Rukman Hertadi

Metabolic regulation and maximal reaction optimization in the central metabolism of a yeast cell

Regulation of fluxes in a metabolic system aims to enhance the production rates of biotechnologically important compounds. Regulation is held via modification the cellular activities of a metabolic system. In this study, we present a metabolic analysis of ethanol fermentation process of a yeast cell in terms of continuous culture scheme. The metabolic regulation is based on the kinetic formulation in combination with metabolic control analysis to indicate the key enzymes which can be modified to enhance ethanol production. The model is used to calculate the intracellular fluxes in the central metabolism of the yeast cell. Optimal control is then applied to the kinetic model to find the optimal regulation for the fermentation system. The sensitivity results show that there are external and internal control parameters which are adjusted in enhancing ethanol production. As an external control parameter, glucose supply should be chosen in appropriate way such that the optimal ethanol production can be achieve...

A new strategy of glucose supply in a microbial fermentation model

Strategy of glucose supply to achieve an optimal productivity of ethanol production of a yeast cell is one of the main features in a microbial fermentation process. Beside a known continuous glucose supply, in this study we consider a new supply strategy so called the on-off supply. An optimal control theory is applied to the fermentation system to find the optimal rate of glucose supply and time of supply. The optimization problem is solved numerically using Differential Evolutionary algorithm. We find two alternative solutions that we can choose to get the similar result: either long period process with low supply or short period process with high glucose supply.

Molecular modeling on porphyrin derivatives as β5 subunit inhibitor of 20S proteasome

The ubiquitin-proteasome system plays an important role in protein quality control. Currently, inhibition of the proteasome has been validated as a promising approach in anticancer therapy. The 20S core particle of the proteasome harbors β5 subunit which is a crucial active site in proteolysis. Targeting proteasome β5 subunit which is responsible for the chymotrypsin-like activity of small molecules has been regarded as an important way for achieving therapeutics target. In the present study, a series of porphyrin derivatives bearing either pyridine or pyrazole rings as meso-substituents were designed and evaluated as an inhibitor for the β5 subunit of the proteasome by employing molecular docking and dynamics simulations. The molecular docking was performed with the help of AutoDock 4.2, while molecular dynamics simulation was done using AMBER 14. All compounds bound to the proteasome with similar binding modes, and each porphyrin-proteasome complex was stable during 30 ns MD simulation as indicated by root-mean-square-deviation (RMSD) value. An analysis on protein residue fluctuation of porphyrin binding demonstrates that in all complexes, porphyrin binding produces minor fluctuation on amino acid residues. The molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation shows that the binding affinities of mono-H2PyP, bis-H2PzP, and tetra-H2PyP were comparable with that of the potential inhibitor, HU10. It is noted that the electrostatic interaction increases with the number of meso-substituents, which was favourable for porphyrin binding. The present study shows that both electrostatic and van der Waals interaction are the main force which controls the interaction of porphyrin compounds with the proteasome.

Stability and Mobility of Lid Lipmnk in Acetonitrile by Molecular Dynamics Simulations Approach

Published by Oriental Scientific Publishing Company

Simple and Easy Method to Synthesize Chicken Eggshell Based Hydroxyapatite

Hydroxyapatite is a common material applied in orthophedia and dentistry. The application of this material is currently expanded to biotechnology field, such as to be used as support materials for enzymes immobilization. Hydroxyapatite can be synthesized by utilizing chicken eggshell waste in household and food industries. This work is aiming to provide a simple and easy method to synthesize hydroxyapatite from chicken eggshell. The synthesis of hydroxyapatite was firstly carried out by reacting chicken eggshell powder (calcium precursor) with (NH4)2HPO4 via modified precipitation at room temperature and normal atmospheric pressure. The mixture was then stirred variably for 1, 2, 3, and 24 hours. X-ray diffraction (XRD) analysis suggests that hydroxyapatite powder derived from this procedure formed a single-phase crystal and it was completely formed after the reaction has run for 1 hour. The scanning electron microscopy (SEM) image showed that the synthesized hydroxyapatite forms a rice-like pattern. The size of hydroxyapatite crystal measured at (002) plane was about 45 nm. Our result showed that simple modified precipitation at room temperature and normal atmospheric pressure in one hour reaction has successfully synthesized hydroxyapatite from chicken eggshell.

The Role of Electrostatic Interactions on Klentaq1 Insight for Domain Separation

We investigated the relationship between the thermostability of Klentaq1 and factors stabilizing interdomain interactions. When thermal adaptation of Klentaq1 was analyzed at the atomic level, the protein was stable at 300 and 350 K. It gradually unfolded at 373 K and almost spontaneously unfolded at 400 K. Domain separation was induced by disrupting electrostatic interactions in two salt bridges formed by Lys354-Glu445 and Asp371-Arg435 on the interface domain. The role of these interactions in protein stability was evaluated by comparing free energy solvation (ΔΔGsolv) between wild type and mutants. Substitution of Asp371 by Glu or Asn, and also Glu445 by Asn resulted in a positive value of ΔΔGsolv, suggesting that mutations destabilized the protein structure. Nevertheless, substitution of Glu445 by Asp gave a negative value to ΔΔGsolv reflecting increasing protein stability. Our results demonstrate that interactions at the interface domains of Klentaq1 are essential factors correlated with the Klentaq1 thermostability.