Structural Aspects and Prediction of Calmodulin-Binding Proteins

Calmodulin (CaM) is an important intracellular protein that binds Ca²⁺ and functions as a critical second messenger involved in numerous biological activities through extensive interactions with proteins and peptides. CaM’s ability to adapt to binding targets with different structures is related to the flexible central helix separating the N- and C-terminal lobes, which allows for conformational changes between extended and collapsed forms of the protein. CaM-binding targets are most often identified using prediction algorithms that utilize sequence and structural data to predict regions of peptides and proteins that can interact with CaM. In this review, we provide an overview of different CaM-binding proteins, the motifs through which they interact with CaM, and shared properties that make them good binding partners for CaM. Additionally, we discuss the historical and current methods for predicting CaM binding, and the similarities and differences between these methods and their relative success at prediction. As new CaM-binding proteins are identified and classified, we will gain a broader understanding of the biological processes regulated through changes in Ca²⁺ concentration through interactions with CaM.     

Lysin Motif (LysM) Proteins: Interlinking Manipulation of Plant Immunity and Fungi

The proteins with lysin motif (LysM) are carbohydrate-binding protein modules that play a critical role in the host-pathogen interactions. The plant LysM proteins mostly function as pattern recognition receptors (PRRs) that sense chitin to induce the plant’s immunity. In contrast, fungal LysM blocks chitin sensing or signaling to inhibit chitin-induced host immunity. In this review, we provide historical perspectives on plant and fungal LysMs to demonstrate how these proteins are involved in the regulation of plant’s immune response by microbes. Plants employ LysM proteins to recognize fungal chitins that are then degraded by plant chitinases to induce immunity. In contrast, fungal pathogens recruit LysM proteins to protect their cell wall from hydrolysis by plant chitinase to prevent activation of chitin-induced immunity. Uncovering this coevolutionary arms race in which LysM plays a pivotal role in manipulating facilitates a greater understanding of the mechanisms governing plant-fungus interactions.     

Structural Analysis of the Complex between Penta-EF-Hand ALG-2 Protein and Sec31A Peptide Reveals a Novel Target Recognition Mechanism of ALG-2

ALG-2, a 22-kDa penta-EF-hand protein, is involved in cell death, signal transduction, membrane trafficking, etc., by interacting with various proteins in mammalian cells in a Ca²⁺-dependent manner. Most known ALG-2-interacting proteins contain proline-rich regions in which either PPYPXnYP (type 1 motif) or PXPGF (type 2 motif) is commonly found. Previous X-ray crystal structural analysis of the complex between ALG-2 and an ALIX peptide revealed that the peptide binds to the two hydrophobic pockets. In the present study, we resolved the crystal structure of the complex between ALG-2 and a peptide of Sec31A (outer shell component of coat complex II, COPII; containing the type 2 motif) and found that the peptide binds to the third hydrophobic pocket (Pocket 3). While amino acid substitution of Phe⁸⁵, a Pocket 3 residue, with Ala abrogated the interaction with Sec31A, it did not affect the interaction with ALIX. On the other hand, amino acid substitution of Tyr¹⁸⁰, a Pocket 1 residue, with Ala caused loss of binding to ALIX, but maintained binding to Sec31A. We conclude that ALG-2 recognizes two types of motifs at different hydrophobic surfaces. Furthermore, based on the results of serial mutational analysis of the ALG-2-binding sites in Sec31A, the type 2 motif was newly defined.     

A highly luminescent organic crystal with the well-balanced charge transport property: The role of cyano-substitution in the terminal phenyl unit of distyrylbenzene

1,4-bis(2-cyano styryl)benzene (2-CSB) crystal with cyano substituent groups introduced to the terminal phenyl rings of distyrylbenzene (DSB) has been prepared and its luminescence efficiency could be as high as ∼55%. Based on the analyses of cyclic voltammetry and crystal structure, cyano substituents not only lower the LUMO level but also result in a change of the packing mode from the herringbone arrangement to the face-to-face slipped π stacking motif. Then field-effect transistors (FETs) based on high-quality 2-CSB crystals grown by the physical vapor transport method have been fabricated and the highest hole and electron mobilities were measured as 0.66 and 0.29 cm²/Vs, which enhanced the corresponding values of DSB crystal by up to one and two orders of magnitude, respectively. 2-CSB crystal simultaneously combined the high luminescence and the well-balanced mobility is expected to be of interest for the fundamental research of organic light-emitting devices.     

基于超网络理论的军事通信网络复杂性度量方法

针对军事通信网络的结构和功能特点,在建立军事通信超网络描述模型的基础上,定义了超网络邻接矩阵、节点分类连接矩阵、类型匹配指数、超网络模体、模体核和模体熵等概念;通过分析超网络模体的特点,提出使用超网络模体熵来度量网络复杂性,给出了具体的计算方法;最后以某舰艇编队通信网络为例,对比分析了已有网络结构复杂性指标和超网络模体熵所度量的网络特征,说明在网络结构确定的情况下,超网络模体熵可以度量网络的功能复杂性.     

