Rana's Fun with Jolecule

Lysozymes

            In order to explore protein structures I went onto a protein model visualizer, called Jolecule, on http://jolecule.appspot.com/.  Once on the main page, I clicked on the “myoglobin” button, and then the “garden” link in the upper right corner.  This last link brought me to a variety of proteins to select from and learn about.  After I have looked through them, I chose to research the Lysozyme protein. 

            Lysozymes are small protein enzymes that bind to polysaccharide chains and break them apart by hydrolysis.  These enzymes protect humans from danger of bacterial infection by attacking and destroying the cell walls of the bacteria.  The bacteria itself constructs a tough skin of carbohydrate chains (sugars) that are interconnected by short peptide strands.  In order to fight the bacteria, the lysozyme breaks the carbohydrate chains of the bacteria, which in turn, destroys the structural integrity of the cell wall and causes the bacteria to burst.  However, as efficient as it is in killing bacteria, the lysozyme is too large of a molecule to travel between cells, that it cannot rid the entire body of disease.  Lysozymes occur in plant and animal tissues and in secretions such as tears, saliva and mucus.  Also it is greatly found in egg whites.  It is found in our tears, and mucus to resist infection on exposed surfaces.  Lysozyme also provides protection in the blood because blood is the worst place for bacteria to grow.  In general Lysozymes protect many places that are rich in potential food for bacteria.  As well, Lysozyme is added to digest cell debris and release the inclusion bodies. 

Furthermore, Lysozyme is a crystal structure with two structural domains.  One is made up of mainly alpha helices, and the other is mainly beta strands.  The boundary between the two domains forms a split where the substrate binds.  Lysozyme adds a molecule of water to the bond between two sugars, which breaks the bond.  This is catalyzed by two amino acid side chains in the active site of the enzyme.  These active sites are glutamate 35 and aspartate 52.  

- This is the overall picture of the lysozyme protein with the polysaccharide substrate in the center.

- This is one of the glu-35 active sites of the enzyme, which would lie next to the polysaccharide.  

- This is one of the asp-52 active sites of the enzyme, which would lie next to the polysaccharide.  

Rameia's Fun with Jolecule

Cyclooxygenase 

Rameia Ramsey 

 The protein I choose to examine and learn about is Cyclooxygenase. Cyclooxygenase, also known as COX, is an enzyme that is responsible for the creating of prostanoids, which are involved in the inflammatory responses. There are three main groups of prostanoids, which are the prostaglandins, prostacyclins, and thromboxanes. Prostaglandins are mediators of inflammatory and anaphylactic reactions, prostacyclins are seen in the resolution phase of inflammation, and thromboxanes are mediators of vasoconstriction, which is the narrowing of blood vessels from contractions from the muscular walls.

There are two forms of the Cyclooxygenase protein respectively named , COX-1 and COX-2. Both of these versions use arachidonic acid to produce prostaglandin but there are certain features that help make COX-1 unfavorable and COX-2 favorable. There are such things called COX-1 inhibitors, these are agents that hinder the action of the enzyme COX-1. The COX-1 enzyme is found in most cells and helps maintain the stomach’s. For example, inflammatory drugs such as aspirin or ibuprofen block the actions of COX-1 and COX-2. The COX-1 inhibitors are able to decrease inflammation but they can also decrease the protective mucus in one’s stomach, which in turn can cause a variety of health concerns such as an upset stomach or ulcers. This is how a COX-1 inhibitor can be seen as undesirable and unfavored. COX-2 inhibitors are agents that block the enzyme COX-2 which causes inflammation. The COX-2 enzyme converts arachidonic acid to prostaglandin which cause pain and inflammation, such as arthritis, in an individual's body. The COX-2 inhibitors relieves this pain. So drugs such as Bextra and Vioxx are examples of COX-2 inhibitors that help protect against the COX-2 enzyme. This is how COX-2 would be seen as more favorable to than COX-1.

Both COX-1 and COX-2 are tertiary structures because of the fact that the amino acids and the binding site and catalytic regions are almost exactly the same.  COX-1 and COX-2 are both homodimers. A dimer is a chemical compound that is made of two identical or similar monomers. A homodimers would be a dimer made of two identical monomers. They also both contain three high mannose oligosaccharides, a fourth oligosaccharide is found only in COX-2 which helps with its degradation. Each monomer of the dimer has three domains, which are the epidermal growth factor, membrane binding, and catalytic domain. On the other side of the membrane binding domain is the peroxidase active site which contains the heme. The active site of COX-2 is larger than the active site for COX-1. There are many differences between the two. COX-1 is produced under all types of physiological conditions, while COX-2 is produced only during specific conditions like inflammation. This would also explain why COX- 1 is found in the kidneys, stomach, and platelets and COX-2 is found in macrophages, leukocytes, and fibroblasts. They are also produced differently, COX-1 is made continuously while COX-2 is only produced when needed. COX-1 is useful to ones body and does not need the aid of inhibitors, but COX-2 plays a major role in inflammation and therefore inhibitors are needed for the COX-2 enzyme.

