去垢剂在膜蛋白研究中的应用

去垢剂是同时具有亲水极性基团和疏水非极性基团的双极性分子,能够使脂膜解体释放膜蛋白,并在溶液中为去膜状态下的膜蛋白提供疏水环境,维持和保护膜蛋白的疏水跨膜结构,在膜蛋白的结构和功能研究中有重要的意义。去垢剂的双极性和理化特性,如临界胶束浓度能够极大影响去垢剂和膜蛋白间的相互作用。在膜蛋白研究中,需要充分利用去垢剂的结构和特性:一方面,需要利用去垢剂代替脂质分子支持和稳定去膜状态下膜蛋白的结构和功能;另一方面,需要控制去垢剂和膜蛋白的相互作用,以满足膜蛋白结构研究如蛋白质结晶试验的要求。简要介绍了去垢剂在膜蛋白研究中的最新应用进展,涉及去垢剂在膜蛋白离体表达、分离和纯化、以及结构研究中的应用。     

分析超速离心研究多聚酸性氨基酸对SnRK2.6的影响

分析超速离心技术是一种通过检测分子在离心场作用下的沉降行为,分析获得其沉降系数、扩散系数、流体力学半径、摩尔质量、结合常数等水力学和热力学性质的方法,被广泛应用于蛋白质分子溶液性质的研究中.本文利用分析超速离心技术研究了拟南芥Sn RK2.6(sucrose non-fermenting1-related protein kinase 2.6)末端一段多聚酸性氨基酸序列对其溶液性质的影响,并将多聚酸性氨基酸序列Sn RK2.6(333~362)及人源PDI(protein disulfide isomerase)(441~491)连接至拟南芥PYL10(PYR like protein 10)分子末端进行分析,同时结合分子排阻层析和静态光散射技术,研究了上述蛋白质分子的分子质量和聚合状态.结果表明,多聚酸性氨基酸序列可以引起蛋白质分子轴长比增加,在溶液中运动时摩擦系数增加,水合半径明显增大,分子排阻层析洗脱体积明显变小.     

铜绿假单胞菌Psl多糖转运蛋白PslD的表达与纯化研究

条件性致病菌铜绿假单胞菌是细菌生物被膜研究的模式菌,其分泌的胞外多糖Psl在生物被膜形成中起关键作用。PslD为Psl多糖的转运蛋白,由256个氨基酸构成,生物信息学分析揭示其有N端信号肽且为一次跨膜蛋白。分离纯化完整跨膜蛋白需要去垢剂的作用,去垢剂种类繁多且性质不一,研究设计了一套筛选溶解PslD的去垢剂的方案。通过抗组氨酸标签的Western blot分析,n-Decyl-β-D-maltopyranoside (DM),n-Decyl-N,N-dimethylamine-N-oxide(DDAO)及n-Dodecyl-N,N-dimethylamine-N-oxide(LDAO)被认为溶解PslD的效率较高。通过改变总蛋白与去垢剂比例,进一步优化了去垢剂的溶解条件即8 mg/mL总蛋白:质量分数为1%的 LDAO。在此溶解条件下,仅通过第一步Ni柱亲和纯化目的蛋白纯度可到达80%以上,这为进一步结晶尝试及其结构生物学研究奠定基础。     

龙须菜叶绿素-蛋白复合物的分离及鉴定

以海洋经济海藻--龙须菜(Gracilarialemaneiformis)为材料,机械破碎与超声波相结合破碎这种含胶量非常多的细胞,蔗糖密度梯度超速离心纯化其类囊体膜,去垢剂Triton X-100增溶纯化的类囊体膜,再用蔗糖密度梯度超速离心方法分离其叶绿素-蛋白质复合物.P700差示光谱鉴定分离的光系统Ⅰ(PSⅠ)颗粒,并且检测到了具有DCIP光还原活性的光系统Ⅱ(PSⅡ)颗粒.结果表明,尽管海藻类囊体膜增溶困难,但只要条件合适,可以得到具有活性的光系统颗粒.     

