半胱氨酸和巯基乙酸的弱氧化动力学特性研究

为探索研究半胱氨酸和巯基乙酸弱氧化反应之间的异同,选取H_2O_2稀溶液来弱氧化巯基化合物,考察温度、H_2O_2浓度对反应的影响,并进行巯基反应速率分析。结果表明,在低浓度H_2O_2下,增加H_2O_2浓度,半胱氨酸和巯基乙酸的反应速率均明显提高;在20~27.5℃区间,半胱氨酸的平均反应速率高于巯基乙酸。同时通过数据模拟,得到了在T=20℃,pH=6的条件下,H_2O_2弱氧化半胱氨酸和巯基乙酸的动力学方程。     

稻种遗传资源多样性的开发利用及保护

由于近年来栽培稻众多改良品种的育成和大面积推广,使之在很大程度上取代了地方品种,造成栽培稻基因源的大量基因流失,导致栽培稻品种的遗传基础越来越狭窄以至不能承受新病、虫害和不利环境的袭击。同时,由于人们长期施用杀虫剂、灭菌剂和除草剂等化学农药,严重地恶化了农业生态环境。要改变这种恶性循环的局面,开发和利用稻种的遗传资源,以丰富栽培稻品种的遗传基础是非常必要的。稻种基因源包括了亚洲栽培稻、非洲栽培稻、杂草稻、稻属的野生物种以及稻族内的近缘属种,它们是栽培稻品种进一步改良所不可缺少的遗传资源。但是,由于农业生产模式的改变,社会经济和工业化水平的迅速发展和提高,稻种基因源的多样性受到了严重的影响和威胁。一些野生稻种的居群已经迅速地缩小甚至从原产地消失。因此,对稻种基因源及其多样性进行及时有效的保护,并对其进行合理的开发和利用,是保证栽培稻进一步改良和持久生产的最有效方法。     

Cysteine: a potential source of error in amino acid analysis of mercaptoethane sulfonic or hydrochloric acid hydrolysates of proteins and peptides

Hydrolysis of proteins and peptides with mercaptoethane sulfonic acid is liable to produce overestimation of the proline content owing to the production of ninhydrin-positive material (probably cysteine) which coelutes with proline on many ion-exchange analytical systems. A similar error occurs with HCl hydrolysis (especially in the presence of mercaptoethanol or thioglycollic acid) if care is not taken to oxidize cysteine during reconstitution of the hydrolysate before amino acid analysis.     

胶蚧属昆虫资源保护及利用

紫胶虫具有重大的经济价值,我国紫胶虫物种和遗传资源丰富,气候类型和生态环境多样,为发展紫胶生产提供了良好的条件。本文简述了我国紫胶虫的物种资源、遗传多样性和生境,并根据紫胶虫资源状况提出了发展紫胶生产的模式。     

植物叶表面的润湿性及其生态学意义

植物叶表面的润湿性是各种生境中常见的一种现象,表现了叶片对水的亲和能力。叶面的润湿性可以通过测定气、固、液界面的接触角大小确定,接触角θ＜110°的为润湿,θ＞130°的为不润湿,表现出斥水性。影响叶片润湿性的主要因素有叶面蜡质含量与形态,叶面绒毛数量、质地、形态和分布方式,气孔和表皮细胞形态和大小,叶水分状况等。叶表面的化学组成和形态是影响叶润湿性的主要内在原因,但外界环境的变化通过影响表面的结构和形态来影响叶润湿性。叶面的润湿性是植物叶片截流降水的微观基础,水分在润湿性强的叶面上铺展呈膜;在不润湿的叶面上形成水珠,容易在风和重力的作用下离开叶面;铺展的水膜,又会对叶的光合作用产生重要的影响。不同润湿性的叶面,滞留、吸附、过滤各种大气污染物数量不同;这些污染物沉降在叶片表面,与叶面发生相互作用,从而改变叶面的润湿性。植物叶含水量的高低对叶感染病菌有重要的影响,在病菌感染期间如果叶表面完全润湿则有利于病菌侵染;一旦病菌侵染,又会对叶面结构造成破坏,需要考虑润湿性能对防治病虫害的农药液滴持留的影响。对于润湿性小、斥水性大的植物,其叶表面表现出一定的自清洁功能;根据这些高疏水性、具有自清洁性的植物叶面特征,可利用或借鉴生物学信息进行仿生设计或制造新的功能材料。润湿性作为固、气、液三相作用的综合结果,是认识植物界面关系的微观基础,对于植物叶面生态功能的认识具有重要的意义。     

The Mycobacterium tuberculosis small heat shock protein Hsp16.3 exposes hydrophobic surfaces at mild conditions: conformational flexibility and molecular chaperone activity

