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.     

纳米材料-蛋白质界面相互作用的分子机制

纳米材料由于其优异的性能在化工、电子、机械、环境、能源、航天等各个领域已经得到了广泛的应用,并且在生物医学方面的应用越来越受到重视。纳米材料-蛋白质界面相互作用是纳米生物医学领域重要的科学问题,对于纳米材料的生物医学应用以及生物安全性评价至关重要。蛋白质分子与纳米材料在界面的相互作用,一方面可以诱导蛋白质的构象、组装结构甚至功能的改变,另一方面可以引起纳米材料的表面亲疏水性、电荷性质等表面物理化学性质的改变。基于蛋白质与纳米材料相互作用检测技术及结果,本文从分子水平阐述了纳米材料与蛋白质分子在界面之间的相互作用机理及相应的结构与性质的变化,从而可以深化对两者之间复杂的相互作用机制的理解,对于推进纳米材料在生物医学的应用及健康、安全、持续发展具有重要意义。     

分析蛋白质-蛋白质相互作用界面的新方法

疏水性和氢键是蛋白质-蛋白质相互作用中的主要因素.提出一种新的计算方法，从蛋白受体的结合部位推导出蛋白配体相应部位应该具有的疏水性质和氢键性质.应用这种方法可以很容易地找出影响相互作用的关键残基，并且将界面的这两种特征用图形软件显示出来.在应用到实际蛋白-蛋白相互作用中时，发现它的用途并不限于此.它可以作为研究蛋白相互作用的一个基本工具.     

表面等离子体共振技术在蛋白质-蛋白质相互作用研究中的应用

表面等离子共振(SPR)近年来迅速发展为用于分析生物分子相互作用的一项技术.该技术无需标记、特异性强、灵敏度高、样品用量小,可实现在线连续实时检测.目前SPR已被广泛应用于免疫学、蛋白质组学、药物筛选、细胞信号转导、受体/配体垂钓等领域.该文阐述了基于表面等离子体共振技术生物传感器的基本原理和技术流程,综述了SPR在蛋白质-蛋白质相互作用动力学研究、蛋白质结构及功能研究、蛋白质突变和碎片分析、信号转导中的应用以及SPR在蛋白质-蛋白质相互作用研究中的多项关键技术.指出SPR通过与光谱、电化学等多技术联用后,可以获得更加详实的信息.     

蛋白质相互作用预测、设计与调控

蛋白质相互作用是生命活动在分子水平上的基本事件. 蛋白质相互作用的三维图像可以给出关键生命活动过程的分子细节. 了解蛋白质相互作用的原理有助于揭示生命活动的机制, 并在此基础上开展有重要价值的蛋白质设计. 本文对于蛋白质相互作用预测、设计和调控研究的近期进展进行了总结归纳, 介绍了作者实验室在相关领域的研究进展, 并对今后的研究方向进行了展望. 主要包括: (1) 蛋白质相互作用网络、蛋白质相互作用机制和蛋白质复合物结构计算分析; (2) 基于序列、结合位点以及复合物结构的蛋白质相互作用预测; (3)蛋白质相互作用设计方法; (4) 利用化学分子调控蛋白质相互作用的方法; (5) 针对蛋白质相互作用的蛋白质药物设计方法.     

蛋白质相互作用的研究方法

生物体的生理功能主要由细胞中的蛋白质控制和调节。其中,多数蛋白质是通过与配体结合或是作为蛋白质复合物中的一部分参与细胞的代谢过程。因此,研究蛋白质间的相互作用是理解生命活动的基础。本文对现有蛋白质相互作用的研究方法和技术进行了评述。     

基于液质联用技术的蛋白质-蛋白质相互作用研究进展※

蛋白质-蛋白质相互作用调控着细胞内众多生物过程, 蛋白质间相互作用网络的绘制对解析复杂的生物过程至关重要. 面对生物体中复杂的蛋白质-蛋白质相互作用, 液质联用技术不仅具有灵敏度高的鉴定优势, 还可以对数以千计的蛋白质进行定量分析. 因此, 对目标蛋白质进行富集、标记或共分级的处理后, 结合液质联用技术对蛋白质准确而灵敏的鉴定, 这类技术已被广泛应用于复杂样本中蛋白质-蛋白质相互作用网络的解析. 目前基于液质联用技术的几种常用的方式, 包括亲和纯化质谱方法(AP-MS)、近程标记质谱方法(PDB-MS)、化学交联质谱方法(XL-MS)和共分级偶联质谱方法(CF-MS)等. 本综述讨论了这些方法的基本原理、优点和在细胞内解析蛋白质间相互作用的应用.     

