Polarity as a criterion in protein design

Hypothetical proteins can be tested computationally by determiningwhether or not the designed sequence-structure pair has thecharacteristics of a typical globular protein. We have developedsuch a test by deriving quantities with approximately constantvalue for all globular proteins, based on empirical analysisof the exposed and buried surfaces of 128 structurally knownproteins. The characteristic quantities that best appear tosegregate badly designed or deliberately misfolded proteinsfrom their properly folded natural relatives are the polar fractionof side chains on the protein surface and, independently, inthe protein interior. Three of the seven hypothetical structurestested here can be rejected as having too many polar side-chaingroups in the interior or too few on the protein surface. Inaddition, a recently designed nutritional protein is identifiedas being very much unlike globular proteins. These database-derivedcharacteristic quantities are useful in screening designed proteinsprior to experiment and may be useful in screening experimentallydetermined (X-ray, NMR) protein structures for possible errors.     

An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure

A 3-D model of a protein can be constructed from its amino acidsequence and the 3-D structures of one or more homologues byannealing three sets of fragments: the structurally conservedregions, structurally variable regions and the side chains.The method encoded in the computer program COMPOSER was assessedby generating 3-D models of eight proteins whose crystal structuresare already known and for which 3-D structures of homologuesare available. In the structurally conserved regions, differencesbetween modelled and X-ray structures are smaller than the differencesbetween the X-ray structures of the modelled protein and thehomologues used to build the model. When several homologuesare used, the contributions of the known structures are weighted,preferably by the square of sequence similarity; this is especiallyimportant when the similarities of the homologues to the modelledstructure differ greatly. The ‘collar’ extensionapproach, in which a similar region of different length in ahomologue is used to extend the framework, can result in a moreaccurate model. If known homologues comprise more than one relatedgroup of proteins and they are both distantly related to theunknown, then alignment of the sequence to be modelled witheach group of homologues facilitates identification of structurallyconserved regions of the unknown and leads to an improved model.Models have root mean square differences (r.m.s.d.s) with thestructures defined by X-ray analysis of between 0.73 and 1.56Å for all C atoms, for seven of the eight models. Forthe model of mucor pepsin, where the closest homologue has 33%sequence identity and 20% of the residues are in structurallyvariable regions, the r.m.s.d. for the framework region is 1.71Å and the r.m.s.d. for all C atoms is 3.47 Â.     

蛋白质在超滤过程中的膜污染和膜清洗

本文选用四种不同的膜清洗剂对牛血清蛋白溶液超滤后污染的三种超滤膜进行研究，结果表明：在蛋白质的等电点取得在不同ＰＨ值下蛋白质对膜污染的最佳清洗效果，清洗效率与蛋白质的所荷电荷有关。采用适宜的清洗过程将会延长膜使用寿命和增强超滤膜性能。     

重组人白细胞介素-10在大肠杆菌中的表达及生物学活性分析

目的在大肠杆菌中表达重组人白细胞介素-10(Interleukin-10,IL-10),并检测其生物学活性。方法将IL-10基因重组到质粒pET11c中,转化BL21(DE),提取质粒,经酶切鉴定和测序分析;在25℃用低浓度的IPTG诱导表达,对包涵体IL-10稀释复性;经ELISA检测其含量,MC/9细胞增殖法检测其生物学活性。结果工程菌IL-10/pET11c/BL21诱导表达的目的蛋白以可溶性和包涵体两种形式存在,Westernblot鉴定证实为IL-10蛋白,两种形式的IL-10均具有一定的生物学活性。结论已成功地在大肠杆菌中表达了IL-10,为进一步纯化和制备IL-10的基因工程药物打下了基础。     

蛋白质化学修饰的研究进展

蛋白质分子具有极其复杂的结构层次，用化学修饰的方法研究蛋白质分子的结构与功能的关系一直是生物化学和分子生物学领域的热点。人们研究出许多小分子化学修饰剂并进行了多种类型的化学修饰。综述了蛋白质化学修饰领域的研究现状与水平，同时强调蛋白质的化学修饰是生化药物研究开发的重要手段之一。     

