Mechanisms of Allostery and Molecular Recognition in the Small Multidrug Resistance Family

多药耐药小家族的变构和分子识别机制

• 批准号: 10666510
• 负责人: Nathaniel J. Traaseth
• 金额: $ 44.49万
• 依托单位: NEW YORK UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-07-15 至 2024-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10666510
• 关键词: Acids; Active Biological Transport; Antibiotic Resistance; Antibiotics; Articulation; Bacteria; Bacterial Drug Resistance; Binding; Biochemical; Biological; Biological Assay; Charge; Chemical Structure; Chemistry; Clinic; Collaborations; Computing Methodologies; Data; Defense Mechanisms; Development; Drug Efflux; Drug Modelings; Drug Transport; Drug resistance; Effectiveness; Family; Foundations; Goals; Grant; Knowledge; Knowledge Discovery; Mediating; Membrane Proteins; Methods; Modeling; Molecular; Molecular Conformation; Multi-Drug Resistance; Mutagenesis; Nature; Organism; Outcomes Research; Pathogenicity; Pharmaceutical Preparations; Phase; Phenotype; Plant alkaloid; Play; Poison; Positioning Attribute; Property; Proteins; Protons; Pump; Repression; Research; Role; Shapes; Side; Source; Specificity; Structure; Substrate Specificity; System; Testing; Transport Process; Work; base; biophysical analysis; biophysical techniques; comparative; computational platform; deprotonation; design; drug discovery; efflux pump; guanidinium; inhibitor; insight; molecular recognition; multi drug transporter; multiple drug use; mutant; novel; pH gradient; pathogenic bacteria; response; theories; tool

Project Summary Bacterial drug resistance is a worldwide problem that limits the effectiveness of antibiotics in the clinic. While there are several molecular mechanisms that contribute to drug resistant phenotypes, it is well established that efflux pumps play a prominent role in pathogenic bacteria. Indeed, multidrug transporters constitute a fundamental mechanism used by bacteria to survive in the presence of toxic compounds by binding and transporting a broad array of structurally diverse compounds. The long-term goals of this project are to discover novel mechanisms used by multidrug transporters and to harness this knowledge to predict and control function. In this competitive renewal, we are now poised to tackle the major challenge in the field of understanding how efflux pumps achieve broad drug specificity required for conferring multidrug resistance. To accomplish this goal, we need to establish a comprehensive understanding of the catalytic cycle for an efflux pump system amenable to detailed biological, biochemical and biophysical studies. For this reason, our proposal will use EmrE from the SMR family as the model drug transporter since it embodies the minimal level of complexity while retaining the key features shared among all secondary active efflux pumps. Aim 1 will test an occluded-state theory that we hypothesize is widely used by efflux pumps for drug binding. Aim 2 will seek to define the molecular basis for substrate-induced activation of dynamics versus inhibitor-induced repression of dynamics, as well as development of a computational platform for predicting binding and transport. Finally, Aim 3 will set out to determine the molecular basis of binding specificity versus promiscuity through a comparative analysis of two subfamilies within the SMR family that have markedly different specificity profiles. Each of these Aims works synergistically toward our long-term goal of articulating novel transport mechanisms and applying our knowledge to develop models for making predictions about function. A major strength of this project is the integrated nature of the approach which utilizes significant collaboration and a combination of biological, biophysical, and computational methods aimed at unveiling general transport mechanisms designed by nature and shared among other multidrug efflux pumps. The outcomes of this research will make a significant impact in understanding efflux-mediated multidrug resistance, and the approaches and methods developed will be translatable to knowledge discovery in other efflux systems.

项目摘要 细菌耐药性是一个在全球范围内的问题，它限制了抗生素在诊所中的有效性。尽管 有几种有助于药物耐药表型的分子机制，众所周知 外排泵在致病细菌中起重要作用。实际上，多药物转运蛋白构成 通过结合和 运输一系列结构上多样的化合物。该项目的长期目标是发现 多药转运蛋白使用并利用这些知识来预测和控制功能的新型机制。 在这种竞争性的续约中，我们现在准备应对了解如何理解如何的主要挑战 排出泵具有赋予多药耐药性所需的广泛药物特异性。为了实现这一目标， 我们需要对排出泵系统的催化周期建立全面的理解 详细的生物学，生化和生物物理研究。因此，我们的建议将使用 SMR家族作为模型药物转运蛋白，因为它体现了最低的复杂水平，同时保留了 所有次级活动排出泵之间共享的关键功能。 AIM 1将测试我们的封闭状态理论 假设被排出泵广泛用于药物结合。 AIM 2将寻求定义分子基础 底物诱导的动力学激活与抑制剂诱导的动力学抑制以及 开发用于预测结合和运输的计算平台。最后，AIM 3将前往 通过对两个的比较分析，确定结合特异性与滥交的分子基础 SMR家族中具有明显不同特异性曲线的亚家族。这些目标都有效 朝着我们阐明新型运输机制并运用我们的知识的长期目标协同目标 开发模型以进行有关功能的预测。该项目的主要优势是综合性质 利用重大协作以及生物学，生物物理和 计算方法旨在揭示由自然设计并共享的一般运输机制 其他多果外排泵。这项研究的结果将对理解产生重大影响 外排介导的多药电阻，开发的方法和方法将可以翻译成 其他外排系统中的知识发现。

项目成果

Afterglow Solid-State NMR Spectroscopy.

余辉固体核磁共振波谱。

• DOI: 10.1007/978-1-4939-7386-6_3
• 发表时间: 2018
• 期刊: Methods in molecular biology (Clifton, N.J.)
• 作者: Abramov,Gili;Traaseth,NathanielJ
• 通讯作者: Traaseth,NathanielJ

Asymmetric protonation of glutamate residues drives a preferred transport pathway in EmrE

• DOI: 10.1073/pnas.2110790118
• 发表时间: 2021-10-12
• 期刊: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• 影响因子: 11.1
• 作者: Li, Jianping;Her, Ampon Sae;Traaseth, Nathaniel J.
• 通讯作者: Traaseth, Nathaniel J.

Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo.

• DOI: 10.1007/s10822-022-00479-w
• 发表时间: 2022-10
• 期刊: Journal of computer-aided molecular design
• 影响因子: 3.5

Correlating lipid bilayer fluidity with sensitivity and resolution of polytopic membrane protein spectra by solid-state NMR spectroscopy.

• DOI: 10.1016/j.bbamem.2014.05.003
• 发表时间: 2015-01
• 期刊: BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
• 影响因子: 3.4
• 作者: Banigan, James R.;Gayen, Anindita;Traaseth, Nathaniel J.
• 通讯作者: Traaseth, Nathaniel J.

Multiple frequency saturation pulses reduce CEST acquisition time for quantifying conformational exchange in biomolecules.

• DOI: 10.1007/s10858-018-0186-1
• 发表时间: 2018-05
• 期刊: Journal of biomolecular NMR
• 影响因子: 2.7
• 作者: Leninger M;Marsiglia WM;Jerschow A;Traaseth NJ
• 通讯作者: Traaseth NJ