Proteins are complex, high molecular mass, organic compounds that consist of amino acids joined by peptide bonds.
Proteins are essential to the structure and function of all living cells.
Many proteins are enzymes or subunits of enzymes. Other proteins play structural or mechanical roles, such as those that form the structures and joints of cytoskeleton. Still more functions of proteins include the storage and transport of various ligands.
In nutrition, protein serves as a source of amino acid for organisms that do not synthesize those amino acids natively.
There are also some more proteins that are pigmented in nature such as melanin.
For the generation of a representative equilibrium two methods are available:
Monte Carlo simulations and
Molecular Dynamics simulations.
For the generation of non-equilibrium ensembles and for the analysis of dynamic events, the second method is appropriate.
While Monte Carlo simulations are more simple than MD (as they do not require the computation of forces), they do not yield significantly better statistics than MD in a given amount of computer time.
Therefore Molecular Dynamics is the more universal technique for energy minimization.
Reason to perform an energy minimization is the removal of all kinetic energy from the system: if several ’snapshots’ from dynamic simulations is compared, energy minimization reduces the thermal noise in the structures and unstability, so that they can be compared better.
To run a simulation several things are needed like:
A file containing the coordinates for all atoms
Information on the interactions (bond angles, charges, Vander Waals)
Parameters to control the simulation
Processors to run the simulation
The PDB file contains the coordinates for all atoms and is the input structure file for MD Simulation. The interactions are listed in the topology (.top) file and the input parameters are put into a .mdp file.
GROMACS (Groningen Machine for Chemical Simulations) is a molecular dynamics simulation package originally developed in the University of Groningen.
GROMACS is an engine to perform molecular dynamics simulations and energy minimization.
A high performance Molecular Dynamics Program.
It is reasonably well optimized for low memory usage.
The highly optimized code makes GROMACS the fastest program for molecular simulations.
The support of different force fields and the open source (GPL) character make GROMACS very flexible.
It is a high performance research tool which can be run on almost every platform.
This program is free software; it can be redistributed and/or modified under the terms of the GNU General Public License as published by the Free Software Foundation.(A free software licence grants, to the recipients, freedoms in the form of permissions to modify or distribute copyrighted work)
Molecular Dynamics studies depend on the quality of the available experimental data. To generate an accurate minimized structure, information about its primary, secondary and tertiary structure is needed.
There are several publically available databases that contain primary, secondary and tertiary structural on proteins. Two particularly important databases are:
Protein Data Bank (PDB) at http://www.rcsb.org/pdb/.
This is the primary world wide archive of structural data of biological macromolecules.
Expert Protein Analysis System (ExPASy) at http://www.expasy.ch/.
This molecular biology server is dedicated to the analysis of protein sequences and structures.