A computational investigation of thermodynamics, structure, dynamics and solvation behavior in modified water models

We investigate the properties of geometrically modified water models by performing molecular dynamics simulations of perturbations of the extended simple point charge (SPC/E) model of water over a wide range of temperatures at 1 bar. The geometric modification consists of altering the H-O-H angle in SPC/E. The dipole moment is held constant by altering the O-H bond length, while the electrostatic charges are left unchanged. We find that a H-O-H angle of at least 100 degrees is necessary for the appearance of density anomalies and of solubility extrema with respect to temperature for small apolar solutes. We observe the occurrence of two incompatible types of structural order in these models: Tetrahedral, with waterlike translational order for bent models with H-O-H angles in excess of 100 degrees ; and linear, with Lennard-Jones-like orientationally averaged translational order for smaller H-O-H angles. Increasing the H-O-H angle causes the density to increase, while at the same time shifting waterlike anomalies to progressively higher temperatures. For bent models with H-O-H angle greater than SPC/E's, we observe arrest of translational motion at 300 K (115 degrees) and 330 K (120 degrees).     

Photoionization of Al IV (neon-type) from its ground 2s 22p 6 1 S e and excited 2s 22p 53p 3,1 P 0 3 S e states using the R-matrix method

The R-matrix method is used to calculate the total photoionization cross-sections from the ground 2s ²2p ^{6 1} S ^e and the first three excited 2s ²2p ⁵3p ^3,1 S ^e states of Al IV, for photon energies ranging from the first ionization threshold to just above the second threshold of the residual ion Al V. The two lowest LS terms of Al V − 2s ²2p ^{5 2} P ⁰, 2s2p ^{6 2} S ^e, 2s2p ^{6 2} S ^e, represented by sophisticated configuration interaction wavefunctions, are included in the R-matrix calculation. The resulting cross-sections are affected by Rydberg series of resonances converging to the 2s2p ^{6 2} S ^e excited threshold.     

Metal-sensitive and thermostable trypsin from the crevalle jack (<Emphasis Type="Italic">Caranx hippos</Emphasis>) pyloric caeca: purification and characterization

Background

Over the past decades, the economic development and world population growth has led to increased for food demand. Increasing the fish production is considered one of the alternatives to meet the increased food demand, but the processing of fish leads to by-products such as skin, bones and viscera, a source of environmental contamination. Fish viscera have been reported as an important source of digestive proteases with interesting characteristics for biotechnological processes. Thus, the aim of this study was to purify and to characterize a trypsin from the processing by-products of crevalle jack (Caranx hippos) fish.

Results

A 27.5 kDa trypsin with N-terminal amino acid sequence IVGGFECTPHVFAYQ was easily purified from the pyloric caeca of the crevalle jack. Its physicochemical and kinetic properties were evaluated using N-α-benzoyl-_DL-arginine-p-nitroanilide (BApNA) as substrate. In addition, the effects of various metal ions and specific protease inhibitors on trypsin activity were determined. Optimum pH and temperature were 8.0 and 50°C, respectively. After incubation at 50°C for 30 min the enzyme lost only 20% of its activity. K _m , k_cat, and k _cat /K _m values using BApNA as substrate were 0.689 mM, 6.9 s^-1, and 10 s^-1 mM^-1, respectively. High inhibition of trypsin activity was observed after incubation with Cd²⁺, Al³⁺, Zn²⁺, Cu²⁺, Pb²⁺, and Hg²⁺ at 1 mM, revealing high sensitivity of the enzyme to metal ions.

Conclusions

Extraction of a thermostable trypsin from by-products of the fishery industry confirms the potential of these materials as an alternative source of these biomolecules. Furthermore, the results suggest that this trypsin-like enzyme presents interesting biotechnological properties for industrial applications.

     

Properties of model atomic free-standing thin films

We present a computational study of the thermodynamic, dynamic, and structural properties of free-standing thin films, investigated via molecular dynamics simulation of a glass-forming binary Lennard-Jones mixture. An energy landscape analysis is also performed to study glassy states. At equilibrium, species segregation occurs, with the smaller minority component preferentially excluded from the surface. The film's interior density and interface width depend solely on temperature and not the initialization density. The atoms at the surface of the film have a higher lateral diffusivity when compared to the interior. The average difference between the equilibrium and inherent structure energies assigned to individual particles, as a function of the distance from the center of the film, increases near the surface. A minimum of this difference occurs in the region just under the liquid-vapor interface. This suggests that the surface atoms are able to sample the underlying energy landscape more effectively than those in the interior, and we suggest a possible relationship of this observation to the recently reported formation of stable glasses by vapor phase deposition.     

Chiral symmetry breaking in a microscopic model with asymmetric autocatalysis and inhibition

Asymmetric autocatalysis and inhibition have been proposed as key processes in the spontaneous emergence of chiral symmetry breaking in a prebiotic world. An elementary lattice model is formulated to simulate the kinetics of chiral symmetry breaking via autocatalysis and inhibition in a mixture of prochiral reactants, chiral products, and inert solvent. Starting from a chirally unbiased initial state, spontaneous symmetry breaking occurs in spite of equal a priori probability for creating either product enantiomer, and the coupled reaction-diffusion processes subsequently amplify the random early-stage symmetry breaking. The processes of reaction and diffusion are kinetically intertwined in a way leading to competition in the appearance of enantiomeric excess. An effective transition temperature can be identified below which spontaneous symmetry breaking appears. In the absence of inhibition, reactions are predominantly autocatalytic under both reaction control (fast diffusion, slow reaction) or diffusion control (fast reaction, slow diffusion) conditions. In the presence of inhibition, simulations with different system sizes converge to the same transition temperature under reaction control conditions, and in this limit the reactions are predominantly nonautocatalytic.     

Simultaneous determination of structural and thermodynamic effects of carbohydrate solutes on the thermal stability of ribonuclease A

This communication describes a new technique for the study of the effects of carbohydrates on the thermal stability of proteins. This approach combines capillary electrophoresis (CE) and protein charge ladders, collections of proteins that differ incrementally in number of chemically modified charged groups, to provide information on both the thermodynamics (i.e., the free energy, DeltaGN-D, of denaturation), and structural changes (i.e., the effective hydrodynamic radius, RH, of proteins in both the native and denatured states) associated with stability. This information, obtained in a single set of electrophoresis experiments, allows a simple microscopic interpretation of the effects of carbohydrate solutes on protein stability. We use this technique to show that the stabilization of ribonuclease A at pH 8.4 by sucrose and fructose can be explained entirely by the contribution these solutes make to the entropy of formation of the protein-solution interface. There is no need, in this case, to refer to quasichemical concepts such as preferential hydration, binding, or exchange of solutes with water at specific sites on the protein to account for the stabilizing effects observed.