Metal-containing sensor proteins sensing diatomic gas molecules

Diatomic gas molecules such as O2, CO and NO act as signaling molecules in many biological systems, where metal-containing gas sensor proteins sense their effector gas molecules by using prosthetic groups such as heme, iron-sulfur clusters and non-heme iron as the active center for gas sensing. When the gas sensor proteins sense their effector gas molecules, intramolecular and intermolecular signal transductions take place to regulate many physiological functions including gene expression, aerotaxis, and change in metabolic pathways, etc. The metal-containing prosthetic groups in these sensor proteins play a crucial role for selective sensing of their effectors. In this perspective, I will discuss the structure and function of some O2-, CO- and NO-sensor proteins, especially focussing on the structural, biochemical and biophysical properties of the active centers of these sensor proteins.     

Disassembly of noncovalent amphiphilic polymers with proteins and utility in pattern sensing

A simple strategy for pattern recognition of proteins through micellar disassembly is introduced. Five different noncovalently assembled receptors have been generated, and the disassembly was studied by monitoring the encapsulated dye release in response to five different proteins. The disassembly induced fluorescence change of the guest molecule produces protein-specific patterns.     

Surface immobilization of bio-functionalized cubosomes: sensing of proteins by quartz crystal microbalance

A strategy for tethering lipid liquid crystalline submicrometer particles (cubosomes) to a gold surface for the detection of proteins is reported. Time-resolved quartz crystal microbalance (QCM-D) was used to monitor the cubosome-protein interaction in real time. To achieve specific binding, cubosomes were prepared from the nonionic surfactant phytantriol, block-copolymer, Pluronic F-127, and a secondary biotinylated lipid, 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[biotinyl(polyethyleneglycol)-2000], which enabled attachment of the particles to a neutravidin (NAv)-alkanethiol monolayer at the gold surface of the QCM sensor chip. A second set of cubosomes was further functionalized with addition of the glycolipid (G(M1)) to facilitate a specific binding uptake of the protein, cholera toxin B subunit (CT(B)), from solution. QCM-D confirmed the specificity of the cubosome-NAv binding. The analysis of titration experiments, also performed with QCM, suggests that an optimal concentration of cubosomes is required for the efficient packing of the particles at the surface: high cubosome concentrations lead to chaotic cubosome binding onto the surface, sterically inhibiting surface attachment, or require significant reorganization to permit uniform cubosome coverage. The methodology enabled the straightforward preparation of a complex nanostructured edifice, which was then used to specifically capture analyte proteins (cholera toxin B subunit or free NAv) from solution, supporting the potential for development of this approach as a biosensing platform.     

Bioelectrochemistry for sensing amino acids,peptides, proteins and DNA interactions

Oxidative damage to peptides, proteins and DNA is considered to be one of the major causes of cancer and age-related diseases. The interaction of biomolecules, peptides, proteins, nucleic acids and pharmaceuticals with solid electrode surfaces is not only a fundamental phenomenon but also a key to important and novel analytical sensing applications in biosensors, biotechnology, medical devices and drug-delivery schemes. Electrochemical methods can provide insight into the redox mechanisms and the electron-transfer reactions of a variety of fundamental biological processes.     

Simulations of self-assembling systems

The previous focus on the thermodynamics of self-assembly of surfactants in solution through simulations is now being expanded to include phenomena in the fluid dynamic regime. This expansion implies that a formal edifice must be built to link molecular dynamics smoothly to mesoscopic and macroscopic length and time scales. We summarize and comment on recent trends in this area along with new results based on classical approaches. The latter include molecular dynamics as well as off-lattice Monte Carlo simulations and lattice-based Guggenheim-type models.     

A multidimensional sensing device for the discrimination of proteins based on manganese-doped ZnS quantum dots

Lab-on-a-nanoparticle: the triple-channel optical properties of Mn-doped ZnS quantum dots (fluorescence, phosphorescence, and light scattering) are explored to develop a multidimensional sensing device for the discrimination of proteins in a lab-on-a-nanoparticle approach.     

