荧光标记生物大分子及其应用

近年来,对生物大分子进行荧光标记的技术受到很大重视并取得了迅速进展,此技术广泛应用于细胞内外物质的检测、核酸杂交测序及疾病诊断等诸多方面。本文就生物大分子的荧光标记及其应用作一简要综述。     

生物大分子特征谱在疾病诊断中的应用

疾病的不同阶段表达的生物大分子不同,并且随着疾病的发生和发展,生物大分子的表达谱也同时发生改变。这些变化的综合信息可以作为疾病相关的特征性生物大分子谱用于疾病诊断和预后评价。随着多种生物大分子组学技术的迅速发展,人们获得的疾病相关的生物大分子信息量不断扩大,从而实现利用生物大分子特征谱诊断疾病。     

模拟体液中生物大分子对类骨磷灰石矿化的影响

为考察体内生物大分子对羟基磷灰石（hydroxyapatite,HA）基底表面矿化物形成的影响,将牛血清白蛋白（bovine serum albumin,BSA）和硫酸软骨素（chondroitin sulfate,CS）大分子分别浸入模拟体液（SBF）中制备成2种矿化介质,再将HA浸入上述矿化介质中3d观察类骨磷灰石形成过程.结果 发现HA基底表面均沉积有Na＋和CO2-3取代的类骨磷灰石（Ca3.78Na0.02）（Ca5.22Na0.48）（CO3）1.5（OH）.BSA在2SBF中的存在促进了类骨磷灰石晶体在基材表面沉积,有利于其沿（300）晶面择优取向生长.CS对类骨磷灰石晶体的生长呈阻碍作用,获得的晶粒尺寸较小.模拟体液中BSA和CS大分子对类骨磷灰石晶体生长和形貌等均有一定的作用.     

时间分辨荧光各向异性及其在生物大分子研究中的应用

概述了时间分辨荧光各向异性（TRAMS）的工作原理和发展概况，描述了常用荧光探针，标记物及大分子的一般标记方法，讨论了其测定方法，研究特点及生物大分子中的构象及结构变化等研究方面的应用，展望了未来的应用前景。     

生物大分子的电纺及其在药物控释中的应用

随着研究者对于纳米技术以及纳米特性研究兴趣的不断增加,近年来静电纺丝受到越来越多的关注。首先综述了生物大分子静电纺丝的研究进展,主要包括合成高分子和天然生物大分子的静电纺丝以及复合纳米纤维的制备,侧重讨论了各种生物材料的电纺条件以及与生物医用有关的电纺纤维膜性质,如纤维膜形态稳定性、机械性质以及降解行为等。在此基础上,综述了静电纺丝在药物控制释放领域中的应用,针对不同药物的溶解性质,分别讨论了其在电纺纤维中的包埋方法以及释放行为。     

细胞微环境对生物活性大分子疗效的影响

随着药物载体技术的快速发展,将生物活性大分子输送至特定靶细胞治疗各种疾病日益受到关注.虽然生物活性大分子在一些疾病治疗中取得了一定疗效,但靶细胞微环境对其最终疗效影响较大.许多疾病和损伤扰乱了正常细胞外基质（ECM）的体系结构、细胞对ECM的黏附及之后的细胞活动.因此,ECM构建的细胞微环境对维持机体平衡、组织再生及修复起着关键性作用.鉴于此,就ECM构建的细胞微环境对生物活性大分子疗效的影响作一综述,为载药系统的设计及药物合成等提供一定的理论基础.     

自组织神经树在生物样品分析中的应用

作者将自组织神经树动用于生物样品─冠心病患者和对照组（健康人）血液中微量金属元素的综合分析，对少数检验组，预报成功率达１００％，结果表明，该方法性能良好，可作为生物样品分析与疾病诊断的一种有效的辅助手段。     

生物组织的超声散射

生物组织的超声散射特性研究是生物医学超声工程学中最基本、最重要的课题之一，这 研究将有助于建立随质的声散射理论，另一方面，研究生物组织的散射特性，又有可能开拓出一定定量超声诊断的新途径。本文主要综述了生物组织中超声散射特性研究的发展概况及新进展。     

生物组织光传播特性的研究

光在组织中传播与组织的光学性质有关。折射率是组织光学性质最基本的参数,用来评价组织改变光线行进方向的参量。本文以菲涅耳公式为理论依据,尝试用空气—组织界面的反射率、生物组织薄膜的反射率和生物组织反射光的偏振分量,推算生物组织的折射率。 本文还探测了组织的前向散射和后向漫射分布。     

