A Novel Type of Coupling Between Proline and Galactoside Transport in Escherichia coli

Exit of thiomethylgalactoside (TMG) from preloaded cells induced the accumulation of proline. Likewise, proline exit stimulated TMG accumulation. Since a proton ionophore (carbonyl-cyanide-m-chlorophenylhydrazone) abolished these effects, a proton-motive force was implicated as the “intermediate” in the coupling reaction. The evidence suggests that the exit of TMG resulted in proton exit, which produced either a membrane potential (inside negative) or a pH gradient (outside acid) or both. This inwardly directed protonmotive force provided the energy for proline entry and accumulation. Thus the energy coupling was not via a common transport protein but by proton movements which coupled the two separate H⁺-dependent transport processes.     

Multifaceted applications of nanomaterials in cell engineering and therapy

Nanomaterials with superior physiochemical properties have been rapidly developed and integrated in every aspect of cell engineering and therapy for translating their great promise to clinical success. Here we demonstrate the multifaceted roles played by innovatively-designed nanomaterials in addressing key challenges in cell engineering and therapy such as cell isolation from heterogeneous cell population, cell instruction in vitro to enable desired functionalities, and targeted cell delivery to therapeutic sites for prompting tissue repair. The emerging trends in this interdisciplinary and dynamic field are also highlighted, where the nanomaterial-engineered cells constitute the basis for establishing in vitro disease model; and nanomaterial-based in situ cell engineering are accomplished directly within the native tissue in vivo. We will witness the increasing importance of nanomaterials in revolutionizing the concept and toolset of cell engineering and therapy which will enrich our scientific understanding of diseases and ultimately fulfill the therapeutic demand in clinical medicine.     

Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms

Proteins are dynamic entities in cellular solution with functions governed essentially by their dynamic personalities. We review several dynamics studies on serine protease proteinase K and HIV-1 gp120 envelope glycoprotein to demonstrate the importance of investigating the dynamic behaviors and molecular motions for a complete understanding of their structure–function relationships. Using computer simulations and essential dynamic (ED) analysis approaches, the dynamics data obtained revealed that: (i) proteinase K has highly flexible substrate-binding site, thus supporting the induced-fit or conformational selection mechanism of substrate binding; (ii) Ca²⁺ removal from proteinase K increases the global conformational flexibility, decreases the local flexibility of substrate-binding region, and does not influence the thermal motion of catalytic triad, thus explaining the experimentally determined decreased thermal stability, reduced substrate affinity, and almost unchanged catalytic activity upon Ca²⁺ removal; (iii) substrate binding affects the large concerted motions of proteinase K, and the resulting dynamic pocket can be connected to substrate binding, orientation, and product release; (iv) amino acid mutations 375 S/W and 423 I/P of HIV-1 gp120 have distinct effects on molecular motions of gp120, facilitating 375 S/W mutant to assume the CD4-bound conformation, while 423 I/P mutant to prefer for CD4-unliganded state. The mechanisms underlying protein dynamics and protein–ligand binding, including the concept of the free energy landscape (FEL) of the protein–solvent system, how the ruggedness and variability of FEL determine protein’s dynamics, and how the three ligand-binding models, the lock-and-key, induced-fit, and conformational selection are rationalized based on the FEL theory are discussed in depth.     

Remarkable disparity in mechanical response among the extracellular domains of type I and II cadherins

Cadherins, a large family of calcium-dependent adhesion molecules, are critical for intercellular adhesion. While crystallographic structures for several cadherins show clear structural similarities, their relevant adhesive strengths vary and their mechanisms of adhesion between types I and II cadherin subfamilies are still unclear. Here, stretching of cadherins was explored experimentally by atomic force microscopy and computationally by steered molecular dynamics (SMD) simulations, where partial unfolding of the E-cadherin ectodomains was observed. The SMD simulations on strand-swapping cadherin dimers displayed similarity in binding strength, suggesting contributions of other mechanisms to explain the strength differences of cell adhesion in vivo. Systematic simulations on the unfolding of the extracellular domains of type I and II cadherins revealed diverse pathways. However, at the earliest stage, a remarkable similarity in unfolding was observed for the various type I cadherins that was distinct from that for type II cadherins. This likely correlates positively with their distinct adhesive properties, suggesting that the initial forced deformation in type I cadherins may be involved in cadherin-mediated adhesion.