Tryptophan-to-dye fluorescence energy transfer applied to oxygen sensing by using type-3 copper proteins

A fluorescence-based system to sense oxygen in solution is described. The method exploits the sensitivity of the endogenous fluorescence of type-3 copper proteins towards the presence of oxygen by translating the near-UV emission of the protein to label fluorescence in the visible range through a FRET mechanism. The main protein in this study, a recombinant tyrosinase from the soil bacterium Streptomyces antibioticus, has been covalently labeled with a variety of fluorescent dye molecules with emission maxima spanning the whole visible wavelength range. In all cases, the emission of the label varied considerably between O2-bound and O2-free protein with a contrast exceeding that of the Trp emission for some labels. It is shown that different constructs may be simultaneously observed using a single excitation wavelength. Next to the described application in oxygen sensing, the method may be applicable to any protein showing variations in tryptophan fluorescence, for example as a function of ligand binding or catalysis.     

Computational discovery of putative quorum sensing inhibitors against LasR and RhlR receptor proteins of Pseudomonas aeruginosa

Drugs have been discovered in the past mainly either by identification of active components from traditional remedies or by unpredicted discovery. A key motivation for the study of structure based virtual screening is the exploitation of such information to design targeted drugs. In this study, structure based virtual screening was used in search for putative quorum sensing inhibitors (QSI) of Pseudomonas aeruginosa. The virtual screening programme Glide version 5.5 was applied to screen 1,920 natural compounds/drugs against LasR and RhlR receptor proteins of P. aeruginosa. Based on the results of in silico docking analysis, five top ranking compounds namely rosmarinic acid, naringin, chlorogenic acid, morin and mangiferin were subjected to in vitro bioassays against laboratory strain PAO1 and two more antibiotic resistant clinical isolates, P. aeruginosa AS1 (GU447237) and P. aeruginosa AS2 (GU447238). Among the five compounds studied, except mangiferin other four compounds showed significant inhibition in the production of protease, elastase and hemolysin. Further, all the five compounds potentially inhibited the biofilm related behaviours. This interaction study provided promising ligands to inhibit the quorum sensing (QS) mediated virulence factors production in P. aeruginosa.     

Resonance raman investigation of the specific sensing mechanism of a target molecule by gas sensory proteins

Specific sensing of gas molecules such as CO, NO, and O2 is a unique function of gas sensory hemoproteins, while hemoproteins carry out a wide variety of functions such as oxygen storage/transport, electron transfer, and catalysis as enzymes. It is important in gas sensory proteins that the heme domain not only recognizes its target molecule but also discriminates against other gases having similar molecular structures. Coordination of a target molecule to the heme is assumed to alter the protein conformation in the vicinity of heme, and the conformation change is propagated to the effector domain where substrate turnover, DNA binding, or interaction with a signal transduction protein is performed differently than the binding of other gases. To understand the appearance of such a specificity, we focus our attention on the ligand-protein interactions in the distal side of heme. In practice, the metal-ligand vibrations as well as internal modes of ligand and heme are measured with resonance Raman spectroscopy for wild-type and some mutant proteins with full-length or limited sensory regions. On the basis of such observations together with the knowledge currently available, we discuss the mechanism of specific sensing of a diatomic molecule in gas sensory proteins.     

Dissipative Particle Dynamics Simulations of Polymer Brushes: Comparison with Molecular Dynamics Simulations

Summary: The structure of polymer brushes is investigated by dissipative particle dynamics (DPD) simulations that include explicit solvent particles. With an appropriate choice of the DPD interaction parameters , we obtain good agreement with previous molecular dynamics (MD) results where the good solvent behavior has been modeled by an effective Lennard–Jones potential. The present results confirm that DPD simulation techniques can be applied for large length scale simulations of polymer brushes. A relation between the different length scales and is established.

Polymer brush at a solid–liquid interface.     

