Exploring the mechanisms of molecular recognition by flavins

The design and development of chemical models for enzymes depends on the fundamental principles observed in biological systems. Molecular recognition of flavins by various receptors has attracted attention due to their applications as chemical models for flavoenzymes. The area of molecular recognition is being investigated through research at the interface of chemistry and biology. In this review, the literature has been surveyed to provide comprehensive coverage of the synthetic methodology of different flavins and receptors and their molecular-recognition studies. Various applications of flavin-receptor complexes have also been highlighted.     

Chemically modified viruses: principles and applications

The search for novel molecular materials has focused on viruses as natural nanomaterials. Historically studied for their effects as pathogens, recent advances have incorporated viruses as substrates for chemical modification, materials development, and therapeutic design. Here we will discuss recent advances in chemical strategies for modifying viruses, and the applications of these technologies.     

分子动力学模拟与分子生物力学

生物大分子的微观结构动力学决定其生物学功能,其力学-化学耦合规律是分子生物力学的重点关注方向。分子动力学模拟是耦合生物大分子力学-化学性质微观结构动力学基础的有效手段,其结果可用于预测结构-功能关系、指导实验设计和诠释实验结果。本文简要介绍了分子动力学模拟的方法学特点、基本工作原理及其在分子生物力学中的应用,并展望了未来可能的发展方向和应用前景。     

Exploring biologically relevant chemical space with metal complexes

Altering biological processes with small synthetic molecules is a general approach for the design of drugs and molecular probes. Medicinal chemistry and chemical biology are focused predominately on the design of organic molecules, whereas inorganic compounds find applications mainly for their reactivity (e.g. cisplatin as a DNA-reactive therapeutic) or imaging properties (e.g. gadolinium complexes as MRI diagnostics). In such inorganic pharmaceuticals or probes, coordination chemistry in the biological environment or at the target site lies at the heart of their modes of action. However, past and very recent results suggest that it is also worth exploring a different aspect of metal complexes: their ability to form structures with unique and defined shapes for the design of 'organic-like' small-molecule probes and drugs. In such metal-organic compounds, the metal has the main purpose to organize the organic ligands in three-dimensional space. It is likely that such an approach will complement the molecular diversity of organic chemistry in the quest for the discovery of compounds with superior biological activities.     

Fullerene modified supported lipid membrane as sensitive element of sensor for odorants

A supported lipid bilayer membrane (s-BLMs) formed on a freshly cleaved metallic surface by the Tien method was applied for the design of an electrochemical sensor for detection of neutral odorant molecules. The lipid bilayer was modified by saturation with fullerene C₆₀, which possesses electron mediator properties and facilitates a redox reaction occurring at the border of the lipid membrane and metal surface. I₂/I⁻ and ferrocenyl trimethyl bromide were used as electroactive marker ions. The smell compounds adsorb on the surface of the lipid layer and change its structure. As a consequence the ratio of marker ion penetration to the lipid membrane is altered. The magnitude of these changes depends on the amount and chemical structure of adsorbed molecules. The research presented was carried out by cyclic voltammetry. The magnitude of the electrochemical signal generated by smell compounds was correlated with other parameters describing their molecular properties such as: octanol/water partition coefficients and dipole moments.     

Pullulan: biosynthesis,production, and applications

Pullulan is a linear glucosic polysaccharide produced by the polymorphic fungus Aureobasidium pullulans, which has long been applied for various applications from food additives to environmental remediation agents. This review article presents an overview of pullulan’s chemistry, biosynthesis, applications, state-of-the-art advances in the enhancement of pullulan production through the investigations of enzyme regulations, molecular properties, cultivation parameters, and bioreactor design. The enzyme regulations are intended to illustrate the influences of metabolic pathway on pullulan production and its structural composition. Molecular properties, such as molecular weight distribution and pure pullulan content, of pullulan are crucial for pullulan applications and vary with different fermentation parameters. Studies on the effects of environmental parameters and new bioreactor design for enhancing pullulan production are getting attention. Finally, the potential applications of pullulan through chemical modification as a novel biologically active derivative are also discussed.     