An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:25     

中国东西部中小城市景观格局及其驱动力

中小城市的数量及其所承载的城市人口迅速增加是当今和将来全球城市化的最为显著的特征之一.因此,对中小城市的发展规律及其城市化带来的生态和环境影响的研究日趋重要.然而,迄今为止的大多数有关城市化的研究聚焦于大型城市.通过对长三角地区和新疆地区24个中小城市的景观格局分析,结合人口经济数据,探究这两个地区总体城市景观格局的变化,城市间景观格局变化的变异性,以及城市景观格局变化的驱动力,并在此基础之上进行两地区间的对比分析.结果表明,1986年至2000年15a间,长三角地区和新疆地区中小城市的总体景观格局变化基本相似,景观的破碎化程度均不断上升,斑块形状更趋于不规则,景观多样性呈小幅增加;长三角地区中小城市间景观格局变异性下降,而新疆地区中小城市间景观格局变异性上升.长三角地区中小城市景观格局变化的驱动力主要是人口的增加和流动所导致的城市景观变化,新疆地区则为人口的增加和流动所导致的耕地景观面积增加.研究结果有助于解决我国中小城市急速发展所带来的一些生态和环境问题,以及通过土地利用规划来改善我国中小城市的可持续发展.     

纳米-TiO2对变异链球菌和白色假丝酵母菌抗菌机制的研究

目的 采用原子力显微镜对应用抗菌剂纳米Ag-Ti02作用后的口腔两种常见致病菌的分子形貌进行观测,为研究其抑菌机制提供有力的直观影像科学依据和可靠、直观的实验方法.方法 选择两种菌种:白色假丝酵母菌、变形链球菌,采用液体稀释法将纳米Ag-TiO2与两种菌相互作用,分别使用光学显微镜、原子力显微镜观察两种菌的细胞微观形态变化.结果 抗菌剂与两种菌作用后,细菌形态均有不同程度的改变,甚至是死亡.结论 原子力显微镜能直观地显示白色假丝酵母菌,变形链球菌的分子结构,通过本实验在研究纳米Ag-TiO2抗菌剂对白色假丝酵母菌,变形链球菌的抑菌机理形态学改变方面做了进一步的完善.     

A critical examination of the maximum velocity of shortening used in simulation models of human movement

The maximum velocity of shortening of a muscle is an important parameter in musculoskeletal models. The most commonly used values are derived from animal studies; however, these values are well above the values that have been reported for human muscle. The purpose of this study was to examine the sensitivity of simulations of maximum vertical jumping performance to the parameters describing the force–velocity properties of muscle. Simulations performed with parameters derived from animal studies were similar to measured jump heights from previous experimental studies. While simulations performed with parameters derived from human muscle were much lower than previously measured jump heights. If current measurements of maximum shortening velocity in human muscle are correct, a compensating error must exist. Of the possible compensating errors that could produce this discrepancy, it was concluded that reduced muscle fibre excursion is the most likely candidate.     

A muscle-path-plane method for representing muscle contraction during joint movement

Traditional muscle paths (the straight-line model and the viapoint-line model) emphasise either the mechanical properties that arouse joint movement or the morphological characteristics of the muscles. To consider both the factors, a muscle-path-plane (MPP) method is introduced to model the paths of muscles during joint movement. This method is based on the premise that there is a MPP, constructed by origin, insertion and MPP control point, which represents the major direction of the muscle contraction for an arbitrary joint configuration at any time. Then, we can calculate the functions and the lengths of the muscle paths during instantaneous joint movement in MPP by mathematical approaches. Taking the triceps brachii as an example, the lengths of its paths during elbow flexion are calculated and compared with the relative studies reported in the literature. It is concluded that this method can provide an insight into the simulation of the muscle contraction.     

A method to determine whether a musculoskeletal model can resist arbitrary external loadings within a prescribed range

Computational models of the musculoskeletal system are prone to design errors. It is possible to create a model that cannot satisfy equilibrium conditions for a set of external loading conditions. A model is ‘loadable’ if there exists a set of muscle forces that can resist an arbitrary applied force within a prescribed range. In this study, a novel mathematical method is introduced to determine whether models are loadable. In addition, an idealised musculoskeletal model is presented in order to develop the theory behind the mathematical method. The method uses the simplex algorithm to determine feasibility of the linear programming problem and can determine loadability for an arbitrary, continuous range of external forces. The method was applied to a three-dimensional model of the shoulder and correctly determined loadability for a range of externally applied forces.     

Validation of the Boussinesq equation for use in traction field determination

Cell traction force plays an important role in many biological processes. Several traction force microscopy methods have been developed to determine cell traction forces based on the Boussinesq solution. This approach, however, is rooted in a half-space assumption. The purpose of this study was to determine the error induced in the half-space assumption using a finite element method (FEM). It demonstrates that displacement error between the FEM and the Boussinesq equation can be used to measure the accuracy of the Boussinesq equation, although singularity exists in the loading point. For one concentrated force, significant difference between the FEM and the Boussinesq equation occurs in the whole field; this difference decreases with an increase in the plate thickness. However, in the case of the balanced forces, the offset of the balanced forces decreases the errors in the middle area. Overall, this study demonstrates that increasing the thickness of the polyacrylamide gel is important for reducing the error of the Boussinesq equation when determining the displacement field of the gel under loads.