颗粒裂解肽G13结构域在大肠杆菌中的高效融合表达

为高效表达颗粒裂解肽G13结构域并避免G13对宿主菌的毒性, 将人工合成的编码G13的基因片段, PCR扩增后克隆于原核表达载体pThioHisA中, 构建了重组表达载体pThioHisA-G13, 将其转化于大肠杆菌BL21(DE3)中, 经IPTG诱导表达融合蛋白Trx-G13, 表达产物以包涵体的形式存在, 其表达量约占细菌总蛋白的58%。包涵体蛋白经 8 mol/L尿素溶解后, 再经CNBr切割, 阳离子交换层析, 得到纯化的重组G13结构域。琼脂糖扩散法检测表明重组G13结构域多肽具有抗菌活性。     

人颗粒裂解肽片段在大肠杆菌中的表达

目的：建立颗粒裂解肽（NKG5）的原核表达载体系统,并在大肠杆菌中获得表达。方法：采用寡核苷酸合成、PCR扩增得到NKG5编码序列,克隆到pGEM-T载体上,经测序正确后,再切下编码序列连接到重组表达载体pGEx-4T-1中,转化大肠杆菌BL21,用IPTG诱导重组工程菌表达,采用谷胱甘肽偶联的Sepharose 4B纯化重组蛋白。结果：重组菌株可以表达GST-NKG5融合蛋白,用免疫印迹反应鉴定纯化的融合蛋白,在相对分子质量34000处有一条带。结论：获得了在大肠杆菌中低表达的颗粒裂解肽融合蛋白,为后续研究奠定了基础。     

蛋白质PX结构域的结构和功能

本文重点介绍了近年不断发现的许多蛋白质结构中含有一个特异的结构域（hox homolog)－PX结构域。蛋白质通过PX结构域与膜肌醇磷脂结合靶蛋白质结合到细胞膜上,然后发挥蛋白质的各自功能。现已鉴定含PX结构域的蛋白质约有100多种,这些蛋白质参与蛋白质转运和信号转导。     

蛋白质结构与功能中的结构域

结构域是蛋白质亚基结构中的紧密球状区域.结构域作为蛋白质结构中介于二级与三级结构之间的又一结构层次,在蛋白质中起着独立的结构单位、功能单位与折叠单位的作用.在复杂蛋白质中,结构域具有结构与功能组件与遗传单位的作用.结构域层次的研究将会促进蛋白质结构与功能关系、蛋白质折叠机制以及蛋白质设计的研究.     

人类蛋白质结构互作网络——结构域对网络拓扑与蛋白质功能的影响

高通量的蛋白质互作数据与结构域互作数据的出现,使得在蛋白质组学领域内研究人类蛋白质结构互作网络,进一步揭示蛋白质结构与功能间的潜在关系成为可能.蛋白质上广泛分布的结构域被认为是蛋白质结构、功能以及进化的基本功能单元.然而,结合蛋白质的结构信息(例如蛋白质结构域数目、长度和覆盖率等)来研究这些表象后的内部机制仍然面临着挑战.将蛋白质分为单结构域蛋白质与多结构域蛋白质,并进一步结合蛋白质互作信息与结构域互作信息构建了人类蛋白质结构互作网络;通过与人类蛋白质互作网络进行比较,研究了人类蛋白质结构互作网络的特殊结构特征;对于单结构域蛋白质与多结构域蛋白质,分别进行了功能富集分析、功能离散度分析以及功能一致性分析等.结果发现,将结构域互作信息综合考虑进来后,人类蛋白质结构互作网络可以提供更多的单纯的蛋白质互作网络无法提供的细节信息,揭示蛋白质互作网络的复杂性.     

