REDOX REACTIONS IN BIOTECHOLOGY

In short redox reactions involve the oxidation of one compound, while reducing another.
In the concept of biological oxidation associated with combustion and decomposition of organic compounds to release energy, and indeed it is. However, the oxidation of a chemical compound is always associated with a reduction in another, and the same redox reaction does not necessarily have to be associated with the distribution of complex to simple. However, always involves a change in the oxidation state of atoms or groups of atoms, or (chemical groups). The degree of oxidation depends on the number of free electrons in an atom or chemical group. The group that gives electrons is called the reductor, and the recipient - oxidant.

In many metabolic biochemical pathways redox reactions occur in parallel to the transmission of electrons and protons in different physical locations of the cells thus generating small differences in electrical potential. Such a difference in electrical potential stimulates an electrical voltage which is used as the driving force of many chemical reactions and physical changes (electricity has been the basis of action of nerve cells and the nervous system, which controls the operation of the entire body, stimulates the active transport across biological membranes is driven powerful driving action of the protein complex in the process of synthesizing ATP synthesis chemiosmotycznej (ATPase)).

Generation and use of electrical voltage in the cell and in various organelles can be applied to complex electrical device to ground components tethered to a motherboard that separates the direction and strength of the voltage, the voltage generator (electron donor and recipient) are chemical compounds, which may not be subunits performing a task (eg ATPase), controlling the execution of tasks (enzymes and co-enzymes), or regulating the transport of protons and electrons (NAD, FAD, etc.).

SOFTWARES FOR MOLECULAR DYNAMICS CALCULATIONS

The starting point for the method of molecular dynamics (MD) is well defined microscopic description of a physical system consisting of a number of such bodies. Description of the system can be represented in the form of equations of motion of Theoretical Mechanics: Hamiltonian and Lagrangian or express directly by Newton's equations of motion. In the first two cases, the equation of motion must be previously obtained by using the well known formalisms. The method of molecular dynamics, as its name suggests, is used to calculate the property on the basis of the equations of motion, allowing you to get to test the properties of both static and dynamic.

In the molecular dynamics , it is possible to change the temperature in a controlled manner, called a simulated cooling. Apply an alternating sequence of heating and cooling system, so as to finally get frozen in some system configurations (configuration expected to achieve a low-energy).
MD method is based on , the numerical solution of equations of motion using a computer.

Softwares for molecular dynamic calculations

Among the many software packages like VEGAZ ZZ, SPARTAN, NANOENGINEER for molecular dynamics deserve a special mention include: Amber, CHARMM, GROMACS, GROMOS, NAMD, Tinker and Desmond.

DENSITY FUNCTIONAL THEORY - DFT

Density functional theory (DFT, called density functional theory) - pillar several quantum-mechanical methods, used for modeling the structure of chemical molecules or crystals. These methods are alternatives to methods based on the wave functions.
This theory assumes that all properties of a quantum system in a steady state due to the electron density of the ground state. More specifically, it is assumed that all observables are functionals unequivocal electron density of the ground state.
At steady state the potential for movement of outer electrons (the potential of the atomic nuclei or the external electrostatic potential) is independent of time. An extension of DFT for states with varying external potential, such as a sinusoidal alternating current, derived from electromagnetic wave is TDDFT (time-dependent density functional theory). DFT theory is based on two Hohenberg-Kohn theorems.
Density functional theory (DFT) calculations have been used to investigate the physical orign of the perturbation to NMR chamical shifts upon protein binding.

Softwares for Density Funtional Theory

DFT is supported by many quantum chemistry and solid state physics softwares, oftem along with other methods. Versatile sofware pakages for DFT include: the Vienna Ab initio Simulation Package (VASP), QUANTUM-ESPRESSO, ABINIT, GPAW, Gaussian and BigDFT.

MOLECULAR DOCKING

Molecular docking of a method allowing to test one molecule of molecular recognition by another, and thus provide a method for binding and binding affinity for the complex formed by two or more molecules of known structures.

In the case of the receptor protein (RB) and the ligand (L) to be the correct docking to predict how RBL complex binding at equilibrium in aqueous solution described by equation (2)

[RBL] ↔ [RB] + [L] (2)

Figure 1: Azurine-CNT complex [RBL] , receptor - Modified Carbon Nanotube [RB], ligand - Azurine [L] A measure of the stability of the resulting complex is RBL binding free energy - VGB, which is related to the affinity of binding to or otherwise association constant of the complex according to the formula:

VGB = - RT ln (Ka)

, where R - gas constant, T - temperature, and Ka - the association constant concentration equal to the ratio of concentrations of the complex RBL-free ingredients RB and L (Ka = [RBL] / [RB] [L]) .

Docking ligand to the receptor protein comprises two consecutive processes: sampling and scoring. Sampling consists of generating different conformations of ligand-receptor binding site. This is achieved by taking into account both the sampling of conformational flexibility of the ligand and the receptor protein.

Docking methods based on ligand binding and conformational sampling include: matching shapes and ligand binding site in the receptor protein, the search for systematic and stochastic algorithm. The protein conformational sampling is sometimes considered by: soft docking, molecular relaxation, taking into account the docking side chain flexibility and involving multiple conformations of the receptor. The use of evaluation functions are empirical and are based on knowledge or derived from the use of molecular mechanics force fields.

During doking, the interaction energy of the protein with the metal surface is described by three main terms: van der Waals energy described by site-site Lennard-Jones, E.LJ, interactions (which also include weak chemical binding of aromatic residues, sulfur and histidine nitrogen atoms to graphite electrode), adsorbate – metal surface,, Umds. The electrostatic term arises from surface polarization and is represented by an image-charge term.

Softwares for molecular docking

There are a lot of programs for molecular docking, both commercial and free available.
The best-known programs include: Autodock, Autodock Vina, DOCK, DockVision, GOLD, ICM, PSI-DOCK and Vegaz ZZ.

Kitchen salat used for creating silicion nanostructures

Kitchen salt (NaCl) reduces the cost of production of silicon nanostructures. Melting and absorbing heat at a critical magnetotermic moment reduction, salt is not allowed to collapse the pores and clumping of domains in large crystals of silicon. After all the salt can be washed with water and used again. Professor. David Xiulei Ji from Oregon State University believes that the cheap and salt-based industrial-scale production of high quality silicon nanostructures should it become a reality. Previous methods were expensive and allow for a small number of nanostructures. Cheaper technologies did not come true because require the use of high temperatures. Nanostructures can be used for example in photonics, bio-imaging, sensors, drug delivery, energy storage or in thermoelectric materials. Ji believes that the first fire will go batteries whose life is almost two times longer than their modern counterparts. During the experiments Ji NaCl and magnesium were mixed with diatomaceous earth. At 801 degrees Celsius starting to melt salt (and thus the absorption of heat). Importantly, NaCl did not contaminate anything. Americans point out that the process of scaling up to a commercial level seems feasible. In the same wayfrom mixed oxides were obtained SiO2/GeO2 composite Si / Ge. It will be used in the manufacture of semiconductors and thermoelectric materials.

Source: Oregon State University