Hsp16.3, the alpha-crystallin-related small heat shock protein of Mycobacterium tuberculosis that is maximally expressed during the stationary phase and is a major membrane protein, has been reported to form specific trimer-of-trimers structure and to act as an effective molecular chaperone (Chang Z et al., 1996, J. Biol Chem 271:7218-7223). However, little is known about its action mechanism. In this study, Hsp16.3 conformational intermediates with dramatically increased chaperone activities were detected after treatment with very low concentrations of guanidine hydrochloride (0.05 M), urea (0.3 M), or mild heating (30 degrees C). The intermediates showed a significant increase in their capacity to bind the hydrophobic probe 1-anilino-8-naphthalene sulfonate (ANS), indicating an increased exposure of hydrophobic surfaces. Interestingly, the greatest chaperone activities of Hsp16.3 were observed in the presence of 0.3 M guanidine HCl or when heated to 35 degrees C. CD spectroscopy studies revealed no significant changes in protein secondary and tertiary structures at these mild treatments. Our in vitro studies also indicate that long-time-heated Hsp16.3, heated even to temperatures as high as 85 degrees C, has almost the same, if not a slightly greater, chaperone activities as the native protein when cooled to room temperature and its secondary structures also almost recovered. Together, these results suggest that Hsp16.3 modulates its chaperone activity by exposing hydrophobic surfaces and that the protein structure is highly stable and flexible, thus highly adapted for its function.     

The relationship between conservation, thermodynamic stability, and function in the SH3 domain hydrophobic core

To investigate the relationships between sequence conservation, protein stability, and protein function, we have measured the thermodynamic stability, folding kinetics, and in vitro peptide-binding activity of a large number of single-site substitutions in the hydrophobic core of the Fyn SH3 domain. Comparison of these data to that derived from an analysis of a large alignment of SH3 domain sequences revealed a very good correlation between the distinct pattern of conservation observed at each core position and the thermodynamic stability of mutants. Conservation was also found to correlate well with the unfolding rates of mutants, but not to the folding rates, suggesting that evolution selects more strongly for optimal native state packing interactions than for maximal folding rates. Structural analysis suggests that residue-residue core packing interactions are very similar in all SH3 domains, which provides an explanation for the correlation between conservation and mutant stability effects studied in a single SH3 domain. We also demonstrate a correlation between stability and the in vivo activity of mutants, and between conservation and activity. However, the relationship between conservation and activity was very strong only for the three most conserved hydrophobic core positions. The weaker correlation between activity and conservation seen at the other seven core positions indicates that maintenance of protein stability is the dominant selective pressure at these positions. In general, the pattern of conservation at hydrophobic core positions appears to arise from conserved packing constraints, and can be effectively utilized to predict the destabilizing effects of amino acid substitutions.     

Prediction of membrane protein types based on the hydrophobic index of amino acids

A new algorithm to predict the types of membrane proteins is proposed. Besides the amino acid composition of the query protein, the information within the amino acid sequence is taken into account. A formulation of the autocorrelation functions based on the hydrophobicity index of the 20 amino acids is adopted. The overall predictive accuracy is remarkably increased for the database of 2054 membrane proteins studied here. An improvement of about 13% in the resubstitution test and 8% in the jackknife test is achieved compared with those of algorithms based merely on the amino acid composition. Consequently, overall predictive accuracy is as high as 94% and 82% for the resubstitution and jackknife tests, respectively, for the prediction of the five types. Since the proposed algorithm is based on more parameters than those in the amino acid composition approach, the predictive accuracy would be further increased for a larger and more class-balanced database. The present algorithm should be useful in the determination of the types and functions of new membrane proteins. The computer program is available on request.     

Amino acid function relates to its embedded protein microenvironment: A study on disulfide‐bridged cystine

