蛋白质-RNA相互作用界面预测与设计

蛋白质-RNA之间的相互作用是蛋白质在细胞里面行使功能的重要方式之一. 结构生物学家利用实验手段可以得到蛋白质-RNA复合物的三维结构, 通过原子水平的晶体结构来解释蛋白质与RNA的识别过程. 但实验取得蛋白质-RNA的复合物结构非常困难, 耗钱、耗时, 同时受限于其相互作用强度. 因而利用理论的方法对蛋白质-RNA相互作用界面进行预测与设计在生物医学研究中十分重要. 本文主要综述了近期蛋白质-RNA相互作用界面预测与设计方面的进展, 包括以下几个方面: (1) 蛋白质-RNA分子对接算法以及对接前后存在的构象变化的处理; (2) 蛋白质-RNA 识别机制的研究; (3) 基于蛋白质-RNA 相互作用界面的分子设计. 蛋白质-RNA分子对接算法逐步完善将有助于我们对大量未知功能的蛋白质与RNA进行功能注释, 而基于生物大分子相互作用界面的分子设计将在药物设计领域中有广阔的应用前景.     

无机纳米晶-生物界面作用的分子机制

无机纳米晶材料以其独特的光、电、磁、力学性质,成为疾病诊断与治疗功能的关键材料.本文总结了无机纳米晶的表面化学活性、离子释放性、晶相结构、晶格缺陷、表面吸附和表面修饰等与尺寸相关的理化性质与生物效应之间的关系.综述了无机纳米晶与蛋白质、磷脂生物膜间的界面相互作用,探讨了纳米晶-生物界面作用的分子机理.这有助于理解无机纳米晶的生物行为和毒理性质,指导设计安全、高效的纳米晶生物医学材料.     

正负离子表面活性剂复配系统*

正负离子表面活性剂复配系统,由于其带有相反电荷的离子头基间的强静电相互作用,具有强协同效应和高表面活性,在水溶液中可形成丰富的微观结构,表现出复杂的相行为。本文在相关研究的基础上,对于正负离子表面活性剂复配系统在表面（界面）性质,囊泡的制备及稳定性,虫状胶束的生成和性质,双水相系统的性质及其在萃取方面的应用,拟相分离模型、热力学胞腔模型、分子热力学模型及分子模拟等理论研究和作为模板合成纳米材料等方面的研究进展进行了综述。对于双水相系统的研究,指出了一些有待于进一步解决的问题。     

石墨烯材料与蛋白质的相互作用

石墨烯材料凭借其优异的物理化学性质在生物化学以及生物医学领域备受关注,展现出了广阔的应用前景。值得注意的是,石墨烯材料在应用于载药、医学检测与诊断及生物成像等诸多领域时,会不可避免地与生物体内的各种蛋白质分子产生相互作用,进而改变石墨烯材料自身的理化性质并影响蛋白质的构象及生物学功能。因此研究石墨烯材料与蛋白质分子之间的相互作用,对于理解和评估其生物学效应,开发新型生物化学技术,具有至关重要的意义。本文综述了近年来针对石墨烯材料与蛋白质分子相互作用开展的代表性的科学研究,分类介绍了石墨烯家族中的各种材料与蛋白质相互作用的分子机制与规律,并介绍了基于蛋白质分子与石墨烯材料相互作用开发的新型应用技术,最后对这一领域未来的热点研究方向进行了分析和展望。     

载体材料与蛋白质的相互作用及对其构象的影响

蛋白质与载体材料间存在着疏水性、静电等相互作用力。这些作用力不仅决定了蛋白质分子在载体表面吸附的数量,也导致吸附蛋白质分子构象发生变化,引起蛋白质活性的改变。蛋白质的特性(分子量和浓度等)、载体材料的表面结构(表面化学组成和物理结构等)及溶液性质(pH和离子强度等)对蛋白质与载体材料间的相互作用产生影响。利用各种先进的分析技术对载体材料表面的蛋白质分子构象进行表征是这一研究领域的热点。本文对这一方面的最新研究进展进行综述。     

双偏振干涉技术(DPI):生物分子相互作用研究的新工具

双偏振干涉(dual polarization interferometry,DPI)技术是近年来发展起来的一种免标记、实时、高灵敏和高分辨率的表面分析技术.它能够精确测量分子相互作用界面层的密度、厚度和质量的绝对值,可实时获取分子相互作用过程的动力学和结构信息.本文简单介绍了DPI的测量原理、仪器组成并对其与相关检测技术的对比进行了简要的概述;着重介绍了近10年来DPI技术在生物分子相互作用研究方面的应用进展,主要包括蛋白质之间以及与其他分子的相互作用,DNA与各种分子之间的相互作用,生物膜与其他分子的相互作用,蛋白质的吸脱附、聚集和结晶过程监测等;并对DPI技术未来的发展进行了展望.随着技术的不断发展,DPI将会在生物分析、纳米材料表征、能源相关表/界面研究等方面得到广泛应用.     