自组织学习联想神经树在生物样品分析中的应用

本文把自组织学习联想神经树运用于生物样品─—冠心病患者和对照组（健康人）血液中微量金属元素的综合分析，预报成功率达１００％。结果表明，该方法性能良好，可作为生物样品分析与疾病诊断的一种有效的辅助手段。     

An immunoinformatics approach for design and validation of multi-subunit vaccine against Cryptosporidium parvum

An immunoinformatics-based approach is explored for potential multi-subunit vaccine candidates against Cryptosporidium parvum. We performed protein structure based systematic methodology for the development of a proficient multi-subunit vaccine candidate against C. parvum based on their probability of antigenicity, allergenicity and transmembrane helices as the screening criteria. The best-screened epitopes like B-cell epitopes (BCL), Helper T-lymphocytes (HTL) and cytotoxic T- lymphocytes (CTL) were joined by using the appropriate linkers to intensify and develop the presentation and processing of the antigenic molecules. Modeller software was used to generate the best 3D model of the subunit protein. RAMPAGE and other web servers were employed for the validation of the modeled protein. Furthermore, the predicted modeled structure was docked with the two known receptors like TLR2 and TLR4 through ClusPro web server. Based on the docking score, the multi-subunit vaccine docked with TLR2 was subjected to energy minimization by molecular dynamics (MD) simulation to examine their stability within a solvent system. From the simulation study, we found that the residue Glu-107 of subunit vaccine formed a hydrogen bond interaction with Arg-299 of the TLR2 receptor throughout the time frame of the MD simulation. The overall results showed that the multi-subunit vaccine could be an efficient vaccine candidate against C. parvum.     

Self-assembly of short peptides to form hydrogels: Design of building blocks,physical properties and technological applications

Hydrogels are unique supramolecular solid-like assemblies composed mainly of water molecules that are held by molecular networks. Physical hydrogels that are formed by a set of non-covalent interactions to establish a well-ordered scaffold devoid of any chemical cross-linking are especially intriguing for various biotechnological and medical applications. Peptides are particularly interesting building blocks of physical gels because of the role of polypeptides as structural elements in biological systems, the extensive ability for their chemical and biological decoration and functionalization, and the facile synthesis of natural and modified peptides. This review describes the assembly and properties of physical hydrogels that have been formed by the self-association of very simple peptide building blocks. Natural short peptides, as short as dipeptides, can form ordered gel assemblies. Moreover, in the case of N-terminal protection, even a protected amino acid can serve as an efficient hydrogelator. Further elucidation of hydrogelators’ assembly, as well as the characterization of their physical properties, can guide the rational design of building blocks for a desired application. The possible mechanism of self-assembly is discussed in line with the chemical nature of the short peptides. Different methods have been used to induce hydrogel assembly, which may significantly affect the mechanical characteristics of the resulting gels. Here, special emphasis is given to methods that allow either spatial control of hydrogel formation or modulation of physical properties of the gel. Finally, the parameters that influence hydrogelation are described, and insights for their design are provided.     

一种基于分子动力学模拟来识别GPIbα与vWF-A1结合面上重要残基的新方法

目的 发展一种识别受体与配体相互作用中关键氨基酸残基的计算机新方法。方法 GPIb?/vWF-A1的晶体结构取自PDB数据库;利用自由分子动力学模拟,观察GPIb?/vWF-A1复合物结合面上的盐桥和氢键的形成和演化;利用分析计算得到的这些盐桥和氢键的生存率的高低,作为度量相互作用残基对之重要性的判据。结果 在GPIb?/vWF-A1的结合面上,GPIb?的21个残基和vWF-A1的21个残基显著参与了GPIb?和vWF-A1间的相互作用,这些残基中的20个已得到突变实验的证实。结论 该方法能较好地预报和识别受体-配体相互作用中的关键残基,并可为传统的氨基酸残基突变实验和抗凝血栓药物设计提供指导。     

Exploring the use of molecular dynamics in assessing protein variants for phenotypic alterations

With the advent of rapid sequencing technologies, making sense of all the genomic variations that we see among us has been a major challenge. A plethora of algorithms and methods exist that try to address genome interpretation through genotype–phenotype linkage analysis or evaluating the loss of function/stability mutations in protein. Critical Assessment of Genome Interpretation (CAGI) offers an exceptional platform to blind‐test all such algorithms and methods to assess their true ability. We take advantage of this opportunity to explore the use of molecular dynamics simulation as a tool to assess alteration of phenotype, loss of protein function, interaction, and stability. The results show that coarse‐grained dynamics based protein flexibility analysis on 34 CHEK2 and 1719 CALM1 single mutants perform reasonably well for class‐based predictions for phenotype alteration and two‐thirds of the predicted scores return a correlation coefficient of 0.6 or more. When all‐atom dynamics is used to predict altered stability due to mutations for Frataxin protein (8 cases), the predictions are comparable to the state‐of‐the‐art methods. The competitive performance of our straightforward approach to phenotype interpretation contrasts with heavily trained machine learning approaches, and open new avenues to rationally improve genome interpretation.     