去垢剂DDM和β-OG对细胞色素 b6f蛋白复合体中叶绿素a单线激发态寿命的不同影响

据报道, 细胞色素b₆f蛋白复合体(cytochrome b₆f, Cyt b₆f)中叶绿素a (chlorophyll a, Chl a)分子的单线激发态寿命(或荧光寿命)短于甲醇中游离Chl a的单线激发态寿命(~4 ns), 但是文献报道不同来源的Cyt b₆f中Chl a单线激发态寿命并不一致(一种为200 ps左右, 一种结果为600 ps左右). 本研究证明, 不同来源Cyt b₆f中Chl a的单线激发态寿命测定结果的不同, 与Cyt b₆f来源无关, 而与溶解膜蛋白的去垢剂—八烷基葡萄糖苷 (n-Octyl β-D-glucopyranoside, β-OG)和十二烷基麦芽糖苷(n-Dodecylβ-D-maltoside, DDM)有关. 溶解在DDM中的样品和溶解在b-OG中的样品相比, 其Chl a的荧光产率低, 强光照射下抗光破坏的能力强, 单线激发态的寿命更短(~200 ps). 显然, 溶解在DDM中样品的Chl a单线激发态的寿命更接近体内真实的情况.     

血清中GPI—PLD的性质研究

纯化的ＧＰＩ－ＰＬＤ是分子量为１００ｋＤ的单肽链,而血清经凝胶过滤时,该酶为５００ｋＤ。了解酶分子天然状态下的性质,有助于认识其生理功能。采用凝胶过滤、疏水柱层析及超速离心分离并测定该酶活性及磷脂、甘油三酯和胆固醇的浓度。结果说明,ＧＰＩ－ＰＬＤ在血清中不是以肽的多聚体形式存在,而可能是与血脂结合,形成蛋白与脂的复合物,经超速离心后存在于ＨＤＬ的密度区内,但该复合物与富含Ａｐｏ－Ａ１的ＨＤＬ亚类是     

膜蛋白结晶方法学研究进展

膜蛋白执行着物质运输、能量转换和信号转导等重要生物学功能,其分子的三维结构解析对阐述其功能及开展理性药物设计有着十分重要的意义．目前膜蛋白结构解析以X射线单晶衍射技术为主,该技术需要高质量晶体作为衍射对象．然而由于膜蛋白具有两亲性,难以得到高度有序的三维晶体,进而导致其结构解析十分困难．针对此问题,研究者们发展了一些专门面向膜蛋白的结晶方法,如基于去垢剂的方法,基于脂类的方法等．本文回顾了这些方法,并对未来膜蛋白的结晶研究进行了展望．     

2DE-MS中膜蛋白质组的研究进展

2-维凝胶电泳(2DE)具有高分辨率、高通量等特点,已被广泛地用于蛋白质组的研究.然而,2DE-MS在膜蛋白质组学研究方面却有其局限性,主要因为:膜蛋白具有低丰度、难溶、等电点时易沉淀、难酶解等特点.然而随着亚细胞分离技术和直接的生化方法富集等技术的发展,低丰度问题得到了极大的改善;增溶剂(尿素,硫脲),新的两性离子和非离子去垢剂,以及有机溶剂等的利用极大地改善了膜蛋白质组的溶解性能;同时,一些新的2DE技术的利用扩大了常规2DE的分离范围.在膜蛋白裂解方面,将酶解法与化学法(CNBr)相结合,另外先进的质谱技术的发展使得膜蛋白质组的研究在最近几年取得了较大的发展.现对2DE-MS途径中,膜的富集、膜蛋白的提取、分离、酶解、鉴定方面的进展进行综述.     

黑斑双鳍电鳐(Narcine maculata)电器官ACh受体的分离、纯化及其某些特性的研究

我们用超速离心、非离子去垢剂Tritonx—100增溶提取、亲和层析等方法从产于南中国海的黑斑双鳍电鳐(Narcine maculata)的电器官分离、纯化了ACh受体蛋白。这种电鳐的电器官每克湿组织含有与眼镜蛇神经毒素(cobro—toxin)的结合位点可达到～3 nmol。纯化后的受体蛋白,与眼镜蛇神经毒素结合的比活力约10—12 nmol/mg蛋白。受体蛋白经SDS-聚丙烯酰胺凝胶电泳呈现两个主要条带,其表观分子量分别为38,000和53,000。ACh受体与~(125)I标记的眼镜蛇神经毒素结合的复合物在1％Triton X—100存在下用凝胶过滤法测其表观分子量约390,000。等电聚焦测得该复合物的等电点约5.6—5.7。根据超离心分析,纯化的受体蛋白的沉降系数为9S。     

