Exploring the thermal stability and activity of α-chymotrypsin in the presence of spermine

Polyamines such as spermine can have interaction with protein. The aim of the present study was to investigate how spermine could influence the structure, thermal stability, and the activity of α-chymotrypsin. Kinetics, thermodynamics, molecular dynamics (MD), and docking simulations studies were conducted to investigate the effect of spermine on the activity and structure of α-Chymotrypsin (α-Chy) in 50 mM Tris–HCl buffer, with the pH 8, using different spectroscopic techniques as well as molecular docking and MD simulations. The stability and activity of α-Chy were increased in the presence of spermine. The results of the kinetic study showed that the activity of spermine was increased. Enzyme activation was accompanied by changes on the α-Chy conformation. Fluorescence intensity changes showed dynamic quenching during spermine binding. The fluorescence quenching of the α-Chy suggested the more polar location of Trp residues. Near-UV and Far-UV circular dichroism studies also demonstrated the transfer of Trp, Phe, and Tyr residues to a more flexible environment. The increase in the absorption of α-Chy in the presence of spermine was as a result of the formation of spermine–α-Chy complex. Molecular docking results revealed the presence of one binding site with a negative value for the Gibbs free energy of the binding of spermine to α-Chy. Docking study also revealed that van der Waals interactions and hydrogen bonds played a major role in stabilizing the complex.     

Rhodobacteraceae on the marine brown alga Fucus spiralis are abundant and show physiological adaptation to an epiphytic lifestyle

Macroalgae harbour specific microbial communities on their surface that have functions related to host health and defence. In this study, the bacterial biofilm of the marine brown alga Fucus spiralis was investigated using 16S rRNA gene amplicon-based analysis and isolation of bacteria. Rhodobacteraceae (Alphaproteobacteria) were the predominant family constituting 23% of the epibacterial community. At the genus level, Sulfitobacter, Loktanella, Octadecabacter and a previously undescribed cluster were most abundant, and together they comprised 89% of the Rhodobacteraceae. Supported by a specific PCR approach, 23 different Rhodobacteraceae-affiliated strains were isolated from the surface of F. spiralis, which belonged to 12 established and three new genera. For seven strains, closely related sequences were detected in the 16S rRNA gene dataset. Growth experiments with substrates known to be produced by Fucus spp. showed that all of them were consumed by at least three strains, and vitamin B₁₂ was produced by 70% of the isolates. Since growth of F. spiralis depends on B₁₂ supplementation, bacteria may provide the alga with this vitamin. Most strains produced siderophores, which can enhance algal growth under iron-deficient conditions. Inhibiting properties against other bacteria were only observed when F. spiralis material was present in the medium. Thus, the physiological properties of the isolates indicated adaption to an epiphytic lifestyle.     

Aggregation prone regions in human proteome: Insights from large‐scale data analyses

Protein aggregation leads to several burdensome human maladies, but a molecular level understanding of how human proteome has tackled the threat of aggregation is currently lacking. In this work, we survey the human proteome for incidence of aggregation prone regions (APRs), by using sequences of experimentally validated amyloid‐fibril forming peptides and via computational predictions. While approximately 30 human proteins are currently known to be amyloidogenic, we found that 260 proteins (～1% of human proteome) contain at least one experimentally validated amyloid‐fibril forming segment. Computer predictions suggest that more than 80% of the human proteins contain at least one potential APR and approximately two‐thirds (65%) contain two or more APRs; spanning 3–5% of their sequences. Sequence randomizations show that this apparently high incidence of APRs has been actually significantly reduced by unique amino acid composition and sequence patterning of human proteins. The human proteome has utilized a wide repertoire of sequence‐structural optimization strategies, most of them already known, to minimize deleterious consequences due to the presence of APRs while simultaneously taking advantage of their order promoting properties. This survey also found that APRs tend to be located near the active and ligand binding sites in human proteins, but not near the post translational modification sites. The APRs in human proteins are also preferentially found at heterotypic interfaces rather than homotypic ones. Interestingly, this survey reveals that APRs play multiple, often opposing, roles in the human protein sequence‐structure‐function relationships. Insights gained from this work have several interesting implications towards novel drug discovery and development. Proteins 2017; 85:1099–1118. © 2017 Wiley Periodicals, Inc.     

