Modeling of amyloid peptides and proteins

淀粉样肽和蛋白质的建模

• 批准号: 7965568
• 负责人: HOMER ROBERT GUY
• 金额: $ 43.61万
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/7965568
• 关键词: Alzheimer' s Disease; Amyloid beta-Protein; Back; Binding; Biochemical; Bovine Spongiform Encephalopathy; Cell Death; Cereals; Computing Methodologies; Consensus; Creutzfeldt-Jakob Syndrome; Data; Dimensions; Disease; Drug Design; Encephalopathies; Environment; Goals; Heavy Metals; Human; Ion Channel; Learning; Length; Long-Term Potentiation; Membrane; Memory Loss; Methods; Microscopy; Modeling; Neurodegenerative Disorders; Peptides; Pharmaceutical Preparations; Phase; PrPSc Proteins; Prion Diseases; Prions; Process; Property; Proteins; Publishing; Scrapie; Series; Short-Term Memory; Simulate; Solutions; Solvents; Structural Models; Structure; Surface; Tail; Time; United States National Institutes of Health; Viral Proteins; Water; X-Ray Crystallography; amyloid formation; amyloid peptide; aqueous; base; beta barrel; dimer; fibrous protein; improved; interest; molecular dynamics; monomer; neuron apoptosis; neurotoxic; neurotoxicity; programs; research study; simulation; solid state nuclear magnetic resonance; synthetic peptide; two-dimensional

We first became interested in how amyloid beta (Abeta) peptides cause Alzheimers disease in the early 90s when Nelson Arispe and Harvey Pollard, who were then at NIH, approached us with their finding that Abeta peptide forms ion channels in bilayers. In 94 we coauthored highly tentative models of the Abeta channels. Back then the consensus was that Alzheimers was caused by fibrils formed by Abeta. Much has been learned since then about the structures of Abeta assemblies and ion channels, and how they relate to Alzheimers disease. Several other groups also found that Abeta forms channels and have microscopically observed Abeta assemblies in synthetic membranes. Heavy metals and peptides that inhibit the Abeta channels also inhibit Abeta-induced apoptosis of neurons. Microscopy studies have also revealed superstructures of numerous protofibril assemblies that form in solution. Solution NMR studies of Abeta monomers in apolar solvents and solid state NMR studies of fibrils have helped elucidate their structures. Given these new data, some of which are inconsistent with our original models, and the biomedical importance of amyoid-associated neurodegenerative diseases such as Alzheimers, we decided to revive our modeling efforts. We became interested in the prions when others noted sequence similarities in the hydrophobic segments of Abeta and the human prion precursor, Prion Protein, and found that the toxic form, PrPSc, could self-assemble into hexagonal lattices similar to those we had developed in modeling Abeta assemblies. We have constructed the following types of soluble Abeta assemblies: dimers, trimers, tetramers, hexamers, strings of hexamers, dodecamers, AbetaOs (18 subunits), beaded and smooth annular protofibril (36 subunits), protofibrils with mass-per-lengths of 18 and 27kDa/nm that correspond to experimentally determined values, and two-dimensional hexagonal lattices that can extend indefinitely. We have also developed numerous models in which up to 36 Abeta peptides form large assemblies on the membrane surface and then insert through the membrane to form channels, and how heavy metals and synthetic peptides can block these channels. These models were constrained by results of microscopy and biochemical studies of the dimensions, masses, and secondary structures of both soluble and membrane-bound assemblies. Most