Antibody side chain conformations are position‐dependent

Side chain prediction is an integral component of computational antibody design and structure prediction. Current antibody modelling tools use backbone‐dependent rotamer libraries with conformations taken from general proteins. Here we present our antibody‐specific rotamer library, where rotamers are binned according to their immunogenetics (IMGT) position, rather than their local backbone geometry. We find that for some amino acid types at certain positions, only a restricted number of side chain conformations are ever observed. Using this information, we are able to reduce the breadth of the rotamer sampling space. Based on our rotamer library, we built a side chain predictor, position‐dependent antibody rotamer swapper (PEARS). On a blind test set of 95 antibody model structures, PEARS had the highest average χ₁ and accuracy (78.7% and 64.8%) compared to three leading backbone‐dependent side chain predictors. Our use of IMGT position, rather than backbone ϕ/ψ, meant that PEARS was more robust to errors in the backbone of the model structure. PEARS also achieved the lowest number of side chain–side chain clashes. PEARS is freely available as a web application at http://opig.stats.ox.ac.uk/webapps/pears .     

用EST-SSR标记检测我国甘蓝型油菜品种的遗传多样性

杂交育种依然是我国油菜育种的主要方法,杂种优势的利用仍然是提高产量的重要途径.为了解我国甘蓝型油菜的遗传变异,采用16个EST-SSR标记对近年来推广的91个品种的遗传多样性进行了分析.共扩增到100个条带,其中84个多态性带,多态性比率为84%.平均每对引物扩增的带数和多态性带数分别为6.25个和5.25个.多态性信息含量(PIC)变化在0.022-0.926之间,平均为0.677,所揭示的基因型数变化于2-24之间,平均为12.44个.供试材料间遗传距离变幅较大(0.0530-0.7223之间),说明它们具有广泛的遗传变异.其中,杂交种和2000年以后育成品种的遗传基础较宽,遗传多样性分别明显高于常规品种和2000年以前育成的品种.按非加权成对平均数法(UPGMA)进行的聚类分析显示,在遗传距离为0.313处,参试材料可以分为三大类,其中,包含87份材料的第一大类在遗传距离为0.233处又可进一步分为10个亚类.聚类结果与系谱来源基本一致,比较真实反映了所用材料的遗传变异情况.     

应用原子力显微镜分析正常淋巴细胞和Jurkat细胞的形态和机械性质

淋巴细胞形态和机械性质的变化与人的健康、疾病的治疗和诊断有着密切关系。本研究利用原子力显微镜研究淋巴细胞和Jurkat细胞形态和机械性质。结果显示,这2种细胞的形态较为相似,但通过对力曲线的分析得出这2种细胞的机械性质明显不同。正常淋巴细胞粘弹力范围大致为(796.7±248.5)pN,而Jurkat细胞分布于(158.5±37.5)pN;正常淋巴细胞的杨氏模量(0.471kPa±0.081kPa)近4倍于Jurkat细胞(0.0964kPa±0.0229kPa);而Jurkat细胞(4.322mN/m±0.382mN/m)的硬度近2倍于正常淋巴细胞(2.278mN/m±0.488mN/m)。结果表明原子力显微镜能可在临床诊断上区分正常细胞与肿瘤细胞,即使两者形态区别不明显。     

High Resolution NMR-based Model for the Structure of a scFv-IL-1�� Complex: POTENTIAL FOR NMR AS A KEY TOOL IN THERAPEUTIC ANTIBODY DESIGN AND DEVELOPMENT*

Monoclonal antibodies have recently started to deliver on their promise as highly specific and active drugs; however, a more effective, knowledge-based approach to the selection, design, and optimization of potential therapeutic antibodies is currently limited by the surprising lack of detailed structural information for complexes formed with target proteins. Here we show that complexes formed with minimal antigen binding single chain variable fragments (scFv) reliably reflect all the features of the binding interface present in larger Fab fragments, which are commonly used as therapeutics, and report the development of a robust, reliable, and relatively rapid approach to the determination of high resolution models for scFv-target protein complexes. This NMR spectroscopy-based approach combines experimental determination of the interaction surfaces and relative orientations of the scFv and target protein, with NMR restraint-driven, semiflexible docking of the proteins to produce a reliable and highly informative model of the complex. Experience with scFvs and Fabs targeted at a number of secreted regulatory proteins suggests that the approach will be applicable to many therapeutic antibodies targeted at proteins, and its application is illustrated for a potential therapeutic antibody targeted at the cytokine IL-1β. The detailed structural information that can be obtained by this approach has the potential to have a major impact on the rational design and development of an increasingly important class of biological pharmaceuticals.     

NSOM‐ and AFM‐based nanotechnology elucidates nano‐structural and atomic‐force features of a Y. pestis V immunogen‐containing particle vaccine capable of eliciting robust response

It is postulated that unique nanoscale proteomic features of immunogen on vaccine particles may determine immunogen‐packing density, stability, specificity, and pH‐sensitivity on the vaccine particle surface and thus impact the vaccine‐elicited immune responses. To test this presumption, we employed near‐filed scanning optical microscopy (NSOM)‐ and atomic force microscopy (AFM)‐based nanotechnology to study nano‐structural and single‐molecule force bases of Yersinia pestis (Y. pestis) V immunogen fused with protein anchor (V‐PA) loaded on gram positive enhancer matrix (GEM) vaccine particles. Surprisingly, the single‐molecule sensitive NSOM revealed that ～90% of V‐PA immunogen molecules were packed as high‐density nanoclusters on GEM particle. AFM‐based single‐molecule force analyses indicated a highly stable and specific binding between V‐PA and GEM at the physiological pH. In contrast, this specific binding was mostly abrogated at the acidic pH equivalent to the biochemical pH in phagolysosomes of antigen‐presenting‐cells in which immunogen protein is processed for antigen presentation. Intranasal mucosal vaccination of mice with such immunogen loaded on vaccine particles elicited robust antigen‐specific immune response. This study indicated that high‐density, high‐stability, specific, and immunological pH‐responsive loading of immunogen nanoclusters on vaccine particles could readily be presented to the immune system for induction of strong antigen‐specific immune responses.     

