. Taken together, our study indicates that Gal-1 reduces the channel membrane expression to inhibit the currents of Ca_V1.2_CM in a splice-variant specific manner, which diminishes [Ca²⁺]_i elevation, and attenuates cardiomyocyte hypertrophy by inhibiting the phosphorylation of δCaMKII and HDAC4. Furthermore, our work suggests that dysregulated Gal-1 and Ca_V1.2 alternative exon 9* might be attributed to the pathological processes of cardiac hypertrophy, and provides a potential anti-hypertrophic target in the heart.