New approaches to sequencing of complex peptides.

复杂肽测序的新方法。

• 批准号: 7924506
• 负责人: PIETER C DORRESTEIN
• 金额: $ 33.14万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-25 至 2012-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7924506
• 关键词: Actinobacteria class; Actinomyces; Algorithms; Amino Acids; Automation; Biological Factors; Blood capillaries; Cloning; Collaborations; Collection; Complex; Cyanobacterium; Cyclic Peptides; Data Collection; Data Set; Development; Gene Cluster; Generations; Genes; Harvest; Imines; In Vitro; Investigation; Laboratories; Lead; Libraries; Marines; Mass Spectrum Analysis; Medical; Methodology; Methods; Monitor; Orphan; Oxidoreductase; Penicillins; Peptides; Problem Solving; Process; Scientist; Screening procedure; Solutions; Source; Staging; Structure; Technology; Therapeutic Agents; Time; Toxin; Vancomycin; Work; base; capillary; combinatorial; computerized data processing; drug discovery; improved; microbial; novel; novel strategies; programs; protein aminoacid sequence; public health relevance; seglitide

DESCRIPTION (provided by applicant): Nonribosomal peptides (NRPs) such as penicillin, vancomycin and related molecules isolated from microbial sources have been a staple for drug discovery for many decades. We propose to employ multi-stage mass-spectrometry (MSn) for de novo sequencing of NRPs, including cyclic NRPs. Analysis of MSn spectra of a cyclic peptide results in the difficult combinatorial problem of interpreting multiple linear peptides from the same spectrum. This proposal develops new combinatorial algorithms for solving this issue. Since the MSn based mass spectrometry analysis of NPRs is fast and inexpensive and requires minimal amounts of material (<1 5g), this approach opens a possibility of high-throughput sequencing of many unknown NRPs accumulated in large bioactivity marine cyanobacterial screening programs. In parallel to the automation of the NRPs sequencing efforts, we will harvest a set of orphan gene clusters from marine actinomycetes to generate a library of cyclic peptides. The algorithms developed in this proposal will be used to fully characterize this cyclic imine library. This work not only sets the stage for the automated characterization of NRPs but will also be applicable to the characterization of other peptidic natural products such as peptaibols, peptide derived toxins or lantibiotics. PUBLIC HEALTH RELEVANCE: This project describes the development and application of a novel mass spectrometry based method and corresponding algorithms that allow the de novo sequencing of complex therapeutic agents that are non-ribosomally derived.

描述（由申请人提供）：非核糖体肽（nrp），如青霉素、万古霉素和从微生物源分离的相关分子，几十年来一直是药物发现的主要内容。我们建议采用多级质谱法（MSn）对nrp（包括环状nrp）进行从头测序。对环肽的MSn光谱进行分析，会导致难以解释来自同一光谱的多个线性肽的组合问题。本文提出了一种新的组合算法来解决这个问题。由于基于MSn的NPRs质谱分析快速且廉价，并且需要最少的材料（< 15g），因此该方法为在大型生物活性海洋蓝藻筛选计划中积累的许多未知nrp的高通量测序提供了可能。在自动化nrp测序工作的同时，我们将从海洋放线菌中收集一组孤儿基因簇，以生成环状肽库。本提案中开发的算法将用于充分表征该循环亚胺库。这项工作不仅为nrp的自动表征奠定了基础，而且也将适用于其他肽类天然产物的表征，如肽基化合物、肽衍生毒素或抗生素。公共卫生相关性：该项目描述了一种新的基于质谱的方法和相应算法的开发和应用，该方法允许对非核糖体衍生的复杂治疗剂进行从头测序。

项目成果

Viequeamide A, a cytotoxic member of the kulolide superfamily of cyclic depsipeptides from a marine button cyanobacterium.

• DOI: 10.1021/np300321b
• 发表时间: 2012-09-28
• 期刊: Journal of natural products
• 影响因子: 5.1
• 作者: Boudreau PD;Byrum T;Liu WT;Dorrestein PC;Gerwick WH
• 通讯作者: Gerwick WH

Translating metabolic exchange with imaging mass spectrometry.

• DOI: 10.1038/nchembio.252
• 发表时间: 2009-12
• 期刊: Nature chemical biology
• 影响因子: 14.8
• 作者: Yang YL;Xu Y;Straight P;Dorrestein PC
• 通讯作者: Dorrestein PC

The spectral networks paradigm in high throughput mass spectrometry.

• DOI: 10.1039/c2mb25085c
• 发表时间: 2012-10
• 期刊: Molecular bioSystems
• 作者: Guthals A;Watrous JD;Dorrestein PC;Bandeira N
• 通讯作者: Bandeira N

Sequencing cyclic peptides by multistage mass spectrometry.

• DOI: 10.1002/pmic.201000697
• 发表时间: 2011-09
• 期刊: PROTEOMICS
• 影响因子: 3.4
• 作者: Mohimani, Hosein;Yang, Yu-Liang;Liu, Wei-Ting;Hsieh, Pei-Wen;Dorrestein, Pieter C.;Pevzner, Pavel A.
• 通讯作者: Pevzner, Pavel A.

Observing the invisible through imaging mass spectrometry, a window into the metabolic exchange patterns of microbes.

• DOI: 10.1016/j.jprot.2012.05.036
• 发表时间: 2012-08-30
• 期刊: Journal of proteomics
• 影响因子: 3.3
• 作者: Gonzalez DJ;Xu Y;Yang YL;Esquenazi E;Liu WT;Edlund A;Duong T;Du L;Molnár I;Gerwick WH;Jensen PR;Fischbach M;Liaw CC;Straight P;Nizet V;Dorrestein PC
• 通讯作者: Dorrestein PC