TAT蛋白质转导结构域与SV40启动子特异的三锌指结构融合蛋白的表达与纯化

利用蛋白质转导结构域(PTDs)可以将与之融合表达的蛋白质直接送入细胞中。将通过筛选噬菌体展示锌指库得到的特异作用于SV40启动子上9bp序列的三锌指结构的序列插入含有TAT蛋白的蛋白质转导结构域的表达载体pET—TAT-NLS中,构建融合蛋白的表达载体pET-TAT-NLS—clone3。融合蛋白在E．coli BL21(DE3)中得到了可溶性表达,含量约占总蛋白的18％;并通过镍亲和凝胶层析柱得到了较好的纯化融合蛋白。     

人源CBX7功能结构域的重组表达与纯化

CBX7(chromobox 7)在细胞寿命延长和癌症发生中起着重要的调控作用。然而,获取足量的全长CBX7蛋白并用于结构研究极为艰难。实验阐述了CBX7功能结构域CBX7(aa 145～227)重组表达载体构建的详细过程。同时,通过Ni-NTA亲和层析对融合目的蛋白进行了纯化,并利用SDS-PAGE及Western-blot进行了鉴定分析。纯化后的融合蛋白样品通过离子交换和分子筛层析进一步分离剩余杂质。本实验得到的高浓度CBX7蛋白可用于结晶,为后续CBX7的结构和功能研究奠定了基础。     

人源Fank1蛋白质FN3结构域多肽的原核表达，纯化及晶体筛选

目的纯化人源Fank1（fibronectin type Ⅲ and ankyrin repeat domain1）蛋白质N端FN3（fibronectin typeⅢ,Ⅲ型纤黏连蛋白）结构域蛋白,用于晶体生长的三维结构分析。方法将FN3结构域基因片段克隆至原核表达载体pGEX-6P-1中,将菌落PCR和测序鉴定正确的重组质粒转化E.coli BL21（DE3）后获得表达菌株。该菌株经IPTG诱导高效表达出带有GST标签的可溶性的融合蛋白,经过Glutathione Sepha-rose^TM 4B亲和层析、Hiload16／60 superdex200分子筛层析纯化后,蛋白纯度达到95％以上。结果纯化蛋白采用悬滴气相扩散法得到棒状晶体。结论成功制备了高纯度FN3蛋白,获得FN3蛋白质晶体,为进一步的三维结构解析及Fank1功能研究奠定了基础。     

APP17肽对β—淀粉样肽及有关蛋白质表达的影响

本研究选用人类野生型SY5Y及SY5YA4CT基因转染细胞,应用免疫沉淀Western Blot等分析方法研究APP17肽对β-淀粉样肽及有关蛋白质如IDE,NT－3,NF表达的影响,探讨其影响神经元存活和退变的可能机理,结果发现,APP17肽能抑制转染细胞Aβ胞外分泌,并能促进野生型SY5Y细胞中IDE的表达,同时对内源性NT－3和NF的表达也有促进作用,提示：APP17肽抑制Aβ分泌和促进内源性神经营养因子的表达可能是其支持神经元存活,改善神经退变的机理之一。     

重组蛋白G Fc结合区单结构域的纯化及理化性质

蛋白 G 是存在于链球菌 C 群和 G 群胞膜上的一种分子量为65kD 的膜蛋白,完整的蛋白 G 分子主要由四部分组成,其中第三部分能与许多动物的 IgG Fc段特异结合。近年来,蛋白 G 的应用研究已展示出广阔前景,它一方面可与多种标记物(如酶、放射性同位素、胶体金等)连接,用于免疫分析;另一方面,可用作纯化单克隆抗体及多克隆抗体的亲和配基。但是有关蛋白 G 的空间结构及其与 IgG Fc 的结合机制     

链球菌蛋白G的构建、重组表达及鉴定

化学合成链球茵蛋白G的C3D基因片段,通过分子生物学的方法对蛋白G（proteinG）的C3片段进行PCR扩增,拼接形成含有两个和三个重复C3片段的重组链球茵蛋白G,C3片段间以链接区D连接,即形成C3DC3和C3DC3DC3的形式,进而克隆到质粒pET21中,在大肠杆菌BL21（DE3）中表达。重组表达的蛋白经过DEAE—Sepharose和IgG—Sepharose纯化,得到纯化的重组蛋白。采用非竞争性酶免疫法对重组蛋白与不同来源IgG的结合常数进行测定,实验结果显示两种重组链球茵蛋白G均可有效地与小鼠、兔及山羊等多种不同来源抗体特异性结合。这些实验结果为下一步研究奠定了基础。     

