蛋白质-蛋白质相互作用界面统计分析

以作者开发的从蛋白质结合部位推导出其界面所具有的疏水性质和氢键性质的计算程序PP_SITE为基础,利用蛋白质结构数据库(PDB),对蛋白质-蛋白质相互作用界面进行了统计分析.从PDB中挑出非冗余的链间相互作用对,计算出这个数据集中所有链间界面的疏水和氢键相互作用特征.对得到的界面特征进行统计分析,寻找能够明显聚类的界面特征.结果表明，界面大小、氢键和疏水相互作用在界面所占比例以及疏水相互作用的集中程度可以作为分类的依据.     

Exploring bioanalytical applications of assisted protein reassembly

Reassembly of protein from its peptide fragments is a technique that can have many applications in the bioanalytical field. Typically, a reporter protein fragmented into its two peptides is employed as a label in this study. This fragments of peptide can reassemble yielding an active functional reporter. This reassembly of the protein can be assisted by non-covalently interacting peptides or proteins, which are attached to the fragmented reporter. This technique has been employed in several applications including study of protein–protein interactions, antibody screening, immunoassays, and high-throughput screening. This review focuses on different reporters employed in the study of reassembly of proteins and applications of this strategy in bioanalysis.     

Structure-based virtual screening of influenza virus RNA polymerase inhibitors from natural compounds: Molecular dynamics simulation and MM-GBSA calculation

The resistances of matrix protein 2 (M2) protein inhibitors and neuraminidase inhibitors for influenza virus have attracted much attention and there is an urgent need for new drug. The antiviral drugs that selectively act on RNA polymerase are less prone to resistance and possess fewer side effects on the patient. Therefore, there is increased interest in screening compounds that can inhibit influenza virus RNA polymerase. Three natural compounds were found by using molecular docking-based virtual screening, which could bind tightly within the polymerase acidic protein-polymerase basic protein 1 (PA-PB1) subunit of influenza virus polymerase. Firstly, their drug likeness properties were evaluated, which showed that the hepatotoxicity values of all the three compounds indicating they had less or no hepatotoxicity, and did not have the plasma protein biding (PPB) ability, the three compounds needed to be modified in some aspects, like bulky molecular size. The stability of the complexes of PA-hits was validated through molecular dynamics (MD) simulation, revealing compound 2 could form more stable complex with PA subunit. The torsional conformations of each rotatable bond of the ligands in PA subunit were also monitored, to investigate variation in the ligand properties during the simulation, compound 3 had fewer rotatable bonds, indicating that the molecule had stronger rigidity. The bar charts of protein–ligand contacts and contacts over the course of trajectory showed that four key residues (Glu623, Lys643, Asn703 and Trp706) of PA subunit that participated in hydrogen-bond, water bridge and hydrophobic interactions with the hit compounds. Finally, the binding free energy and contributed energies were calculated by using MM-GBSA method. Out of the three compounds, compound 1 showed the lowest total binding free energy. Among all the interactions, the contribution of the covalent binding and the van der Waals energy were more than other items, compound 1 formed more stable hydrogen bonds with the residues of PA subunit binding pocket. This study smoothed the path for the development of novel lead compounds with improved binding properties, high drug likeness, and low toxicity to humans for the treatment of influenza, which provided a good basis for further research on novel and effective influenza virus PA-PB1 interaction inhibitors.     

In silico structure-based design of enhanced peptide inhibitors targeting RNA polymerase PAN-PB1C interaction

Developing antivirals for influenza A virus (FluA) has become more challenging due to high range of antigenic mutation and increasing numbers of drug-resistant viruses. Finding a selective inhibitor to target highly conserved region of protein-protein interactions interface, thereby increasing its efficiency against drug resistant virus could be highly beneficial. In this study, we used in silico approach to derive FluAPep1 from highly conserved region, PA_N-PB1_C interface and generated 121 FluAPep1 analogues. Interestingly, we found that the FluAPep1 interaction region in the PA_N domain are highly conserved in many FluA subtypes. Especially, FluAPep1 targets two pandemic FluA strains, H1N1/avian/2009 and H3N2/Victoria/1975. All of these FluA subtypes PA_N domain (H1N1/H3N2CAN/H3N2VIC/H7N1/H7N2) were superimposed with PA_N domain from H17N10 and the calculated root mean standards deviations were less than 3 Å. FlexPepDock analysis revealed that FluAPep1 exhibited higher binding affinity (score -246.155) with the PA_N domain. In addition, around 86% of non-hot spot mutated peptides (FluAPep28-122) showed enhanced binding affinity with PA_N domain. ToxinPred analysis confirmed that designed peptides were non-toxic. Thus, FluAPep1 and its analogues has potential to be further developed into an antiviral treatment against FluA infection.     