This is an aspirin molecule in the Cyclooxygenase protein.

This is the bonding site of the aspirin molecule.  This is what prevents the arachidonic acid which eventually gets converted into prostaglandin from binding.

This is the tunnel that leads to the active site.

Joshua's Fun with Jolecule Blog Post

Joshua Everett
Fun with Jolecule

Antibodies

Antibodies are molecules that search for viruses, bacteria, and other infectious molecules within an organism. These antibodies are commonly circulating in the blood of humans along with examining all objects that they come into contact with. Specifically when an antibody finds a foreign object in the blood, it attaches to the object and fights off any infection the object might bring to the human. This process can only be fulfilled if the object is a virus and an abundance of antibodies attaches to its surface. On the other hand, if the foreign object in the blood is a type of bacteria, the antibody will attach to the bacteria and only act as a marker protein. This marker will alert more powerful defense molecules to fight off the bacteria from causing infection. Antibodies function in direct correlation with the immune system of individuals, for example, without antibodies people would have a weak immune system and would be unable to fight of disease. Without antibodies, there is not a functional immune system in the body, and individuals would be suffering from constant sickness. 

The basic structure of an antibody is simply a molecule that is made of up of several flexible arms that have binding site at the end of each of them. The abundance of arms help ensure that the antibodies are always prepared to fight off any foreign object no matter what the shape consists of. The binding sites of these flexible arms also are able to work symbiotically to be able to attach to viruses and bacterium despite any complications with the shape. Antibodies, however, vary in their properties and distinctions. Some antibodies only have two arms with binding sites, while others may have ten arms with binding sites. Some antibodies even have additional long flexible linkers that are attached from the molecule to the arms with allows some antibodies to have better coverage over the foreign object they are binding to because of the extra length. Various antibodies originate from genes that are recombined in lymphocytes which are the blood cells that create antibodies. The variety of antibodies creates a system in which only certain antibodies are active when different infections are present in the body. Different antibodies have different binding properties which allow for all viruses and bacterium to be fought off with a different antibody. 

Furthermore, all antibodies are composed of four major chains, two long and heavy chains and two short and light chains. Between two of these chains, a heavy and a short chain, there is room for a binding site from a pocket that is formed between them. These long protein chains vary in length and create many loops which allow them to be appropriately called, hypervariable loops. The loops these chains make form these pockets that allow antibodies to attach to foreign molecules that are attacking the body. The other parts of the antibody molecules have many other chains/arms that are connected to a central domain called an antigen (an antibody generator). This formation stays continually uniform with every antibody. In addition, the antibody structure is also on a quaternary level of protein structure because of the many polypeptide chains that are part of an antibody. In Jolecule, the protein structure depicted only shows one immunogloulin. An antibody will have three of immunologists in its structure. A quaternary structure is considered to be any protein that has more that two polypeptide chains in a molecule. An antibody has many chains, two heavy and two light chains and even more when all three immunogloulins are present, which allows an antibody to fit the criteria of a quaternary structure.   

This picture is depicting the overall structure of what an antibody looks like. The immune system forms antibodies that are made up of three major components, light chains, heavy chains, and a central domain, an antigen. All three parts of the antibody work together to be able to fight of foreign particles. 

This picture depicts the top of the binding site where the chains are forming loops in the molecule. In the immune system, antibodies are produced from the mutated residues contributed by the binding site from the loops shown.

This picture depicts a single protein called an immunogloulin. An immunogloulin is only one of the three immunogloulin in a complete antibody. One immunogloulin contains heavy chains, light chains, and an antigen is attached between the chains.  Two immunogloulins act as the Y structure of an antigen and contains a heavy and light chain. A third immunogloulin acts as a base for the antigen because it only contains two heavy chains and not a light chain and a heavy chain. 

This picture depicts the heavy chain of the antibody goes below the antibody into another domain. In this domain, the heavy chain interacts with other proteins. 