Conformational studies of the alpha-helical 28-43 fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus

To determine whether the alpha-helix in the B3 immunoglobulin binding domain of protein G from group G Streptococcus has conformational stability as an isolated fragment, we carried out a CD and NMR study of the 16-residue peptide in solution corresponding to this alpha-helix. Based on two-dimensional H-NMR spectra recorded at three different temperatures (283, 305, and 313 K), it was found that this peptide is mostly unstructured in water at these temperatures. Weak signals corresponding to i,i+3 or i,i+4 interactions, which are characteristic of formation of turn-like structures, were observed in the ROE spectra at all temperatures. The absence of a stable three-dimensional structure of the investigated peptide supports an earlier study (Blanco and Serrano, Eur J Biochem 1995, 230, 634-649) of a possible mechanism for folding of other (B1 and B2) immunoglobulin binding domains of Protein G. (c) 2008 Wiley Periodicals, Inc. Biopolymers 89: 1032-1044, 2008.This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com.     

Deep-learning contact-map guided protein structure prediction in CASP13

We report the results of two fully automated structure prediction pipelines, “Zhang-Server” and “QUARK”, in CASP13. The pipelines were built upon the C-I-TASSER and C-QUARK programs, which in turn are based on I-TASSER and QUARK but with three new modules: (a) a novel multiple sequence alignment (MSA) generation protocol to construct deep sequence-profiles for contact prediction; (b) an improved meta-method, NeBcon, which combines multiple contact predictors, including ResPRE that predicts contact-maps by coupling precision-matrices with deep residual convolutional neural-networks; and (c) an optimized contact potential to guide structure assembly simulations. For 50 CASP13 FM domains that lacked homologous templates, average TM-scores of the first models produced by C-I-TASSER and C-QUARK were 28% and 56% higher than those constructed by I-TASSER and QUARK, respectively. For the first time, contact-map predictions demonstrated usefulness on TBM domains with close homologous templates, where TM-scores of C-I-TASSER models were significantly higher than those of I-TASSER models with a P-value <.05. Detailed data analyses showed that the success of C-I-TASSER and C-QUARK was mainly due to the increased accuracy of deep-learning-based contact-maps, as well as the careful balance between sequence-based contact restraints, threading templates, and generic knowledge-based potentials. Nevertheless, challenges still remain for predicting quaternary structure of multi-domain proteins, due to the difficulties in domain partitioning and domain reassembly. In addition, contact prediction in terminal regions was often unsatisfactory due to the sparsity of MSAs. Development of new contact-based domain partitioning and assembly methods and training contact models on sparse MSAs may help address these issues.     

Synthesis, folding, and structure of the beta-turn mimic modified B1 domain of streptococcal protein G

The mechanism of beta-sheet formation remains a fundamental issue in our understanding of the protein folding process, but is hampered by the often encountered kinetic competition between folding and aggregation. The role of local versus nonlocal interactions has been probed traditionally by mutagenesis of both turn and strand residues. Recently, rigid organic molecules that impose a correct chain reversal have been introduced in several small peptides to isolate the importance of the long-range interactions. Here, we present the incorporation of a well-studied beta-turn mimic, designated as the dibenzofuran-based (DBF) amino acid, in the B1 domain of streptococcal protein G (B1G), and compare our results with those obtained upon insertion of the same mimic into the N-terminal beta-hairpin of B1G (O Melnyk et al., 1998, Lett Pept Sci 5:147-150). The DBF-B1G domain conserves the structure and the functional and thermodynamical properties of the native protein, whereas the modified peptide does not adopt a native-like conformation. The nature of the DBF flanking residues in the modified B1G domain prevents the beta-turn mimic from acting as a strong beta-sheet nucleator, which reinforces the idea that the native beta-hairpin formation is not driven by the beta-turn formation, but by tertiary interactions.     

