人热休克蛋白转录因子1 DNA结合结构域的表达、纯化和晶体生长

目的:获得大量热休克转录因子1(HSF1)DNA结合结构域(DBD)蛋白,用于晶体生长的三维结构解析。方法:将DBD基因片段克隆至原核表达载体pGEX-6P-1中并获得高效表达,经过Glutathione SepharoseTM 4B亲和层析、ResourceQ纯化后,蛋白纯度达到95%以上。结果:圆二色谱仪分析蛋白质的二级结构结果显示α螺旋占33%,β折叠占15%;采用悬滴气相扩散法得到了针状DBD晶体。结论:纯化的蛋白质与同源性达68%的Kluyveromyceslactis的DBD有相似的空间构象。获得的蛋白质晶体为进一步的三维结构解析奠定了基础。     

孕烷X受体配体结合结构域蛋白晶体的X线衍射结构解析

目的:利用X线衍射技术解析孕烷X受体(PXR)配体结合结构域(LBD)蛋白晶体的3维结构。方法:对PXR蛋白LBD(130~434氨基酸残基)序列进行密码子优化并化学合成后克隆至pRSFDuet-1表达载体,再将载体导入大肠杆菌BL21(DE3),对PXR-LBD蛋白进行原核表达与分离纯化;采用晶体筛选试剂盒筛选蛋白结晶条件,采用悬滴法获得目标蛋白的晶体;对获得的蛋白晶体进行X线晶体衍射检测,并收集相关数据建立PXR-LBD的三维结构。结果:获得了PXR-LBD的高质量晶体并利用X线衍射解析了该蛋白质晶体的结构数据,使用Phenix.refine软件和COOT软件等对结构进行修正,最终获得了高分辨率的3维结构数据。结论:完成了孕烷X受体配体结合结构域蛋白晶体的X线衍射结构解析,为研究和开发PXR相关药物奠定了基础。     

神经富亮氨酸重复蛋白家族研究进展

神经富亮氨酸重复(neural leucine-rich repeat,NLRR)蛋白家族是一类进化上保守、功能多样的Ⅰ型跨膜蛋白.NLRR主要表达于神经组织,肺部、心脏、肝、肾也有微量表达.自1996年Taguchi在发育的小鼠神经系统中发现了新的LRR蛋白质mNLRR-1和mNLRR-2后,一系列含有类似结构的NLRR蛋白质在小鼠、大鼠、爪蟾、斑马鱼和人类等种属中被发现.NLRR蛋白家族成员同源性高,主要含有一些共同的蛋白质结构域:LRR(leucine-rich repeat)、AFR(amino-flanking region)、CFR(carboxy-flanking region)、IgC2(immunoglobulin-like C2 type domain)和FNⅢ(fibronectin type Ⅲ-like domain)等.迄今为止,已有实验证明NLRR作为细胞黏附分子或配体受体分子在神经发育与再生过程中发挥着重要作用.主要对NLRR的时空表达模式、结构及主要生物学功能等进行了综述.     

重组黄热病毒E蛋白结构域Ⅲ作为亚单位疫苗的抗原性和免疫原性

目的：表达纯化黄热病毒（YFV）囊膜蛋白（E蛋白）结构域Ⅲ,研究其作为亚单位疫苗预防YFV、日本脑炎病毒（JEV）感染的可能。方法：扩增YFVE蛋白结构域Ⅲ（YFDⅢ）的cDNA片段333bp,将其连接到原核表达载体pET-32a（＋）中,构建原核表达载体pET-YFDⅢ,转化感受态大肠杆菌Rosetta（DE3）,IPTG诱导表达重组YFDⅢ;用纯化的YFDⅢ免疫新西兰兔和BALB/c鼠,检测相关抗体滴度。结果：在大肠杆菌中可溶性表达了YFDⅢ融合蛋白,表达量约占菌体蛋白的50%;Western印迹及ELISA分析表明,纯化的YFDⅢ具有良好的抗原性和免疫原性;利用纯化的YFDⅢ免疫新西兰兔,获得了高达1∶4×105滴度的抗YFV抗体和1∶2×104滴度的抗JEV抗体;利用纯化的YFDⅢ免疫BALB/c鼠,获得了1∶7×104滴度的抗YFV抗体和1∶2×103滴度的抗JEV抗体。结论：重组YFDⅢ有较好的免疫原性,具有开发成亚单位疫苗的潜能。     