Jazmean's Fun with Jolecule

Glucocorticoid Receptor

After playing around in Jolecule, I decided to learn more about the different proteins they had available for viewing. The protein that peeked my interest was the Glucocorticoid Receptor. As presented in Jolecule, this protein is in its tertiary structure due to the folding of the protein.This protein is responsible for controlling stress response in the nucleus. The receptor binds to cortisol (cortisol is a steroid hormone that is produced by the adrenal gland) and then travels to the nucleus and binds to the DNA within the nucleus. This process of binding can trigger either two responses; the expression of anti-inflammatory proteins in the nucleus is up regulated or the expression of pro-inflammatory proteins in the cytosol is repressed. Inflammatory proteins are responsible for the healing of tissue when there is an injury present. These proteins can cause redness, heat, and pain at the site of the injury. If the inflammatory proteins persist for too long, the pain at the injury site can become chronic. Glucocorticoids stop this from happening. Because of this, glucocorticoids (as noted by NCBI) are widely used for the suppression of chronic inflammatory diseases such as asthma. Glucoorticoids receptors are also gaining interest within the field of Psychology as these receptors are also responsible for the response of stress in the brain. Psychologists believe that further understanding how the Glucocorticoid Receptor works will help in understanding how psychological diseases develop such as depression.

The Glucocorticoid Receptor is modular in structure. This means that within the receptor, there are different structural parts that have multiple functions. Like all steroid receptors, the Glucocorticoid Receptor has a variable domain, DNA binding domain, hinge region, and hormone binding domain. The variable domain is different for each steroid receptor. For GR, it has the N-terminus which directs the delivery of the protein to the correct organelle. The DNA binding domain controls which gene will be activated when it comes in contact with the DNA within the nucleus. The hinge region is responsible for the movement of the receptors to the nucleus and the hormone binding domain is responsible for the affect of the response of the receptor.

This shows the DNA Binding Domain. This is the only DNA Binding Domain in the Glucocorticoid Receptor 

This is the Hinge Region.

This is the N Terminal 

This is the overall protein

The Carbon Fixer, Rubisco Protein by Nida Ali

Rubisco, the Carbon Fixer Protein

Through the Jolecule program, I chose the Rubisco protein, which is known as the carbon fixer. Rubisco is used to catalyze the first major step of carbon fixation in the Calvin Cycle. Rubisco is often referred to as the most abundant protein in the world. It goes through the Calvin cycle by undergoing photosynthesis and molecular synthesis, which is seen in all plants. Carboxylation or even oxygenation of RubP, also known as ribulose-1,5-bisphosphate, is catalyzed by the Rubisco protein with carbon dioxide or oxygen. Since carbon is “locked” in highly oxidized forms, carbon dioxide gas, oxidation with carbon will allow it to be "fixed" into organic forms. Rubisco takes carbon dioxide and attaches it to ribulose bisphosphate. Rubisco then takes the chain and shortens them into two identical phosphoglycerate pieces that each contain three carbon atoms. Rubisco produces phosphoglycerate which is then recycled to create more ribulose bisphosphate in order to continue on the process of the carbon fixing cycle.

Rubisco contains a three-dimensional structure and the protein strands coil on themselves in a Quaternary structure which makes their function possible. Rubisco is composed of eight large protein chains, which forms four dimers, as well as eight small protein chains, which assembles the small subunit. A dimer is a macromolecular complex quaternary protein structure. The active sites of Rubisco are located on the large subunits between the dimer pairs. Rubisco's catalytic properties/function relies on the large subunits of the protein. In order for this enzyme to do its job, a Mg2+ ion must be positioned in an active site and a CO2 molecule added. This CO2 then reacts to produce a 6-carbon intermediate molecule. Thus, the specific shape of each active site only allows for the binding of certain molecules which then allows rubisco to carry out its function.

Here is an overview of a version of Rubisco from a photosynthetic bacteria. It is displayed as a Quaternary structure of inter-twist alpha helices with kinks. This complex protein needs the Quaternary arrangement of the polypeptide chain in order for it to be a functional protein.

Carbon is removed from Co2 and is added into ribulose bisphosphate, a short sugar chain with five carbon atoms. Since carbon is “locked” in highly oxidized forms, it must be“fixed” into more organic forms through the oxidation with carbon. Here there are two tertiary forms of the protein which combine to display a functional protein in the form of a Quaternary structure. This zoomed in picture highlights the folds of the protein, which is displaying the various points of attraction from the secondary structure and therefore create kinks within the strands.

In order for Carbon Fixation to occur, the Mg metal ion is required for the coordinate reactions. The Mg ion is positioned in an active site.

Rubisco accepts both Carbon Dioxide and O2 as a substrate, but here Mg ions coordinate with Oxygen atoms in order to undergo Carbon Fixation. The activation site of this enzyme requires the addition and activation of Carbon Dioxide to Lysine.

