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Protein Families - Coursework Example

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The paper deals with the analysis of protein families using bioinformatics programs such as Crescendo/CHARMM/Amber etc. Reportedly, the general protein analysis involves
the development of methods to predict structure and function of proteins.
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Protein Families
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"Protein Families"

Download file to see previous pages The analysis of a single gene sequence is done by establishing similarity with other known genes, determining phylogenetic trees and evolutionary relationships; identifying well-defined domains in the sequence, identifying physical properties, binding sites and modification sites comprising of the protein sequence features.
For analysis of complete genomes and to determine which gene families are present in the protein and which are not present, several techniques such as location of genes on the chromosomes, correlation with function or evolution, expansion of duplication of gene families, identification of missing enzymes, and presence or absence of biochemical pathways are considered. Large scale events that have affected the evolution of organisms are also studied for genome analysis.
When genes or genomes are analyzed with respect to functional data the techniques used are expression analysis, micro array data, mRNA concentration measurements, protein concentration measurements, proteomics, and covalent modifications. For analysis of gene and genomes from a functional perspective, comparative analyses of biochemical pathways are made along with deletion or mutant genotypes vs. phenotypes and identification of essential genes, or genes involved in specific processes in structure and functions of the organisms.
Analysis of protein structure and functions are done with the help of computer simulations which are used as tools to investigate protein structure and dynamics under a wide variety of conditions....
When genes or genomes are analysed with respect to functional data the techniques used are expression analysis, micro array data, mRNA concentration measurements, protein concentration measurements, proteomics, and covalent modifications. For analysis of gene and genomes from a functional perspective, comparative analyses of biochemical pathways are made along with deletion or mutant genotypes vs. phenotypes and identification of essential genes, or genes involved in specific processes in structure and functions of the organisms (Lengauer, 2002).
Analysis of protein structure and functions are done with the help of computer simulations which are used as tools to investigate protein structure and dynamics under a wide variety of conditions, ranging from ligand binding and enzyme-reaction mechanisms to denaturation (in which protein molecules become biologically inactive) and protein re-folding (Ponder and Case, 2003). In all these simulations, the energy of a protein is represented as a function of its atomic coordinates. These functions are known as force fields as forces on individual atoms are related to the gradient of this potential energy function (Ponder and Case, 2003).

The protein force fields are represented using a simple equation that shows the potential energy function (Source, Ponder and Case, 2003)



Source, Ponder and Case, 2003

The summations shown here are on bonds, torsions and angles and this equation represents the very basic potential energy function that can reproduce only the essential features of protein energy at an atomic level. According to Ponder and Case (2003), the combination of potential energy function and the other parameters constitute a force field. ...Download file to see next pagesRead More
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