肺炎链球菌SP0306蛋白的表达纯化及结晶研究

SP0306蛋白是肺炎链球菌TIGR4菌株中的一种假想的转录因子,但其蛋白三维结构及生物学功能尚未明了,生物信息学分析提示其可能调控碳水化合物代谢相关基因的表达。成功构建了SP0306蛋白的全长表达载体PET28a-sp0306,利用大肠杆菌BL21(DE3)菌株进行原核表达,获得了以可溶形式表达的目的蛋白。经Ni-NTA柱亲和层析及DEAE阴性离子交换层析纯化后,获得了高纯度的目的蛋白。采用悬滴气相扩散法获得了质量较好的SP0306蛋白晶体,并初步进行了晶体X射线衍射,为其最终的三维结构解析及生物学功能研究奠定了基础。     

UHRF2结构域突变体的原核表达与纯化

目的构建UHRF2各个以结构域为基础的突变体原核表达载体,在大肠埃希菌中表达并对融合蛋白进行纯化和鉴定。方法以pCMV-3xFlag—UHRF2为模板,PCR扩增UHRF2的各个结构域基因片段,各PCR产物经酶切后连接到pGEX-4T-1载体上;将重组载体转化大肠埃希菌（BL21菌株）,IPTG诱导表达各GST融合蛋白,超声波破碎细菌,离心收获蛋白并经谷胱甘肽琼脂糖凝胶4B（glutathione sepharose 4B）亲合纯化;纯化的蛋白经SDS-PAGE电泳后用考马斯亮蓝染色或免疫印记实验鉴定各蛋白表达情况。结果成功构建了UHRF2结构域突变体的原核表达载体,各突变体蛋白表达正确。结论UHRF2各结构域突变体的成功构建便于用GST pull—down实验研究UHRF2参与与其它蛋白相互作用的结构域,为了解UHRF2功能打下了基础。     

HIV-1逆转录酶的表达、纯化及晶体生长条件的摸索

利用大肠杆菌原核表达系统对HIV-1 RT蛋白进行表达,纯化以及晶体生长条件的搜索。以PNL4-3为模板,通过聚合酶链式反应扩增出HIV-1 RT蛋白的基因,将扩增出的目的基因克隆到表达载体Pet-duet中,构建HIV-1逆转录酶的重组质粒,重组质粒转化表达菌株BL21(DE3)进行诱导表达。HIV-1逆转录酶主要以可溶形式表达,经亲和柱Ni2+-NTA,阴离子交换柱MONOQ,分子筛进行纯化后获得了蛋白,其纯度达到85%-90%,基本满足了晶体生长条件的要求。对晶体生长条件行了初筛,最终并获得了HIV-1 RT的蛋白晶体,为蛋白晶体的优化以及蛋白结构的研究奠定了基础。     

肺炎链球菌SPD1587蛋白的表达纯化及晶体生长研究

SPD1587蛋白是肺炎链球菌D39菌株中的一种转录因子,其在鼻咽部定植和肺部感染过程中发挥着重要作用。生物信息学分析提示其具有与A群链球菌的转录因子Mga蛋白相似的结构,目前其三维结构尚未被解析。成功构建了SPD1587蛋白的全长表达载体PET28a-spd1587,利用大肠杆菌BL21(DE3)菌株进行原核表达,获得了以可溶形式表达的目的蛋白。经Ni-NTA柱亲和层析及DEAE阴离子交换层析纯化后,获得了高纯度的目的蛋白。采用悬滴气相扩散法获得了SPD1587蛋白晶体。     