A molecular dynamics simulation of bacteriophage T4 lysozyme

An analysis of a 400 ps molecular dynamics simulation of the164 amino acid enzyme T4 lysozyme is presented. The simulationwas carried out with all hydrogen atoms modeled explicitly,the inclusion of all 152 crystallographic waters and at a temperatureof 300 K. Temporal analysis of the trajectory versus energy,hydrogen bond stability, r.m.s. deviation from the startingcrystal structure and radius of gyration, demonstrates thatthe simulation was both stable and representative of the averageexperimental structure. Average structural properties were calculatedfrom the enzyme trajectory and compared with the crystal structure.The mean value of the C displacements of the average simulatedstructure from the X-ray structure was 1.1 ± 0.1 Å;differences of the backbone and angles between the averagesimulated structure and the crystal structure were also examined.Thermal-B factors were calculated from the simulation for heavyand backbone atoms and both were in good agreement with experimentalvalues. Relationships between protein secondary structure elementsand internal motions were studied by examining the positionalfluctuations of individual helix, sheet and turn structures.The structural integrity in the secondary structure units waspreserved throughout the simulation; however, the A helix didshow some unusually high atomic fluctuations. The largest backboneatom r.m.s. fluctuations were found in non-secondary structureregions; similar results were observed for r.m.s. fluctuationsof non-secondary structure and angles. In general, the calculatedvalues of r.m.s. fluctuations were quite small for the secondarystructure elements. In contrast, surface loops and turns exhibitedmuch larger values, being able to sample larger regions of conformationalspace. The C difference distance matrix and super-positioninganalyses comparing the X-ray structure with the average dynamicsstructure suggest that a ‘hinge-bending’ motionoccurs between the N- and C-terminal domains.     

Controlled release of insecticide carbaryl from sodium alginate,sodium alginate/gelatin,and sodium alginate/sodium carboxymethyl cellulose blend beads crosslinked with glutaraldehyde

Interpenetrating network polymeric beads of sodium alginate (NaAlg) and its blend with gelatin (gels) or sodium carboxymethyl cellulose (NaCMC) have been prepared by crosslinking with a common crosslinking agent, glutaraldehyde (GA), for the release of insecticide carbaryl (Carb). The prepared beads were characterized by Fourier transform infrared spectroscopy and scanning electron microscopy. Scanning electron microscopy confirmed the spherical nature and surface morphology of the particles. Bead characteristics, such as carbaryl entrapment efficiency, particle size, equilibrium swelling degree, and carbaryl release kinetics, were determined. The effects of the preparation conditions, such as Carb/NaAlg ratio, time of exposure to GA, blend ratio, and temperature of release medium on the carbaryl release, were investigated for 25 days at 25°C. It was observed that the carbaryl release decreased with increase in crosslinking of network, while it increased with increase in Carb/NaAlg ratio and temperature. The release of carbaryl also increased with increase in Gel or NaCMC content in the blend beads. The highest carbaryl release was found to be 100%, for the beads that were prepared with 1 : 1 NaAlg/Gel at 16 days. The diffusion coefficients have been calculated for the transport of insecticide through the polymeric beads, using initial time approximation method. These values were also consistent with the carbaryl release data. The carbaryl release from most of the bead formulations followed the Fickian trend. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 99: 1310–1319, 2006     

人血浆蛋白C的纯化与鉴定

目的　建立人血浆蛋白C的纯化与鉴定方法。方法　利用DEAE SephadexA 5 0代替氯化钡 ,对血浆进行预处理 ,再经DEAE SepharoseFF离子交换和肝素 SepharoseCL 6B亲和层析进行分离纯化 ,用活化的部分凝血活酶时间 (APTT)测定组分活性 ,非还原型SDS PAGE测定其相对分子质量 ,Westernblot鉴定其特异性。结果获得相对分子质量为 6 2 0 0 0的蛋白条带 ,此条带可与人蛋白C单克隆抗体发生特异性反应。结论　已成功地从血浆中分离到蛋白C ,为其规模化生产奠定了基础。     

Ⅱ型B族链球菌表面免疫相关蛋白基因的克隆和原核表达

目的重组表达Ⅱ型B族链球菌表面免疫相关蛋白(Surfaceimmunogenicprotein,SIP)基因,为进一步免疫学研究提供目标蛋白。方法用PCR的方法从GBSⅡ型标准株的基因组DNA中扩增出SIP基因,用T/A克隆法将其插入pMD18T载体,构建原核表达载体pET32aSIP,用BL21(DE3)/pET系统表达TrixSIP融合蛋白,SDSPAGE和质谱分析鉴定表达产物,并对表达蛋白进行初步纯化。结果PCR扩增产物经测序,证实与GenBank中Ⅰa/c型GBS的SIP的基因序列同源性为99%。SDSPAGE显示,经IPTG诱导后BL21(DE3)/pET32aSIP总蛋白中出现一条相对分子质量为66000的新蛋白带。质谱分析和蛋白质库的比较证实其为B族链球菌表面免疫相关蛋白(SIP)的可能性分数为74。结论已成功表达并初步纯化SIP,为SIP在细菌致病中的作用研究以及相关疫苗的制备奠定了基础。     

EDTA滴定法精确测定可溶性氯化物中氯含量

介绍了利用EDTA滴定法精确测定可溶性氯化物中氯含量的原理、条件和方法。试样溶解后,先在强酸性介质中用AgNO3沉淀Cl-离子,沉淀过滤后,加入过量Ni(CN)42-发生置换反应,然后在pH9.5的氨性缓冲溶液中,以紫脲酸铵为指示剂,用EDTA标准溶液滴定置换出的Ni2 离子。结果表明,改进后的本法,准确、干扰小、终点现象明显,是一种准确的测氯方法。测定结果的变异系数仅为0.18%,回收率为98.3%～100.9%。