乳腺癌中耐药蛋白P-gp、GST-π、Topo-Ⅱ的表达

目的明确乳腺癌中是否存在P-gp、GST-π、TopoⅡ三种原发耐药蛋白;三种耐药蛋白的表达与乳腺癌的组织类型、细胞分化程度、TNM分期是否相关;是否影响乳腺癌患者的预后。方法采用S-P免疫组化方法,检测260例乳腺癌患者中P-gp、TopoⅡ、GST-π的表达情况,同时取10例乳腺病及10例癌旁乳腺组织作对照。结果乳腺癌中三种耐药蛋白呈异质性表达。P-gp、GST-π和TopoⅡ在良性病变中弱表达,在伴有早期浸润的乳腺导管内癌和乳腺浸润性导管癌中的表达同样明显高于乳腺导管内癌;其中P-gp和GST-π表达和预后相关,差异显著(P<0.01,P<0.05)。结论乳腺癌在发生早期浸润的同时就伴随着耐药的发生;P-gp和GST-π是乳腺癌患者预后的影响因素,综合检测优于单一检测。     

Unique Behavioral Characteristics and microRNA Signatures in a Drug Resistant Epilepsy Model

Background

Pharmacoresistance is a major issue in the treatment of epilepsy. However, the mechanism underlying pharmacoresistance to antiepileptic drugs (AEDs) is still unclear, and few animal models have been established for studying drug resistant epilepsy (DRE). In our study, spontaneous recurrent seizures (SRSs) were investigated by video-EEG monitoring during the entire procedure.

Methods/Principal Findings

In the mouse pilocarpine-induced epilepsy model, we administered levetiracetam (LEV) and valproate (VPA) in sequence. AED-responsive and AED-resistant mice were naturally selected after 7-day treatment of LEV and VPA. Behavioral tests (open field, object exploration, elevated plus maze, and light-dark transition test) and a microRNA microarray test were performed. Among the 37 epileptic mice with SRS, 23 showed significantly fewer SRSs during administration of LEV (n = 16, LEV sensitive (LS) group) or VPA (n = 7, LEV resistant/VPA sensitive (LRVS) group), while 7 epileptic mice did not show any amelioration with either of the AEDs (n = 7, multidrug resistant (MDR) group). On the behavioral assessment, MDR mice displayed distinctive behaviors in the object exploration and elevated plus maze tests, which were not observed in the LS group. Expression of miRNA was altered in LS and MDR groups, and we identified 4 miRNAs (miR-206, miR-374, miR-468, and miR-142-5p), which were differently modulated in the MDR group versus both control and LS groups.

Conclusion

This is the first study to identify a pharmacoresistant subgroup, resistant to 2 AEDs, in the pilocarpine-induced epilepsy model. We hypothesize that modulation of the identified miRNAs may play a key role in developing pharmacoresistance and behavioral alterations in the MDR group.     

Developmental change of endogenous glutamate and gamma-glutamyl transferase in cultured cerebral cortical interneurons and cerebellar granule cells,and in mouse cerebral cortex and cerebellum in vivo

The developmental change of endogenous glutamate, as correlated to that of gamma-glutamyl transferase and other glutamate metabolizing enzymes such as phosphate activated glutaminase, glutamate dehydrogenase and aspartate, GABA and ornithine aminotransferases, has been investigated in cultured cerebral cortex interneurons and cerebellar granule cells. These cells are considered to be GABAergic and glutamatergic, respectively. Similar studies have also been performed in cerebral cortex and cerebellum in vivo. The developmental profiles of endogenous glutamate in cultured cerebral cortex interneurons and cerebellar granule cells corresponded rather closely with that of gamma-glutamyl transferase and not with other glutamate metabolizing enzymes. In cerebral cortex and cerebellum in vivo the developmental profiles of endogenous glutamate, gamma-glutamyl transferase and phosphate activated glutaminase corresponded with each other during the first 14 days in cerebellum, but this correspondence was less good in cerebral cortex. During the time period from 14 to 28 days post partum the endogenous glutamate concentration showed no close correspondence with any particular enzyme. It is suggested that gamma-glutamyltransferase regulates the endogenous glutamate concentration in culture neurons. The enzyme may also be important for regulation of endogenous glutamate in brain in vivo and particularly in cerebellum during the first 14 days post partum. Gamma-glutamyl transferase in cultured neurons and brain tissue in vivo appears to be devoid of maleate activated glutaminase.Abbreviations used Asp-T aspartate aminotransferase (EC 2.6.1.1) - GABA-T GABA aminotransferase (EC 2.6.1.19) - GAD glutamate decarboxylase (EC 4.1.1.15) - gamma-GT gamma-glutamyl transferase (gamma-glutamyl transpeptidase) (EC. 2.3.2.2) - Glu glutamate - GDH glutamate dehydrogenase (EC 1.4.1.3) - GS glutamine synthetase (EC 6.3.1.2) - MAG maleate activated glutaminase - Orn-T ornithine aminotransferase (EC 2.6.1.13) - PAG phosphate activated glutaminase (EC 3.5.1.1)