Using Homology Modeling, Molecular Dynamics and Molecular Docking Techniques to Identify Inhibitor Binding Regions of Somatostatin Receptor 1

The G protein coupled receptor(GPCR), one of the members in the superfamily, which consists of thousands of integral membrane proteins, exerts a wide variety of physiological functions and responses to a large portion of the drug targets. The 3D structure of somatostatin receptor 1(SSTR1) was modeled and refined by means of homology modeling and molecular dynamics simulation. This model was assessed by Verify-3D and Vadar, which confirmed the reliability of the refined model. The interaction between the inhibitor cysteamine, somatostatin(SST) and SSTR1 was investigated by a molecular docking program, Affinity. The binding module not only showed the crucial residues involved in the interaction, but also provided important information about the interaction between SSTR1 on the one hand and ligands on the other, which might be the significant evidence for the structure-based design.     

α2A肾上腺素受体的同源模建及与Yohimbine的对接研究

通过对比多个与α2A-肾上腺素受体同属G-蛋白偶联受体的视紫红质蛋白序列,选择以相似性最大的牛视紫红质蛋白为模板,同源模建了α2A-肾上腺素受体的跨膜结构,并在结构中找到了体积为0.090 nm3,已被报导的活性残基包围的活性位点.运用分子力学与动力学方法研究了此结构突变前后与抑制剂Yohimbine的对接情况,得到了与文献报道相吻合的结果.同时对接研究结果发现,在α2A-肾上腺素受体的结合位点周围的一个由色氨酸和两个苯丙氨酸组成的局部疏水区对抑制剂有稳定作用,并且天冬氨酸113作为氢键受体也对稳定抑制剂有重要作用.     

促红细胞生成素(EPO)受体(EBP)激活剂的理论突变设计

采用分子动力学模拟的方法, 构建了人促红细胞生成素模拟肽与其受体胞外结合片段的相互作用的分子动力学模型. 通过对该模型的结构研究和理论分析, 对模拟肽与受体结合机制提出了新的理论解释. 根据EBP活性口袋的静电势分布, 对二聚体小肽激活剂的每条链上的部分氨基酸进行了突变, 分别用电性更强的氨基酸来代替部分疏水氨基酸, 计算结果显示, 突变后的二聚体小肽激活剂对EBP的“亲和力”明显增强.     

糖尿病大鼠肝细胞膜中胰岛素受体巯基的检测

采用四氧嘧啶腹腔注射法建立糖尿病大鼠实验模型,用巯基试剂盒紫外可见分光光度法研究四氧嘧啶所致糖尿病模型大鼠肝脏细胞膜中胰岛素受体的性质变化.实验结果表明,糖尿病大鼠肝脏组织细胞膜胰岛素受体的自由巯基含量明显低于正常大鼠,每克蛋白质降低了22%(P＜0.05),提示糖尿病大鼠肝细胞膜胰岛素受体存在氧化损伤.     

Analysis of Peptide Ligand Binding to FGFR1

Simulating annealing algorithm was used in docking computation to predict a selected peptide VYMSPF(P2) binding site on the ectodomain of FGFR1.The peptide is located on the hydrophobic surface of the receptor,which is critical for FGF binding.The synthesized peptide can effectively inhibit the mitogenic activity of afGF,and has a potential to become a therapeutic agent as an aFGF antagonist.     

Homology modeling, agonist binding site identification, and docking in octopamine receptor of Periplaneta americana

AY333178 (from Periplaneta americana, 628 AAs) was selected as a target octopamine receptor (OAR) class OAR2 for this study using Discovery Studio (DS Modeling1.1/1.2, Accelrys Inc.). Blast similarity search was performed and identified that AY333178 contains N-terminal domain of GPCR. Based upon Blast and Pfam results, Rhodopsin 1U19 (protein data bank) was considered as an ideal homologue and used as a template for homology modeling due to its higher X-ray resolution at 2.2A. Sequence alignment between AY333178 and 1U19 was done using Align123 followed by a manual modification. The final alignment was carefully evaluated and evidenced to be matching the conserved residue data for class A GPCR fairly well. The 3D model of AY333178 was generated with MODELER, and further refined using CHARMm. Superimposition of the model was done over the template 1U19. Two fairly consistent profiles were observed demonstrating AY333178 model was reasonable and could be employed for the further docking study. Agonist docking into OAR2 model was done using LigandFit. The superimposition of two top poses of representative agonists was performed with a soft surface generated. Those models are considered to be used in designing new leads for hopefully more active compounds. Further research on the comparison of models for the agonists may elucidate the mechanisms of OAR2-ligand interactions.     