尤文肉瘤EWS-FLI1蛋白HLA-A2.1限制性CTL表位的预测、筛选及鉴定

目的预测、筛选及合成尤文肉瘤EWS-FLI1蛋白HLA-A2.1限制性细胞毒性T淋巴细胞(Cytotoxic T Lymphocyte,CTL)表位,初步鉴定EWS-FLI1表位肽。方法综合运用BIMAS、SYFPEITHI、Predep和IEDB方案对EWS-FLI1蛋白进行HLA-A~*0201限制性CTL表位的预测,应用多项式方案、量化基序方案对预测的CTL表位进行筛选,并将筛选的CTL表位与HLA-A~*0201分子进行动力学模拟,应用标准Fmoc方案合成CTL表位肽;通过表位多肽刺激CTL释放颗粒溶素的检测,以及靶细胞杀伤实验验证表位多肽的免疫效应。结果综合预测得出了8个可能的表位肽,进一步筛选确定其中4个肽为候选合成表位,应用分子动力模拟初步验证了4个候选表位肽与HLA-A2.1分子的结合力,合成的各条肽经色谱分析纯度均在98%以上,经质谱分析各肽的分子量测定值与理论值相符,颗粒溶素释放实验及靶细胞杀伤实验证实了筛选的表位均能产生刺激效应,其中,表位肽QIQLWQFLL(EWS-FLI1 304)的刺激效应最为显著。结论综合运用多个方案可提高预测效率,分子动力学模拟可初步验证表位肽与HLA-A~*0201的结合力,所合成的多肽为高纯度肽,通过免疫学实验初步鉴定了EWS-FLI1的表位。     

HLA-B27 and antigen presentation: At the crossroads between immune defense and autoimmunity

The HLA-B27 is historically studied as a susceptibility factor in spondyloarthropathies and, primarily, in ankylosing spondylitis (AS). Over the recent years however, it has been rediscovered as protective factor against some severe viral infections. This is due to the high capacity of virus-specific, HLA-B27-restricted CD8+ T cells for both intrinsic (i.e. polyfunctionality, high avidity, low sensitivity to Treg cell-mediated suppression) and extrinsic (i.e. rapid and efficient antigen processing and presentation) factors. It is tempting to speculate that these two aspects are not independent and that the association of B27 molecules to autoimmunity is the downside of this superior functional efficacy which, in given genetic backgrounds and environmental conditions, can support a chronic inflammation leading to spondyloarthropathies. Still, the pathogenic role of HLA-B27 molecules in AS is elusive. Here, we focus on the biology of HLA-B27 from the genetics to the biochemistry and to the structural/dynamical properties of B27:peptide complexes as obtained from atomistic molecular dynamics simulation. Overall, the results point at the antigen presentation as the key event in the disease pathogenesis. In particular, an extensive comparison of HLA-B*2705 and B*2709 molecules, that differ in a single amino acid (Asp116 to His116) and are differentially associated with AS, indicates that position 116 is crucial for shaping the entire peptide-presenting groove.     

A Multiscale Computational Approach to Dissect Early Events in the Erb Family Receptor Mediated Activation,Differential Signaling,and Relevance to Oncogenic Transformations

We describe a hierarchical multiscale computational approach based on molecular dynamics simulations, free energy-based molecular docking simulations, deterministic network-based kinetic modeling, and hybrid discrete/continuum stochastic dynamics protocols to study the dimer-mediated receptor activation characteristics of the Erb family receptors, specifically the epidermal growth factor receptor (EGFR). Through these modeling approaches, we are able to extend the prior modeling of EGF-mediated signal transduction by considering specific EGFR tyrosine kinase (EGFRTK) docking interactions mediated by differential binding and phosphorylation of different C-terminal peptide tyrosines on the RTK tail. By modeling signal flows through branching pathways of the EGFRTK resolved on a molecular basis, we are able to transcribe the effects of molecular alterations in the receptor (e.g., mutant forms of the receptor) to differing kinetic behavior and downstream signaling response. Our molecular dynamics simulations show that the drug sensitizing mutation (L834R) of EGFR stabilizes the active conformation to make the system constitutively active. Docking simulations show preferential characteristics (for wildtype vs. mutant receptors) in inhibitor binding as well as preferential enhancement of phosphorylation of particular substrate tyrosines over others. We find that in comparison to the wildtype system, the L834R mutant RTK preferentially binds the inhibitor erlotinib, as well as preferentially phosphorylates the substrate tyrosine Y1068 but not Y1173. We predict that these molecular level changes result in preferential activation of the Akt signaling pathway in comparison to the Erk signaling pathway for cells with normal EGFR expression. For cells with EGFR over expression, the mutant over activates both Erk and Akt pathways, in comparison to wildtype. These results are consistent with qualitative experimental measurements reported in the literature. We discuss these consequences in light of how the network topology and signaling characteristics of altered (mutant) cell lines are shaped differently in relationship to native cell lines. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. These authors contributed equally     