非对称纳米材料的性质及其应用

具有非对称结构的纳米材料显示出独特的物理和化学性质,在生物传感、靶向药物运载以及分子检测等生物医学领域具有良好的应用前景.本文就非对称纳米材料的性质及其应用方面的最新研究进展进行了综述.首先,我们从三个不同方面讨论了非对称纳米材料的性质及相关应用,即表面双亲性、催化特性和生物相容性;然后着重强调了非对称纳米材料在生物医学上的应用,如生物传感、靶向运载、基因疫苗以及杀菌剂;最后,我们对非对称纳米材料在制备技术的改进及其在食品安全领域的应用作出了展望.     

金属纳米材料表面配体聚集效应

金属纳米材料表面配体不仅可以稳定金属纳米颗粒,辅助合成特定尺寸和形貌的纳米材料,还可用于调控金属纳米颗粒的表面化学性质。由于现有表征技术的局限性,金属纳米材料表面有机配体的结构和功能一直以来并未被深入研究。得益于分子结构明确金属纳米团簇和其他模型纳米材料体系的发展,配体在金属纳米材料表面的精确配位结构及其对催化过程的促进作用正不断被揭示出来。金属表面有机分子配位不仅可以调控表面金属电子结构,还可以分割表面原子周期性结构。表面有机配体的聚集可以进一步在金属表面构筑3D空间结构,改变纳米材料亲疏水性,并影响催化底物和反应中间体与表面的相互作用强弱和吸附构型。此外,有机配体与表面金属所组成的界面还可以构筑新的活性位点,改变催化反应路径,从而提升催化反应活性和选择性。金属纳米材料表面有机配体的聚集效应使得异相纳米材料可以同时表现出均相催化和酶催化的优势。     

生物材料表界面与蛋白质及细胞的相互作用的研究进展

材料接触生物环境首先是通过其界面,这种材料界面与生物环境中的生物分子及细胞之间的相互作用决定着材料生物功能的实现。因此,调控材料与生物体的界面相互作用几乎是所有生物材料的研究及应用首先和必然面对的关键共性问题。本文综述了近年来我们课题组在生物表界面领域的研究及其最新进展。从分子层面上设计生物功能表面入手,建立了一系列普适、高效、简单易行的表面功能化新方法用于改变材料表面的物理化学性质,进而调控材料表面与蛋白质或细胞/细菌之间的相互作用。     

无机纳米-生物界面作用的SERS研究

探索生命体对无机纳米材料的生物应答机制是高效、安全、可控地应用无机纳米材料的基础,其关键在于准确理解在生物体系中无机纳米材料与生物分子间的纳米.生物界面作用.本文主要探讨了在纳米-生物界面具有拉曼增强效应的金、银纳米材料;介绍了表面增强拉曼光谱(surface-enhanced raman spectroscopy,SERS)原位研究金、银等无机纳米材料表/界面吸附的核酸、蛋白质、磷脂等生物分子,以及细胞、病毒和细菌等与金、银纳米材料表/界面作用的研究进展;综述了SERS技术在探索纳米-生物界面作用机制、生物分子测定、生物分子界面行为监测中的应用.     

结构蛋白质组学研究进展

蛋白质结构与其生物学功能直接相关，蛋白质功能的调控也主要依赖于其构象和相互作用的动态调节。对蛋白质结构和功能的研究一直是生命科学领域的研究热点，也是当前蛋白质组学研究的重要发展方向。该综述重点讨论了近年来基于质谱的结构蛋白质组学主要分析方法的原理、进展和应用，主要包括非变性质谱法、限制性蛋白质酶切法、化学交联法、氢氘交换法、共价化学标记法、热稳定性分析法等；最后对结构蛋白质组学的发展进行了总结与展望。     

Optical manipulation with nanoscale chiral fields and related photochemical phenomena