Jube's Fun with Jolecule

                                                                  Antibody Protein 

        I studied the antibody protein. Also known as immunoglobulins, antibodies are specialized cells of the immune system that work to prevent antigens from attacking the body. They work to detect foreign particles and fight it off to defend the body’s immune system. Using jolecule, I was able to see the specific arrangement of an antibody. Antibodies are Y shaped, and they are composed of two antigen binding sites. Each binding site has a heavy chain and a light chain. This variation allows the binding sites to vary from one antibody to the next. The following figures highlight some of the essential aspects of the protein.

           Figure 1: Y Shaped Structure                     

   Figure 2: Constant Region  

Figure 3: Antigen Binding Site

Figure 1 shows the Y shaped structure of the antibody. This structure is beneficial because it can be modified so that the antibody can attach to the specific shape of the protein or sugar molecules attached to the antigen. Furthermore, figure 2 shows the constant region of the structure which functions to communicate with the other proteins in the immune system to determine how to get rid of the antigen. The ends of the heavy (green) chain and light (purple) chain are the constant regions of this structure. In contrast, the tips of the antibody (where the chain labels are in figure 1) represent the antigen binding site as depicted by figure 3. Figure 3 shows an overhead view of where the antigen binds to the chains. When binded, the immune system will be able to attack the antigen to protect the body.

Evidently, all three figures show the tertiary structure of the protein because the light chain and heavy chain are both apparent. To add, the polypeptide chains have folded into their functional shape. As a result, interactions between the chains allow for them to stabilize so that they can function efficiently. Essentially, the presence of both chains contribute to the function of the protein because both chains work together to attach to the antigen present so that it can, ultimately, be destroyed.

Sara Fun with Jolecule Article

Sara Bearden

Cyclooxygenase

        After playing around in the program Jolecule I chose to learn more about the protein Cyclooxygenase.  This protein is know to be the site of pain-killing.  This protein is involved in the first step of creating postaglandins from a common fatty acid.  These postaglandins are what deliver and strengthen pain signals, induce inflammation, and control the constriction of muscle cells. There are different postaglandins that control different processes but, they are all created form the cyclooxygenase protein.  In order to create postaglandins the cyclooxygenase adds two oxygen molecules to arachidonic acid to start a set of reactions that will create a host of unusual molecules.  As we know the drug aspirin is used as a pain killer well, that drug blocks the binding of the arachidonic acid in the cyclooxygenase active site. That leads to a different product so new messages are delivered and we end up not feeling pain and don't launch an inflammation response.  There are two isomers of this protein and they are used for different purposes.  COX-1 is used for creating postaglandins in order to send basic housekeeping messages to the body in different cells.  COX-2 is used only in certain cells in order to signal pain and inflammation.

         The quaternary structure of this protein is a dimer of identical subunits so there are two active sites of cyclooxygenase and two peroxide active sites ( activate the heme groups that participate in the cyclooxygenase reaction). By having this structure the active sites are close by allowing the reaction to occur quicker and smoother. Each subunit has a knob that is covered with hydrophobic amino acids which allows anchorage to the membrane of the endoplasmic reticulum.  Therefore, the structure doesn't move and the acid that is used for the reaction can find the protein to do the reaction. The cyclooxygenase active site is reached by a tunnel in the protein which leads the arachidonic acid to the enzyme for processing and starting the reaction.  Aspirin can block this site so the reaction cannot occur and leading to different messages being delivered where we end up with feeling no pain. 

 This photo shows how the active site of cyclooxygenase is deep inside the protein.  The ribbon in front of it is the tunnel that would lead the arachodine acid to the active site to bind and start the set of reactions.  At that site is also where the aspirin would go and stop the binding from happening.

 The two active sites of the protein are shown in this photo.  The top one would be the the cyclooxygenase active site where the bottom would be the peroxide active site.  As shown in the photo the two sites are near each other and this is due to the structure of the protein.

 This screenshot shows some of the structures the atoms formed within the shape of cyclooxygenase.  These pentagon shapes are showing how they are non-polar because there are no water molecules around them.  Therefore, the bonds are equally sharing the electrons. Also making the whole protein non-polar which, means it's hydrophobic.

The last screenshot is an overview of the structure of the protein.  You can see the alpha helices intertwine with each other to form the the quaternary structure of a dimer.  There is are two identical subunits that are apart of the dimer which allows for double the active sites and with the alpha helices as a tertiary structure the active sites are in proximity of each other.