Investigation of Latent Free Energy in Noncovalent Networks

非共价网络中潜在自由能的研究

• 批准号: 9330920
• 负责人: MARCEY L WATERS
• 金额: $ 36.55万
• 依托单位: UNIV OF NORTH CAROLINA CHAPEL HILL
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-08-15 至 2020-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9330920
• 关键词: Active Sites; Adopted; Affinity; Behavior; Binding; Binding Sites; Biological; Biological Models; Biological Process; Biology; Biotin; Catalysis; Catenanes; Communication; Complement; Complex; Computer Simulation; Coupled; Coupling; Development; Entropy; Enzymes; Equilibrium; Event; Exhibits; Financial compensation; Free Energy; Goals; Health; Human; Hydrogen Bonding; Individual; Investigation; Ligand Binding; Ligands; Link; Measures; Modeling; Molecular; Molecular Conformation; Mutate; Mutation; Outcome; Peptides; Pharmaceutical Chemistry; Play; Post-Translational Protein Processing; Prevalence; Process; Property; Protein Engineering; Proteins; Resolution; Rest; Roentgen Rays; Role; Scheme; Signal Transduction; Stimulus; Streptavidin; Structure; Study models; System; Testing; Thermodynamics; base; complex biological systems; computer studies; design; driving force; enzyme activity; falls; infancy; inhibitor/antagonist; insight; molecular recognition; mutant; novel; protein folding; protein function; public health relevance; receptor; response; role model

 DESCRIPTION (provided by applicant): Noncovalent networks (NCNs) in proteins play a critical role in biological function: communication through NCNs contributes to ligand binding, catalysis, allostery, and signal transduction, but the mechanisms by which NCNs contribute to these processes is not generally recognized. One possible mechanism for communication through a network is via the storage and release of latent free energy. Notably, each individual noncovalent interaction in an NCN is not necessarily optimized; instead, the NCN as a whole is optimized within the constraints of the protein. Because of this, NCNs store latent free energy. This provides the thermodynamic driving force for a protein to respond when it contacts an external stimulus, resulting in a downstream outcome. Changes in the balance of forces in the NCN result in the release of latent free energy, but the molecular mechanisms by which this occurs are poorly understood. Despite the critical role NCNs play in biological function, they are difficult to study in complex biological systems. However, simple model systems for molecular recognition generally do not encode enough complexity to adequately model the properties of a NCN. Herein, we propose to use two protein-like supramolecular assemblies of intermediate complexity to study the role of latent free energy in noncovalent network gated protein actuation, including responses to structural mutations (Aim 1) and recognition of a guest via induced-fit binding (Aim 2). These systems include a peptidic catenane and a peptidic macrocyclic host containing multiple beta-turns, intra- and interstrand H-bonds, and aromatic interactions that are all in communication. In the catenane, we will determine how a specific change in one part of a NCN can be compensated for (or not) by the rest of the network, and thus provide insight into mechanisms for storing and releasing latent free energy (Aim 1). The effect of mutations in each region of the network will be assessed experimentally and computationally to probe the structure, dynamics, and thermodynamics of the resultant catenane. Both enthalpic and entropic mechanisms for responding to a stimulus will be investigated. The host-guest system (Aim 2) will be utilized to investigate the coupling of the NCN in the host to the binding affinity of the guest. Stabilization of a protein's NCN upon binding has been proposed to provide significant enhancement of binding affinities (i.e. streptavidin-biotin). We will test this hypothesis by tunin the stability of the NCN in the host and experimentally and computationally characterizing its structure and response to a guest. Together, these studies will elucidate mechanisms by which NCNs utilize latent free energy in protein actuation and will provide a new conceptual model for protein function with applications to protein design and inhibitor development.

 描述（应用程序提供）：蛋白质中的非共价网络（NCN）在生物学功能中起关键作用：通过NCN进行通信有助于配体结合，催化，变构和信号翻译，但是NCN对这些过程有助于这些过程的机制通常不识别。通过网络通信的一种可能的机制是通过潜在自由能的存储和释放。值得注意的是，NCN中的每个单独的非共价相互作用不一定优化。取而代之的是，NCN作为一个整体在蛋白质的约束中进行了优化。因此，NCNS存储潜在自由能。这为蛋白质接触外部刺激时提供了热力学驱动力，从而导致下游结果。 NCN力平衡的变化导致潜在自由能的释放，但是尽管NCN在生物学功能中起着至关重要的作用，但这种情况的分子机制仍很难在复杂的生物系统中研究。但是，用于分子识别的简单模型系统通常没有编码足够的复杂性来充分对NCN的性质进行建模。在本文中，我们建议使用中间复杂性的两个蛋白质的超分子组件来研究潜在自由能在非共价网络门控蛋白激活中的作用，包括对结构突变的反应（AIM 1）以及通过诱导的拟合结合来识别来宾的识别（AIM 2）。这些系统包括宠物链球菌和一个宠物大环宿主，其中包含多个β-扭转，内部和链间H键以及芳香相互作用，这些相互作用都在通信中。在Catenane中，我们将确定如何通过网络的其余部分来补偿NCN的一部分的特定变化，从而深入了解存储和释放潜在自由能的机制（AIM 1）。将通过实验和计算评估网络中每个区域的突变的影响，以探测所得链烷烷的结构，动力学和热力学。焓和熵机制均应研究刺激的反应。将利用主机 - 乐器系统（AIM 2）调查主机中NCN与来宾的结合亲和力的耦合。已经提出了结合后蛋白质NCN的稳定化，以显着增强结合亲和力（即链霉亲和素生物素）。我们将通过Tunin在主机中的NCN稳定性以及实验和计算表征其对来宾的结构和响应来检验这一假设。总之，这些研究将阐明NCN在蛋白质激活中利用潜在的自由能，并将为蛋白质功能提供新的概念模型，并应用于蛋白质设计和抑制剂开发。