酶催化过程的全程模拟

酶催化包括底物到活性区的输运、选择催化化学反应及产物释放等复杂过程,由于复杂的蛋白质环境效应,任一化学和非化学过程都有可能是决定酶活性的关键步骤。为了全面认识酶催化活性,我们对几类酶催化过程进行了广泛的组合量子/分子力学(QM/MM)和经典分子力学(MM)动力学模拟(MD)研究,详细地讨论了整个酶催化过程的分子机制、关键残基的作用和蛋白质环境效应,丰富了对酶催化活性的认识。随着多尺度模型和计算模拟方法的进一步完善与发展,有望实现超大复杂生物酶催化过程的全程模拟研究,为酶工程领域的相关研究提供支持。     

自组装的分子动力学模拟

简要回顾了近年来国内外分子动力学模拟自组装的研究,对已报道的建模方法、可视化表现以及相关应用略作概述,并以此为基础对自组装过程的分子动力学模拟研究所面临的问题和尚需深入的内容进行了讨论。基于自组装、相变和涨落的固有联系,提出了以研究波动为手段,和以频率相关热容为研究对象的探索方向。希望能够为分子动力学模拟推动自组装研究提供有益的参考。     

Simulations on radiation-cured polyethylene

Simulations of the simultaneous crosslinking and chain scission reactions that are induced in bulk amorphous polyethylene by irradiation have been implemented with a computer. A detailed study of the various defect structures in the network is reported, to show that dangling ends have the highest population among these defects, especially at higher crosslink densities. The calculated sol fractions compare very favorably with previously published experimental studies. We find that there is about 1 chain scission for every 9 crosslinked units, i.e., one scission per 4.5 crosslinks. This is fewer scissions than had previously been deduced by application of the Charlesby-Pinner method.     

Simulations of shearing of capillary bridges

Capillary bridges are considered as the major source of interaction forces acting in wet particulate systems. We study the dynamic shear resistance by using a lattice Boltzmann numerical scheme for a binary fluid. The shear resistance force showed very little dependence on surface tension and contact angle. Instead, the shear resistance is a dynamic phenomenon and a major contributing factor is the distortion of the flow field caused by the presence of interfaces. This distortion of the flow field is geometry-dependent: in smaller diameter bridges the proportion of this distorted flow field becomes larger and it makes a major contribution to the shear resistance force. In other words multiple bridges have an enhancement effect on shear resistance.     

分子聚集体的光谱模拟

采用Frenkel激子理论研究了一维线性和二维人字形分子聚集体的吸收和发射光谱.通过引入激子离域长度的概念,将聚集体与单分子的光谱线形函数联系起来.计算的光谱结果表明,聚集体的光谱与分子在聚集体中的排列紧密相关.分析了一维J聚集光谱发生红移以及二维人字形分子聚集体吸收光谱形成J和H激子谱带的内在原因.模拟得到的聚集体的...     

An aptamer-based signal-on and multiplexed sensing platform for one-spot simultaneous electronic detection of proteins and small molecules

One-spot signal-on and simultaneous electronic detection of lysozyme and adenosine is achieved based on target-induced release of aptamers and back-filling hybridization of the resulting single stranded DNAs with redox-tags conjugated aptamers.     

端羟基聚丁二烯/增塑剂共混物相容性的分子动力学模拟和介观模拟

应用分子动力学(MD)和介观动力学(MesoDyn)模拟方法对固体推进剂中端羟基聚丁二烯(HTPB)与增塑剂癸二酸二辛酯(DOS)、硝化甘油(NG)的相容性进行了研究. 采用MD模拟方法在COMPASS力场下, 对纯物质、HTPB/增塑剂共混物的密度、内聚能密度、溶度参数和共混物分子间的Flory-Huggins作用参数及结合能等进行了模拟计算, 通过比较溶度参数差值(Δδ)的大小、模拟前后体系密度变化情况均可以预测HTPB与增塑剂的相容性, 结合能的分析揭示了HTPB/增塑剂共混物组分间的相互作用及本质. 将Flory-Huggins作用参数转化为MesoDyn模拟的输入参数, 采用MesoDyn模拟方法对HTPB/增塑剂共混体系的介观形貌与动力学演变过程进行了研究, 通过模拟得到的等密度图、自由能密度和有序度参数等可以判断共混体系的相容性. MD和MesoDyn模拟结果均表明: HTPB/DOS属于相容体系, 而HTPB/NG属于不相容体系, 其结论与实验结果一致.