Investigation of Latent Free Energy in Noncovalent Networks

非共价网络中潜在自由能的研究

基本信息

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
项目类别：
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

项目摘要

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（由申请人提供）：蛋白质中的非共价网络 (NCN) 在生物功能中发挥着关键作用：通过 NCN 进行的通信有助于配体结合、催化、变构和信号转导，但 NCN 促进这些过程的机制并不明确。普遍认为，通过网络进行通信的一种可能机制是通过潜在自由能的存储和释放，NCN 中的每个单独的非共价相互作用不一定是优化的。正因为如此，NCN 储存了潜在的自由能，从而为蛋白质在接触外部刺激时做出反应提供了热力学驱动力，从而导致下游结果的力平衡发生变化。 NCN 会导致潜在自由能的释放，但人们对这种情况发生的分子机制知之甚少，尽管 NCN 在生物功能中发挥着关键作用，但它们很难在复杂的生物系统中进行研究。分子识别通常不会编码足够的复杂性在此，我们建议使用两种中等复杂性的类蛋白质超分子组装体来研究潜在自由能在非共价网络门控蛋白质驱动中的作用，包括对结构突变的反应（目标 1）和识别通过诱导拟合结合形成客体（目标 2），这些系统包括肽链烷和含有多个 β 转角、链内和链间氢键的肽大环宿主。在索烷中，我们将确定 NCN 某一部分的特定变化如何被网络的其余部分补偿（或不补偿），从而深入了解存储和释放的机制。潜在自由能（目标 1）。将通过实验和计算来评估网络每个区域的突变影响，以探究所产生的索烷的结构、动力学和热力学。宿主-客体系统（目标 2）将用于研究宿主中的 NCN 与客体的结合亲和力的耦合，已提出结合后蛋白质 NCN 的稳定性可显着增强结合亲和力（我们将通过调节 NCN 在宿主中的稳定性并通过实验和计算表征其结构和对客体的反应来检验这一假设。 NCN 在蛋白质驱动中利用潜在自由能的机制，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。