In our previous study, we have shown that the microenvironments around conserved amino acids are also conserved in protein families (Bandyopadhyay and Mehler, Proteins 2008; 72:646–659). In this study, we have hypothesized that amino acids perform similar functions when embedded in a certain type of protein microenvironment. We have tested this hypothesis on the microenvironments around disulfide‐bridged cysteines from high‐resolution protein crystal structures. Although such cystines mainly play structural role in proteins, in certain enzymes they participate in catalysis and redox reactions. We have performed and report a functional annotation of enzymatically active cystines to their respective microenvironments. Three protein microenvironment clusters were identified: (i) buried‐hydrophobic, (ii) exposed‐hydrophilic, and (iii) buried‐hydrophilic. The buried‐hydrophobic cluster encompasses a small group of 22 redox‐active cystines, mostly in alpha‐helical conformations in a –C‐x‐x‐C‐ motif from the Oxido‐reductase enzyme class. All these cystines have high strain energy and near identical microenvironments. Most of the active cystines in hydrolase enzyme class belong to buried hydrophilic microenvironment cluster. In total there are 34 half‐cystines detected in buried hydrophilic cluster from hydrolases, as a part of enzyme active site. Even within the buried hydrophilic cluster, there is clear separation of active half‐cystines between surface exposed part of the protein and protein interior. Half‐cystines toward the surface exposed region are higher in number compared to those in protein interior. Apart from cystines at the active sites of the enzymes, many more half‐cystines were detected in buried hydrophilic cluster those are part of the microenvironment of enzyme active sites. However, no active half‐cystines were detected in extremely hydrophilic microenvironment cluster, that is, exposed hydrophilic cluster, indicating that total exposure of cystine toward the solvent is not favored for enzymatic reactions. Although half‐cystines in exposed‐hydrophilic clusters occasionally stabilize enzyme active sites, as a part of their microenvironments. Analysis performed in this work revealed that cystines as a part of active sites in specific enzyme families or folds share very similar protein microenvironment regions, despite of their dissimilarity in protein sequences and position specific sequence conservations. Proteins 2016; 84:1576–1589. © 2016 Wiley Periodicals, Inc.     

Characterization of cysteine thiol modifications based on protein microenvironments and local secondary structures

We have demonstrated earlier that protein microenvironments were conserved around disulfide‐bridged cystine motifs with similar functions, irrespective of diversity in protein sequences. Here, cysteine thiol modifications were characterized based on protein microenvironments, secondary structures and specific protein functions. Protein microenvironment around an amino acid was defined as the summation of hydrophobic contributions from the surrounding protein fragments and the solvent molecules present within its first contact shell. Cysteine functions (modifications) were grouped into enzymatic and non‐enzymatic classes. Modifications studied were—disulfide formation, thio‐ether formation, metal‐binding, nitrosylation, acylation, selenylation, glutathionylation, sulfenylation, and ribosylation. 1079 enzymatic proteins were reported from high‐resolution crystal structures. Protein microenvironments around cysteine thiol, derived from above crystal structures, were clustered into 3 groups—buried‐hydrophobic, intermediate and exposed‐hydrophilic clusters. Characterization of cysteine functions were statistically meaningful for 4 modifications (disulfide formation, thioether formation, sulfenylation, and iron/zinc binding) those have sufficient amount of data in the current dataset. Results showed that protein microenvironment, secondary structure and protein functions were conserved for enzymatic cysteine functions, in contrast to the same function from non‐enzymatic cysteines. Disulfide forming enzymatic cysteines were tightly packed within intermediate protein microenvironment cluster, have alpha‐helical conformation and mostly belonged to CxxC motif of electron transport proteins. Disulfide forming non‐enzymatic cysteines did not belong to conserved motif and have variable secondary structures. Similarly, enzymatic thioether forming cysteines have conserved microenvironment compared to non‐enzymatic cystienes. Based on the compatibility between protein microenvironment and cysteine modifications, more efficient drug molecules could be designed against cysteine‐related diseases.     

Lateral plasma membrane compartmentalization links protein function and turnover

Biological membranes organize their proteins and lipids into nano‐ and microscale patterns. In the yeast plasma membrane (PM), constituents segregate into a large number of distinct domains. However, whether and how this intricate patchwork contributes to biological functions at the PM is still poorly understood. Here, we reveal an elaborate interplay between PM compartmentalization, physiological function, and endocytic turnover. Using the methionine permease Mup1 as model system, we demonstrate that this transporter segregates into PM clusters. Clustering requires sphingolipids, the tetraspanner protein Nce102, and signaling through TORC2. Importantly, we show that during substrate transport, a simple conformational change in Mup1 mediates rapid relocation into a unique disperse network at the PM. Clustered Mup1 is protected from turnover, whereas relocated Mup1 actively recruits the endocytic machinery thereby initiating its own turnover. Our findings suggest that lateral compartmentalization provides an important regulatory link between function and turnover of PM proteins.     

Biosynthetic pathway to neuromelanin and its aging process

Using model compounds of the melanic component of neuromelanin (NM) prepared by tyrosinase oxidation at various ratios of dopamine (DA) and cysteine (Cys) under physiological conditions, we examined a biosynthetic pathway to NM and its aging process by following the time course of oxidation to NM and the subsequent structural modification of NM under various heating conditions. Chemical degradation methods were applied to the synthetic NM. 4‐Amino‐3‐hydroxyphenylethylamine (4‐AHPEA) and thiazole‐2,4,5‐tricarboxylic acid (TTCA) were used as markers of benzothiazine and benzothiazole units, respectively. By following the time course of the biosynthetic pathway of synthetic NM, we found that neurotoxic molecules are trapped in NM. An aging simulation of synthetic NM showed that benzothiazine units in NM are gradually converted to benzothiazole during the aging process. Thus, natural NM was found to be similar to aged (heated) NM prepared from a 2:1 molar ratio of DA and Cys.     