整合素αMβ2 I-结构域的基因合成和蛋白表达

目的：利用大肠杆菌表达系统表达整合素αMβ2 I-结构域,并对其进行纯化。方法与结果：利用DNAWorks在线引物程序设计经过密码子优化的整合素αMβ2 I-结构域的寡核苷酸序列;采用PCR介导的基因拼装法合成αMβ2 I-结构域DNA模板,将其克隆至原核表达载体pET11d-6h上,并转化大肠杆菌,获得表达菌株;经IPTG诱导,αMβ2 I-结构域在大肠杆菌BL21（DE3）中获得高效表达,表达产物经Ni-NTA琼脂糖层析柱纯化后,纯度达到90％以上;电喷雾电离质谱测定表明纯化所得的蛋白精确的相对分子质量为23720.0,与预期值相符;肽指纹质谱图谱鉴定其为目的蛋白。结论：αMβ2 I-结构域的高效表达,为进一步研究其与配体的结合及其复合物晶体结构奠定了基础。     

MNDA及MNDA-HIN200片段在大肠杆菌中克隆、表达及纯化

MNDA蛋白是与免疫反应相关的HIN-200家族成员之一,可作为模式识别受体来识别外源性双链DNA,它在人类免疫性疾病中发挥重要作用.通过PCR扩增获得的MNDA全长cDNA和MNDA-H1N200基因片段克隆到原核表达载体pET-28a中,使其N端带有一个His标签,将重组质粒转化到大肠杆菌BL21(DE3)表达菌株,经IPTG诱导后,分别经过亲和层析和分子筛层析对MNDA和MNDA-HIN200进行纯化.DNA测序表明,构建的重组质粒正确,筛选了蛋白最适表达菌株BI21(DE3);由于PYD(88aa)结构域之间的相互作用影响MNDA的表达量度聚集状态,因此设计了PYD缺失的只含有HIN-200结构域的突变体MNDA-HIN200,最终获得了大量的、均一性好、高纯度的MNDA-HIN200蛋白,为MNDA的蛋白的晶体筛选和结构解析奠定基础.     

X-ray diffraction of heavy-atom labelled two-dimensional crystals of rhodopsin identifies the position of cysteine 140 in helix 3 and cysteine 316 in helix 8

We have used site-specific heavy-atom labelling and X-ray diffraction to localize single amino acid residues in the cytoplasmic domain of the integral membrane protein rhodopsin, the dim-light photoreceptor of retinal vertebrate rod cells. Two-dimensional orthorhombic crystals of the space group p22(1)2(1) (a=59.5(+/-1) A and b=82.7(+/-1.5) A) were produced from detergent-solubilized, partially delipidated rhodopsin. To obtain milligram amounts of two-dimensional crystals, which are required for X-ray diffraction, the yield of the crystalline material was significantly increased by reconstitution of rhodopsin in the presence of cholesterol (1:2 to 1:10 mol/mol) and by adding polar organic solvents to the dialysis buffer. The native cysteine residues C140 and C316 were then selectively labelled with mercury using the sulphydryl-specific reagent p-chloromercuribenzoate (1.6-2.1 mol Hg per mol rhodopsin). The labelling did not affect the unit cell dimensions. Optical absorption spectra of labelled and native two-dimensional rhodopsin crystals showed the characteristic 11-cis-retinal peak at 498 nm, which corresponds to the dark state of rhodopsin. The in-plane position of the mercury label was calculated at 9.5 A resolution from the intensity differences in the X-ray diffraction patterns of labelled and native crystals using Fourier difference methods and the phase information from electron crystallography. The label positions were in excellent agreement with the positions of C140 at the cytoplasmic end of helix 3 and of C316 in the cytoplasmic helix 8 recently obtained from three-dimensional rhodopsin crystals. Whereas these high-resolution diffraction studies were performed under cryogenic conditions (100 K), our results were obtained at room temperature with fully hydrated membranes and in the absence of loop-loop crystal contacts. To study the structural changes of the cytoplasmic loops involved in activation and signal transduction, our more physiological conditions offer important advantages. Furthermore, the localization of C316 is the first direct proof that the electron density on top of helix 1 observed by cryo-electron microscopy is a part of the C-terminal loop. Our approach is of particular interest for investigations of other membrane proteins, for which 3D crystals are not available. Structural constraints from heavy-atom labels at strategic sites enable the assignment of a position in the amino acid sequence to features visible in a low-resolution density map and the study of conformational changes associated with different functional states of the membrane protein.     

