Selective reaction of hydroxylamine with chromophore during the photocycle of pharaonis phoborhodopsin

Crystals of alpha-momorcharin (MMC) were cross-linked and soaked in an 80% acetonitrile--water mixture and X-ray data were collected to 2.2 A resolution. MMC is a ribosome-inactivating protein with a sugar chain on Asn-227. In previous studies, the whole conformation of the sugar chain could not be obtained in the aqueous system. Here the structure of MMC in a low water system is shown to be similar to the native one, but the sugar chain on Asn-227 is defined by the electron density map. Several oxygen atoms of the oligosaccharide formed intramolecular hydrogen bonds to the protein moiety. The conformation of the residues in the active center is similar to that in the aqueous system. Our results show conformational alteration of the tetrasaccharide of MMC in organic media. They indicate that the oligosaccharides are more rigid in organic solvents. X-ray determination in organic media may be used to solve some structures of oligosaccharides linked to glycoproteins.     

Pentahaem cytochrome c nitrite reductase: reaction with hydroxylamine,a potential reaction intermediate and substrate

The pentahaem enzyme cytochrome c nitrite reductase catalyses the reduction of nitrite to ammonia, a key reaction in the biological nitrogen cycle. The enzyme can also transform nitrogen monoxide and hydroxylamine, two potential bound reaction intermediates, into ammonia. Structural and mechanistic aspects of the multihaem enzyme are discussed in comparison with hydroxylamine oxidoreductase, a trimeric protein with eight haem molecules per subunit.     

A self-organized chemical model and reaction cascade

Some reaction cascades in biological systems are analyzed by a self-organized chemical model, an autocatalytic reaction. This model is described by the coupling of a primary system which stabilizes the initial stage of the reaction rapidly and a partial system which controls the primary system slowly. By the internal force caused by a trigger above the threshold, the coupled system in near-equilibrium is broken and changed into a new state. From the rate equation for the coupled system, a dimensionless nonlinear state equation, n = -n3 - un - v, is derived, where n is the concentration of intermediate, and u, v are dynamic variables of the system. This equation is similar to a nonequilibrium tri-molecular reaction. By using this chemical network theory, fibrin polymerization. F + F----fm----fp + X, where F is a fibrinogen molecule, fm is a fibrin monomer, fp is fibrin polymer, and X is small peptides released from fibrinogen, is discussed as an excellent example of the enzyme reaction cascade.     

Specific chemical cleavage of diphtheria toxin with hydroxylamine. Purification and characterization of the modified proteins

Specific chemical cleavage of diphtheria toxin with hydroxylamine was performed to remove peptides of 10 and 7 kDa from the carboxyl terminus. The resulting modified proteins of 51 and 48 kDa (HA51DT and HA48DT, respectively) were purified and characterized with respect to structural and biological properties. The 51-kDa toxin binds to ATP-agarose, as does intact diphtheria toxin, while HA48DT does not bind to the nucleotide matrix. Neither modified toxin binds to the membranes of diptheria toxin-sensitive cells, and, consequently, neither is toxic. However, when covalently linked to a membrane binding moiety, both HA51DT and HA48DT are toxic. Cell-killing ability during a short exposure time indicated that concanavalin A (Con A) derivatives of diphtheria toxin and HA51DT are equally toxic, ConA HA48DT being somewhat less toxic, while the conjugate of ConA to A-chain kills a small number of cells only at inordinately high concentration (1 microM). We have thus separated the cell membrane binding function of diphtheria toxin from its membrane permeation function by removing specific small peptides from the carboxyl terminus. These modified toxins may have applications in the preparation of highly potent hybrid toxins.     

The smallest chemical reaction system with bistability

Background  

Bistability underlies basic biological phenomena, such as cell division, differentiation, cancer onset, and apoptosis. So far biologists identified two necessary conditions for bistability: positive feedback and ultrasensitivity.     

A multi-scaled approach for simulating chemical reaction systems

In this paper we give an overview of some very recent work, as well as presenting a new approach, on the stochastic simulation of multi-scaled systems involving chemical reactions. In many biological systems (such as genetic regulation and cellular dynamics) there is a mix between small numbers of key regulatory proteins, and medium and large numbers of molecules. In addition, it is important to be able to follow the trajectories of individual molecules by taking proper account of the randomness inherent in such a system. We describe different types of simulation techniques (including the stochastic simulation algorithm, Poisson Runge–Kutta methods and the balanced Euler method) for treating simulations in the three different reaction regimes: slow, medium and fast. We then review some recent techniques on the treatment of coupled slow and fast reactions for stochastic chemical kinetics and present a new approach which couples the three regimes mentioned above. We then apply this approach to a biologically inspired problem involving the expression and activity of LacZ and LacY proteins in E. coli, and conclude with a discussion on the significance of this work.