Regio- and stereospecific analysis of glycerolipids

In recent years researchers have recognized the potential value of comprehensive lipid profiling (lipidomics), which was invented and promoted by lipidologists who recognized the many valuable applications that grew out of the fields of DNA profiling (genomics) and protein profiling (proteonomics). Through lipid class-selective intrasource ionization and subsequent analysis of two-dimensional cross-peak intensities, the chemical identity and mass composition of individual molecular species of most lipid classes can now be determined in a chloroform extract. There remains, however, the necessity to distinguish the enantiomers and isobaric regioisomers resulting from enzymatic and chemical reactions, which conventional high performance liquid chromatography/mass spectrometry (HPLC/MS) has been slow to accommodate, and tandem MS unable to provide. While reversed-phase HPLC can separate regioisomers, normal-phase HPLC can resolve diastereomers, and chiral-phase HPLC can effect dramatic resolution of enantiomers, the full potential of the combined systems has seldom been exploited. The present chapter calls attention to both recent and earlier combinations of these methodologies with mass spectrometry, which allows the HPLC/ESI (electrospray ionization)-MS/MS separation and identification of enantiomeric diacylglycerols, triacylglycerols, and glycerophospholipids as well as their isobaric regioisomers. These developments permit further expansion of lipid profiling (lipidomics) and better understanding of lipid metabolism.     

Molecular dynamics simulations of the interaction of phospholipid bilayers with polycaprolactone

The molecular interaction between common polymer chains and the cell membrane is unknown. Molecular dynamics simulations offer an emerging tool to characterise the nature of the interaction between common degradable polymer chains used in biomedical applications, such as polycaprolactone, and model cell membranes. Herein we characterise with all-atomistic and coarse-grained molecular dynamics simulations the interaction between single polycaprolactone chains of varying chain lengths with a phospholipid membrane. We find that the length of the polymer chain greatly affects the nature of interaction with the membrane, as well as the membrane properties. Furthermore, we next utilise advanced sampling techniques in molecular dynamics to characterise the two-dimensional free energy surface for the interaction of varying polymer chain lengths (short, intermediate, and long) with model cell membranes. We find that the free energy minimum shifts from the membrane-water interface to the hydrophobic core of the phospholipid membrane as a function of chain length. Finally, we perform coarse-grained molecular dynamics simulations of slightly larger membranes with polymers of the same length and characterise the results as compared with all-atomistic molecular dynamics simulations. These results can be used to design polymer chain lengths and chemistries to optimise their interaction with cell membranes at the molecular level.     

Charge-transfer processes and redox reactions in planar lipid monolayers and bilayers

Supported bilayer lipid membranes (BLMs) and lipid monolayers have been known for quite sometime and are attracting sustained interest since they open new research vista and offer practical approaches in biosensor development and molecular device applications. Central to these areas of interest are electric processes and redox reactions where the movement of ions and electrons plays a pivotal role. In this paper an overview of the major findings in this field is presented. Further, we summarize the work on planar lipid bilayers and monolayers that have been done in the past few years in a number of laboratories. Supported planar BLMs and their closely related systems provide the foundation for a variety of lipid bilayer-based molecular sensors that are sensitive, versatile, as well as potentially inexpensive (i.e., disposable), and open to all sorts of experimentation.     

Tailored recombinant elastin-like polymers for advanced biomedical and nano(bio)technological applications

The genetic engineering of protein-based polymers is a method that enables, in an easy way, the design of complex and highly functional macromolecules. As examples of this approach, different molecular designs are presented, with increasing degree of complexity, showing how the controlled increase in their complexity yields (multi)functional materials with more selected and sophisticated properties. The simplest designs show interesting properties already, but the adequate introduction of given chemical functions along the polymer chain provides an opportunity to expand the range of properties to enhanced smart behavior and self-assembly. Finally, examples are given where those molecular designs further incorporate selected bioactivities in order to develop materials for the most cutting edge applications in biomedicine and nano(bio)technology.     

Microalgal lipids biochemistry and biotechnological perspectives

In the last few years, there has been an intense interest in using microalgal lipids in food, chemical and pharmaceutical industries and cosmetology, while a noteworthy research has been performed focusing on all aspects of microalgal lipid production. This includes basic research on the pathways of solar energy conversion and on lipid biosynthesis and catabolism, and applied research dealing with the various biological and technical bottlenecks of the lipid production process. In here, we review the current knowledge in microalgal lipids with respect to their metabolism and various biotechnological applications, and we discuss potential future perspectives.     

细胞穿透肽在肿瘤治疗中的应用

随着人类对基因组信息解读的不断深入,越来越多的生物大分子作为候选药物进入生物治疗领域。但细胞表面的脂质双层膜具有选择通透性,这种天然屏障作用在保护细胞的同时也限制了绝大多数生物大分子进入细胞内部发挥治疗效应。目前流行的入胞转运方式如电穿孔、脂质体转染等均存在对细胞的额外毒副作用,且作用范围局限于体外实验。细胞穿透肽是一类以非受体依赖方式,非经典内吞方式直接穿过细胞膜进入细胞的多肽。它们可以与多种生物活性物质连接并携带其进入细胞,这一特性为它们成为理想的药物载体提供了可能。本文对使用细胞穿透肽作为载体转运具有抗癌作用的生物大分子进入细胞的抗癌实验予以介绍。     