of our models of assemblies composed of six or more subunits involve hexamers in which the C-termini segments (residues 29-42) form a six-stranded antiparallel beta barrel. However, in our final 36-peptide models of annular protofibrils and channels, six of these barrels merge to form a large 36-stranded beta-barrel). Our collaborators have found that Abeta channels can be blocked by low concentrations of two small drugs (MRS2481 and MRS2485synthesized by Ken Jacobson at NIH) and histadine-containing peptides (e.g., His4). We have modeled how these drugs and peptides may bind in the central region of our favored model of the channels. This is an exciting finding because so far all agents that block the channels also inhibit Abeta-induced neurotoxicity. Thus, the models may be useful for structure-based design of drugs to treat Alzheimer's disease. We have also simulated how some of these assemblies could morph or grow into models of fibrils that are based on solid state NMR studies. We are using both atomically complete and coarse graining molecular dynamic simulations to better understand the structures of these Abeta oligomers, how they assemble, and how larger assemblies can form from smaller assemblies. The atomically complete simulations using GROMACS, CHARMM, or NAMD programs are better for analyzing precise interactions within relatively ordered assemblies; however only short time scales can be analyzed. We have been using coarse-grained methods with Discrete Molecular Dynamics (DMD) simulations to analyze longer time scales and less ordered assemblies. We have also used steered dynamics simulations to analyze transitions between different types of assemblies. Prion Protein (PrP) can exist in two forms, the normal PrPC form and a toxic PrPSc form that causes Creutzfeldt-Jakob disease, bovine spongiform encephalopathy, scrapie, and other spongiform encephalopathies. PrPSc can form different types of assemblies; i.e., two-dimensional hexagonal lattices, fibrils, and membrane-bound. Aspects of the PrP and PrP-associated diseases resemble those of Abeta and Alzheimers. The most hydrophobic portion of the 230 residue-long PrP protein (residues 111-135) has a sequence quite similar to the hydrophobic segment of Abeta that we propose to form a six-stranded antiparallel beta-barrel. Experimental studies indicate that PrP protein can span membranes and that sub-peptides of the hydrophobic region are neurotoxic and can form ion channels in bilayers. PrPSc can assemble in water into a P3 hexagonal lattice that has three parallel axes of three-fold symmetry. We have constructed PrPSc lattice models with the axis of the putative hydrophobic beta-barrels on one of the three-fold axes of a P3 hexagonal lattice. In these models, residues 111-135 form a beta-hairpin and three of theses hairpins associate about an axis of three-fold symmetry to form a six-stranded beta barrel. In addition, a triple-stranded beta helix formed by residues 50-91 is proposed to surround the hydrophobic beta-barrel and shield it from water. The segment forming the beta-helix includes an octapeptide sequence (HGGGWGQP) that is repeated five times. Membrane-penetrating tails of some viral proteins have a repetitive octapeptide sequence that has been shown to form a similar triple-stranded beta helix. These models are consistent with experimental findings that the beta content of N-terminus region increases when PrPC converts to PrPSc. The structure of the C-terminus helical domain of PrPC has been determined in numerous NMR studies and one X-ray crystallography study. In our