肿瘤坏死因子与其受体相互作用的计算机模拟研究

利用同源模建方法,以ＴＮＦＲ５５受体胞外区的晶体结构为参考模板,预测了ＴＮＦＲ７５受体胞外区Ｃｙｓ１８～Ｐｈｅ１４７片段的三维结构．根据Ｒ５５受体胞外区与ＬＴ相结合的复合物的晶体结构,预测了ＴＮＦ与Ｒ５５及Ｒ７５胞外区的复合物的三维结构,模拟了ＴＮＦ与受体之间的相互作用．由于ＴＮＦ与受体的作用形式是三聚体对三聚体,因此在模拟ＴＮＦ与受体相互作用时选择了包括一个非对称的ＴＮＦ三聚体和一个受体（Ｒ５５或Ｒ７５）单体的模拟系统．结合已有的突变体实验结果,利用计算机模拟分析手段,发现了一些ＴＮＦ突变体之所以具有受体选择性的三维结构基础和发挥了关键作用的氨基酸残基以及这些残基之间的主要作用形式．研究深化了对已有的突变体实验结果的认识,建立了不同的实验结果之间的内在关联,为以后有目的的新型突变体设计和实验研究打下了基础．     

人白介素6受体结合功能域的构效关系研究

以分子对接（docking）方法研究人白介素6受体胞外区配基结合功能域“WSXWS”区氨基酸残基定点突变对受体与配基人白介素6结合时的相互作用能量、分子间相互作用的影响,从分子力学、分子动态学分析了人白介素6受体胞外区功能域关键氨基酸残基在受体与配基结合中的构象变化以及与人白介素6间的相互作用.     

人白介素6受体胞外区三维结构的同源模拟

IL-6受体是造血因子超家族成员,其胞外区细胞因子结合结构域（CBD）是受体结合配基和偶联gp130转导IL-6信号的功能域.据预测,IL-6R功能域的β片层折叠模式和人生长激素受体（hGH-R）及CD₄的晶体结构十分相似.应用计算机同源模拟技术,以hGH-R和CD₄的三维结构为模板,模建了hIL-6R功能域（106～322位）的三维结构,初步描述了其结构保守区的构象特征.文章研究模建的hIL-6R三维结构模式为探讨可溶性IL-6R点突变的结果,以及进行三维定量分析IL-6R胞外区功能域的构效关系提供了空间结构基础.     

TNF受体（P55）胞外区基因的克隆及其在大肠杆菌中的表达

TNF与多种疾病密切相关。为了获得大量具有生物学活性的可溶性TNF受体用以拮抗TNF的毒性作用,在原核表达系统中表达了TNFR（P55）的胞外区与TrxA的融合蛋白。将TNFR（P55）胞外区去信号肽的前三个结构域基因克隆入融合蛋白表达载体pET-32a,在大肠杆菌BL21（DE3）中高效表达了TrxA-TNFR融合蛋白。表达产物以包涵体形式存在,经过变性和复性,并经镍金属鳌和柱亲和层析纯化,得到了纯度较高的可溶性受体蛋白的初纯品。免疫学实验及L929细胞体外实验均表明：该蛋白具有TNFR（P55）特异的抗原性、与TNF结合的活性以及良好的抑制TNF的TNF生物学活性。     

应用进化踪迹及分子动力学模拟研究beta2肾上腺素受体突变活性

β2肾上腺素受体(β2adrenergic receptor,β2AR)是G蛋白耦联受体(G protein coupled receptors,GPCRs)超家族中的一员,也是研究治疗哮喘的关键药物受体靶标.采用进化踪迹(evolutionary trace,ET)方法分析肾上腺素受体家族跨膜区片段序列,识别出了44个保守的残基,然后将β2肾上腺素受体以及受体D130N活性突变体、D79N失活突变体进行分子动力学模拟,试图找出与受体不同功能状态相关的结构动力学特征.发现受体DRY motif中的D130远离R131而转向K149残基这一结构特征与受体活性高度关联,此外,从残基相互作用的变化推断出了受体helix 2,4 and 6伴随着受体活化而发生的运动.这些研究结果对进一步探索β2肾上腺素受体突变体的激活机制以及所诱发疾病的分子机理提供了依据.     

hIL-6与其受体作用的结构基础及拮抗剂的研究进展

通过对大量的分子生物学实验及晶体衍射结果的分析 ,从分子水平揭示人白细胞介素 6(hIL 6 )与其受体相互作用的结构模式及结合表位 .hIL 6属于促红细胞生成素受体超家族 ,首先和hIL 6受体α低亲和力结合 ,两者形成的复合物再与hIL 6受体 β(gp130 )的胞外区相互作用形成高亲和力三聚体 ,但是hIL 6不能单独和gp130结合 ,需要借助于hIL 6受体α的桥梁作用才能将二者联系起来进而促进六聚体的形成 .hIL 6是一种能够介导细胞表面信号转导 ,调节机体免疫及造血干细胞增殖和分化的细胞因子 ,许多疾病的发病机理及发展进程都和hIL 6过表达有关 .基于对hIL 6与其受体相互作用方式的探究 ,为hIL 6小分子拮抗剂的药物设计提供了理论模型 ,在此基础上已研究开发了许多不同种类的hIL 6新型分子拮抗剂 ,其中部分拮抗剂已应用于临床指导 .     