Differential interaction of peptides derived from C-terminal domain of human apolipoprotein E with platelet activating factor analogs

Apolipoprotein-derived peptides are promising candidates for the treatment of various inflammatory conditions and the main mechanism proposed for the protective action of these peptides includes binding to pro-inflammatory lipid mediators with high affinity and facilitating their sequestration/metabolism/clearance in the body. Molecules that act as pro-inflammatory lipid mediators differ considerably in their molecular structures, chemical compositions and physicochemical properties. Importance of the properties of pro-inflammatory lipid mediators on the biological activity of apolipoprotein-derived peptides has not been studied in detail. In this study, we characterized the physicochemical properties of aggregates containing lyso-PAF, acetyl-PAF and butanoyl-PAF, three closely related pro-inflammatory lipid mediators, and studied their interaction with peptides derived from the C-terminal domains of human apolipoprotein E. These PAF-analogs differ only in the chemical composition of the functional groups they carry at the sn-2 positions. Our results show that physicochemical properties of aggregates containing lyso-PAF, acetyl-PAF and butanoyl-PAF differ considerably and affect their apolipoprotein-derived peptides-binding capacity.     

Molecular engineering of the cellulosome complex for affinity and bioenergy applications

The cellulosome complex has evolved to degrade plant cell walls and, as such, combines tenacious binding to cellulose with diverse catalytic activities against amorphous and crystalline cellulose. Cellulolytic microorganisms provide an extensive selection of domains; those with affinity for cellulose, cohesins and their dockerin binding partners that define cellulosome stoichiometry and architecture, and a range of catalytic activities against carbohydrates. These robust domains provide the building blocks for molecular design. This review examines how protein modules derived from the cellulosome have been incorporated into chimaeric proteins to provide biosynthetic tools for research and industry. These applications include affinity tags for protein purification, and non-chemical methods for immobilisation and presentation of recombinant protein domains on cellulosic substrates. Cellulosomal architecture provides a paradigm for design of enzymatic complexes that synergistically combine multiple catalytic subunits to achieve higher specific activity than would be obtained using free enzymes. Multimeric enzymatic complexes may have industrial applications of relevance for an emerging carbon economy. Biocatalysis will lead to more efficient utilisation of renewable carbon-fixing energy sources with the added benefits of reducing chemical waste streams and reliance on petroleum.     

GM1 locates to mature amyloid structures implicating a prominent role for glycolipid-protein interactions in Alzheimer pathology

While the molecular mechanisms underlying Alzheimer's disease (AD) remain largely unknown, abnormal accumulation and deposition of beta amyloid (Aβ) peptides into plaques has been proposed as a critical pathological process driving disease progression. Over the last years, neuronal lipid species have been implicated in biological mechanisms underlying amyloid plaque pathology. While these processes comprise genetic features along with lipid signaling as well as direct chemical interaction of lipid species with Aβ mono- and oligomers, more efforts are needed to spatially delineate the exact lipid-Aβ plaque interactions in the brain. Chemical imaging using mass spectrometry (MS) allows to probe the spatial distribution of lipids and peptides in complex biological tissues comprehensively and at high molecular specificity. As different imaging mass spectrometry (IMS) modalities provide comprehensive molecular and spatial information, we here describe a multimodal ToF-SIMS- and MALDI-based IMS strategy for probing lipid and Aβ peptide changes in a transgenic mouse model of AD (tgAPP_ArcSwe). Both techniques identified a general AD-associated depletion of cortical sulfatides, while multimodal MALDI IMS revealed plaque specific lipid as well as Aβ peptide isoforms. In addition, MALDI IMS analysis revealed chemical features associated with morphological heterogeneity of individual Aβ deposits. Here, an altered GM1 to GM2/GM3 ganglioside metabolism was observed in the diffuse periphery of plaques but not in the core region. This was accompanied by an enrichment of Aβ1–40arc peptide at the core of these deposits. Finally, a localization of arachidonic acid (AA) conjugated phosphatidylinositols (PI) and their corresponding degradation product, lyso-phosphatidylinositols (LPI) to the periphery of Aβ plaques was observed, indicating site specific macrophage activation and ganglioside processing.     