超滤-高效液相色谱法检测pHLA复合物中的抗原肽北大核心CSCD

重组HLA-Ⅰ类分子/抗原肽复合物(pHLA复合物)在研究人类T细胞特异性免疫应答中有重要用途。pHLA复合物的制备以基因工程及蛋白体外稀释折叠复性技术为基础,在体外复性体系中重组HLA-Ⅰ类分子正确折叠,并结合抗原肽形成复合物。本研究建立了一种超滤-高效液相色谱法(超滤-HPLC法)定量检测重组pHLA复合物中的抗原肽,尤其针对少量制备产物中抗原肽的检测。通过将重组HLA-Ⅰ类分子和抗原肽加入到复性缓冲液中,使重组HLA-Ⅰ类分子的重链(heavy chain,HC)与轻链(β2m)复性折叠,与含锚定残基的VYF抗原肽结合形成pHLA复合物,经超滤去除未结合的游离抗原肽VYF而保留复合物,最后将pHLA复合物经酸处理破坏其相互作用从而释放抗原肽,再超滤收集VYF抗原肽并进行HPLC检测,所测得的VYF抗原肽即为重组HLA-Ⅰ类分子与抗原肽相互作用所结合的抗原肽。结果显示,制备的重组pHLA复合物可被HLA-Ⅰ分子构象特异性抗体W6/32识别,这说明重组HLA-Ⅰ类分子折叠构象正确,可鉴定为pHLA复合物;而超滤-HPLC法也可检测到pHLA复合物中含有抗原肽VYF,因此将超滤-HPLC法用于检测pHLA复合物的方法可行。与Western blotting法相比,超滤-HPLC法定量检测抗原肽浓度范围为0–9μg/mL,可根据复合物中结合的抗原肽量来优化不同结合条件,以提高HLA-Ⅰ类分子折叠效率并促进HLA-Ⅰ类分子结合抗原肽,还可根据pHLA复合物结合的抗原肽含量计算复性体系中形成pHLA复合物的制备率。因此文中所建立的超滤-HPLC法可用于pHLA复合物制备过程的质量控制,在T细胞特异性免疫研究、人工抗原呈递细胞以及特异性四聚体探针应用开发方面都具有优势。     

Symmetric primary and tertiary structure mutations within a symmetric superfold: a solution, not a constraint, to achieve a foldable polypeptide

In previous studies designed to increase the primary structure symmetry within the hydrophobic core of human acidic fibroblast growth factor (FGF-1) a combination of five mutations were accommodated, resulting in structure, stability and folding kinetic properties similar to wild-type (despite the symmetric constraint upon the set of core residues). A sixth mutation in the core, involving a highly conserved Met residue at position 67, appeared intolerant to substitution. Structural analysis suggested that the local packing environment of position 67 involved two regions of apparent insertions that distorted the tertiary structure symmetry inherent in the beta-trefoil architecture. It was postulated that a symmetric constraint upon the primary structure within the core could only be achieved after these insertions had been deleted (concomitantly increasing the tertiary structure symmetry). The deletion of these insertions is now shown to permit mutation of position 67, thereby increasing the primary structure symmetry relationship within the core. Furthermore, despite the imposed symmetric constraint upon both the primary and tertiary structure, the resulting mutant form of FGF-1 is substantially more stable. The apparent inserted regions are shown to be associated with heparin-binding functionality; however, despite a marked reduction in heparin-binding affinity the mutant form of FGF-1 is surprisingly approximately 70 times more potent in 3T3 fibroblast mitogenic assays. The results support the hypothesis that primary structure symmetry within a symmetric protein superfold represents a possible solution, rather than a constraint, to achieving a foldable polypeptide.     

Integrating statistical pair potentials into protein complex prediction

The biophysical study of protein-protein interactions and docking has important implications in our understanding of most complex cellular signaling processes. Most computational approaches to protein docking involve a tradeoff between the level of detail incorporated into the model and computational power required to properly handle that level of detail. In this work, we seek to optimize that balance by showing that we can reduce the complexity of model representation and thus make the computation tractable with minimal loss of predictive performance. We also introduce a pair-wise statistical potential suitable for docking that builds on previous work and show that this potential can be incorporated into our fast fourier transform-based docking algorithm ZDOCK. We use the Protein Docking Benchmark to illustrate the improved performance of this potential compared with less detailed other scoring functions. Furthermore, we show that the new potential performs well on antibody-antigen complexes, with most predictions clustering around the Complementarity Determining Regions of antibodies without any manual intervention.     

