Structural basis of phosphatidylglycerol recognition and trafficking at the outer membrane

外膜磷脂酰甘油识别和运输的结构基础

• 批准号: BB/L00335X/1
• 负责人: Michael Overduin
• 金额: $ 60.31万
• 依托单位: University of Birmingham
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FL00335X%2F1
• 关键词: Structural; basis; phosphatidylglycerol; recognition; trafficking

The overall aim of this project is to determine how bacteria recognize and organize lipids in their outer membraneThe challenge we are tackling here is best described by Bruce Albert, the Editor of Science, who recently stated "I am painfully aware of the huge gap that remains in our understanding of even the simplest cells. Consider, for example, the common bacterium E. coli, which served as a predominant model organism in the early years of molecular biology. It is very sobering to report that more than 50 years later, nearly a quarter of the more than 4000 proteins encoded by its genome have functions that remain unknown. Might some new functional classes of biological molecules, common to all cells, be discovered by a focus on such proteins?" [Science, 2012, 337: 6102]. We intend to fill this gap of biological knowledge by defining the function and mechanism of an E.coli coli protein called YraP. According to the Interpro database there are at least 6746 proteins with similarity to YraP which have been sequenced from a wide range of bacterial species including many pathogens, and hence there is broader relevance to many micro-organisms and infectious diseases. Moreover, as a unique bacterial gene that is expressed in response to stress, YraP offers potential opportunities for the design of antimicrobial agents, especially once suitable screening assays and mechanistic insights are available. The diversity of YraP-related proteins, which typically are composed of a pair of BON domains, includes haemolysins, mechanosensitive channels, the membrane-pore forming protein Secretin, and several eukaryotic proteins. This suggests a common function involving lipid recognition or membrane manipulation, as first proposed by C Yeats and A Bateman in 2003, although how they are related at a structural and mechanistic level remains unclear.Our primary focus is on solving the atomic resolution structures and molecular interactions of YraP, providing the first experimental insights into how the BON domain engages the phospholipid components of the protective outer membrane that surrounds all Gram negative bacteria. The outer membrane's main function is to form a semi-permeable layer that controls the influx and efflux of nutrients and other materials including drug molecules. The proteins inserted into outer membranes include 90 lipid modified proteins like YraP as well as pores, channels and antigens that act as targets of immune responses. These lipoproteins are embedded into a bilayer composed of immunogenic lipopolysaccharides, phospholipids and glycolipids. We will investigate how YraP binds and organizes lipids and contributes to trafficking them to the outer membrane of bacteria. In order to develop the first mechanistic understanding of YraP function, we will use biophysical methods including nuclear magnetic resonance spectroscopy (NMR). Visualising the atoms of the protein structures and ligand interactions of YraP will provide valuable insights into the functional roles of the amino acid residues and lipids they contact. These principles of PG recognition and outer membrane specificity could aid in the discovery of molecular inhibitors and new classes of antimicrobial agents, with YraP playing a key role in controlling cell permeability and ensuring viability during bacterial stress.This project represents collaborative science, involving a joint structure-function analysis of a novel target by two research groups from the Institute of Microbiology and Infection and the Henry Wellcome Building for Biomolecular NMR Spectroscopy (HWB-NMR), respectively. We will combine the molecular and cellular insights of Ian Henderson's bacteriology group, which has just discovered the role of YraP in lipid trafficking, along with the structural biological expertise within Michael Overduin's group, which specialises in elucidating protein:lipid recognition and trafficking mechanisms.

