Ubiquitin Structure Research Paper
Graphical Analysis of the Structure of the Ubiquitin Protein Molecule Using the VMD Computer Program
Author’s Name
Chemical Engineering Department, University of New Hampshire - Durham
ABSTRACT
VMD is a molecular visualization program developed by the Theoretical and Computational Biophysics group of the University of Illinois at Urbana-Champaign with the goal of displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Therefore, The VMD program is vital when it comes to the display and analysis of protein primary, secondary, tertiary, and quaternary structure. The focus of the study, conducted through the means of VMD, was directed towards Ubiquitin, a regulatory protein found in nearly every eukaryotic tissue and associated with the function of degradation of defective and superfluous proteins in the organism. A special emphasis was given to the graphical analysis of protein backbone conformation and secondary structure, general atom distribution, and hydrophobic versus hydrophilic behavior and its connection with polar and non-polar region distribution. As a culmination of the study, it was concluded that the structure of the Ubiquitin molecule adheres to the scientific principles of protein structure and function.
INTRODUCTION
The current study focused on the graphical analysis of the structure of the Ubiquitin protein molecule using the VMD computer program. VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, and lipid bilayer assemblies. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and
Author’s Name
Chemical Engineering Department, University of New Hampshire - Durham
ABSTRACT
VMD is a molecular visualization program developed by the Theoretical and Computational Biophysics group of the University of Illinois at Urbana-Champaign with the goal of displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Therefore, The VMD program is vital when it comes to the display and analysis of protein primary, secondary, tertiary, and quaternary structure. The focus of the study, conducted through the means of VMD, was directed towards Ubiquitin, a regulatory protein found in nearly every eukaryotic tissue and associated with the function of degradation of defective and superfluous proteins in the organism. A special emphasis was given to the graphical analysis of protein backbone conformation and secondary structure, general atom distribution, and hydrophobic versus hydrophilic behavior and its connection with polar and non-polar region distribution. As a culmination of the study, it was concluded that the structure of the Ubiquitin molecule adheres to the scientific principles of protein structure and function.
INTRODUCTION
The current study focused on the graphical analysis of the structure of the Ubiquitin protein molecule using the VMD computer program. VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, and lipid bilayer assemblies. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and
Cited: Kuriyan, John. The Molecules of Life. New York: Taylor and Francis Group, 2013. Print. Theoretical and Computational Biophysics Group.VMD User’s Guide. NIH Biomedical Research Center for Macromolecular Modeling, 23 Dec. 2014. Web. 22 Jan. 2015. Theoretical and Computational Biophysics Group.VMD. University of Illinois at Urbana-Champaign, 20 Mar. 2006. Web. 22 Jan. 2015. Wikipedia. Wikimedia Foundation Inc., n.d. Web. 22 Jan. 2015.