Chiral light-matter interaction occurs when the system consists of the matter and the light has a chiral structure, which is generically called the chiro-optical effect. Circular dichroism and optical rotation are representative spectroscopic methods based on chiro-optical effects. Chiro-optical effects have been widely utilized to detect chiral materials in the system. The chiro-optical effect also has the potential to create chiral materials from achiral materials and chiral optical fields, and to generate chiral optical fields from chiral matter systems. To achieve that, the design and observation of chiral optical field structures are essential. In this article, we describe local chiral optical fields generated in the peripheries of nanomaterials (typically metal nanostructures) irradiated with light. We summarize basic characteristics of nanoscale local chiral optical fields, methods to observe/control the chiral optical field structures at nanomaterials. Then some chemical, optical, and mechanical effects of designed chiral optical fields are described. Chiral nanostructures were created from achiral nanomaterials combined with circularly polarized light. Nucleation of chiral crystals of achiral molecules was achieved by circularly polarized light with the aid of plasmonic materials. Circularly polarized luminescence was observed from achiral fluorescent molecules conjugated with chiral plasmonic nanostructures. On mechanical characteristics, optical forces exerted on chiral materials were found to be dependent on the handedness of incident circularly polarized light, which can be utilized to discriminate the chirality of the material. The concept can be further generalized to the spin-dependent asymmetric light-matter interactions, which will create not only the molecular- and nano-scale chiral structures but also various novel functions of materials that are correlated with the handedness degree of freedom.     

Self-assembled Supramolecular Artificial Transmembrane Ion Channels: Recent Progress and Application

Natural protein channels have evolved with fantastic spatial structures, which play pivotal physiological functions in all living systems. Learning from nature, chemical scientists have developed a myriad of artificial transmembrane ion channels by using various chemical strategies, among which the non-covalent supramolecular ion channels exhibit remarkable advantages over other forms(e.g., single-molecule ion channel), which exhibited facile preparation methods, easier structural modification and functionalization. In this review, we have systematically summarized the recent progress of supramolecular self-assembled artificial transmembrane ion channels, which were classified by different self-assembly mechanisms, such as hydrogen bonds, π-π interactions, etc. Detailed preparation process and self-assembly strategies of the supramolecular ion channels have been described. Moreover, potential biomedical applications of the supramolecular ion channels have also been carefully discussed in this review. Finally, future opportunities and challenges facing this field were also elaborately discussed. It is anticipated that this review could provide a panoramic sketch and future directions towards the construction of novel artificial ion channels with novel functions and biomedical applications.     

Hypervalent nonbonded interactions of a divalent sulfur atom. Implications in protein architecture and the functions

In organic molecules a divalent sulfur atom sometimes adopts weak coordination to a proximate heteroatom (X). Such hypervalent nonbonded S···X interactions can control the molecular structure and chemical reactivity of organic molecules, as well as their assembly and packing in the solid state. In the last decade, similar hypervalent interactions have been demonstrated by statistical database analysis to be present in protein structures. In this review, weak interactions between a divalent sulfur atom and an oxygen or nitrogen atom in proteins are highlighted with several examples. S···O interactions in proteins showed obviously different structural features from those in organic molecules (i.e., π(o) → σ(s)* versus n(o) → σ(s)* directionality). The difference was ascribed to the HOMO of the amide group, which expands in the vertical direction (π(o)) rather than in the plane (n(o)). S···X interactions in four model proteins, phospholipase A? (PLA?), ribonuclease A (RNase A), insulin, and lysozyme, have also been analyzed. The results suggested that S···X interactions would be important factors that control not only the three-dimensional structure of proteins but also their functions to some extent. Thus, S···X interactions will be useful tools for protein engineering and the ligand design.     

Bioactive Structure of Membrane Lipids and Natural Products Elucidated by a Chemistry‐Based Approach

Determining the bioactive structure of membrane lipids is a new concept, which aims to examine the functions of lipids with respect to their three‐dimensional structures. As lipids are dynamic by nature, their “structure” does not refer solely to a static picture but also to the local and global motions of the lipid molecules. We consider that interactions with lipids, which are completely defined by their structures, are controlled by the chemical, functional, and conformational matching between lipids and between lipid and protein. In this review, we describe recent advances in understanding the bioactive structures of membrane lipids bound to proteins and related molecules, including some of our recent results. By examining recent works on lipid‐raft‐related molecules, lipid–protein interactions, and membrane‐active natural products, we discuss current perspectives on membrane structural biology.     

