VMD or Visual Molecular Dynamics is a computer program that can be used to design, animate, and model molecules especially organic molecules so that they can be visualized in 3-dimensional graphics for analysis and better understanding of their molecular structure and components. For the most part VMD is used to view and analyze the molecular stimulations, but the program also contains rendering tools that can be used to modify the dimensional and sequential data of the molecules. The data can be applied in various ways. Biochemists can rearrange and form amino acids to observe mutagenesis or functions of the proteins, it can also be useful to predict and understand catalytic mechanisms stimulated by proteins.
VMD can be useful to a range of audience, molecular structural data obtained from VMD can be integrated with bioinformatics, which will then provide useful information to researchers of biological system, not only individuals involved with the field of biological science, but also theoretical and experimental researchers of chemical science can utilize the information to scrutinize the chemical structure of molecules. It can also be used in educational institutions to display molecules in a very descriptive manner to students, to give them a broader idea of the structural function.
On the organic level VMD is most likely used to model proteins, nucleic acids, and lipid bi-layer assemblies, VMD can also read Protein Data Bank (PDB) files so any protein structures can be found in the VMD database, VMD can create very detailed graphic of molecular dynamics stimulation, then using the variety of tools that are included in the program structures of these organic molecules are then modified and analyzed to view the experimental molecule.
One of the major molecule structure created and analyzed in VMD by biologists is the molecule of hemoglobin. Hemoglobin is an essential element of an animal body, iron containing oxygen transport protein in red blood cells, it transports oxygen from lungs to the rest of the body of animals, so it can be used by cells. Hemoglobin plays a significant role in function of an organism, likewise deficiency of hemoglobin causes severe damage to the body. So modeling, and animating hemoglobin molecule structure in 3-D graphics, the diseases and problems caused by decrease of hemoglobin can be discussed and explored more thoroughly, for cure or other diseases that can be caused from the absence of sufficient hemoglobin in the body. The molecular dynamic stimulations of hemoglobin can illustrate the mutations in the genes of hemoglobin proteins, which then can be examined, and modified in order to study the cause, also to predict future possible mutation in hemoglobin genes and their effect.
The shape of the protein chains that produce the building blocks and other structures used in life is mostly determined by weak chemical bonds that are easily broken and remade. These chains can shorten, lengthen, and change shape in response to the input or withdrawal of energy. The changes in the chains alter the shape of the protein and can also alter its function or cause it to become either active or inactive. The ATP molecule can bond to one part of a... ... middle of paper ... ...
BioPure Corporation, which was founded in 1984 by entrepreneurs Carl Rausch and David Judelson, is a privately owned biopharmaceutical firm specializing in the ultra purification of proteins for human and veterinary use. In 1998 Biopure pioneered the development of oxygen therapeutics using “Hemoglobin”, a new class of pharmaceuticals that are intravenously administered to deliver oxygen to the body's tissues. Biopure's two products, Hemopure for human use, and Oxyglobin for animal veterinary use, both represented a new Oxygen based treatment approach for managing patients' oxygen requirements in a broad range of potential medical applications. The factor distinguishing Biopure’s two products from other blood substitute products being developed by two possible rivals, Baxter International and Northfeild Laboratories, is that its hemoglobin based source is bovine rather than human and was derived from the blood cells of cattle. Both of Biopure’s blood substitute products were in the final stages of the approval process of the Food and Drug Administration (FDA) in 1998. Oxyglobin had just received the FDA’s approval for commercial release declaring it safe and effective for medical use. Hemopure was entering final Phase 3 clinical trials and was optimistically expected to see final FDA approval for release in 1999. The FDA approval of Oxyglobin and its possible subsequent release into the veterinary market caused concern over whether the early release of Hemoglobin would impinge BioPure’s ability to price Hemopure when the product finally received approval. Given that the two products were almost identical in properties and function, it was thought that the early release of Oxyglobin would create an unrealistic price expectation for Hemopure if released first.
Zhang X., Tang H., Ye C. and Liu M. (2006). Structure-based drug design: NMR-based approach for ligand-protein interactions. Drug Discovery Today: Technologies. 3 (3), pp. 241-245.
