基于大分子拥挤原理的介孔二氧化硅中青霉素酰化酶的共价组装

To improve the covalent immobilization of penicillin acylase （PA）, macromolecular crowding theory was applied to its immobilization. Influence of mass ratio of enzyme to the silica, as well as, activation time with glutaraldehyde on the activity of assembled PA, was studied. In the mesopores, the effect of fl-cyclodextrin （β-CD） on the immobilization of the enzyme was also investigated. It was remarkable that the coupled yield and relative activity reached 99.5% and 92.3%, respectively, when penicillin acylase assembled covalently in the mesopores. The results here indicate that mimicked macromolecule crowding could significantly ameliorate the performance of covalently immobilized PA.     

基于自适应混合非支配个体排序策略的改进型NSGA-Ⅱ算法

针对经典快速非支配排序遗传算法(NSGA-Ⅱ)中基于拥挤距离的种群多样性保持策略不能客观反映个体间真实拥挤程度的问题,提出了一种基于自适应混合非支配个体排序策略的改进型NSGA-Ⅱ算法(NSGA-Ⅱ^h)。首先,设计一种新的循环聚类个体排序策略;然后,根据Pareto分层信息来对基于经典拥挤距离和循环聚类的两种个体排序策略进行自适应的选择;最终,实现对进化后期的种群多样性保持机制的改进。通过5个标准测试函数进行算法验证,并与经典的NSGA-Ⅱ、多目标粒子群优化算法(MOPSO)和GDE3等算法进行对比分析,NSGA-Ⅱ^h算法获得了80%的最优反向世代距离(IGD)值,且显著性水平为5%的双尾t检验结果表明,新算法具有明显统计意义上的性能优势。改进算法不仅能提高进化种群的分布性,而且能增强算法的收敛性,有效提高了优化效果。     

大分子拥挤环境下多糖对蛋白肽的修饰研究

采用胃蛋白酶适度水解大豆分离蛋白得到蛋白肽,在大分子拥挤环境下通过Maillard反应制备蛋白肽-葡聚糖共价复合物(Hydrolated Soy Protein Isolated-Dextran Conjugates,HDC),采用十二烷基磺酸钠-聚丙烯酰胺凝胶电泳(SDS-PAGE)技术证实大豆7S球蛋白和葡聚糖发生了共价结合,并通过乳化剪切机、荧光分光光度计、差示扫描量热仪和粒度分布仪等对其接枝度、溶解性、热稳定性、抗氧化性和乳化性能进行系统分析。结果表明:大分子拥挤环境下大豆水解蛋白肽-葡聚糖60℃反应4 h就可以形成较高接枝度的共价复合物,溶解性较大豆分离蛋白(Soybean protein isolated,SPI)和大豆分离蛋白-葡聚糖(Soybean Protein Isolated-Dextran Conjugates,SDC)有所提高,热稳定性好,HDC的自由基清除率明显高于大豆水解蛋白和它与葡聚糖的混合物,达到66.39%,且羟自由基清除率高于维生素C,HDC的乳液粒径最小并具有优越的乳化稳定性。     

Liquid–Liquid Phase Separation in the Presence of Macromolecular Crowding and State-dependent Kinetics

Biomolecular condensates formed via liquid–liquid phase separation (LLPS) are increasingly being shown to play major roles in cellular self-organization dynamics in health and disease. It is well established that macromolecular crowding has a profound impact on protein interactions, particularly those that lead to LLPS. Although synthetic crowding agents are used during in vitro LLPS experiments, they are considerably different from the highly crowded nucleo-/cytoplasm and the effects of in vivo crowding remain poorly understood. In this work, we applied computational modeling to investigate the effects of macromolecular crowding on LLPS. To include biologically relevant LLPS dynamics, we extended the conventional Cahn–Hilliard model for phase separation by coupling it to experimentally derived macromolecular crowding dynamics and state-dependent reaction kinetics. Through extensive field-theoretic computer simulations, we show that the inclusion of macromolecular crowding results in late-stage coarsening and the stabilization of relatively smaller condensates. At a high crowding concentration, there is an accelerated growth and late-stage arrest of droplet formation, effectively resulting in anomalous labyrinthine morphologies akin to protein gelation observed in experiments. These results not only elucidate the crowder effects observed in experiments, but also highlight the importance of including state-dependent kinetics in LLPS models, and may help in designing further experiments to probe the intricate roles played by LLPS in self-organization dynamics of cells.     

