Molecular Structure Determination by Mass Spectrometry and Computational Modeling

通过质谱和计算模型测定分子结构

• 批准号: 10735319
• 负责人: Joshua S Sharp
• 金额: $ 48.6万
• 依托单位: UNIVERSITY OF MISSISSIPPI
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-06-01 至 2027-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10735319
• 关键词: Address; Amino Acids; Antibody Binding Sites; Antithrombin III; Area; Binding; Biological Sciences; Blood; Blood Proteins; Buffers; Carbohydrate Chemistry; Carbohydrates; Cell model; Cells; Chromatography; Complex; Complex Mixtures; Computer Analysis; Computer Models; Computer Simulation; Coupled; Data; Development; Dose; Emerging Technologies; Engineering; Epitopes; Family; Freezing; Generations; Health; Heparin; High Pressure Liquid Chromatography; Histones; Human; Hydrogen Peroxide; Hydrophobic Interactions; Hydroxyl Radical; Immune response; Immunoglobulin G; In Situ; In Vitro; Individual; Ion Exchange; Ions; Label; Life; Liquid Chromatography; Mass Spectrum Analysis; Measurement; Measures; Mediating; Membrane Proteins; Methods; Modernization; Modification; Molecular; Molecular Conformation; Molecular Structure; Monoclonal Antibodies; Mus; Organelles; Ovalbumin; Patients; Pharmaceutical Preparations; Pharmacology; Plasma; Play; Polysaccharides; Post-Translational Protein Processing; Protein Analysis; Protein Conformation; Protein Dephosphorylation; Protein Footprinting; Protein Isoforms; Protein Structure Databases; Proteins; Proteome; Reagent; Reporting; Reproducibility; Research Personnel; Resolution; Role; Side; Site; Solvents; Structure; Surface; System; TNF gene; Techniques; Technology; Testing; Time; Tissues; Whole Blood; Work; adalimumab; biophysical properties; carbohydrate structure; cell injury; chemical stability; conformer; dosimetry; dynamic system; experience; experimental study; flexibility; high standard; improved; in vivo; innovation; mechanical force; molecular mechanics; molecular modeling; mouse model; protein aggregation; protein complex; protein structure; reaction rate; structural biology; therapeutic protein; three dimensional structure; tool; tool development

PROJECT SUMMARY/ABSTRACT Structural biology plays a central role in modern molecular bioscience, enabling both a greater understanding and new mechanisms of manipulation of biomolecular action. However, despite tremendous development in tools for the generation of high resolution molecular models, large families of biomolecules and biomolecular complexes are still poorly represented in databases of protein structure due to limitations of current technology, and methods for probing protein structure within mammalian tissue are few. One method that has been used successfully to qualitatively study the structure of several of these families is hydroxyl radical protein footprinting (HRPF), an emerging technology that has been used to study changes in protein topography by measuring changes in the apparent rate of reaction between hydroxyl radicals generated in situ and amino acid side chains on the protein surface. Our initial work has developed HRPF into a quantitative measurement of protein topography at the individual amino acid level, accurately measuring the average solvent accessible surface areas (<SASA>) of many individual amino acids in a single experiment. In this renewal, we will expand our technology into structural systems that change dynamically with time, including protein posttranslational modification systems, large heteromeric protein complexes, and protein:carbohydrate complexes. The core technology we will develop to enable these studies is high performance liquid chromatography coupled inline with amino acid resolution HRPF (LC-HR-HRPF). Inline liquid chromatography allows the separation of protein conformers and immediate quantitative measurement of the purified conformers’ topographies by HR-HRPF before the dynamic system has a chance to re-equilibrate, freezing the structural information in the stable chemical footprint. We will also develop technology for analysis of protein structure within mammalian whole blood, enabling the study of protein structure and interactions within highly complex native systems. We will develop flow systems to precisely and carefully deliver hydrogen peroxide to blood for protein labeling without damaging cells, and will demonstrate the technology with the structural analysis of monoclonal antibodies dosed into a mouse model. Finally, we will develop technologies to probe the topography of complex carbohydrates, enabling us to measure which parts of carbohydrates mediate interactions with proteins, even in complex mixtures of glycans. We will develop both reducing-end specific and non-specific labeling strategies for probing carbohydrate topography. Together, these advances represent potential transforming technologies for the structural analysis of biomedically important and highly challenging systems.

项目总结/文摘

项目成果

The structure of a virus-encoded nucleosome.

病毒编码的核小体的结构。

• DOI: 10.1038/s41594-021-00585-7
• 发表时间: 2021-05
• 期刊: Nature structural & molecular biology
• 影响因子: 16.8
• 作者: Valencia-Sánchez MI;Abini-Agbomson S;Wang M;Lee R;Vasilyev N;Zhang J;De Ioannes P;La Scola B;Talbert P;Henikoff S;Nudler E;Erives A;Armache KJ
• 通讯作者: Armache KJ

Intrinsic Buffer Hydroxyl Radical Dosimetry Using Tris(hydroxymethyl)aminomethane.

• DOI: 10.1021/jasms.9b00088
• 发表时间: 2020-02-05
• 期刊: Journal of the American Society for Mass Spectrometry
• 影响因子: 3.2
• 作者: Roush AE;Riaz M;Misra SK;Weinberger SR;Sharp JS
• 通讯作者: Sharp JS

Peracylation Coupled with Tandem Mass Spectrometry for Structural Sequencing of Sulfated Glycosaminoglycan Mixtures without Depolymerization.

• DOI: 10.1021/jasms.0c00178
• 发表时间: 2020-10-07
• 期刊: Journal of the American Society for Mass Spectrometry
• 影响因子: 3.2
• 作者: Liu H;Liang Q;Sharp JS
• 通讯作者: Sharp JS

Enabling Real-Time Compensation in Fast Photochemical Oxidations of Proteins for the Determination of Protein Topography Changes.

• DOI: 10.3791/61580
• 发表时间: 2020-09-01
• 期刊: Journal of visualized experiments : JoVE
• 作者: Misra SK;Sharp JS
• 通讯作者: Sharp JS

Cryo-EM reveals the architecture of placental malaria VAR2CSA and provides molecular insight into chondroitin sulfate binding.

• DOI: 10.1038/s41467-021-23254-1
• 发表时间: 2021-05-19
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Wang K;Dagil R;Lavstsen T;Misra SK;Spliid CB;Wang Y;Gustavsson T;Sandoval DR;Vidal-Calvo EE;Choudhary S;Agerbaek MØ;Lindorff-Larsen K;Nielsen MA;Theander TG;Sharp JS;Clausen TM;Gourdon P;Salanti A
• 通讯作者: Salanti A