人白细胞介素－2的两个部分拮抗剂

通过定点诱变技术得到6个生物活性剧烈下降的人白细胞介素-2(IL-2)突变体,其中两个突变体即15Val-IL-2和126Asp-IL-2可以在一定浓度范围内使IL-2的生物效应降低.在对高亲和力IL-2受体(IL-2R)的竞争抑制实验中,15Val-IL-2和126Asp-IL-2又表现了一定的竞争能力.这些结果表明15Val-IL-2和126Asp-IL-2的部分拮抗天然IL-2的作用.结合IL-2二级结构分析及对IL-2与IL-2R相互作用的已有认识,可认为15Val-IL-2和126Asp-IL-2的部分拮抗作用产生的原因在于替换残基在空间上对IL-2与IL-2R βγ亚基结合微环境的轻微扰动,干扰了IL-2有关残基与IL-2R βγ亚基的结合,但尚不能完全阻止其与IL-2R βγ亚基的结合.     

TCR-CD3复合物跨膜区自组装的分子机制

目的 T细胞受体-共受体复合物（TCR-CD3）在适应性免疫应答中起着重要作用,其亚基间的相互作用一直是研究热点。由于传统实验的局限性,对于跨膜蛋白TCR-CD3复合物的研究不能深入到微观层面。方法 利用分子动力学模拟方法（包括粗粒化模拟、拉伸动力学、全原子模拟）分析TCR-CD3复合物的自组装机制。结果 通过粗粒化模拟（CGMD）发现,TCR-CD3复合物在组装过程中存在着αβ依次结合δε’、γε、ζζ’的组装顺序,并阐述了α^R253突变会降低α^K258与δε’的相互作用。结论 本文论证了仅存在TCR-CD3复合物的跨膜区不足以介导TCR-CD3复合物亚基间的特异性相互作用。拉伸动力学（SMD）和全原子模拟（AAMD）的结果说明,ζζ’与TCR-CD3其余部分之间的胞外区相互作用强于跨膜区,同时ζζ’的缺失对αβδε’γε的稳定性影响最小,而δε’的缺失对αβγεζζ’的稳定性影响最大。     

人白介素6与其受体结合特定结构域的预测

借助人白介素6的核磁共振构象, 以人生长因子受体为模板同源模建的人白介素6受体空间构象, 通过表观静电势分析, 结合空间构象的互补性对人白介素6与其受体进行分子对接, 在分子力学优化、分子动力学动态模拟的基础上获得稳定的复合物结构, 从理论上预测人白介素6与其受体相互作用的结构域, 进一步确定影响人白介素6与其受体相互作用的特定位点, 为确定靶蛋白人白介素6的活性部位、利用计算机寻找和辅助设计新的拮抗剂提供理论依据.     

Furin／kexin蛋白质前体加工酶抑制剂的理性再设计

许多重的生物过程,如酶原激活、肽激素合成、病毒蛋白加工和受体成熟,均须蛋白质前体加工酶的剪切处理。因此,蛋白质前体加工酶可能是一种新药开发的对象,综合利用同源模建技术和序列的进化踪迹分析手段,研究了蛋白质前体加工酶furin/kexin与水蛭抑制剂(eglinC）突变体的相互作用模式,阐释furin/kexin各个亚类的底物/抑制剂特异性的共性和差异性的序列结构基础。在此基础上,利用界面再设计策略（核心算法为异型自洽系综最优化）进行了furin/kexin抑制剂的理性再设计,分别以模建的水蛭抑制剂-furin,水蛭 素-kex2复合物结构为模板,对水蛭 抑制剂P1,P2和P4位置进行设计,计算结果显示这三个位置均是偏好碱性残基,与已有的实验结论一致,另外针对furin/kexin各亚类在S′端有较多的特异性残基位置这一特点,对抑制剂P′端的残基位置实施改造,设计furin和kex2的特异性更高的抑制剂,对于furin,设计得到的最好突变体是P2′Glu-P3′Asp-P4′Arg;而对于kex2,最好的突变体是P2′Arg-P3′Arg-P4′Glu。结构分析显示furin和kex2与相应的水蛭 抑制剂突变体形成石油同的相互作用模式,这里我们给出了综合利用同源模建技术,序列的进化踪迹分析和理性再设计进行酶-抑制剂相互作用研究及抑制剂改造的方案;同时提供了合理的理论设计方案。为进一步的实验设计提供理性的指导。     