糖-蛋白质特异性识别在生物材料领域的应用

糖类不仅是组成生命体的基本物质之一,还是很多生理和病理过程中分子识别和细胞间相互作用的基础。糖的生物学功能可通过与蛋白质的相互作用来实现。这种可逆的特异性识别在信号传导、细胞粘附、增殖、分化、病菌感染和免疫应答等生命过程中具有重要意义。本文着重介绍了糖-蛋白质相互作用的种类和机理,综述了糖-蛋白质特异性识别作用在生物材料领域的应用进展,包括将糖类作为靶向分子修饰到纳米粒子或载体分子表面进行药物传递和基因转染,利用糖-蛋白质非共价作用力进行分子组装,以及制备糖基化表面用于调控蛋白粘附和细胞行为。由于糖类特殊的生物学性能和种类的多样性,基于糖-蛋白质特异性识别有望用于制备更加实用和智能的生物材料。     

免疫系统蛋白质相互作用的研究方法

对于相互作用蛋白的研究,有助于了解蛋白在细胞内如何发挥其生理功能.在人类基因组计划草图公布以后,基于蛋白质组学的蛋白谱研究逐渐得到重视,在此背景下,蛋白质相互作用的研究也逐步受到关注.对于蛋白质组学研究范围内所有蛋白质的相互作用的研究,被称作"相互作用组"[1].     

纳米颗粒与蛋白质分子的相互作用

纳米技术的快速发展和广泛应用前景,引起了人们对纳米生物效应和安全性问题的普遍关注。为保证纳米技术的健康持续发展,纳米颗粒与生物体的相互作用以及产生的生物学效应不容忽视。为充分了解纳米颗粒物产生的生物学效应,阐明纳米颗粒如何进入生物体以及与生物体相互作用的分子过程至关重要。在总结国内外相关研究的基础上,本文介绍了纳米颗粒进入机体的主要途径,并系统综述了纳米颗粒与蛋白质分子的相互作用及其表征方法,以及纳米颗粒与蛋白质相互作用对蛋白质结构功能和纳米颗粒生物效应的影响。     

Emerging Supramolecular Therapeutic Carriers Based on Host–Guest Interactions

Recent advances in host–guest chemistry have significantly influenced the construction of supramolecular soft biomaterials. The highly selective and non‐covalent interactions provide vast possibilities of manipulating supramolecular self‐assemblies at the molecular level, allowing a rational design to control the sizes and morphologies of the resultant objects as carrier vehicles in a delivery system. In this Focus Review, the most recent developments of supramolecular self‐assemblies through host–guest inclusion, including nanoparticles, micelles, vesicles, hydrogels, and various stimuli‐responsive morphology transition materials are presented. These sophisticated materials with diverse functions, oriented towards therapeutic agent delivery, are further summarized into several active domains in the areas of drug delivery, gene delivery, co‐delivery and site‐specific targeting deliveries. Finally, the possible strategies for future design of multifunctional delivery carriers by combining host–guest chemistry with biological interface science are proposed.     

Argentophilic Interactions

The decade 1990–2000 saw a growing interest in aurophilic interactions in gold chemistry. These interactions were found to influence significantly a variety of structural and other physical characteristics of gold(I) compounds. The attention paid to this unusual and counterintuitive type of intra‐ and intermolecular bonding between seemingly closed‐shell metal centers has rapidly been extended to also include silver chemistry. Hundreds of experimental and computational studies have since been dedicated to the argentophilicity phenomenon. The results of this development are reviewed herein focusing on molecular systems where two or more silver(I) centers are in close contact leading to specific structural characteristics and a variety of novel physical properties. These include strongly modified ligand‐to‐metal charge‐transfer processes observed in absorption and emission spectroscopy, but also colossal positive and negative thermal expansion on the one hand and unprecedented negative linear compressibility of crystal parameters on the other.     

壳聚糖基生物医用材料及其应用研究进展

壳聚糖是一种极具发展潜力的天然生物材料,其在生物医学领域的研究和应用越来越受到重视。阐述了壳聚糖及其衍生物作为生物医用材料的特性,介绍了壳聚糖基生物医用材料的应用现状和发展趋势。     

Analysis of renal stones by FTIR spectroscopy

A study of the chemical composition of renal stones is important for understanding their etiology. And the therapy for the stone disease is usually based on the analysis of calculi, permitting a porper management of the disease and the prevention of its recurrence. FTIR spectroscopy has been used for urinary stones analysis. The routine, easy and rapid measurements give unambiguous information about the stone composition. Especially a precise wavelength scale of the Fourier method is helpful here. A relatively good spatial resolution is important as very often the stones are composed of core and various layers of different chemical composition. A quantitative determination of the proportion of various materials in calculi is also possible.     

