Struct. Invest. of Hsp70 and TGFb by Solution Studies and High-Perform. Comput.

结构。

• 批准号: 8699784
• 负责人: Emre H. Brookes
• 金额: $ 12.39万
• 依托单位: UNIVERSITY OF TEXAS HLTH SCIENCE CENTER
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-08-01 至 2016-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8699784
• 关键词: Affect; Binding; Biological; Biological Assay; Cell Differentiation process; Cell Proliferation; Cell membrane; Complement; Complex; Computer Analysis; Computer software; Computing Methodologies; Data; Data Analyses; Development; Diffusion; Extracellular Matrix Proteins; Grant; Investigation; Knockout Mice; Knowledge; Malignant Neoplasms; Mammals; Mediating; Methodology; Methods; Modeling; Molecular; Molecular Chaperones; Molecular Conformation; Neoplasm Metastasis; Neurodegenerative Disorders; Neutrons; Nucleotides; Peptides; Performance; Phenotype; Physiological; Play; Process; Protein Isoforms; Proteins; Radial; Reaction; Relative (related person); Resolution; Roentgen Rays; Role; Signal Transduction; Simulate; Solutions; Solvents; Structure; System; Techniques; Tertiary Protein Structure; Testing; Tissues; Validation; Variant; Viscosity; analytical ultracentrifugation; base; biological systems; heat-shock proteins 110; human disease; in vivo; macromolecular assembly; macromolecule; molecular dynamics; novel; receptor; research study; response; sedimentation coefficient; software development; therapeutic development; three dimensional structure; tumor growth

DESCRIPTION (provided by applicant): This grant proposes the development of a novel methodology, based on computational approaches and experiments performed under physiological solution conditions, to complement high-resolution methods for the structure determination of biological macromolecules and their assemblies, and the application of this methodology to two relevant cases, Hsp70 and TGF¿. Starting with high-resolution structures, the developed software will generate alternative conformations using molecular dynamics. The conformations will be grouped into equivalence classes (ECs). Small angle X-ray and/or neutron scattering profiles, radius of gyration and hydrodynamic molecular parameters, such as the sedimentation coefficient, translational and rotational diffusion coefficients, and intrinsic viscosity, will be computed for each EC. The ECs will be globally fitted to experimental data, resulting in a distribution of contributing ECs. This information will provide important structural and dynamic detail obtained under physiological conditions and help to validate corresponding data from other high-resolution techniques. The proposed analysis strategy is based on well-established first principles and has universal applicability to any biological systems asking similar questions. We will test our software on two systems where relevant open questions remain. Hsp70 chaperones are 2-domain proteins that mediate a large number of protein processing and folding reactions. Upon binding ATP or ADP, Hsp70s undergo conformational changes that result in release or binding of their protein substrates. These processes are important in neurodegenerative disease and cancer. No crystal structure of an Hsp70 in an ATP state has ever been determined. A structure of the related protein Hsp110 bound to ATP has been determined and has been proposed to model for the Hsp70:ATP conformation, but this has not been tested directly. Controversy exists regarding the interpretation of the crystal structures of Hsp70s. The conformational state of Hsp70 in its nucleotide-free, ADP, and ATP states, and with and without bound peptide substrates will be analyzed under solution conditions where conformations will not be influenced by crystal packing forces or solvent components that are not physiological. TGF¿s are proteins which regulate cell proliferation, cell differentiation, and expression of extracellular matrix proteins. Three isoforms have arisen in mammals which play prominent roles in human disease, especially cancer. TGF¿1 and -¿3 can have opposing roles in tumor growth and metastasis. Understanding the origins of these differences in activity requires a detailed understanding of their structural dynamics. Dimeric TGF¿ binds with receptors TRII and TRI to signal across cell membranes, and can exist in an open or closed state. The open and closed ternary states TGF¿:TRII:TRI form differing signaling complexes. The proposed analysis method will quantify the extent which TGF¿1 and -¿3 exist in their ternary complexes with their receptors in an open state. For both cases, our method will provide additional detail by quantifying multiple conformations existing in solution rather than insisting on a single state.