Biomarkers for ischemic stroke subtypes: A protein-protein interaction analysis

According to the Trial of Org 10172 in Acute Stroke Treatment, ischemic stroke is classified into five subtypes. However, the predictive biomarkers of ischemic stroke subtypes are still largely unknown. The utmost objective of this study is to map, construct and analyze protein-protein interaction (PPI) networks for all subtypes of ischemic stroke, and to suggest the predominant biological pathways for each subtypes. Through 6285 protein data retrieved from PolySearch2 and STRING database, the first PPI networks for all subtypes of ischemic stroke were constructed. Notably, F2 and PLG were identified as the critical proteins for large artery atherosclerosis (LAA), lacunar, cardioembolic, stroke of other determined etiology (SOE) and stroke of undetermined etiology (SUE). Gene ontology and DAVID analysis revealed that GO:0030193 regulation of blood coagulation and GO:0051917 regulation of fibrinolysis were the important functional clusters for all the subtypes. In addition, inflammatory pathway was the key etiology for LAA and lacunar, while FOS and JAK2/STAT3 signaling pathways might contribute to cardioembolic stroke. Due to many risk factors associated with SOE and SUE, the precise etiology for these two subtypes remained to be concluded.     

Macrocyclic peptides as regulators of protein-protein interactions

Protein-protein interactions are attractive but challenging targets for drug discovery. Recent technological progress and examples using macrocyclic peptides as protein interaction modulators are reviewed.     

利用内禀荧光探针研究蛋白相互作用中硫氧还蛋白的氧化还原态

细胞内蛋白质的氧化还原状态直接影响细胞的增殖、分化及凋亡,而氧化还原状态的改变对调控细胞的生存或死亡尤为重要。硫氧还蛋白(Thioredoxin, TRX)是一种广泛存在于生物体内的氧化还原调节蛋白,其在细胞内氧化还原状态的变化是发挥其氧化还原调控作用的重要过程。以TRX为对象并以其中的色氨酸残基(Trp)作为内禀荧光探针,利用蛋白质定点突变、SDS-聚丙烯酰胺凝胶电泳(SDS-PAGE)、荧光光谱和圆二色谱等技术和方法,研究TRX与谷胱甘肽过氧化物酶(glutathione peroxidase, GPX3)相互作用过程中氧化还原态的变化。通过观测TRX以及突变体中色氨酸荧光光谱的变化,研究蛋白相互作用的电子转移模式以及TRX氧化态-还原态之间的相互转化。结果表明氧化态的TRX与还原态的GPX3之间存在相互作用并发生电子交换,解释了二者之间电子传递模式为GPX3将电子传递给TRX,为揭示TRX在细胞信号传递过程中的物理化学机制提供了实验依据。     

Real-time observation of temperature-dependent protein-protein interactions using real-time dual-color detection system

This study examined the ability of a real-time dual-color detection system to allow direct observations of the kinetics of temperature-dependent protein-protein interaction at a single-molecule level. The primary target protein was an Alexa Fluor^® 488-labeled actin conjugate, which had been pre-incubated with an unlabeled rabbit anti-actin antibody (IgG). The complementary fluorescent protein was Alexa Fluor^® 633-labeled goat anti-rabbit IgG antibody, which interacts with the rabbit anti-actin antibody (IgG) bound to the Alexa Fluor^® 488-labeled actin conjugate. The individual protein molecules labeled with different fluorescent dyes in solution were effectively focused, interacted with the other protein molecules at 500 aM, and detected directly in real-time using the dual-wavelength (λ_ex = 488 and 635 nm) laser-induced fluorescence detection system. The kinetics of the protein-protein interactions were examined at different temperatures (12-32 °C). At concentrations in the aM range, the number of bound complex molecules through the protein-protein interaction decreased gradually with time at a given temperature, and increased with decreasing temperature at a set time. A high concentration (above 500 pM) of the protein sample caused aggregation and nonspecific binding of the protein molecules, even though the protein molecules were not an example of complementary binding. The results demonstrated that the real-time kinetics of a protein-protein interaction could be analyzed effectively at the single-molecule level without any time delay using the real-time dual-color detection system.     

蛋白质-蛋白质分子对接中打分函数研究进展

分子对接是研究分子间相互作用与识别的有效方法.其中,用于近天然构象挑选的打分函数的合理设计对于对接中复合物结构的成功预测至关重要.本文回顾了蛋白质-蛋白质分子对接组合打分函数中一些主要打分项,包括几何互补项、界面接触面积、范德华相互作用能、静电相互作用能以及统计成对偏好势等打分项的计算方法.结合本研究小组的工作,介绍了目前普遍使用的打分方案以及利用与结合位点有关的信息进行结构筛选的几种策略,比较并总结了常用打分函数的特点.最后,分析并指出了当前蛋白质-蛋白质对接打分函数所存在的主要问题,并对未来的工作进行了展望.     

Insight into the structures of Interleukin-18 systems

Structure-based molecular designs play a critical role in the context of next generation drug development. Besides their fundamental scientific aspects, the findings established in this approach have significant implications in the expansions of target-based therapies and vaccines. Interleukin-18 (IL-18), also known as interferon gamma (IFN-γ) inducing factor, is a pro-inflammatory cytokine. The IL-18 binds first to the IL-18α receptor and forms a lower affinity complex. Upon binding with IL-18β a hetero-trimeric complex with higher affinity is formed that initiates the signal transduction process. The present study, including structural and molecular dynamics simulations, takes a close look at the structural stabilities of IL-18 and IL-18 receptor-bound ligand structures as functions of time. The results help to identify the conformational changes of the ligand due to receptor binding, as well as the structural orders of the apo and holo IL-18 protein complexes.