Show your understanding of the structure of nucleic acids by describing the similarities and differences between DNA, mRNA and tRNA. Your descriptions should include drawings with labels of the nucleotide structures and the overall structures of each where applicable.
These discoveries about the structure of DNA allowed scientists to explore the genome and develop a stronger understanding of genes. Within a decade of its discovery, other scientists had identified the genes responsible for specific diseases and traits. The discovery of the structure of DNA created a basis for ...
To help people with chronic anemia a synthetic version of Erythropoietin was produced called r-HuEPO, while provin...
James Danilli intended to further explain in the Davson and danilli model observations on the surface tensions in the lipid bilayers and even though there were some flaws ...
receptor complex site. After I design an analog of Tamoxifen, I will then use the Gaussian 03W
Red blood cells with normal hemoglobin (HbA) move easily through the bloodstream, delivering oxygen to all of the cells of the body. Normal red blood cells are shaped like doughnuts with the centers partially scooped out and are soft and flexible.
In this experiment, we determined the isotonic and hemolytic molar concentrations of non-penetrating moles for sheep red blood cells and measured the absorbance levels from each concentration. The results concluded that as the concentration increased the absorbance reading increased as well. A higher absorbance signifies higher amounts of intact RBCs. The isotonic molar concentration for NaCl and glucose is 0.3 M. The hemolysis molar concentration for NaCl and glucose is 0.05 M. Adding red blood cells to an isotonic solution, there will be no isotonic pressure and no net movement. The isotonic solution leaves the red blood cells intact. RBC contain hemoglobin which absorbs light, hemoglobin falls to the bottom of the tube and no light is absorbed. Determining the isotonic concentration of NaCl and glucose by finding the lowest molar concentration. In contrast to isotonic molar concentration, hemolysis can be determined by finding the
I have always been fascinated by Biology and Computer Science which propelled me to take up my undergraduate studies in the field of Bioinformatics. As a part of my undergraduate curriculum, I have been exposed to a variety of subjects such as “Introduction to Algorithms”, “System Biology”, “PERL for Bioinformatics”, “Python”, “Structure and Molecular Modeling” and “Genomics and Proteomics” which had invoked my interest in areas such as docking algorithms, protein structure prediction, practical aspects of setting and running simulation, gene expression prediction through computational analysis. These fields have both a strong computational flavour as well as the potential for research which is what attracts me towards them.
Proteins are considered to be the most versatile macromolecules in a living system. This is because they serve crucial functions in all biological processes. Proteins are linear polymers, and they are made up of monomer units that are called amino acids. The sequence of the amino acids linked together is referred to as the primary structure. A protein will spontaneously fold up into a 3D shape caused by the hydrogen bonding of amino acids near each other. This 3D structure is determined by the sequence of the amino acids. The 3D structure is referred to as the secondary structure. There is also a tertiary structure, which is formed by the long-range interactions of the amino acids. Protein function is directly dependent on this 3D structure.
Red Blood Cells contain hemoglobin molecules to help bind to oxygen to bring to other tissues. Without this function, cells would not be able to go through the process of cellular respiration and can only survive a short time. Red Blood Cells are also able to carry bicarbonate as a waste product and carry a variety of hormones to communicate between organs.
There are four main levels of a protein, which make up its native conformation. The first level, primary structure, is just the basic order of all the amino acids. The amino acids are held together by strong peptide bonds. The next level of protein organization is the secondary structure. This is where the primary structure is repeated folded so that it takes up less space. There are two types of folding, the first of which is beta-pleated sheets, where the primary structure would resemble continuous spikes forming a horizontal strip. The seco...
Chemical reactions involve the making and breaking of bonds. It is essential that we know what bonds are before we can understand any chemical reaction. To understand bonds, we will first describe several of their properties. The bond strength tells us how hard it is to break a bond. Bond lengths give us valuable structural information about the positions of the atomic nuclei. Bond dipoles inform us about the electron distribution around the two bonded atoms. From bond dipoles we may derive electronegativity data useful for predicting the bond dipoles of bonds that may have never been made before.