一种新的多目标粒子群优化算法

论文提出了一种基于拥挤度和动态惯性权重聚合的多目标粒子群优化算法,该算法采用Pareto支配关系来更新粒子的个体最优值,用外部存档策略保存搜索过程中发现的非支配解;采用适应值拥挤度裁剪归档中的非支配解,并从归档中的稀松区域随机选取精英作为粒子的全局最优位置,以保持解的多样性;采用动态惯性权重聚合的方法以使算法尽可能地逼近各目标的最优解。仿真结果表明,该算法性能较好,能很好地求解多目标优化问题。     

基于拥挤距离的多目标粒子群算法

该算法通过引用NSGA-II中的拥挤距离,确定外部档案中非支配解的拥挤度,依据竞标赛选择方法选出每个粒子的全局最优位置,引导每个粒子向处于较稀松区域的非支配解搜索,提高了解的多样性。动态变异算子的引入,减缓了算法的收敛速度,增大了解的搜索区域,避免了算法早熟收敛或陷入局部最优。实验结果表明,算法CDMOPSO比NSGA-II具有更好的收敛性和维持种群多样性的能力。     

基于适应值共享的多生境排挤遗传算法

针对优化多模函数时单纯使用共享和排挤机制的遗传算法所存在的缺陷,提出了基于适应值共享的多生境排挤遗传算法。基本思想是：按照共享的思想在对个体的适应值进行调整的同时,将排挤选择和相似个体中适应度最差个体被替换的策略分别应用于选择算子和群体的进化中。理论分析和数值实验表明,该算法很好地维持了种群多样性,对于各类多峰函数具有较强的搜索能力。     

纤维分级对漂白云杉木浆纤维悬浮液屈服性能的影响

采用沉降和流变实验,研究了纤维分级对漂白云杉木浆纤维悬浮液屈服性能的影响,并分析了压缩屈服应力和剪切屈服应力的耦合相关性,通过Froude数(剪切屈服应力与压缩屈服应力的比值)表征。结果表明,分级前后各长度组分纤维(4种纤维悬浮液)的凝结集聚因子介于26.1～37.8之间,其与纤维长径比近似呈线性关系;所有长度组分纤维悬浮液的压缩屈服应力和剪切屈服应力均随集聚因子的增大而呈指数式增大;对同种纸浆,Froude数随集聚因子的增大而降低,并逐渐达到稳态值。     

Physicochemical Characterization of Polymer-Stabilized Coacervate Protocells

The bottom-up construction of cell mimics has produced a range of membrane-bound protocells that have been endowed with functionality and biochemical processes reminiscent of living systems. The contents of these compartments, however, experience semidilute conditions, whereas macromolecules in the cytosol exist in protein-rich, crowded environments that affect their physicochemical properties, such as diffusion and catalytic activity. Recently, complex coacervates have emerged as attractive protocellular models because their condensed interiors would be expected to mimic this crowding better. Here we explore some relevant physicochemical properties of a recently developed polymer-stabilized coacervate system, such as the diffusion of macromolecules in the condensed coacervate phase, relative to in dilute solutions, the buffering capacity of the core, the molecular organization of the polymer membrane, the permeability characteristics of this membrane towards a wide range of compounds, and the behavior of a simple enzymatic reaction. In addition, either the coacervate charge or the cargo charge is engineered to allow the selective loading of protein cargo into the coacervate protocells. Our in-depth characterization has revealed that these polymer-stabilized coacervate protocells have many desirable properties, thus making them attractive candidates for the investigation of biochemical processes in stable, controlled, tunable, and increasingly cell-like environments.     

Fluorescence Correlation Spectroscopy Analysis of Effect of Molecular Crowding on Self-Assembly of β-Annulus Peptide into Artificial Viral Capsid

Recent progress in the de novo design of self-assembling peptides has enabled the construction of peptide-based viral capsids. Previously, we demonstrated that 24-mer β-annulus peptides from tomato bushy stunt virus spontaneously self-assemble into an artificial viral capsid. Here we propose to use the artificial viral capsid through the self-assembly of β-annulus peptide as a simple model to analyze the effect of molecular crowding environment on the formation process of viral capsid. Artificial viral capsids formed by co-assembly of fluorescent-labelled and unmodified β-annulus peptides in dilute aqueous solutions and under molecular crowding conditions were analyzed using fluorescence correlation spectroscopy (FCS). The apparent particle size and the dissociation constant (K_d) of the assemblies decreased with increasing concentration of the molecular crowding agent, i.e., polyethylene glycol (PEG). This is the first successful in situ analysis of self-assembling process of artificial viral capsid under molecular crowding conditions.