Introducing a combinatorial DNA-toolbox platform constituting defined protein-based biohybrid-materials

The access to defined protein-based material systems is a major challenge in bionanotechnology and regenerative medicine. Exact control over sequence composition and modification is an important requirement for the intentional design of structure and function. Herein structural- and matrix proteins provide a great potential, but their large repetitive sequences pose a major challenge in their assembly. Here we introduce an integrative “one-vector-toolbox-platform” (OVTP) approach which is fast, efficient and reliable. The OVTP allows for the assembly, multimerization, intentional arrangement and direct translation of defined molecular DNA-tecton libraries, in combination with the selective functionalization of the yielded protein-tecton libraries. The diversity of the generated tectons ranges from elastine-, resilin, silk- to epitope sequence elements. OVTP comprises the expandability of modular biohybrid-materials via the assembly of defined multi-block domain genes and genetically encoded unnatural amino acids (UAA) for site-selective chemical modification. Thus, allowing for the modular combination of the protein-tecton library components and their functional expansion with chemical libraries via UAA functional groups with bioorthogonal reactivity. OVTP enables access to multitudes of defined protein-based biohybrid-materials for self-assembled superstructures such as nanoreactors and nanobiomaterials, e.g. for approaches in biotechnology and individualized regenerative medicine.     

Dynamic Crosslinking of Polyethylene by Hydrogen Bonding Grafted Motifs: A Molecular Dynamics Simulation Study

The recyclability of polyethylene-based is an important social and environmental issue. Dynamic crosslinking of polyethylene by multiple hydrogen bonding motifs provides an opportunity for complete recyclability. This approach is based on producing reversible covalent bonds in the crosslinking polyethylene networks to produce vitrimers. It is employed molecular dynamics simulation to study the effect of mole percent of randomly grafted 1-(7-oxo-7,8-dihydro-1,8-naphthyridin-2-yl) poly(ethylene-co-[2-hydroxyethyl methacrylate])s (ODIN-PEHEMAs), on thermal stability of the vitrimers. The crosslinking nature and dynamics of these grafted polyethylene chains are analyzed focusing on free volume, specific volume, radial distribution function, and mean squared displacement. The addition of hydrogen bonding units increased the free volumes, but the mole percent of side chains is not enough to affect the dynamics of the main chains in vicinity of the glass transition temperature. The simulation results show that for 1.67-mole percent of randomly grafted ODIN-PEHEMAs, the mean squared displacement, MSD, dramatically increases in vicinity of 312.5 K, which is in good agreement with the experimental results due to the physical cross-linking breakage at room temperature. With increasing the mole percent of ODIN (4.33, 8.33, and 10.67 mole percent), the breakage of physical cross-links shifted to higher temperatures.     

上气道内流动现象与压力分布模拟

目的用计算流体力学模拟的方法和体外模型实验的手段,研究呼吸时真实结构的上气道内的流动状态和压力分布,同时验证数值模拟模型的准确性。方法首先基于磁共振图像,借助Mimics软件重建上气道三维结构。在此真实几何结构基础上,建立上呼吸道内流动的有限元分析模型,以及制作相应的实体模型。模拟并测量呼吸流量为200、400和600 m L/s时的情况,并将数值模型预测的壁面压力分布与实测结果比较。结果如果气道内气流流量相同,吸气时气道两端的压差比呼气时大,即吸气时气道阻力比呼气时大。不同点压力分布的数值计算结果与实体模型测量结果一致。数值模拟结果表明,吸气时气道悬雍垂以及会厌后的舌后区域流动速度较高,悬雍垂下舌后区有涡旋产生。呼气时矢状位鼻咽顶端靠近后壁处,冠状位鼻咽、会厌下口咽处均有涡旋产生。结论数值模型可以准确地模拟上气道的流动状态和压力分布,直观地反映上气道内流动特点。作为非侵入式的工具,气道模型和数值模拟可以在探索阻塞性睡眠呼吸暂停(obstructive sleep apnea,OSA)的发病机制和有效治疗方法的过程中发挥重要作用。