Two human TNF receptors have similar extracellular, but distinct intracellular, domain sequences

Tumor necrosis factor (TNF) is a cytokine with a wide range of biological activities in inflammatory and immunologic responses. These activities are mediated by specific cell surface receptors of 55 kDa and 75 kDa apparent molecular masses. A 75-kDa TNF receptor cDNA was isolated using partial amino acid sequence information and the polymerase chain reaction (PCR). When expressed in COS-1 cells, the cDNA transfers specific TNF-binding properties comparable to those of the native receptor. The predicted extracellular region contains four domains with characteristic cysteine residues highly similar to those of the 55-kDa TNF receptor, the nerve growth factor (NGF) receptor, and the CDw40 and OX40 antigens. The consensus sequence of the TNF receptor extracellular domains also has similarity to the cysteine-rich sequence motif LIM. In marked contrast to the extracellular regions, the intracellular domains of the two TNF receptors are entirely unrelated, suggesting different modes of signaling and function.     

A 20 amino acid synthetic peptide of a region from the 55 kDa human TNF receptor inhibits cytolytic and binding activities of recombinant human tumour necrosis factor in vitro.

Tumour Necrosis Factor (TNF) and Lymphotoxin (LT) can exert a wide range of effects on cells and tissues and they are important effector molecules in cell mediated immunity. All these effects are induced subsequent to the binding of these cytokines to specific membrane receptors. Recently, two of these membrane receptors of 55 and 75 kDa, have been identified which share some amino acid (AA) homology in their N-terminal extracellular domains but differ in their intracellular domains. We synthesized two synthetic 20 AA peptides from hydrophilic regions of the N-terminal extracellular domains of the 55 kDa receptor; peptide A shares homology with both 55 and 75 kDa receptors, peptide B is unique. We found peptide B inhibits both the binding and cytolytic activity of recombinant human TNF when tested on murine L929 cells in vitro. Polyclonal antiserum generated against peptide B will block binding of 125I-labelled TNF to these cells in vitro. However, peptide A and antiserum prepared against peptide A are without effect in these same assay systems. These data suggest that the 20 AA sequences from AA 175 to 194 in the N-terminal extracellular domain of the 55 kDa TNF receptor are expressed on the cell surface and are involved in the binding of TNF.     

Recombinant 55-kDa tumor necrosis factor (TNF) receptor. Stoichiometry of binding to TNF alpha and TNF beta and inhibition of TNF activity.

The extracellular domain of the 55-kDa TNF receptor (rsTNFR beta) has been expressed as a secreted protein in baculovirus-infected insect cells and Chinese hamster ovary (CHO)/dhfr- cells. A chimeric fusion protein (rsTNFR beta-h gamma 3) constructed by inserting the extracellular part of the receptor in front of the hinge region of the human IgG C gamma 3 chain has been expressed in mouse myeloma cells. The recombinant receptor proteins were purified from transfected cell culture supernatants by TNF alpha- or protein G affinity chromatography and gel filtration. In a solid phase binding assay rsTNFR beta was found to bind TNF alpha with high affinity comparable with the membrane-bound full-length receptor. The affinity for TNF beta was slightly impaired. However, the bivalent rsTNFR beta-h gamma 3 fusion protein bound both ligands with a significantly higher affinity than monovalent rsTNFR beta reflecting most likely an increased avidity of the bivalent construct. A molecular mass of about 140 kDa for both rsTNFR beta.TNF alpha and rsTNFR beta.TNF beta complexes was determined in analytical ultracentrifugation studies strongly suggesting a stoichiometry of three rsTNFR beta molecules bound to one TNF alpha or TNF beta trimer. Sedimentation velocity and quasielastic light scattering measurements indicated an extended structure for rsTNFR beta and its TNF alpha and TNF beta complexes. Multiple receptor binding sites on TNF alpha trimers could also be demonstrated by a TNF alpha-induced agglutination of Latex beads coated with the rsTNFR beta-h gamma 3 fusion protein. Both rsTNFR beta and rsTNFR beta-h gamma 3 were found to inhibit binding of TNF alpha and TNF beta to native 55- and 75-kDa TNF receptors and to prevent TNF alpha and TNF beta bioactivity in a cellular cytotoxicity assay. Concentrations of rsTNFR beta-h gamma 3 equimolar to TNF alpha were sufficient to neutralize TNF activity almost completely, whereas a 10-100-fold excess of rsTNFR beta was needed for similar inhibitory effects. In view of their potent TNF antagonizing activity, recombinant soluble TNF receptor fragments might be useful as therapeutic agents in TNF-mediated disorders.     

