Proteins are biological macromolecules found in all biological organisms, which are polymers of amino acids joined together by peptide bonds. They contain elements such as hydrogen, nitrogen, oxygen, carbon, and sulfur which form the structural material of bodily tissues and major components of muscles, tendons, blood vessels, bones, teeth, skin and hair. Protein structures are imperative to the functioning of all living cells and viruses. Each type of protein is different in its sequence of amino acids. The position of the chemically distinct chains gives each type of protein individual properties.
Protein structure levels are primary, secondary, tertiary, and quaternary structures.
- The primary structure refers to the protein sequence or linear number and order of the amino acids.
- In the secondary structure, the chains of amino acids are organized into regular structures also known as alpha-helixes and beta-pleated sheets, which are held together by hydrogen bonds.
- The tertiary structure is the three-dimensional shape of a single protein molecule influenced by hydrogen bonding, disulfide linkages, electrostatic interactions, and hydrophobic interaction. The structure is held together by interactions between the side chains.
- Not too different from tertiary structure in terms of chain interaction is the quaternary structure. It is composed of a combination of two or more chains to complete a unit. Determination of quaternary structure uses various experimental techniques that require samples of proteins.
The structures of protein can evolve, like a protein domain, which can function and exist independently. DNA sequences can also create unnaturally existing DNAs like recombinant proteins. Elements such as these and more keep protein structures complex.
As developments in structural biology evolve, scientists, researchers, and students continue to study and understand the complexities of protein structures. Prediction, visualization, and analysis of the protein structures can now be studied using animation sequences. Here are some steps on how to create protein structure animation:
- Download a tool designed for animated visualization, analysis, and drawing of protein structure and protein prediction. A number of molecular animation programs can be purchased or downloaded from the web for free. Different applications can provide ball and stick animations of molecular structures, virtual reality 3D animation, display molecular dynamics simulations, show an alpha helix, DNA and DNA polymerase, homeoboxes, beta sheet, etc. Such software is packed with tools for drawing, viewing, and structure manipulation among other tasks. Examples are Windows Protein Data Bank, Movie Mol, Visual Molecular Dynamics, Anthreprot, Storm, WinPep, and Protein Advisor.
- Once the software is installed, follow tutorials prior to employing the utility. Be familiar with the available features to help you navigate easily. For instance, Protein Advisor, which is available for Macintosh computers, allows easy navigation and manipulation of all entries in the Protein Data Bank. It provides visualization of biomolecular structures using animation and stereo views. Special viewing capabilities are likewise featured. It also allows the user to find all atoms within a specified distance and can be manipulated with the logging window. Other capabilities include dragging residues on a sequence based structure; 3D structure comparison, which allows you to extract common substructures of proteins; 3D structure drawing that allows you to draw and label residues on bases and compounds, Id code search for specified structures, etc.
Proteins, being critical components of biological organisms, facilitate most of life’s functions. The study of protein structure and protein function is highly crucial to biochemistry, as well as to the biophysical, biotechnology, and pharmaceutical industries.