lattice models, three C-terminus helical domains, based on the NMR structures of PrPC, surround another three-fold axis, with the C-termini α-helices forming a triple-stranded coiled-coil, which is a commonly observed structural motif of fibrous proteins. The models were constrained to have the dimensions and lattice type of the experimentally observed lattice. They were constrained further to be consistent with other experimental results, such as formation of the lattice when substantial portions of the PrP protein are deleted. Our models of a membrane bound hexagonal lattice assemble have similar properties. In these models, the hydrophobic beta-barrel spans the bilayer, and a more collapsed beta-helix formed by the octapeptide repeats extends into the aqueous phase. In our fibril models, residues 111-135 form a continuous beta-strand, and six of these strands assembles into a hexameric antiparallel beta barrel. An overlapping dimeric structure of the helical domain observed in the crystal structures was used to model an elongated trimeric helical domain of fibrils. This domain is in series with the elongated beta domains. An alternative model in which the C-termini domains form a triple-stranded beta-helix was also developed. We plan to publish these preliminary models this year, and to perform additional simulations of refine the models.

我们第一次对淀粉样蛋白β (Abeta)肽如何导致阿尔茨海默病产生兴趣是在90年代初，当时在美国国立卫生研究院的Nelson Arispe和Harvey Pollard找到我们，他们发现Abeta肽在双层结构中形成离子通道。1994年，我们共同撰写了Abeta通道的高度试探性模型。当时的共识是阿尔茨海默氏症是由β形成的原纤维引起的。从那时起，人们对β组装和离子通道的结构以及它们与阿尔茨海默病的关系有了更多的了解。其他几个研究小组也发现β形成通道，并在显微镜下观察到β在合成膜中的组装。抑制Abeta通道的重金属和多肽也抑制Abeta诱导的神经元凋亡。显微镜研究也揭示了在溶液中形成的许多原纤维组合的上层结构。β单体在极性溶剂中的溶液核磁共振研究和原纤维的固态核磁共振研究有助于阐明它们的结构。鉴于这些新数据，其中一些与我们的原始模型不一致，以及淀粉样蛋白相关的神经退行性疾病（如阿尔茨海默氏症）的生物医学重要性，我们决定恢复我们的建模工作。当其他人注意到Abeta和人类朊病毒前体prion Protein的疏水片段序列相似时，我们开始对朊病毒感兴趣，并发现毒性形式PrPSc可以自组装成六边形晶格，类似于我们在模拟Abeta组装时开发的那些晶格。我们已经构建了以下类型的可溶性Abeta组合：二聚体、三聚体、四聚体、六聚体、六聚体串、十二聚体、abetos（18个亚基）、串珠状和光滑的环状原纤维（36个亚基）、质量长度为18和27kDa/nm的原纤维（与实验确定的值相对应），以及可以无限延伸的二维六边形晶格。我们还开发了许多模型，其中多达36个Abeta肽在膜表面形成大组装，然后插入膜形成通道，以及重金属和合成肽如何阻断这些通道。这些模型受到显微镜和生化研究结果的约束，这些研究包括可溶性和膜结合的组装体的尺寸、质量和二级结构。我们的大多数由六个或更多亚基组成的组件模型涉及六聚体，其中c端片段（残基29-42）形成六股反平行β桶。然而，在我们最终的环形原原纤维和通道的36个肽模型中，这些桶中的6个合并形成一个大的36股β -桶)。我们的合作者发现，低浓度的两种小药物（MRS2481和mrs2485由NIH的Ken Jacobson合成）和含组胺肽（例如His4）可以阻断Abeta通道。我们已经模拟了这些药物和多肽如何在我们喜欢的通道模型的中心区域结合。这是一个令人兴奋的发现，因为到目前为止，所有阻断通道的药物都能抑制β诱导的神经毒性。因此，该模型可用于基于结构的药物设计，以治疗阿尔茨海默病。我们还模拟了其中一些组件如何变形或生长成基于固态核磁共振研究的原纤维模型。我们正在使用原子完整和粗粒分子动力学模拟来更好地理解这些Abeta低聚物的结构，它们如何组装，以及如何从较小的组装形成较大的组装。使用GROMACS， CHARMM或NAMD程序的原子完全模拟更适合分析相对有序的组件内的精确相互作用；然而，只能分析很短的时间尺度。我们一直在使用离散分子动力学（DMD）模拟的粗粒度方法来分析更长的时间尺度和更少的有序装配。我们还使用转向动力学仿真来分析不同类型组件之间的转换。朊蛋白（PrP）可以以两种形式存在，正常的PrPC形式和有毒的PrPSc形式，后者可导致克雅氏病、牛海绵状脑病、痒病和其他海绵状脑病。PrPSc可以形成不同类型的组件；即二维六边形晶格、原纤维和膜结合。PrP和PrP相关疾病的一些方面类似于β和阿尔茨海默病。230个残基长的PrP蛋白中最疏水的部分（残基111-135）的序列与我们提出的Abeta的疏水片段非常相似，形成了一个六链反平行β -桶。实验研究表明，PrP蛋白可以跨膜，疏水区的亚肽具有神经毒性，并可以在双层中形成离子通道。PrPSc可以在水中组装成P3六边形晶格，它有三个平行的三重对称轴。我们建立了PrPSc晶格模型，假设疏水β -桶的轴在P3六边形晶格的三重轴之一上。在这些模型中，残基111-135形成了一个发夹，其中三个发夹围绕着一个三重对称的轴相互联系，形成了一个六股的β桶。此外，提出了由残基50-91形成的三链β螺旋，以包围疏水性β桶并使其免受水的侵害。形成β -螺旋的片段包括一个重复五次的八肽序列（HGGGWGQP）。一些病毒蛋白的穿膜尾部具有重复的八肽序列，已显示形成类似的三链β螺旋。这些模型与实验结果一致，即当PrPC转化为PrPSc时，n端区β含量增加。PrPC的c端螺旋结构已经在许多核磁共振研究和一个x射线晶体学研究中确定。在我们的晶格模型中，基于PrPC的核磁共振结构，三个c端螺旋结构域围绕着另一个三重轴，其中c端为&amp；#945；-螺旋形成三股螺旋状线圈，这是纤维蛋白的常见结构基序。模型必须具有实验观测到的晶格的尺寸和晶格类型。他们进一步受到限制，以与其他实验结果一致，例如当PrP蛋白的大部分被删除时晶格的形成。我们的膜结合六边形晶格组合模型具有类似的性质。在这些模型中，疏水β -桶横跨双分子层，由八肽重复形成的更塌陷的β -螺旋延伸到水相。在我们的纤维模型中，残基111-135形成了一个连续的β链，其中6个链组装成一个六聚体反平行的β桶。在晶体结构中观察到的重叠二聚体螺旋结构被用来模拟原纤维的细长三聚体螺旋结构。这个结构域和加长的结构域串联在一起。另一种模型，其中c端结构域形成三链β -螺旋也被开发。我们计划在今年发表这些初步模型，并进行额外的模拟来完善这些模型。