Volume 21, Issue 2 , May and June 2014, , Pages 362-369
Abstract
Background: Molecular dynamics method to simulate the thermodynamic behavior of materials in the solid phase, liquid and gas using the force, velocity and position of particles. Among these factors, the most important factor is power. Classical molecular dynamics simulations, Classical potential energy ...
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Background: Molecular dynamics method to simulate the thermodynamic behavior of materials in the solid phase, liquid and gas using the force, velocity and position of particles. Among these factors, the most important factor is power. Classical molecular dynamics simulations, Classical potential energy is obtained. potential classic, is a function of the location and position of electrons in atoms or nuclei of atoms is dependent. purpose of this study compare the energy calculated for a number of biologically important proteins.
Materials and Methods: Molecular dynamics simulation provide an appropriate way to microscopic atomic and molecular modeling. The calculations were performed on a personal computer with the program hyperchem. No changes were made and geometry of all atoms, Dihedral angles and bonds were self-change.
Results: The final energy of protein structures using Monte-Carlo simulations, molecular dynamics and Langevin dynamics was performed. Optimize the geometry and the interaction energies calculated with different methods, for several proteins, including nerve growth factor receptor and enzyme protein was comparable effective learning.
Conclusion: Molecular dynamics simulations of quantum and classical potential energy of the electron Schrödinger equation is calculated. Simulation methods using a set of non-equilibrium transport properties and consider the effects of quantum mechanics are developed. Energy potential and the degree during the heat simulations almost constant that indicates the stability of the temperature structure of these proteins are listed.
Volume 20, Issue 5 , March and April 2014, , Pages 659-664
Abstract
Abstract
Introduction: Cholinergic neurons play an important role in muscle contraction, in learning and memory. Choline acetyltransferase is the enzyme that is responsible for the synthesis of acetylcholine and is a specific marker for choiinergic neurons. Computational methods investigate on Choline ...
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Abstract
Introduction: Cholinergic neurons play an important role in muscle contraction, in learning and memory. Choline acetyltransferase is the enzyme that is responsible for the synthesis of acetylcholine and is a specific marker for choiinergic neurons. Computational methods investigate on Choline acetyltransferase enzyme.
Aim: The aim of the present work was to describe and characterize the molecular structure vibrational properties of choline acetyltransferase crystalline-structure. In this work, the structures of a coordination compound modeling the choline acetyltransferase computationally. Thus, it is worthwhile to collect information on their structures by the means of computational chemistry as well.
Materials and Methods: Monte Carlo simulations are based on pair wise additive potentials of the form . In concepts and algorithms of classical MD simulations the atoms of a biopolymer move according to the Newtonian equations of motion. These studies provided insights into the steric, electrostatic, hydrophobic, and hydrogen bonding properties and other structural features influencing the choline acetyltransferasewas
Results: Potential energies for the three force fields of MM+, AMBER and OPLS at Monte Carlo simulation were compared. Geometry of optimized variables of Bond length (B),Bond Angle (A) and Dihedral Angle (D) investigated. The potential energy (kcal/mol) via time (ps) during Molecular Dynamic (MD) simulation at300 K in gas (R2 = 0.7656) and water (R2 = 0.9794) environments studied to stabilized structure of choline acetyltransferase accepted.
Conclusion: These results also were revealed that the solvation of Choline acetyltransferase molecule is the major component for the interaction potential energy and it was clearly shown that the role of the solute-solvent interactions is more pronounced in Choline acetyltransferase molecule and it’s active site solvation
Volume 20, Issue 3 , September and October 2013, , Pages 331-337
Abstract
Introduction: The insulin-like growth factor naturally exists in the Central Nervous System (CNS) and plays a significant role in cellular multiplication and differentiation during growth and maturation of the brain. These factors are expressed with their bond proteins and their receptors in the damaged ...
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Introduction: The insulin-like growth factor naturally exists in the Central Nervous System (CNS) and plays a significant role in cellular multiplication and differentiation during growth and maturation of the brain. These factors are expressed with their bond proteins and their receptors in the damaged areas of the brain. This indicates the role of IGFs systems in the brain damage.
Objective: Molecular simulation is a direct computational method for studying the structural changes of a wide spectrum of physical and biological issues. Computationally, experimental force fields have various forms in simulation of folding insulin-like growth factor.
Materials and Methods: In this study, the transfer temperature for IGF1 was modulated. The system was balanced and was studied and analyzed through dynamic molecular method within 500 Pico seconds.
Results: Studying the changes occurred in the potential energy of the three force fields showed that Amber force field is better than MM+ and OPLS force field and also MD simulation, at least in this model, is more effective than MC and LD methods.
Conclusion: Low temperatures make the structure more stable while high temperatures are on the contrary.