Design of glycolysis

The design of the glycolytic pathway resulting from the continuous refinement of evolution is discussed with regard to three aspects. 1. Functional and structural properties of individual enzymes. The catalytic constants of the glycolytic enzymes are remarkably optimized; the turnover numbers are within one order of magnitude. The same is true for the molarities of catalytic centres in the cytosol, as is noted for yeast. Functional properties of the enzymes are reflected in their tertiary and quaternary structures. 2. Regulatory mechanisms of single enzymes. A classification of the various types of enzymic control mechanisms operating in the glycolytic pathway is given. In addition to the usual Michaelis-Menten saturation kinetics and the various types of inhibition there is control by positive and negative effectors based on oligomeric structures (fast acting, fine control) as well as regulation by chemical interconversion structures (fast acting, fine control) as well as regulation by chemical based on enzymes cascades (slow acting, very effective). 3. Functional and regulatory mechanisms of the whole glycolytic reaction pathway. A prominent feature is the high enzyme:substrate ratio, which guarantees fast response times. However, a quantitative treatment of the overall kinetics is limited by an incomplete knowledge of the enzymes' dynamic and chemical compartmentation as well as some of their control properties. From an analysis of the oscillatory state, certain control points in the glycolytic chain can be located that coincide with major branching points to other metabolic pathways. These points are controlled by fast-acting cooperative enzymes that operate in a flip-flop mechanism together with the respective antagonistic enzymes, preventing futile cycles. The gating enzymes leading to the glycogen store and the citric acid cycle are of the slow-acting but very effective interconvertible type. The combination of all the complex and intricate features of design yields a glycolytic network that enables the cell to respond to its various metabolic needs quickly, effectively and economically.     

Design of carbohydrate multiarrays

Recently, microarray technology has increasingly been widely applied in glycobiology. This technology has rather evident potential advantages: unlimited number of carbohydrate ligands coated onto one small sized chip, enormously low consumption of both carbohydrate ligands and carbohydrate-binding proteins to be tested, etc. Literature data demonstrate that three approaches are used for glycoarray design. The first one is based on the physical adsorption of glycomolecules on a surface (as in a common ELISA), the second one-on covalent immobilization, and the third one-on a streptavidin-biotin system. In all of the described methods, carbohydrate ligands were placed on chips as a 2D monolayer and high sensitivity was achieved due to fluorescent detection. Notably, a tendency of stepping from model chips toward real multiarrays, where the number of carbohydrate ligands can be up to two hundred, has been observed the last 2 years, this already producing a number of interesting findings when studying carbohydrate-binding proteins. In 2005 new construction, 3D glycochip was described, where 150 mum diameter polyacrylamide gel elements serve as microreactors instead of 2D dots. As a result of the 3D placement of a ligand, two orders of magnitude increase of its density is possible, this providing principal signal improvement during fluorescent detection and increasing method sensitivity. At the same time, carbohydrate consumption is low, i.e., approximately 1 pmol per gel element. Copolymerization chemistry enables the immobilization of several glycomolecule classes to the gel, in particular, aminospacered oligosaccharides, polyacrylamide conjugates, and even 2-aminopyridine derivatives of oligosaccharides, which are widely used in the structural analysis of glycoprotein N-chains.     

电压钳控制电流钳的设计

研究证明,传统膜片钳放大器在电流钳模式下记录到的快速电压信号会存在失真,且造成失真的根本原因是由于膜片钳的探头电路设计.为了克服这些缺陷重新设计了一种探头,新探头电路不仅能像传统的电压跟随器一样测量瞬态电压,而且适用于传统的电压钳工作模式.此外,一种命名为电压钳控制的电流钳技术被应用来改进传统的膜片钳放大器.用可变的低通滤波器来调整电压钳模块的响应速度,从而在实现膜电位钳位的同时准确记录快速电压信号.桥平衡电路用来消除命令电流流过串联电阻时带来的电压误差.而传统膜片钳中的快电容补偿环节则被改进用来补偿电极分布电容和探头放大器输入电容并提高电流钳模式下系统的响应速度.细胞模型实验结果表明,改进后的膜片钳放大器能够满足电生理研究中快速电位变化测量的需要.     

Evolution of Integrated Design

There is an intricate integration of parts in the bodies ofanimals which can in some cases and to some extent be demonstratedquantitatively and must presumably be maintained in evolution.There is intricate fit between parts packed together in thebodies of animals so that changes in the relative sizes of organsmay make complex rearrangement necessary. These points are illustratedby examples concerning the legs of dogs and the heads of ostariophysanfishes.     

Design of fluidized-bed fermentors

Designing a fluidized-bed bioreactor requires choosing the best support particle (if any). Effectiveness factors (proportional to reactor volumetric productivity) are derived for flocs, solid spherical supports, porous supports, and adsorbent supports. The derivation demonstrates a mathematical procedure for reducing the diffusion/uptake equations for many components (substrates and inhibitory products) to a single equation, and for identifying the limiting component. With solid supports there exists a film thickness that maximizes the effectiveness, and the design objective is to keep the film near this optimum throughout the bed. This involves consideration of the effect of support particle density and film growth on bed stratification. Other considerations in picking support particles are obtaining reasonable values for bed height and diameter, minimizing mass transfer resistance between liquid and biomass, and preventing surface shear from stripping off the biomass.     

Design of luminescence photobiosensors

The potential of immobilized enzyme membranes in biosensors has been explored in our group for several years. Although part of our work has been mainly devoted to electrochemical transducers and oxidases for the design of enzyme electrodes, the demand for ultrasensitive and highly selective sensors led us to consider the use of luminescent enzyme systems associated to optical transduction. When considering the need for operational and reliable biosensors in biotechnology, immobilization and stability of the sensing element still remain, in most cases, an unavoidable problem. We recently proposed a very fast and reliable procedure for preparing enzymatic membranes from Pall (Biodyne Immunoaffinity membranes) supplied in a pre-activated form. Both the firefly and bacterial systems as well as peroxidase for the chemiluminescent determination of various analytes, could be bound to such a support. Based on this approach, a fibre-optic sensor with immobilized enzymes has been designed which permits bio- or chemiluminescent analysis of ATP, NADH or H₂O₂ respectively. With the NADH-based system, other analytes could be detected using coupled dehydrogenases. This device appears very promising and includes the convenience of both the luminescence sensitivity as well as the handling of the biosensor design.     

Design of protease inhibitors

There is a general parallelism in the strategy followed in the design of hormonal peptide analogs and protease inhibitors. However, in the latter, one more dimension has been added with the development of mechanism-based inhibitors, a dimension that is not yet available for hormonal peptides because of the lack of knowledge about receptor mechanisms. The recently advanced concepts of transition state and bi-product analogs have made possible the development of highly potent active-site directed reversible protease inhibitors of great therapeutic potential.