The heat capacity of proteins

The heat capacity plays a major role in the determination of the energetics of protein folding and molecular recognition. As such, a better understanding of this thermodynamic parameter and its structural origin will provide new insights for the development of better molecular design strategies. In this paper we have analyzed the absolute heat capacity of proteins in different conformations. The results of these studies indicate that three major terms account for the absolute heat capacity of a protein: (1) one term that depends only on the primary or covalent structure of a protein and contains contributions from vibrational frequencies arising from the stretching and bending modes of each valence bond and internal rotations; (2) a term that contains the contributions of noncovalent interactions arising from secondary and tertiary structure; and (3) a term that contains the contributions of hydration. For a typical globular protein in solution the bulk of the heat capacity at 25°C is given by the covalent structure term (close to 85% of the total). The hydration term contributes about 15 and 40% to the total heat capacity of the native and unfolded states, respectively. The contribution of non-covalent structure to the total heat capacity of the native state is positive but very small and does not amount to more than 3% at 25°C. The change in heat capacity upon unfolding is primarily given by the increase in the hydration term (about 95%) and to a much lesser extent by the loss of noncovalent interactions (up to ～5%). It is demonstrated that a single universal mathematical function can be used to represent the partial molar heat capacity of the native and unfolded states of proteins in solution. This function can be experimentally written in terms of the molecular weight, the polar and apolar solvent accessible surface areas, and the total area buried from the solvent. This unique function accurately predicts the different magnitude and temperature dependences of the heat capacity of both the native and unfolded states, and therefore of the heat capacity changes associated with folding/unfolding transitions. © 1995 Wiley-Liss, Inc.     

Lethal mutations in the major homology region and their suppressors act by modulating the dimerization of the rous sarcoma virus capsid protein C‐terminal domain

An infective retrovirus requires a mature capsid shell around the viral replication complex. This shell is formed by about 1500 capsid protein monomers, organized into hexamer and pentamer rings that are linked to each other by the dimerization of the C‐terminal domain (CTD). The major homology region (MHR), the most highly conserved protein sequence across retroviral genomes, is part of the CTD. Several mutations in the MHR appear to block infectivity by preventing capsid formation. Suppressor mutations have been identified that are distant in sequence and structure from the MHR and restore capsid formation. The effects of two lethal and two suppressor mutations on the stability and function of the CTD were examined. No correlation with infectivity was found for the stability of the lethal mutations (D155Y‐CTD, F167Y‐CTD) and suppressor mutations (R185W‐CTD, I190V‐CTD). The stabilities of three double mutant proteins (D155Y/R185W‐CTD, F167Y/R185W‐CTD, and F167Y/I190V‐CTD) were additive. However, the dimerization affinity of the mutant proteins correlated strongly with biological function. The CTD proteins with lethal mutations did not dimerize, while those with suppressor mutations had greater dimerization affinity than WT‐CTD. The suppressor mutations were able to partially correct the dimerization defect caused by the lethal MHR mutations in double mutant proteins. Despite their dramatic effects on dimerization, none of these residues participate directly in the proposed dimerization interface in a mature capsid. These findings suggest that the conserved sequence of the MHR has critical roles in the conformation(s) of the CTD that are required for dimerization and correct capsid maturation. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins

A previously developed computer program for protein design, RosettaDesign, was used to predict low free energy sequences for nine naturally occurring protein backbones. RosettaDesign had no knowledge of the naturally occurring sequences and on average 65% of the residues in the designed sequences differ from wild-type. Synthetic genes for ten completely redesigned proteins were generated, and the proteins were expressed, purified, and then characterized using circular dichroism, chemical and temperature denaturation and NMR experiments. Although high-resolution structures have not yet been determined, eight of these proteins appear to be folded and their circular dichroism spectra are similar to those of their wild-type counterparts. Six of the proteins have stabilities equal to or up to 7kcal/mol greater than their wild-type counterparts, and four of the proteins have NMR spectra consistent with a well-packed, rigid structure. These encouraging results indicate that the computational protein design methods can, with significant reliability, identify amino acid sequences compatible with a target protein backbone.     