Use of a fusion protein to obtain crystals suitable for X-ray analysis: crystallization of a GST-fused protein containing the DNA-binding domain of DNA replication-related element-binding factor, DREF.

Crystals of glutathione-S-transferase (GST)-fused protein containing the DNA-binding domain of DNA replication-related element-binding factor, DREF, were obtained under crystallization conditions similar to those for GST. Preliminary X-ray crystallographic analysis revealed that crystals of the GST-fused protein belong to space group P6(1)22 or P6(5)22 with unit cell dimensions a = b = 140.4 A, c = 93.5 A and gamma = 120 degrees, having one molecule in the crystallographic asymmetric unit. The crystals diffract to 2.5 A resolution. The cell dimensions are related to those of GST crystals thus far reported. Crystallization of the DNA-binding domain that was cleaved from the fused protein by thrombin was also carried out using several methods under numerous conditions, but efforts to produce well-ordered large crystals were unsuccessful. A possible application of GST-fusion proteins for small target proteins or domains to obtain crystals suitable for X-ray structure determination is proposed.     

Design and structural thermodynamic studies of the chimeric protein derived from spectrin SH3 domain

A number of the chimeric constructs with spectrin SH3 domain were designed for structural and thermodynamic studies of protein self-assembly and protein-ligand interactions. SH3 domains, components of many regulatory proteins, operate through weak interactions with proline-rich regions of polypeptide chains. The recombinant construct (WT-CIIA) studied in this work was constructed by linking the peptide ligand PPPVPPYSAG to the domain C-terminus via a long 12-residue linker to increase the affinity of this ligand for the spectrin domain, thereby ensuring a stable positioning of the polyproline helix to the conserved ligand-binding site in orientation II, which is regarded as untypical of the interaction between this domain and oligopeptides. A comparison of fluorescence spectra of the initial domain and the recombinant protein WT-CIIA suggests that the ligand sticks to the conservative binding site. However, analysis of the equilibrium urea-induced unfolding has demonstrated that this is an unstable contact, which leads to a two-stage unfolding of the chimeric protein. The protein WT-CIIA was crystallized; a set of X-ray diffraction data with a resolution of 1.75 Å was recorded from individual crystals. A preliminary analysis of these diffraction data has demonstrated that the crystals belong to space group P32 with the following unit cell parameters: a = b = 36.39, c = 112.17 Å, a = β = 90.0, and γ = 120.0.     

Purification and crystallization of a complex between human interferon γ receptor (extracellular domain) and human interferon γ

X-ray diffraction quality crystals have been obtained from a complex between interferon γ and the extracellular domain of its high-affinity cell surface receptor. The crystals were obtained from interferon γ/interferon γ receptor complexes purified by size exclusion chromatography. Diffraction quality crystals required analyzing these complex samples by isoelectric focusing gels to select purified complex fractions devoid of unbound interferon γ. These studies used interferon γ receptor engineered with an eight amino acid N-terminal deletion to eliminate heterogeneity generated due to proteolytic cleavage. In addition, the receptor was expressed in an E. coli secretion cell line which eliminated the need to refold the protein. Hexagonal crystals were grown from 1.6 M ammonium phosphate solutions and belong to a spacegroup of P6₅22 with unit cell dimensions a = 145.9 Å and c = 180.3 Å. These crystals diffract to at least 2.9 Å resolution when exposed to synchrotron radiation. SDS PAGE analysis of the crystals demonstrated that both interferon γ and the receptor were present. Analysis of the x-ray diffraction data revealed that the crystals contain complexes with a stoichiometry of 2:1 receptor: ligand within the crystallographic asymmetric unit and consist of approximately 55% solvent. © 1996 Wiley-Liss, Inc.     