Modeling and simulation of the human delta opioid receptor

A model for the human delta opioid receptor has been generated via sequence alignment, structure building using the crystal structure of bovine rhodopsin as a template, and refinement by molecular dynamics simulation. The model building suggested that, in addition to the previously postulated interaction between D128 and Y308, an internal salt bridge also exists between residues D128 and R192, both of which are conserved in all the opioid receptors. The model and salt bridge were then shown to be stable during a 20-nsec simulation in a lipid bilayer. It is therefore proposed that both of these interactions play a role in stabilizing the inactive state of the receptor. The model is also used in an effort to rationalize many of the mutational studies performed on delta opioid receptors, and to suggest a plausible explanation for the differences between known delta opioid agonists and antagonists.     

Structural insights into the interaction of insulin-like growth factor 2 with IGF2R domain 11

The insulin-like growth factor II/mannose-6-phosphate receptor (IGF2R) mediates trafficking of mannose-6-phosphate (M6P)-containing proteins and the mitogenic hormone IGF2. IGF2R also plays an important role as a tumor suppressor, as mutation is frequently associated with human carcinogenesis. IGF2 binds to domain 11, one of 15 extracellular domains on IGF2R. The crystal structure of domain 11 and the solution structure of IGF2 have been reported, but, to date, there has been limited success when using crystallography to study the interaction of IGFs with their binding partners. As an approach to investigate the interaction between IGF2 and IGF2R, we have used heteronuclear NMR in combination with existing mutagenesis data to derive models of the domain 11-IGF2 complex by using the program HADDOCK. The models reveal that the molecular interaction is driven by critical hydrophobic residues on IGF2 and IGF2R, while a ring of flexible, charged residues on IGF2R may modulate binding.     

TNF-Induced shedding of TNF receptors in human polymorphonuclear leukocytes: role of the 55-kDa TNF receptor and involvement of a membrane-bound and non-matrix metalloproteinase

A down-modulation of both the 55-kDa (TNF-R55) and the 75-kDa (TNF-R75) TNF receptors is observed in neutrophils exposed to a variety of stimuli. Proteolytic cleavage of the extracellular region of both receptors (shedding) and, with TNF, internalization of TNF-R55 and shedding of TNF-R75 are the proposed mechanisms. We have characterized the TNF-induced shedding of TNF receptors in neutrophils and determined the nature of the involved proteinase. Neutrophils exposed to TNF release both TNF receptors. A release of TNF receptors comparable to that observed with TNF was induced with TNF-R55-specific reagents (mAbs and a mutant of TNF) but not with the corresponding TNF-R75-specific reagents. A hydroxamic acid compound (KB8301) almost completely inhibited shedding of TNF-R55 and to a lesser degree shedding of TNF-R75. KB8301 also inhibited FMLP-induced shedding to a similar extent. Shedding was also inhibited by 1,10-phenanthroline, but this effect was considered nonspecific as the compound, at variance with KB8301, almost completely inhibited TNF and FMLP-induced PMN activation. Diisopropylfluorophosphate partially inhibited shedding of TNF-R75, suggesting the contribution of a serine proteinase to the release of this receptor. Shedding activity was not affected by matrix metalloproteinases inhibitors nor was it released in the supernatants of FMLP-stimulated neutrophils. These results suggest that TNF induces release of its receptors, that such a release is mediated via TNF-R55, and that a membrane-bound and non-matrix metalloproteinase is involved in the process. The possibility that ADAM-17, which we show to be expressed in neutrophils, might be the involved proteinase is discussed.     

Structural delineation and phase-dependent activation of the costimulatory CD27:CD70 complex

CD27 is a tumor necrosis factor (TNF) receptor, which stimulates lymphocytes and promotes their differentiation upon activation by TNF ligand CD70. Activation of the CD27 receptor provides a costimulatory signal to promote T cell, B cell, and NK cell activity to facilitate antitumor and anti-infection immunity. Aberrant increased and focused expression of CD70 on many tumor cells renders CD70 an attractive therapeutic target for direct tumor killing. However, despite their use as drug targets to treat cancers, the molecular basis and atomic details of CD27 and CD70 interaction remain elusive. Here we report the crystal structure of human CD27 in complex with human CD70. Analysis of our structure shows that CD70 adopts a classical TNF ligand homotrimeric assembly to engage CD27 receptors in a 3:3 stoichiometry. By combining structural and rational mutagenesis data with reported disease-correlated mutations, we identified the key amino acid residues of CD27 and CD70 that control this interaction. We also report increased potency for plate-bound CD70 constructs compared with solution-phase ligand in a functional activity to stimulate T-cells in vitro. These findings offer new mechanistic insight into this critical costimulatory interaction.