土壤病毒生态学研究方法

病毒是地球上最丰富的生物实体,每克土壤中可包含数以亿计的病毒,它不仅影响土壤中其它微生物的群落组成、土壤元素的生物地球化学循环,还会影响土壤微生物的物种进化,甚至影响植物、动物和人体健康。目前人们对土壤中病毒的种类及丰度、分布特征以及功能引起的生态环境效应还知之甚少。在概述病毒生态学研究方法的基础上,对土壤病毒的提取、纯化、定量及分子生态学方法等基本流程进行了比较分析,以期建立一套快速简便、高效稳定的适用于土壤病毒研究的方法,并用于研究土壤病毒的多样性及分布特征,探讨病毒在环境中的生存和传播机制,为土壤病毒的防控及开发利用提供支撑。     

松嫩平原苏打盐渍化旱田土壤表观电导率空间变异

在松嫩平原西部吉林省大安市乐胜乡,于2013年4月20日选择盐碱程度不均一的典型盐渍化旱田地块,面积为4.8 hm~2作为研究样地。利用EM38大地电导率仪测定结合田间定点采样,并通过经典统计和地统计相结合的方法研究了盐渍化旱田土壤表观电导率空间变异特征,分析了土壤表观电导率与土壤盐碱指标之间的关系。结果表明,盐渍化旱田土壤水平方向表观电导率(EC_h)经对数转换后具有强空间自相关,其变异特征主要是与地形地貌和水文状况等结构性因素有关。垂直方向表观电导率(EC_v)经对数转换后具有中等空间自相关性,其变异特征受结构性因素和随机因素共同作用。EC_h和EC_v半方差模拟的最优模型分别为球状模型和指数模型。Pearson分析表明土壤表观电导率(EC_h和EC_v)与土壤盐碱指标EC_(1∶5)、pH_(1∶5)、SAR、SC、Na~+、CO_3~(2-)、HCO_3~-呈正相关关系(P0.05),EC_h与土壤盐碱指标相关系数均大于EC_v。在实际应用中可以用EC_h来指示土壤的盐碱程度。回归分析表明土壤表观电导率(EC_h和EC_v)与土壤盐碱指标呈线性相关,且EC_h回归模型的决定系数均大于EC_v回归模型的决定系数,可用水平方向土壤表观电导率(EC_h)来计算土壤盐碱指标,进行土壤盐渍化的快速评估。     

孔雀河下游断流河道的环境特征及物种间关系

基于孔雀河下游断流河道的环境因子和植被样地数据,采用聚类与CCA排序法,分析了生境的退化特征以及物种间的相互关系,结果表明:1)断流河道退化生境分为绿洲-荒漠过渡类型、轻度荒漠化类型和盐土荒漠化类型。绿洲-荒漠过渡类型地下水位低、盐分含量相对较低,植被盖度相对较高,土壤维持着原砂质壤土,为潜在退化型;轻度荒漠化类型地下水位、土壤质地与含盐量与前者基本相同,土壤未明显退化,但植被盖度低于10%,植物种类与个体数目都较低,属于轻度退化型;盐土荒漠化类型地下水位高、盐分含量高,土壤机械组成中砂粒比重较大、无建群种幸存,属于重度退化型。2)绿洲-荒漠过渡类型总体联结性为显著正联结,正负联结比小于1,生态系统表现为建群种维系物种关系的不稳定状态;轻度荒漠化类型总体联结性为不显著负联结,正负联结比小于1,表现出生态系统进入退化演替的阶段;盐土荒漠化类型总体联结性为显著正联结,正负联结比大于1,表现出重度退化群落的种间平衡状态,物种间以达到稳定共存,其中,真盐生植物对这种平衡的维持起着重要的作用。3)CCA排序表明,绿洲-荒漠过渡类型形成以胡杨为中心的种间正联结,幸存于盐分适中、水分养分相对较高的生境;轻度荒漠化类型,形成以多枝柽柳与刚毛柽柳相互依存的不显著负联结,幸存于土壤养分、水分相对较低的生境;盐土荒漠化类型形成以盐爪爪、盐节木、盐穗木等真盐生植物维系的显著正联结,幸存于土壤贫瘠、地下水位浅、盐分含量高、沙化严重的生境。