Vibrational spectroscopy with metasurface optics (VISMO) for high-throughput identification of protein post-translational modifications

超表面光学振动光谱 (VISMO) 用于蛋白质翻译后修饰的高通量鉴定

• 批准号: 10761601
• 负责人: Jack Hu
• 金额: $ 28.99万
• 依托单位: PUMPKINSEED TECHNOLOGIES INC
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-22 至 2024-09-21
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10761601
• 关键词: Amino Acid Sequence; Amino Acids; Antigens; Arthritis; Autoimmune Diseases; Binding; Biological Assay; Biological Markers; Biological Process; Biological Response Modifier Therapy; Catalogs; Cell Signaling Process; Cell physiology; Cells; Charge; Chemicals; Complement; Detection; Development; Diabetes Mellitus; Diagnosis; Dimensions; Disease; Disease Pathway; Enzyme-Linked Immunosorbent Assay; Etiology; Fingerprint; Fluorescence; Foundations; Growth; Health; Health Transition; Human; Immune response; Immunoassay; Individual; Inflammation; Ions; Kinetics; Label; Legal patent; Length; Ligands; Location; Malignant Neoplasms; Mass Spectrum Analysis; Measurement; Measures; Metabolic; Methodology; Methods; Mission; Modernization; Monitor; Nanostructures; Nerve Degeneration; Neurodegenerative Disorders; Noise; Nucleic Acids; Nucleic acid sequencing; Nutrient; Optics; Pathway interactions; Peptide Sequence Determination; Peptides; Phase; Physiology; Post-Translational Protein Processing; Posttranslational Amino Acid Modification; Property; Proteins; Proteome; Proteomics; Pumpkins; Raman Spectrum Analysis; Regulation; Research Personnel; Resolution; Sampling; Signal Transduction; Small Business Innovation Research Grant; Spectrum Analysis; Speed; Structure; Technology; Tertiary Protein Structure; Therapeutic; Time; Treatment Efficacy; analog; cell type; chemical cleavage; improved; insight; interest; machine learning algorithm; miniaturized sensor; novel sequencing technology; novel therapeutics; parallelization; prevent; protein aminoacid sequence; protein function; protein profiling; protein protein interaction; protein structure; sensor; single molecule; small molecule; success; synthetic peptide; therapeutic development; transcriptome; treatment response

Project Summary/Abstract Proteins are critical to a wide array of cellular processes - from cell signaling to immune responses, nutrient transport, growth, and metabolic regulation. Proper function of proteins depends sensitively on the type, location, and abundance of post-translational modifications (PTMs). Aberrations in PTM properties can degrade protein function and compromise the physiology and function of the cells in which they reside. Indeed, altered PTMs have been implicated in a variety of diseases, including cancers, auto-immune diseases, neurodegenerative diseases, and inflammation. Nucleic acid sequencing gives almost no insight into PTM attributes, and sensitive and high-throughput characterization and quantification of PTMs remains a daunting challenge for mass spectroscopy (MS) and immunoassays. Pumpkinseed is developing an optics-based and label-free approach to measure protein PTMs, termed Vibrational Spectroscopy with Metasurface Optics (VISMO). VISMO offers high-speed analysis of millions of proteins – including their sequence, structure, and interactions – with three key advantages over other proteomics solutions: (1) In a label-free format, we uniquely identify each molecule via its vibrational scattering spectra, rather than relying on lower-resolution fluorescent tagging. (2) Using nanostructured Si chips, we create highly efficient optical resonators that both dramatically amplify the signal-to-noise ratio – even for very low abundance biomarkers – and increase sample throughput, with simultaneous measurement of ~3 million proteins per square centimeter. (3) We use cutting-edge machine learning (ML) algorithms to dissect information-rich features from the vibrational spectra, including the wavenumbers that correspond to the primary, secondary, and tertiary structure of the protein, as well as changes related to protein or small-molecule binding. Our Phase I proposal will develop this revolutionary platform for sensitive, high-throughput, and high-resolution protein detection, including their abundance, sequence, and PTMs. Aim 1 develops sensors that enable sensitive, few-to-single-molecule spectroscopy, builds our catalog of spectra for particular amino acids, short peptide sequences, and PTMs; and develops machine learning (ML) algorithms that provide interpretability to each molecule’s optical scattering signature. Aim 2 advances our methods for protein sequencing using chemical cleavage and our patented ‘sequencing by subtraction’ methodology. Phase I results will form the foundation of our Phase II proposal, with potentially far-reaching impacts on whole-proteome sequencing and protein-profiling of the vast repertoire of cell types. Biotherapeutic companies and academic researchers studying intact, native proteins will value the high-resolution that Pumpkinseed’s platform offers compared to existing ELISA-type assays, and the higher-sensitivity and throughput compared to traditional mass spectrometry. Our approach provides a new methodology for probing protein structure and interactions in order to reveal new dimensions of disease etiology and distinct opportunities for new therapeutic development.

项目概要/摘要 蛋白质对于多种细胞过程至关重要 - 从细胞信号传导到免疫反应、营养 运输、生长和代谢调节。蛋白质的正常功能敏感地取决于类型， 位置和翻译后修饰 (PTM) 的丰度。 PTM 特性的畸变可以 降低蛋白质功能并损害其所在细胞的生理学和功能。的确， 改变的 PTM 与多种疾病有关，包括癌症、自身免疫性疾病、 神经退行性疾病和炎症。核酸测序几乎无法深入了解 PTM PTM 的属性、敏感且高通量的表征和定量仍然是一个令人畏惧的问题 质谱 (MS) 和免疫分析面临的挑战。 Pumpkinseed 正在开发一种基于光学的 测量蛋白质 PTM 的无标记方法，称为超表面光学振动光谱 （维莫）。 VISMO 可以对数百万种蛋白质进行高速分析，包括它们的序列、结构和 相互作用 - 与其他蛋白质组学解决方案相比具有三个关键优势：（1）以无标记格式，我们 通过其振动散射光谱唯一地识别每个分子，而不是依赖于较低分辨率 荧光标记。 (2) 使用纳米结构硅芯片，我们创建了高效的光学谐振器 显着放大信噪比——即使对于丰度非常低的生物标志物——并增加样本 吞吐量，可同时测量每平方厘米约 300 万个蛋白质。 (3) 我们使用 尖端机器学习 (ML) 算法可从振动频谱中剖析信息丰富的特征， 包括对应于蛋白质的一级、二级和三级结构的波数，如 以及与蛋白质或小分子结合相关的变化。我们的第一阶段提案将开发这个 用于灵敏、高通量和高分辨率蛋白质检测的革命性平台，包括其 丰度、序列和 PTM。目标 1 开发能够灵敏、少分子到单分子的传感器 光谱学，建立特定氨基酸、短肽序列和 PTM 的光谱目录； 并开发机器学习 (ML) 算法，为每个分子的光学提供可解释性 散射签名。目标 2 改进了我们使用化学切割进行蛋白质测序的方法以及我们的 获得专利的“减法测序”方法。第一阶段的结果将构成我们第二阶段的基础 该提案对整个蛋白质组测序和蛋白质分析具有潜在的深远影响 细胞类型的库。研究完整天然蛋白质的生物治疗公司和学术研究人员 与现有的 ELISA 型检测相比，将重视 Pumpkinseed 平台提供的高分辨率，并且 与传统质谱分析相比，具有更高的灵敏度和通量。我们的方法提供了一种新的 探索蛋白质结构和相互作用以揭示疾病新维度的方法 病因学和新疗法开发的独特机会。