Collaborative Research: Integrating Geochemistry and Proteomics to Assess Protein Sources and Their Fate in Marine Systems

合作研究：整合地球化学和蛋白质组学来评估海洋系统中的蛋白质来源及其命运

• 批准号: 0825790
• 负责人: David Goodlett
• 金额: $ 51.92万
• 依托单位: University of Washington
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-01 至 2012-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0825790&HistoricalAwards=false
• 关键词: Collaborative; Research; Integrating; Geochemistry; Proteomics

Proteins represent the major source for organic nitrogen in the ocean. Yet the identification of individual proteins and important mechanisms controlling their preservation has been stalled by the analytical and mathematical challenges in deciphering the vast suite of possible structures and complex suite of degradation products. In this study, researchers at the Chesapeake Biological Laboratory and the University of Washington will conduct a novel interdisciplinary study to harness and integrate recent developments and advances in biomedical proteomics and bioinformatics to follow the geochemical fate of proteins in marine systems. The integration of proteomics approaches to geochemical analysis is expected to allow the research team to identify individual proteins in both living materials and their detrital products -- the process involved in transforming proteins into biomarkers of both organic sources and the catalytic (i.e. enzymatic) agents responsible for their degradation. The project has three major goals: 1. Identification of the dominant proteins expressed in autotrophs prior to becoming detritus. These proteins represent the primary precursors for long term protein preservation and knowledge of their amount, distribution and amino acid signatures are needed to follow subsequent alterations. 2. Identification of peptides and modified products resulting from algal protein degradation and their interaction in the complex matrices of particles and sediments. With these observed sequence tags, the researchers propose to assign individual protein homologies, functions, and sources across a range of environments. 3. Application of advances in proteomics (including database mining and bioinformatics) to identify specific structures (e.g. á-helices, â-sheets, hydrophobic cores) or chemical modifications (glycation, phosphorylation etc.) that are selectively retained during the degradation process and act as mechanisms for long term preservation of organic nitrogen. Broader Impacts: This project will feature several approaches to provide for interdisciplinary student training in marine chemistry and proteomics as well as disseminate results to a broad audience. In the more traditional role, this project will support a doctoral student and key postdoctoral fellow. Undergraduate students will be involved in the summer at CBL through an active on-site REU program. The team will expand the impact of this work to the broader educational community through science teacher training.

蛋白质是海洋中有机氮的主要来源。然而，由于破译大量可能的结构和复杂的降解产物所面临的分析和数学挑战，对单个蛋白质和控制其保存的重要机制的识别已经陷入停滞。在这项研究中，切萨皮克生物实验室和华盛顿大学的研究人员将进行一项新颖的跨学科研究，以利用和整合生物医学蛋白质组学和生物信息学的最新发展和进步，以跟踪海洋系统中蛋白质的地球化学命运。将蛋白质组学方法与地球化学分析相结合，预计将使研究团队能够识别生物材料及其碎屑产物中的单个蛋白质，该过程涉及将蛋白质转化为有机来源和负责其降解的催化（即酶）剂的生物标志物。该项目有三个主要目标： 1. 鉴定在自养生物变成碎屑之前表达的主要蛋白质。这些蛋白质代表了长期蛋白质保存的主要前体，需要了解它们的数量、分布和氨基酸特征来跟踪后续的改变。 2. 鉴定藻类蛋白质降解产生的肽和修饰产物及其在颗粒和沉积物的复杂基质中的相互作用。通过这些观察到的序列标签，研究人员建议在一系列环境中分配单个蛋白质的同源性、功能和来源。 3. 应用蛋白质组学（包括数据库挖掘和生物信息学）的进展来识别在降解过程中选择性保留的特定结构（例如á-螺旋、â-折叠、疏水核心）或化学修饰（糖化、磷酸化等），并作为有机氮长期保存的机制。更广泛的影响：该项目将采用多种方法，为海洋化学和蛋白质组学的跨学科学生提供培训，并向广大受众传播结果。在更传统的角色中，该项目将支持一名博士生和关键博士后研究员。本科生将通过活跃的 REU 现场项目参与 CBL 的暑期活动。该团队将通过科学教师培训将这项工作的影响扩大到更广泛的教育界。