描述（应用程序提供）：这项赠款提出了一种新方法的发展，基于在物理溶液条件下执行的计算方法和实验，以补充高分辨率方法，以确定生物学大分子及其组装的结构，以及将这种方法应用于两个相关的情况，HSP70和TGF启动型号的结构，将这种方法应用于开发的型号，以启动摩尔型结构，以启动摩尔型结构，从而启动了开发的型结构。组成将分为等效类（EC）。小角度X射线和/或中性散射曲线，回旋的半径和流体动力学分子参数，例如沉积系数，转化和旋转扩散系数以及内在的粘度，每个EC都将计算。 ECS将在全球范围内适合实验数据，从而导致EC的分布。该信息将提供在物理条件下获得的重要结构和动态细节，并有助于验证其他高分辨率技术的相应数据。提出的分析策略基于建立良好的第一原则，并对任何生物系统提出类似问题具有普遍的适用性。我们将在仍然存在相关开放问题的两个系统上测试我们的软件。 HSP70伴侣是二域蛋白，可介导大量蛋白质加工和折叠反应。在结合ATP或ADP时，HSP70的均质变化导致其蛋白质底物的释放或结合。这些过程在神经退行性疾病和癌症中很重要。尚未确定ATP状态下HSP70的晶体结构。已经确定了与ATP结合的相关蛋白HSP110的结构，并已提出为HSP70：ATP构象建模，但尚未直接测试。关于HSP70S晶体结构的解释存在争议。 HSP70在无核苷酸，ADP和ATP状态中的构象状态，以及没有结合的肽底物的构象状态，将在溶液条件下进行分析，在溶液条件下，构象不会受到不受生理生理的晶体堆积力或溶剂成分的影响。 TGFS是调节细胞增殖，细胞分化和细胞外基质蛋白表达的蛋白质。哺乳动物中出现了三种同工型，这些同工型在人类疾病，尤其是癌症中起着重要作用。 TGF¿1和 - 3可以在肿瘤生长和转移中具有相反的作用。了解这些活动差异的起源需要详细了解它们的结构动力学。二聚体TGF与受体TRII和TRI结合，以跨细胞膜发出信号，并且可以以开放或封闭状态存在。开放和封闭的三元状态TGF¿：TRII：TRI形成了区分信号传导复合物。提出的分析方法将量化其受体处于开放状态的三元复合物中的TGF¿1和 - 3的程度。对于这两种情况，我们的方法都将通过量化解决方案中存在的多个注意事项而不是坚持单个状态来提供其他细节。

项目成果

US-SOMO HPLC-SAXS module: dealing with capillary fouling and extraction of pure component patterns from poorly resolved SEC-SAXS data.

• DOI: 10.1107/s1600576716011201
• 发表时间: 2016-10-01
• 期刊: Journal of applied crystallography
• 影响因子: 6.1
• 作者: Brookes E;Vachette P;Rocco M;Pérez J
• 通讯作者: Pérez J

Characterization of size, anisotropy, and density heterogeneity of nanoparticles by sedimentation velocity.

• DOI: 10.1021/ac501722r
• 发表时间: 2014-08-05
• 期刊: ANALYTICAL CHEMISTRY
• 影响因子: 7.4
• 作者: Demeler, Borries;Tich-Lam Nguyen;Gorbet, Gary E.;Schirf, Virgil;Brookes, Emre H.;Mulvaney, Paul;El-Ballouli, Ala'a O.;Pan, Jun;Bakr, Osman M.;Demeler, Aysha K.;Uribe, Blanca I. Hernandez;Bhattarai, Nabraj;Whetten, Robert L.
• 通讯作者: Whetten, Robert L.