蛋白质相互作用研究的新技术与新方法

目前,蛋白质相互作用已成为蛋白质组学研究的热点. 新方法的建立及对已有技术的改进标志着蛋白质相互作用研究的不断发展和完善．在技术改进方面,本文介绍了弥补酵母双杂交的蛋白定位受限等缺陷的细菌双杂交系统;根据目标蛋白特性设计和修饰TAP标签来满足复合体研究要求的串联亲和纯化技术,以及在双分子荧光互补基础上发展的动态检测多个蛋白质间瞬时、弱相互作用的多分子荧光互补技术．还综述了近两年建立的新方法：与免疫共沉淀相比,寡沉淀技术直接研究具有活性的蛋白质复合体;减量式定量免疫沉淀方法排除了蛋白质复合体中非特异性相互作用的干扰;原位操作的多表位－配基绘图法避免了样品间差异的影响,以及利用多点吸附和交联加固研究弱蛋白质相互作用的固相蛋白质组学方法.     

Improvement of protein stability in protein microarrays

Protein stability in microarrays was improved using protein stabilizers. PEG 200 at 30% (w/v) was the most efficient stabilizer giving over 4-fold improvement in protein stability compared to without the stabilizer. PEG 200 above 10% (w/v) in the array solution prevented the evaporation of water in the sample and thereby improved protein stability in the microarray. When the streptavidin-biotin binding reaction was performed under optimized conditions, biotin-BSA-fluorescein isothiocyanate (FITC) was detected from 1 ng ml^–1 to 5 g ml^–1 by fluorescence analysis.     

A solubility-enhancement tag (SET) for NMR studies of poorly behaving proteins

Protein-fusion constructs have been used with great success for enhancing expression of soluble recombinant protein and as tags for affinity purification. Unfortunately the most popular tags, such as GST and MBP, are large, which hinders direct NMR studies of the fusion proteins. Cleavage of the fusion proteins often re-introduces problems with solubility and stability. Here we describe the use of N-terminally fused protein G (B1 domain) as a non-cleavable solubility-enhancement tag (SET) for structure determination of a dimeric protein complex. The SET enhances the solubility and stability of the fusion product dramatically while not interacting directly with the protein of interest. This approach can be used for structural characterization of poorly behaving protein systems, and would be especially useful for structural genomics studies.     

Characterization of a mammalian Golgi-localized protein complex, COG, that is required for normal Golgi morphology and function

Multiprotein complexes are key determinants of Golgi apparatus structure and its capacity for intracellular transport and glycoprotein modification. Three complexes that have previously been partially characterized include (a) the Golgi transport complex (GTC), identified in an in vitro membrane transport assay, (b) the ldlCp complex, identified in analyses of CHO cell mutants with defects in Golgi-associated glycosylation reactions, and (c) the mammalian Sec34 complex, identified by homology to yeast Sec34p, implicated in vesicular transport. We show that these three complexes are identical and rename them the conserved oligomeric Golgi (COG) complex. The COG complex comprises four previously characterized proteins (Cog1/ldlBp, Cog2/ldlCp, Cog3/Sec34, and Cog5/GTC-90), three homologues of yeast Sec34/35 complex subunits (Cog4, -6, and -8), and a previously unidentified Golgi-associated protein (Cog7). EM of ldlB and ldlC mutants established that COG is required for normal Golgi morphology. "Deep etch" EM of purified COG revealed an approximately 37-nm-long structure comprised of two similarly sized globular domains connected by smaller extensions. Consideration of biochemical and genetic data for mammalian COG and its yeast homologue suggests a model for the subunit distribution within this complex, which plays critical roles in Golgi structure and function.     

Human dihydrofolate reductase and thymidylate synthase form a complex in vitro and co-localize in normal and cancer cells

Enzymes involved in thymidylate biosynthesis, thymidylate synthase (TS), and dihydrofolate reductase (DHFR) are well-known targets in cancer chemotherapy. In this study, we demonstrated for the first time, that human TS and DHFR form a strong complex in vitro and co-localize in human normal and colon cancer cell cytoplasm and nucleus. Treatment of cancer cells with methotrexate or 5-fluorouracil did not affect the distribution of either enzyme within the cells. However, 5-FU, but not MTX, lowered the presence of DHFR-TS complex in the nucleus by 2.5-fold. The results may suggest the sequestering of TS by FdUMP in the cytoplasm and thereby affecting the translocation of DHFR-TS complex to the nucleus. Providing a strong likelihood of DHFR-TS complex formation in vivo, the latter complex is a potential new drug target in cancer therapy. In this paper, known 3D structures of human TS and human DHFR, and some protozoan bifunctional DHFR-TS structures as templates, are used to build an in silico model of human DHFR–TS complex structure, consisting of one TS dimer and two DHFR monomers. This complex structure may serve as an initial 3D drug target model for prospective inhibitors targeting interfaces between the DHFR and TS enzymes.