新多肽配体GE11与表皮生长因子受体的结合能力分析

应用亲和毛细管电泳（ACE）分析方法,对表皮生长因子受体（EGFR）和新多肽配体GE11之间的结合能力进行分析。结果表明,EGFR与多肽配体GE11之间存在特异性相互作用,考察EGFR在不同浓度GE11溶液中的迁移情况,采用非线性、双倒数、Y-倒数和X-倒数4个数据处理方法得到较好的数据拟合,并测得结合常数。该文为筛选多肽配体以及测定受体与多肽配体之间的结合常数提供了简便的方法,将有力推动肿瘤靶向药物输送的研究。     

Searching for Peptide Ligands of Interleukin-2 Receptor α Chain in Phage-displayed Peptide Library

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神经介素B受体与拮抗剂、激动剂的分子模拟研究

大鼠神经介素B受体(rat neuromedin B receptor, rNMBR)属于G蛋白偶联受体(G-protein coupled receptor, GPCR) A家族的成员. GPCR的结构特征和在信号传导中的重要作用决定了其可以作为很好的药物靶标. 关于rNMBR与内源性激动剂神经介素B (neuromedin B, NMB)以及与非肽类拮抗剂pd168368作用机制的研究对于合理设计受体药物分子有重要的指导意义. 在这一研究中, 我们使用同源模建, 构建受体的三维结构, 进行分子对接和分子动力学的计算. 基于受体三维结构, 通过10 ns的空载受体、激动剂-受体、拮抗剂-受体的分子动力学模拟, 探讨受体与激动剂与拮抗剂的作用机制. 研究表明rNMB-R中跨膜(transmembrane, TM)螺旋3, 5, 6, 7参与配体的结合. NMB与受体的结合, 使受体转变为活性构象, 而受体同拮抗剂pd168368恰好相反.     

多巴胺第三受体蛋白三维结构及其活性位点氨基酸残基

基于牛视紫红质模板蛋白,同源模建多巴胺第三受体（D₃R）蛋白三维结构,在1-棕榈酰-2-油酰-卵磷脂（POPC）膜-水模型环境,开展300 ns分子动力学模拟提炼优化其结构,取得稳定的D₃R蛋白三维结构（2B08-D₃R）.在该蛋白基础上,采用MP2/6-31G（d,p）方法,计算多巴胺（Dop）与氨基酸残基相互作用的结合能,确定五个残基（Asp117、Ser208、His272、Phe269和Thr276）为活性位点.五个活性位点残基分别位于D₃R蛋白跨膜螺旋区TM3、TM5和TM6,组成活性空腔结构.多巴胺分子以其苯基平面与TM2-TM7包围的圆柱体空腔平行和非共价键结合方式保留在D₃R蛋白中,与D₃R蛋白结合能E_b为-97.8 kJ·mol^-1基于3PBL D₃R突变体晶体结构,构建了另外一个含有多巴胺分子的D₃R蛋白结构（Dop-3PBL-D₃R）,确定在该蛋白结构中,多巴胺的活性位点氨基酸是Asp83、His272、Phe269、Phe268和Trp265.在该蛋白结构中,多巴胺分子同样以其苯基平面与TM2-TM7包围的圆柱体空腔平行和非共价键方式结合,与该蛋白相互作用的结合能是-80.5 kJ·mol^-1.     

确定蛋白质-短肽复合物结构的新方法

大部分蛋白质 -蛋白质复合物的三维结构在接触表面都显示出很好的几何匹配 .由于蛋白质的表面几何形状和其它的一些物理化学性质在分子的专一性相互作用中起了主要作用 ,所以 ,接触表面几何形状的互补常常被认为是蛋白质分子识别的基础 .一般来说 ,蛋白质接触表面的几何匹配只涉及 5到 1 0几个紧密堆积的氨基酸残基 ,因此 ,蛋白质与蛋白质配体之间的识别计算可以通过蛋白质与突变周围的或与蛋白质表面紧密接触的配体肽段的识别计算来实现 . Stoddard等 [1] 已经利用从 MBP上选取的八肽成功地计算出接近晶体结构的 MBP-受体复合物 .许多研…     

建立短肽抑制剂与酶识别的模式──基于表面静电互补和溶剂化能的Docking计算方法

提出了把简化的接触表面静电互补模型与溶剂化能模型相结合的新的Docking计算方法.编写了计算模拟程序ESCOLD,并用于酶-短肽体系的Docking计算.对3个已知X射线晶体结构的酶-抑制剂肽链复合物中的六肽用ESCOLD重新进行了Docking计算.用溶剂化能作为评价函数,正确地预测出接近实验结果的六肽取向.     

The Structural Basis of Peptide Binding at Class A G Protein-Coupled Receptors

G protein-coupled receptors (GPCRs) represent the largest membrane protein family and a significant target class for therapeutics. Receptors from GPCRs’ largest class, class A, influence virtually every aspect of human physiology. About 45% of the members of this family endogenously bind flexible peptides or peptides segments within larger protein ligands. While many of these peptides have been structurally characterized in their solution state, the few studies of peptides in their receptor-bound state suggest that these peptides interact with a shared set of residues and undergo significant conformational changes. For the purpose of understanding binding dynamics and the development of peptidomimetic drug compounds, further studies should investigate the peptide ligands that are complexed to their cognate receptor.     