A contact energy function considering residue hydrophobic environment and its application in protein fold recognition

The three-dimensional （3D） structure prediction of proteins ：is an important task in bioinformatics. Finding energy functions that can better represent residue-residue and residue-solvent interactions is a crucial way to improve the prediction accu- racy. The widely used contact energy functions mostly only consider the contact frequency between different types of residues; however, we find that the contact frequency also relates to the residue hydrophobic environment. Accordingly, we present an improved contact energy function to integrate the two factors, which can reflect the influence of hydrophobic interaction on the stabilization of protein 3D structure more effectively. Furthermore, a fold recognition （threading） approach based on this energy function is developed. The testing results obtained with 20 randomly selected proteins demonstrate that, compared with common contact energy functions, the proposed energy function can improve the accuracy of the fold template prediction from 20% to 50%, and can also improve the accuracy of the sequence-template alignment from 35% to 65%.     

Prediction of human protein function from post-translational modifications and localization features

We have developed an entirely sequence-based method that identifies and integrates relevant features that can be used to assign proteins of unknown function to functional classes, and enzyme categories for enzymes. We show that strategies for the elucidation of protein function may benefit from a number of functional attributes that are more directly related to the linear sequence of amino acids, and hence easier to predict, than protein structure. These attributes include features associated with post-translational modifications and protein sorting, but also much simpler aspects such as the length, isoelectric point and composition of the polypeptide chain.     

A new method for quantifying residue conservation and its applications to the protein folding nucleus

The conservation of residues in columns of a multiple sequence alignment (MSA) reflects the importance of these residues for maintaining the structure and function of a protein. To date, many scores have been suggested for quantifying residue conservation, but none has achieved the full rigor both in biology and statistics. In this paper, we present a new approach for measuring the evolutionary conservation at aligned positions. Our conservation measure is related to the logarithmic probabilities for aligned positions, and combines the physicochemical properties and the frequencies of amino acids. Such a measure is both biologically and statistically meaningful. For testing the relationship between an amino acid's evolutionary conservation and its role in the Phi-value defined protein folding kinetics, our results indicate that the folding nucleus residues may not be significantly more conserved than other residues by using the biological-relevance weighted statistical scoring method suggested in this paper as an alternative to entropy-based procedures.     

Regional covariation and its application for predicting protein contact patches

Correlated mutation analysis (CMA) is an effective approach for predicting functional and structural residue interactions from multiple sequence alignments (MSAs) of proteins. As nearby residues may also play a role in a given functional interaction, we were interested in seeing whether covarying sites were clustered, and whether this could be used to enhance the predictive power of CMA. A large‐scale search for coevolving regions within protein domains revealed that if two sites in a MSA covary, then neighboring sites in the alignment also typically covary, resulting in clusters of covarying residues. The program PatchD( http://www.uhnres.utoronto.ca/labs/tillier/ ) was developed to measure the covariation between disconnected sequence clusters to reveal patch covariation. Patches that exhibit strong covariation identify multiple residues that are generally nearby in the protein structure, suggesting that the detection of covarying patches can be used in conjunction with traditional CMA approaches to reveal functional interaction partners. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

基于功能与空间格局的区域生态系统保管策略

本研究以位于长江流域的湖北省兴山县为研究区域,着重讨论了基于功能与空间格局的生态系统保育策略,即以改善生态系统功能为评价指标,以调整生态因子的空间格局为手段的生态系统保育策略。根据该县的地理位置,我们以生态系统功能中的水源函养为森林生态系统保育的评价指标。利用基于地理信息系统的水涵养能力。利用生态系统中水涵养能力的空间异质性和变化－位置效应在生态因子改变中的作用,我们提出了“基于空间格局的森林扩展”的策略。将该策略应用于兴山县的生态系统保育,以期达到保育森林与改善水涵养能力的双重目的。本研究为保育,管理和持续利用长江流域和其他遭遇同样问题的区域的生态系统提供了有价值的信息。     

30种植物叶蛋白中氨基酸组成及含量的测定与营养价值评价

评价植物叶蛋白的营养价值,既要考虑“量”,看植物叶蛋白含量的高低,也要考虑“质”,看必需氨基酸的含量及配比[1]。作者取叶蛋白含量50%以上的30种植物进行氨基酸含量测定[2],并进行营养价值评价。1　方　　法应用日立83550型氨基酸自动分析仪进行氨基酸含量的测定,并与?..