该项目的总体目的是确定细菌如何在其外膜中认识并组织脂质我们在这里所面临的挑战中如何描述，科学编辑布鲁斯·阿尔伯特（Bruce Albert）最好描述，他最近指出：“我最近在理解我们对最简单细胞的理解中仍然存在巨大的差距。清醒地报告，在50多年后，由其基因组编码的4000多个蛋白质中有近四分之一的功能可能是未知的。 [Science，2012，337：6102]。我们打算通过定义称为YRAP的大肠杆菌蛋白的功能和机制来填补这一生物知识的空白。根据Interpro数据库，至少有6746个蛋白质与YRAP相似，这些蛋白已从包括许多病原体在内的广泛的细菌物种进行了测序，因此与许多微生物和传染病的相关性更广泛。此外，作为一种针对压力表示的独特细菌基因，YRAP为设计抗菌剂的设计提供了潜在的机会，尤其是一旦提供了合适的筛选分析和机械见解。通常由一对BON结构域组成的与YRAP相关蛋白的多样性包括血液蛋白，机械敏感通道，形成膜的蛋白质分泌素和几种真核蛋白。 This suggests a common function involving lipid recognition or membrane manipulation, as first proposed by C Yeats and A Bateman in 2003, although how they are related at a structural and mechanistic level remains unclear.Our primary focus is on solving the atomic resolution structures and molecular interactions of YraP, providing the first experimental insights into how the BON domain engages the phospholipid components of the protective outer membrane that surrounds所有革兰氏阴性细菌。外膜的主要功能是形成一个半渗透层，该层控制营养物质和其他材料（包括药物分子）的流入和外排。插入外膜的蛋白质包括90个脂质改性蛋白，例如YRAP，以及充当免疫反应靶标的孔，通道和抗原。这些脂蛋白被嵌入由免疫原性脂多糖，磷脂和糖脂组成的双层中。我们将研究YRAP如何结合和组织脂质，并有助于将它们运送到细菌外膜上。为了发展对YRAP功能的首次机械理解，我们将使用包括核磁共振光谱（NMR）在内的生物物理方法。可视化蛋白质结构的原子和YRAP的配体相互作用将为它们接触的氨基酸残基和脂质的功能作用提供宝贵的见解。 These principles of PG recognition and outer membrane specificity could aid in the discovery of molecular inhibitors and new classes of antimicrobial agents, with YraP playing a key role in controlling cell permeability and ensuring viability during bacterial stress.This project represents collaborative science, involving a joint structure-function analysis of a novel target by two research groups from the Institute of Microbiology and Infection and the Henry Wellcome Building for分子NMR光谱（HWB-NMR）分别。我们将结合伊恩·亨德森（Ian Henderson）的细菌学组的分子和细胞洞察，该组刚刚发现了yrap在脂质运输中的作用，以及迈克尔·奥弗杜因（Michael Overduin）组中的结构生物学专业知识，该群体专门研究阐明蛋白质：脂质识别和运输机制。

项目成果

An acid-compatible co-polymer for the solubilization of membranes and proteins into lipid bilayer-containing nanoparticles.

• DOI: 10.1039/c8nr01322e
• 发表时间: 2018-06-07
• 期刊: Nanoscale
• 影响因子: 6.7
• 作者: Hall SCL ;Tognoloni C ;Charlton J ;Bragginton ÉC ;Rothnie AJ ;Sridhar P ;Wheatley M ;Knowles TJ ;Arnold T ;Edler KJ ;Dafforn TR
• 通讯作者: Dafforn TR

Mechanism of intermediate filament recognition by plakin repeat domains revealed by envoplakin targeting of vimentin.

• DOI: 10.1038/ncomms10827
• 发表时间: 2016-03-03
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Fogl C;Mohammed F;Al-Jassar C;Jeeves M;Knowles TJ;Rodriguez-Zamora P;White SA;Odintsova E;Overduin M;Chidgey M
• 通讯作者: Chidgey M

A novel pathway for outer membrane protein biogenesis in Gram-negative bacteria.

• DOI: 10.1111/mmi.13082
• 发表时间: 2015-08
• 期刊: Molecular microbiology
• 影响因子: 3.6
• 作者: Jeeves M;Knowles TJ
• 通讯作者: Knowles TJ

Structure of dual BON-domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation.

• DOI: 10.7554/elife.62614
• 发表时间: 2020-12-14
• 期刊: eLife
• 影响因子: 7.7
• 作者: Bryant JA;Morris FC;Knowles TJ;Maderbocus R;Heinz E;Boelter G;Alodaini D;Colyer A;Wotherspoon PJ;Staunton KA;Jeeves M;Browning DF;Sevastsyanovich YR;Wells TJ;Rossiter AE;Bavro VN;Sridhar P;Ward DG;Chong ZS;Goodall EC;Icke C;Teo AC;Chng SS;Roper DI;Lithgow T;Cunningham AF;Banzhaf M;Overduin M;Henderson IR
• 通讯作者: Henderson IR