Localized surface plasmon resonance properties and biomedical applications of copper selenide nanomaterials

Nanomaterials with localized surface plasmon resonance (LSPR) locating in the near-infrared region have broad application prospects in the field of biomedicine. However, the biggest problem that limits the biomedical application of such nanomaterials lies in two aspects: First, the potential long-term in vivo toxicity caused by the metabolism of many nanomaterials with LSPR effect; Second, most of current nanomaterials with LSPR effect are difficult to achieve LSPR wavelength tunability in the near-infrared region to adapt to different biomedical applications. Copper selenide nanomaterials are composed of selenium and copper, which are necessary nutrient elements for human life. Because of the active and flexible chemical properties of selenium and copper, copper selenide nanomaterials can not only be effectively degraded and utilized in human body, but also be endowed with various physicochemical properties by chemical modification or doping. Recently, copper selenide nanomaterials have shown unique properties such as LSPR in the near-infrared region, making them attractive for near-infrared thermal ablation, photoacoustic imaging, disease marker detection, multimode imaging, and so on. Currently, to the best of our knowledge, there is no review on the LSPR properties of copper selenide nanomaterials and its biomedical applications. This review first discusses the relationship between the physicochemical properties and the LSPR of copper selenide nanomaterials and then summarizes the latest progress in the application of copper selenide nanomaterials in biological detection, diagnosis, and treatment of diseases. In addition, the advantages, and prospects of copper selenide nanomaterials in biomedicine are also highlighted.     

Electrochemical Sensors Using Two‐Dimensional Layered Nanomaterials

Two‐dimensional (2D) layered nanomaterials, e.g. graphene and molybdenum disulfide (MoS₂), have rapidly emerged in material sciences due to their unique physical, chemical and mechanical properties. In the meanwhile, there is a growing interest in constructing electrochemical sensors for a wide range of chemical and biological molecules by using these 2D nanomaterials. In this review, we summarize recent advances on using graphene and MoS₂ for the development of electrochemical sensors for small molecules, proteins, nucleic acids and cells detection. We also provide our perspectives in this rapidly developing field.     

Protein–Nanoparticle Interaction‐Induced Changes in Protein Structure and Aggregation

Large surface area, small size, strong optical properties, controllable structural features, variety of bioconjugation chemistries, and biocompatibility make many different types of nanoparticles (NPs), such as gold NPs, useful for many biological applications, such as biosensing, cellular imaging, disease diagnostics, drug delivery, and therapeutics. Recently, interactions between proteins and NPs have been extensively studied to understand, control, and utilize the interactions involved in biomedical applications of NPs and several biological processes, such as protein aggregation, for many diseases, including Alzheimer's disease. These studies also offer fundamental knowledge on changes in protein structure, protein aggregation mechanisms, and ways to unravel the roles and fates of NPs within the human body. This review focuses on recent studies on the roles and uses of NPs in protein structural changes and aggregation processes.     

Langmuir monolayers as models to study processes at membrane surfaces

The use of new sophisticated and highly surface sensitive techniques as synchrotron based X-ray scattering techniques and in-house infrared reflection absorption spectroscopy (IRRAS) has revolutionized the monolayer research. Not only the determination of monolayer structures but also interactions between amphiphilic monolayers at the soft air/liquid interface and molecules dissolved in the subphase are important for many areas in material and life sciences. Monolayers are convenient quasi-two-dimensional model systems. This review focuses on interactions between amphiphilic molecules in binary and ternary mixtures as well as on interfacial interactions with interesting biomolecules dissolved in the subphase. The phase state of monolayers can be easily triggered at constant temperature by increasing the packing density of the lipids by compression. Simultaneously the monolayer structure changes are followed in situ by grazing incidence X-ray diffraction or IRRAS. The interactions can be indirectly determined by the observed structure changes. Additionally, the yield of enzymatic reaction can be quantitatively determined, secondary structures of peptides and proteins can be measured and compared with those observed in bulk. In this way, the influence of a confinement on the structural properties of biomolecules can be determined. The adsorption of DNA can be quantified as well as the competing adsorption of ions at charged interfaces. The influence of modified nanoparticles on model membranes can be clearly determined. In this review, the relevance and utility of Langmuir monolayers as suitable models to study physical and chemical interactions at membrane surfaces are clearly demonstrated.     

Assemblies of carbon and boron-nitrogen nanotubes and fullerenes: Structure and properties

This review concerns assemblies of the main carbon nanostructures (fullerenes and nanotubes) generated by interactions between similar and dissimilar species. The two major families of these nanomaterials are reviewed: (1) assemblies with weak (van der Waals) bonds between fullerenes and/or nanotubes (fullerites, nanopeapods, nanotube bundles, and nanotubular crystals) and (2) assemblies formed by covalently bonded (polymerized) fullerenes and/or nanotubes (covalent crystals of small fullerenes C _{n < 60} , nanobuds, ropes of polymerized nanotubes, and covalent networks built of nanotubes). Data are systematized on their atomic structures, stability factors, electronic structures, chemical bonding, physical and chemical properties, and potential fields of application. Related heteronanomaterials (assemblies of boron-nitrogen fullerene-like molecules and/or nanotubes) are reviewed briefly.