自由电子激光在生物学中的应用

同步辐射的发展和应用已经极大的推动了自然科学包括生物学的巨大发展,其中结构生物学更是离不开X射线衍射分析,小角散射等。X射线自由电子激光(XFEL)相比同步辐射具有更高强度,完全相干等特点,被称为第四代光源。科学家已经利用XFEL实现了尺度约为1微米的蛋白质晶体的高分辨率结构解析,并且也实现了单颗粒的病毒的低分辨重构。未来,XFEL将会为生物学的发展打开一扇新的大门。     

Crystallization and preliminary x-ray analysis of complexes of porcine pancreatic elastase with two natural inhibitors

Two different natural protease inhibitors, the squash inhibitor MCEI III and the third domain of turkey ovomucoid inhibitor OMTKY3, were crystallized in complexes with porcine pancreatic elastase (PPE). About 700 conditions were screened altogether. Crystals of the complex between MCEI III and PPE were grown in citrate buffer with and without ammonium acetate. X-ray diffraction data were collected to 1.9 angstroms resolution at room temperature using synchrotron radiation. The crystals belong to space group P2(1), with unit-cell parameters a = 49.17, b = 44.59, c = 67.08 angstroms, beta = 110.97 degrees. Crystals of the OMTKY3/PPE complex were obtained in the presence of ammonium sulfate, MES buffer and polyethylene glycol monomethylether (PEG). These crystals of this complex diffracted to 2.1 angstroms resolution and belongs to space group I222, with unit-cell parameters a = 84.58, b = 84.61, c = 89.92 angstroms and diffracted to 2.2 angstroms resolution. The diffraction data were collected using a conventional rotating anode X-ray generator at room temperature. In both cases the presence of inhibitor in the crystals was confirmed by crystallography.     

Characterization of the knob domain of the adenovirus type 5 fiber protein expressed in Escherichia coli.

The adenovirus fiber protein is used for attachment of the virus to a specific receptor on the cell surface. Structurally, the protein consists of a long, thin shaft that protrudes from the vertex of the virus capsid and terminates in a globular domain termed the knob. To verify that the knob is the domain which interacts with the cellular receptor, we have cloned and expressed the knob from adenovirus type 5 together with a single repeat of the shaft in Escherichia coli. The protein was purified by conventional chromatography and functionally characterized for its interaction with the adenovirus receptor. The recombinant knob domain bound about 4,700 sites per HeLa cell with an affinity of 3 x 10(9) M-1 and blocked adenovirus infection of human cells. Antibodies raised against the knob also blocked virus infection. By gel filtration and X-ray diffraction analysis of protein crystals, the knob was shown to consist of a homotrimer of 21-kDa subunits. The results confirm that the trimeric knob is the ligand for attachment to the adenovirus receptor.     

Crystallization and preliminary X-ray analysis of the complex between a mouse Fab fragment and a single IgG-binding domain from streptococcal protein G.

The Fab fragment of a mouse immunoglobulin G1, complexed with a single IgG-binding domain from streptococcal protein G, has been crystallized in a form suitable for analysis by X-ray diffraction. The needle-shaped crystals were grown from polyethylene glycol 4000 using vapour diffusion methods and diffract to 2.3 A resolution. The space group is P2(1)2(1)2(1) (a = 64.5 A, b = 70.5 A and c = 120.1 A), with one Fab-protein G domain complex in the asymmetric unit. Solution of the three-dimensional structure of the complex will permit a detailed analysis of the molecular interactions between protein G and the Fab portion of IgG.     

The expression, purification and crystallization of the epsilon subunit of the F1 portion of the ATPase of Escherichia coli.

The epsilon subunit of the F0F1-ATPase from Escherichia coli has been expressed in E. coli as a fusion protein with glutathione S-transferase from the parasitic helminth Schistosoma japonicum. The epsilon subunit released by thrombin treatment of the purified fusion protein carried two amino acid changes, A1G and M2S, and was obtained in a yield of about five milligrams per litre of cultured cells. The two amino acid changes were shown not to affect function. The protein has been crystallized in a form suitable for X-ray diffraction structure analysis. The crystals are hexagonal, space group P6(1)22 (or P6(5)22), with a = b = 94.9 A, c = 57.1 A and gamma = 120 degrees. The diffraction from small crystals extends to at least 2.9 A resolution.