RON蛋白与CXC趋化因子受体4蛋白的表达与去势抵抗型前列腺癌患者阿比特龙耐药的相关性

目的：研究受体酪氨酸激酶（RON）蛋白与CXC趋化因子受体4（CXCR4）蛋白的表达与去势抵抗型前列腺癌（CRPC）患者阿比特龙耐药的相关性。方法：选取2017年1月至2020年2月我院收治的127例接受阿比特龙治疗的CRPC患者,根据是否耐药分为观察组（n=32,阿比特龙耐药患者）、对照组（n=95,缓解患者）。采用免疫组化与蛋白免疫印迹检测比较两组RON、CXCR4蛋白表达,采用Logistic回归分析进行RON、CXCR4蛋白与耐药的单因素、多因素分析,采用受试者工作特征曲线（ROC）及ROC下面积（AUC）分析RON、CXCR4蛋白预测耐药的价值,并在阿比特龙耐药细胞株中加入RON、CXCR4抑制剂,观察两者对阿比特龙耐药细胞凋亡指标［半胱氨酸蛋白酶（caspase）-3、caspase-9、细胞凋亡率］的影响。结果：免疫组化显示,观察组RON阳性表达率（71.88%,23/32）较对照组（27.37%,26/95）高;观察组CXCR4阳性表达率（65.63%,21/32）较对照组（12.63%,12/95）高;蛋白免疫印迹检测显示,观察组RON、CXCR4蛋白较对照组高（P<0.05）;RON、CXCR4蛋白与耐药均呈正相关（P<0.05）;加入RON、CXCR4抑制剂后,RON、CXCR4表达被成功抑制,且caspase-3、caspase-9、细胞凋亡率均高于阿比特龙耐药细胞株（P<0.05）;Transwell实验检测细胞迁移及侵袭显示,抑制RON、CXCR4表达,细胞迁移及侵袭细胞数目均显著降低（P<0.05）;RON蛋白预测阿比特龙耐药的AUC为0.789,截断值＞4.11,敏感度为84.37%,特异度为61.05%（P<0.05）;CXCR4蛋白预测阿比特龙耐药的AUC为0.825,截断值＞3.42,敏感度为75.00%,特异度为80.00%（P<0.05）;RON+CXCR4蛋白预测阿比特龙耐药的AUC为0.884（95%CI：0.815～0.934）,敏感度为87.50%,特异度为83.16%（P<0.05）。 结论：CRPC患者RON、CXCR4蛋白表达显著增加,与患者阿比特龙耐药密切相关,有望成为预测耐药的标志物,抑制RON、CXCR4蛋白表达,可促进CRPC阿比特龙耐药细胞的凋亡。     

Identification of peptide-mediated interactions between human PTTG and SH3 domains in pALL gene expression profile

Human pituitary tumor-transforming gene (PTTG) plays an essential role in the development and progression of pediatric acute lymphoblastic leukemia (pALL). PTTG has two SH3-binding peptide motifs that can be recognized by a variety of SH3-containing proteins in the pALL through peptide-mediated interactions. In this study, the gene expression profile of pALL was examined in detail by integrating computational modeling and experimental assay, aiming to identify those potential partner proteins of human PTTG. The binding potency of domain candidates to peptide motifs was ranked using knowledge-based scoring and fluorescence titration. A number of SH3 domains found in a variety of pALL proteins were identified as potent binders with moderate or high affinity for PTTG. It is revealed that the PTTG peptide motifs show different affinity profiles for various candidate proteins, indicating that the PTTG selectivity is optimized across pALL gene expression space. The PTTG peptides were then mutated rationally to target the SH3 domains of identified partner proteins by competing with the native peptide motifs.     

Optimizing the Kinetics and Thermodynamics of DNA i‐Motif Folding

Under slightly acidic conditions, single cytidine‐rich DNA strands can form four‐stranded structures called i‐motifs. The stability of the i‐motif structure is based on the intercalation of hemiprotonated C–C⁺ base pairs. In addition, the stability of these structures is influenced by pH, temperature, salt concentration, number of cytidines per C‐rich stretch, and length of sequence; it also depends on the nucleotides in the connecting loop regions. Here, we investigated the influence of the loop nucleotides on i‐motif stability, structure, and kinetics of folding, in five structures with the same loop‐size but different adenosine and thymidine residues within the loop. The stabilities of the i‐motif structures were determined by CD melting, and structure and kinetics of folding were studied by static and time‐resolved NMR experiments.     

Fluorescent Probes for G‐Quadruplex Structures

Mounting evidence supports the presence of biologically relevant G‐quadruplexes in single‐cell organisms, but the existence of endogenous G‐quadruplex structures in mammalian cells remains highly controversial. This is due, in part, to the common misconception that DNA and RNA molecules are passive information carriers with relatively little structural or functional complexity. For those working in the field, however, the lack of available tools for characterizing DNA structures in vivo remains a major limitation to addressing fundamental questions about structure–function relationships of nucleic acids. In this review, we present progress towards the direct detection of G‐quadruplex structures by using small molecules and modified oligonucleotides as fluorescent probes. While most development has focused on cell‐permeable probes that selectively bind to G‐quadruplex structures with high affinity, these same probes can induce G‐quadruplex folding, thereby making the native conformation of the DNA or RNA molecule (i.e., in the absence of probe) uncertain. For this reason, modified oligonucleotides and fluorescent base analogues that serve as “internal” fluorescent probes are presented as an orthogonal means for detecting conformational changes, without necessarily perturbing the equilibria between G‐quadruplex, single‐stranded, and duplex DNA. The major challenges and motivation for the development of fluorescent probes for G‐quadruplex structures are presented, along with a summary of the key photophysical, biophysical, and biological properties of reported examples.