Industrial potential of lipoxygenases

Lipoxygenases (LOXs) are iron- or manganese-containing oxidative enzymes found in plants, animals, bacteria and fungi. LOXs catalyze the oxidation of polyunsaturated fatty acids to the corresponding highly reactive hydroperoxides. Production of hydroperoxides by LOX can be exploited in different applications such as in bleaching of colored components, modification of lipids originating from different raw materials, production of lipid derived chemicals and production of aroma compounds. Most application research has been carried out using soybean LOX, but currently the use of microbial LOXs has also been reported. Development of LOX composition with high activity by heterologous expression in suitable production hosts would enable full exploitation of the potential of LOX derived reactions in different applications. Here, we review the biological role of LOXs, their heterologous production, as well as potential use in different applications. LOXs may fulfill an important role in the design of processes that are far more environmental friendly than currently used chemical reactions. Difficulties in screening for the optimal enzymes and producing LOX enzymes in sufficient amounts prevent large-scale application so far. With this review, we summarize current knowledge of LOX enzymes and the way in which they can be produced and applied.     

Lipopeptides as anti-infectives: a practical perspective

Lipopeptide antibiotics represent an old class of antibiotics that were discovered over 50 years ago, which includes the old polymyxins but also new entries, such as the recently approved daptomycin. They generally consist of a hydrophilic cyclic peptide portion attached to a fatty acid chain which facilitates insertion into the lipid bilayer of bacterial membranes. This review presents an overview of this class of antibiotics, focusing on their therapeutic applications and putting particular emphasis on chemical modifications introduced to improve their activity.     

Designing dendrimers for biological applications

Dendrimers are branched, synthetic polymers with layered architectures that show promise in several biomedical applications. By regulating dendrimer synthesis, it is possible to precisely manipulate both their molecular weight and chemical composition, thereby allowing predictable tuning of their biocompatibility and pharmacokinetics. Advances in our understanding of the role of molecular weight and architecture on the in vivo behavior of dendrimers, together with recent progress in the design of biodegradable chemistries, has enabled the application of these branched polymers as anti-viral drugs, tissue repair scaffolds, targeted carriers of chemotherapeutics and optical oxygen sensors. Before such products can reach the market, however, the field must not only address the cost of manufacture and quality control of pharmaceutical-grade materials, but also assess the long-term human and environmental health consequences of dendrimer exposure in vivo.     

Enzymatic modification of phospholipids for functional applications and human nutrition

Rapid progress in biochemistry of phospholipids and evolution of modern bioengineering has brought forth a number of novel concepts and technical advancements in the modification of phospholipids for industrial applications and human nutrition. Highlights cover preparation of novel phospholipid analogs based on the latest understanding of pivotal role of phospholipids in manifold biological processes, exploration of remarkable application potentials of phospholipids in meliorating human health, as well as development of new chemical and biotechnological approaches applied to the modification of phospholipids. This work reviews the natural occurrence and structural characteristics of phospholipids, their updated knowledge on manifold biological and nutritional functions, traditional and novel physical and chemical approaches to modify phospholipids as well as their applications to obtain novel phospholipids, and brief introduction of the efforts focusing on de novo syntheses of phospholipids. Special attention is given to the summary of molecular structural characteristics and catalytic properties of multiple phospholipases, which helps to interpret experimental phenomena and to improve reaction design. This will of course provide fundamental bases also for the development of enzymatic technology to produce structured or modified phospholipids.     

Study of curcumin behavior in two different lipid bilayer models of liposomal curcumin using molecular dynamics simulation

Liposomal formulation of curcumin is an important therapeutic agent for the treatment of various cancers. Despite extensive studies on the biological effects of this formulation in cancer treatment, much remains unknown about curcumin–liposome interactions. Understanding how different lipid bilayers respond to curcumin molecule may help us to design more effective liposomal curcumin. Here, we used molecular dynamics simulation method to investigate the behavior of curcumin in two lipid bilayers commonly used in preparation of liposomal curcumin, namely dipalmitoylphosphatidylcholine (DPPC) and dimyristoylphosphatidylglycerol (DMPG). First, the free energy barriers for translocation of one curcumin molecule from water to the lipid bilayer were determined by using the potential of mean force (PMF). The computed free energy profile exhibits a global minimum at the solvent–headgroup interface (LH region) for both lipid membranes. We also evaluated the free energy difference between the equilibrium position of curcumin in the lipid bilayer and bulk water as the excess chemical potential. Our results show that curcumin has the higher affinity in DMPG compared to DPPC lipid bilayer (?8.39 vs. ?1.69 k_BT) and this is related to more hydrogen bond possibility for curcumin in DMPG lipid membrane. Next, using an unconstrained molecular dynamic simulation with curcumin initially positioned at the center of lipid bilayer, we studied various properties of each lipid bilayer system in the presence of curcumin molecule that was in full agreement with PMF and experimental data. The results of these simulation studies suggest that membrane composition could have a large effect on interaction of curcumin–lipid bilayer.