Graphene‐polymer nanocomposites for biomedical applications

Despite the significant efforts in the synthesis of new polymers, the mechanical properties of polymer matrices can be considered modest in most cases, which limits their application in demanding areas. The isolation of graphene and evaluation of its outstanding properties, such as high thermal conductivity, superior mechanical properties, and high electronic transport, have attracted academic and industrial interest, and opened good perspectives for the integration of graphene as a filler in polymer matrices to form advanced multifunctional composites. Graphene‐based nanomaterials have prompted the development of flexible nanocomposites for emerging applications that require superior mechanical, thermal, electrical, optical, and chemical performance. These multifunctional nanocomposites may be tailored to synergistically combine the characteristics of both components if proper structural and interfacial organization is achieved. The investigations carried out in this aim have combined graphene with different polymers, leading to a variety of graphene‐based nanocomposites. The extensive research on graphene and its functionalization, as well as polymer graphene composites, aiming at applications in the biomedical field, are reviewed in this paper. An overview of the polymer matrices adequate for the biomedical area and the production techniques of graphene composites is presented. Finally, the applications of such nanocomposites in the biomedical field, particularly in drug delivery, wound healing, and biosensing, are discussed.     

Segmented polyurethanes derived from novel siloxane–carbonate soft segments for biomedical applications

A novel macrodiol based on mixed silicone and carbonate chemistries was synthesized and used as a soft segment precursor in the synthesis of two series of segmented polyurethane (PU) copolymers varying in hard segment content and soft segment molecular weight. The hard segments in these copolymers were derived from 4,4‐methylene diphenyl diisocyanate and 1,4‐butane diol. The phase transitions, microphase separation behavior, and mechanical properties of the copolymers were investigated using a variety of experimental methods. When compared with segmented PU copolymers having predominately poly(dimethyl siloxane) soft segments, these siloxane–carbonate soft segment copolymers exhibit enhanced intersegment mixing, and consequently relatively low mechanical modulus. With relatively low modulus and siloxane units in the soft phase, the siloxane–carbonate PUs have potential for use in cardiac and orthopedic biomedical applications. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011     

Midkine Interaction with Chondroitin Sulfate Model Synthetic Tetrasaccharides and Their Mimetics: The Role of Aromatic Interactions

Midkine (MK) is a neurotrophic factor that participates in the embryonic central nervous system (CNS) development and neural stem cell regulation, interacting with sulfated glycosaminoglycans (GAGs). Chondroitin sulfate (CS) is the natural ligand in the CNS. In this work, we describe the interactions between a library of synthetic models of CS-types and mimics. We did a structural study of this library by NMR and MD (Molecular Dynamics), concluding that the basic shape is controlled by similar geometry of the glycosidic linkages. Their 3D structures are a helix with four residues per turn, almost linear. We have studied the tetrasaccharide-midkine complexes by ligand observed NMR techniques and concluded that the shape of the ligands does not change upon binding. The ligand orientation into the complex is very variable. It is placed inside the central cavity of MK formed by the two structured beta-sheets domains linked by an intrinsically disordered region (IDR). Docking analysis confirmed the participation of aromatics residues from MK completed with electrostatic interactions. Finally, we test the biological activity by increasing the MK expression using CS tetrasaccharides and their capacity in enhancing the growth stimulation effect of MK in NIH3T3 cells.     

Binding of Glycans to the SARS CoV-2 Spike Protein,an Open Question: NMR Data on Binding Site Localization,Affinity, and Selectivity

We have used NMR experiments to explore the binding of selected glycans and glycomimetics to the SARS CoV-2 spike glycoprotein (S-protein) and to its receptor binding domain (RBD). STD NMR experiments confirm the binding of sialoglycans to the S-protein of the prototypic Wuhan strain virus and yield dissociation constants in the millimolar range. The absence of STD effects for sialoglycans in the presence of the Omicron/BA.1 S-protein reflects a loss of binding as a result of S-protein evolution. Likewise, no STD effects are observed for the deletion mutant Δ143–145 of the Wuhan S-protein, thus supporting localization of the binding site in the N-terminal domain (NTD). The glycomimetics Oseltamivir and Zanamivir bind weakly to the S-protein of both virus strains. Binding of blood group antigens to the Wuhan S-protein cannot be confirmed by STD NMR. Using ¹H,¹⁵N TROSY HSQC-based chemical shift perturbation (CSP) experiments, we excluded binding of any of the ligands studied to the RBD of the Wuhan S-protein. Our results put reported data on glycan binding into perspective and shed new light on the potential role of glycan-binding to the S-protein.     

The Application of Micro‐ and Nanomotors in Classified Drug Delivery

Micro and nanomotors (MNMs) are micro/nanoscale devices that are able to convert chemical or external energy into mechanical motion. Based on a multitude of propulsion mechanisms, synthetic MNMs have been developed over the past decades for diverse biomedical applications, particularly drug delivery. Herein, we set out the classification of drugs delivered by MNMs, such as small molecules, nucleic acid, peptides, antibodies, and other proteins, and discuss their current limitations and possibilities in in vivo applications. Challenges and future perspectives are also discussed. With the increasing research enthusiasm in this field and the strengthening of multidisciplinary cooperation, intelligent MNMs will appear in the near future, which will have a profound impact on all related fields.