The Binding Mode of a Tau Peptide with Tubulin

The microtubule‐associated protein Tau promotes the polymerization of tubulin and modulates the function of microtubules. As a consequence of the dynamic nature of the Tau–tubulin interaction, the structural basis of this complex has remained largely elusive. By using NMR methods optimized for ligand–receptor interactions in combination with site‐directed mutagenesis we demonstrate that the flanking domain downstream of the four microtubule‐binding repeats of Tau binds competitively to a site on the α‐tubulin surface. The binding process is complex, involves partial coupling of different interacting regions, and is modulated by phosphorylation at Y394 and S396. This study strengthens the hypothesis of an intimate relationship between Tau phosphorylation and tubulin binding and highlights the power of the INPHARMA NMR method to characterize the interaction of peptides derived from intrinsically disordered proteins with their molecular partners.     

多肽片段连接方法及肽硫酯和肽醛的合成*

本文综述了多肽和蛋白质合成中的片段连接方法,这是近年来多肽和蛋白质合成领域中方法学上的重要进展.该方法使用非保护的多肽片段,无需酶或化学活化试剂,在缓冲溶液中能够高产率地获得多肽和蛋白质.还介绍了与多肽片段连接有关的肽硫酯和肽醛的合成方法.     

压电胰岛素-C肽微阵列免疫传感器研究

以AT切型、基频10MHz的镀金膜石英晶体作为换能器,将抗人胰岛素和C肽单克隆抗体固定在石英晶体电极表面,用2×5检测池固定夹具构建一种新型压电胰岛素-C肽微阵列免疫传感器.研究了抗体固定方法、抗体工作浓度、固定量、一致性以及传感器的响应参数如检测温度、时间和特异性等的影响.该微阵列传感器在胰岛素浓度为2.5～160.0mIU/L、C肽浓度为0.375～12.0ng/mL范围内响应特性良好,压电晶体频率偏移值与胰岛素和C肽浓度呈良好的线性关系.将此微阵列传感器用于人血清标本的测定,结果与放射免疫法符合(r为0.92和0.94).此微阵列传感器具有灵敏度高、特异性好,低密度阵列结构,检测通量较高,不需标记,操作简单、能实时在线检测和重复使用等优点,能用于临床实验诊断,具有临床推广应用价值.     

Study on Synthesis and Binding Ability of a New Anion Receptor Containing NH Binding Sites

A new colorimetric recognition receptor 1 based on the dual capability containing NH binding sites of selectively sensing anionic guest species has been synthesized. Compared with other halide anions, its UV/Vis absorption spectrum in dimethyl sulfoxide showed the response toward the presence of fluoride anion with high selectivity, and also displayed dramatic color changes from colorless to yellow in the presence of TBAF （5 × 10^-5 mol/L）. The similar UV/Vis absorption spectrum change also occurred when 1 was treated with AcO^- while a little change with H2PO^-4 and OH^-. Receptor 1 has almost not affinity abilities to Cl^-, Br^- and I^-. The binding ability of receptor 1 to fluoride with high selectivity over other halides contributes to the anion size and the ability of forming hydrogen bonding. While the different ability of binding with geometrically triangular （AcO^-）, tetrahedral （H2PO^-4 ） and linear （OH^-） anions maybe result from their geometry configuration.     

Screening and Identification of a Targeting Peptide to nGLP-1R from Phage Display Peptide Library

<正>In order to provide the structure information for designing new exendin-4 analogues,a phage display peptide library was screened by targeting the N-terminal extracellular domain of GLP-1R(nGLP-1R).After four rounds of selection,nine sequences were obtained,four of them have higher affinity for nGLP-1R than the others.We chose two of them named X and Y peptides.Isletβ-cell proliferation assay suggested that X and Y peptides didn't have any activity to increase isletβ-cell proliferation.In other words,X and Y peptides were not agonists to GLP-1R.However, the conservative motifs of X and Y peptides provided us useful information to design new exendin-4 analogues.     

Antagonist binding in the rat muscarinic receptor A study by docking and X-ray crystallography

A series of agonists to the rat muscarinic receptor have been docked computationally to the active site of a homology model of rat M1 muscarinic receptor. The agonists were modelled on the X-ray crystal structure of atropine, which is reported here and the docking studies are shown to reproduce correctly the order of experimental binding affinities for the agonists as well as indicate where there appear to be inconsistencies in the experimental data. The crystal and molecular structure of atropine (tropine tropate; -[hydroxymethyl]benzeneacetic acid 8-methyl[3.2.1]oct-3-yl ester C₁₇H₂₃NO₃) has been determined by X-ray crystallography using an automated Patterson search method, and refined by full-matrix least-squares to a final R of 0.0452 for 2701 independent observed reflections and 192 parameters using Mo K radiation, λ = 0.71073 Å at 150 K. The compound crystallises in space group Fdd2 with Z = 16 molecules per unit cell.