Modifying the Thioester Linkage Affects the Structure of the Acyl Carrier Protein

At the center of many complex biosynthetic pathways, the acyl carrier protein (ACP) shuttles substrates to appropriate enzymatic partners to produce fatty acids and polyketides. Carrier proteins covalently tether their cargo via a thioester linkage to a phosphopantetheine cofactor. Due to the labile nature of this linkage, chemoenzymatic methods have been developed that involve replacement of the thioester with a more stable amide or ester bond. We explored the importance of the thioester bond to the structure of the carrier protein by using solution NMR spectroscopy and molecular dynamics simulations. Remarkably, the replacement of sulfur with other heteroatoms results in significant structural changes, thus suggesting more rigorous selections of isosteric substitutes is needed.     

Analytical Description of NMR Relaxation Highlights Correlated Dynamics in Intrinsically Disordered Proteins

The dynamic fluctuations of intrinsically disordered proteins (IDPs) define their function. Although experimental nuclear magnetic resonance (NMR) relaxation reveals the motional complexity of these highly flexible proteins, the absence of physical models describing IDP dynamics hinders their mechanistic interpretation. Combining molecular dynamics simulation and NMR, we introduce a framework in which distinct motions are attributed to local libration, backbone dihedral angle dynamics and longer‐range tumbling of one or more peptide planes. This model provides unique insight into segmental organization of dynamics in IDPs and allows us to investigate the presence and extent of the correlated motions that are essential for function.     

Revealing Conformational Variants of Solution‐Phase Intrinsically Disordered Tau Protein at the Single‐Molecule Level

Intrinsically disordered proteins, such as tau protein, adopt a variety of conformations in solution, complicating solution‐phase structural studies. We employed an anti‐Brownian electrokinetic (ABEL) trap to prolong measurements of single tau proteins in solution. Once trapped, we recorded the fluorescence anisotropy to investigate the diversity of conformations sampled by the single molecules. A distribution of anisotropy values obtained from trapped tau protein is conspicuously bimodal while those obtained by trapping a globular protein or individual fluorophores are not. Time‐resolved fluorescence anisotropy measurements were used to provide an explanation of the bimodal distribution as originating from a shift in the compaction of the two different families of conformations.     

Cation Translocation around Single Polyoxometalate–Organic Hybrid Cluster Regulated by Electrostatic and Cation–π Interactions

We report herein an interesting dynamic translocation process of countercations around one polyoxometalate(POM)–organic hybrid anionic cluster at various concentrations and temperatures. It was found that both electrostatic interactions and cation–π interactions regulate the position of small countercations around single clusters. The dynamic geometry and the symmetry of the hybrid macroions are largely affected by the type of counterions, as shown by nuclear magnetic resonance (NMR) spectroscopy studies and all‐atom molecular dynamics simulation. It is also shown that electrostatic interactions dominate over cation–π interactions in determining the locations of the counterions in the current system.     

无序蛋白质在生物分子凝聚相形成与调控中的作用

生物分子凝聚形成生物体内的多种无膜细胞器,其独特的物理化学性质使其具有多样的生物学功能,包括感知外界环境的变化、调节蛋白在细胞内的浓度、调控信号转导途径以及选择性富集特定蛋白质和RNA等。同时,生物分子凝聚相的错误形成与调控会导致多种人类疾病,如神经退行性疾病、癌症和病毒性疾病等。无序蛋白质在生物分子凝聚相的形成和调控中发挥了重要作用。本文通过总结分析无序蛋白在生物分子凝聚相形成中的作用以及化学小分子对生物分子凝聚相的调控,探讨了通过靶向无序蛋白进行配体设计来获得调控生物分子凝聚相化学探针及药物的可能性,并展望了揭示无序蛋白及化学分子调控生物凝聚相机制应重点关注的问题。     

Differences between G‐Protein‐Stabilized Agonist–GPCR Complexes and their Nanobody‐Stabilized Equivalents

Protein nanobodies have been used successfully as surrogates for unstable G‐proteins in order to crystallize G‐protein‐coupled receptors (GPCRs) in their active states. We used molecular dynamics (MD) simulations, including metadynamics enhanced sampling, to investigate the similarities and differences between GPCR–agonist ternary complexes with the α‐subunits of the appropriate G‐proteins and those with the protein nanobodies (intracellular binding partners, IBPs) used for crystallization. In two of the three receptors considered, the agonist‐binding mode differs significantly between the two alternative ternary complexes. The ternary‐complex model of GPCR activation entails enhancement of ligand binding by bound IBPs: Our results show that IBP‐specific changes can alter the agonist binding modes and thus also the criteria for designing GPCR agonists.     

天然无序蛋白质:序列-结构-功能的新关系

天然无序蛋白质是一类新发现的蛋白质,它们在天然条件下没有确定的三维结构,却具有正常的生物学功能,广泛参与信号传递、DNA转录、细胞分裂和蛋白质聚集等重要的生理与病理过程.无序蛋白质的发现是对传统的蛋白质"序列-结构-功能"范式的挑战.在这篇综述里,我们首先回顾了蛋白质的传统范式以及无序蛋白质的发现过程,然后介绍无序蛋白质在结构、序列、功能等方面的特征与相互作用,并以分子识别过程为例,进一步阐述目前国际上对无序蛋白质所具有优势的一些认识与观点.我们还分析了无序蛋白质研究在生命科学和医学等领域的应用前景,并介绍了国内在无序蛋白质领域的研究现状.