大肠杆菌发酵生产重组人颗粒溶素

目的:在FUS-50L生物反应器中利用补料分批培养技术培养表达含重组质粒pET28a( )-GNLY的大肠杆菌BL21(DE3)pLysS株,生产重组颗粒溶素(GNLY)。方法:选取含pET28a( )-GNLY的BL21(DE3)pLysS菌株单个克隆分级培养,将制备的二级种子液接种于发酵罐中。在发酵过程中,控制溶氧为30%～50%,温度为37℃;在基础培养基内生长4h后,补加以甘油为碳源的补料,继续生长到11h;加入葡萄糖至终浓度为1%,30℃诱导表达6h;收集菌体,纯化制备目的蛋白。利用Western印迹检测重组蛋白的抗原性,用CFU方法检测其生物学活性。结果:发酵液中最终菌体密度达80g/L;纯化所得重组蛋白约占菌体总蛋白的5%,含量为60mg/L;经鉴定所获重组颗粒溶素有较好的免疫学活性和生物学活性。结论:用含重组质粒pET28a( )-GNLY的大肠杆菌BL21(DE3)pLysS表达系统,可得到具有生物活性的重组颗粒溶素,为大批量生产提供了条件。     

NMR-assisted protein structure prediction with MELDxMD

We describe the performance of MELD-accelerated molecular dynamics (MELDxMD) in determining protein structures in the NMR-data-assisted category in CASP13. Seeded from web server predictions, MELDxMD was found best in the NMR category, over 17 targets, outperforming the next-best groups by a factor of ~4 in z-score. MELDxMD gives ensembles, not single structures; succeeds on a 326-mer, near the current upper limit for NMR structures; and predicts structures that match experimental residual dipolar couplings even though the only NMR-derived data used in the simulations was NOE-based ambiguous atom–atom contacts and backbone dihedrals. MELD can use noisy and ambiguous experimental information to reduce the MD search space. We believe MELDxMD is a promising method for determining protein structures from NMR data.     

短短芽孢杆菌GZDF3中PilZ结构域基因的挖掘和糖基转移酶的原核表达

【背景】PilZ结构域是最早发现的环二鸟苷酸(Cyclic diguanylate,c-di-GMP)受体信号分子,与c-di-GMP结合后可以调控目标基因或者蛋白的活性,在细菌的生长过程中发挥着至关重要的作用,而短短芽孢杆菌中PilZ结构域的研究相对缺乏。【目的】挖掘短短芽孢杆菌GZDF3菌株中的PilZ结构域蛋白基因,并进行重组表达,为研究其功能奠定基础。【方法】从Pfam数据库中下载PilZ结构域模型,HMMScan软件扫描GZDF3全基因组序列,在保守结构域数据库(Conserved domain database,CDD)中分析蛋白保守结构域,Protein BLAST比对分析;采用ExPASy在线软件预测蛋白的基本理化性质;构建重组表达载体进行蛋白重组表达。【结果】GZDF3基因中存在5个含有PilZ结构域的蛋白编码基因,其中命名为Gene4836的基因经Protein BLAST比对分析显示其编码糖基转移酶,Gene1423为YcgR超家族蛋白编码基因,Gene1723编码透明质酸合成酶,属于糖基转移酶超家族2,其余Gene2571、Gene2956编码假定蛋白;Gene4836的编码产物分子量为24.08 kD,等电点为6.39,为酸性亲水性蛋白;C端有一个PilZ结构域;0.5 mmol/L乳糖诱导、30°C培养20 h,表达出一大小约为25kD的重组蛋白,与生物信息学预测结果相符。【结论】首次对短短芽孢杆菌含有PilZ结构域蛋白编码基因进行原核表达,并成功纯化出重组蛋白,为后续研究其功能奠定了基础。     

Enhanced cell-free protein expression by fusion with immunoglobulin Ckappa domain

While cell-free systems are increasingly used for protein expression in structural and functional studies, several proteins are difficult to express or expressed only at low levels in cell-free lysates. Here, we report that fusion of the human immunoglobulin kappa light chain constant domain (Ckappa) at the C terminus of four representative proteins dramatically improved their production in the Escherichia coli S30 system, suggesting that enhancement of cell-free protein expression by Ckappa fusion will be widely applicable.