Auto Dock Auto Dock is an automated docking tool. It is designed to predict how small molecules, such as substrates, bind to a receptor of known 3D structures. Auto Dock actually consists of two main programs: one performs the docking of the ligand to a set of grids describing the target protein; and the other Auto Grid pre-calculates these grids. In addition to using them for docking, the atomic affinity grids can be visualized. A graphical user interface called Auto Dock Tools or ADT was utilized to generate grids, calculate dock score and evaluate the conformers. Rasmol: RASMOL [Raster Display of Molecules] is a molecular graphics program intended for the structural visualization of proteins, nucleic acids and small biomolecules. The program reads in molecular coordinate files and interactively displays the molecule on the screen in variety of representations and color schemes. DOCKING METHODOLOGY: The structure of β-ketoacyl-acyl carrier protein synthase (KAS) which is an essential target for novel antibacterial drug design was retrieved from PDB [10]. A comparative protein - ligand dock analysis was performed using 1HNJ to evaluate the algorithm and scoring function efficiency between Auto Dock 3.0 and experimental activities. The molecules selected for docking studies are from the selected article [11, 12]. The docking studies were done on ecKAS III (pdb id: 1HNJ) receptor. All these molecules as well as the bound ligand of the protein 1HNJ were docked by using the software Auto Dock and the score values are predicted. The protein ligand interactions were also studied. All molecules were drawn using ChemDraw Ultra 8.0 tool and energy minimized using Chem 3D Ultra 8.0 software. Automated docking was used to locate the ap... ... middle of paper ... ... this method the ligands were kept manually into receptors and minimised to reduce the steric clashes among the atoms in the molecule. Now a days the docking is done by recent computational resources. The recent docking studies involve the systemic methods, random methods and simulation methods. Systemic method: In this method the main fragments are first doc ked into the binding site of a target molecule. They will be very helpful when the target core is very hard to interact. Random method: This method involves the simultaneous changes of a ligand molecule. The scored ligands will be used for the further steps. Simulation method: In this method both the target and ligand are treated on being flexible. In this method the preparation of the ligand are mapped on a grid. Then the energy values of the grid are minimised to fix the ligand into a receptor.
Pang, A., Warren, M. J. and Pickersgill, R. W. (2011), Structure of PduT, a trimeric bacterial microcompartment protein with a 4Fe–4S cluster-binding site. Acta Crystallographica D, 67: 91–96. doi: 10.1107/S0907444910050201
the strands to seperate, then cooled to allow the primers in the solution to b...
called an active site. This active site is made by a few of the amino
The sequence of BRCA1 protein shows that there are quite a few of cysteine residues. These cysteine residues form disulfide bonds which help stabilize the secondary structure of the protein. The secondary structure of BRCA1 protein indicates that there are alpha helices and beta turns which are connected by loops and turns. The 3D structure of BRCA1/BARD1 RING-domain heterodimer is shown in figure 1.
consists of a polyhedral head and a tail. The tail is used to inject DNA into a
The three-dimensional contour limits the number of substrates that can possibly react to only those substrates that can specifically fit the enzyme surface. Enzymes have an active site, which is the specific indent caused by the amino acid on the surface that fold inwards. The active site only allows a substrate of the exact unique shape to fit; this is where the substance combines to form an enzyme- substrate complex. Forming an enzyme-substrate complex makes it possible for substrate molecules to combine to form a product. In this experiment, the product is maltose.
...Coauthor, ChemBioChem 2006, 7, 1-10; b) A. Author, B. Coauthor, Angew. Chem. 2006, 118, 1-5; Angew. Chem. Int. Ed. 2006, 45, 1-5.))
“This knowledge will help us design drugs that mimic the viral effects on these proteins to either activate a host’s immune response or shut it down,” said Dr. Michael Gale, associate ...
Myoglobin consist of single polypeptide chain that made up of 153 amino acid and ahs a size of 18 kDa. Its three-dimensional structure was first determined by X-ray crystallography by John Kendrew in 1957. Myoglobin is a typical globular protein in that it is a highly folded compact structure with most of the hydrophobic amino acid residues buried in the interior and many of the polar residues on the surface. X-ray crystallography revealed that the single polypeptide chain of myoglobin consist of entirely of eight (labelled A-H) alpha-helical. Within a hydrophobic crevice formed by the folding polypeptide chain is the heme prosthetic group. This nonopolypepetide unit is noncovalently bound to myoglobin and is essential for the biological activity of the protein.
"The Species of the Secondary Protein Structure. Virtual Chembook - Elmhurst College. Retrieved July 25, 2008, from http://www.cd http://www.elmhurst.edu/chm/vchembook/566secprotein.html Silk Road Foundation. n.d. - n.d. - n.d.
To examine the interaction between two molecules in solution without isolating the compound Jobfs method is used. Although unstable compounds tend to be generated, this is not a reflection of weak interactions. In some cases, the transition metal species cannot be crystallized from the solution and separated from the other species present. Without Jobfs Method this composition can be very difficult to deduce.
For example, some of the proteins contain pleckstrin homology domains that bind phosphoinositide and others contain C2 domains that bind membrane lipids in the presence of Ca2+, some proteins contain positively charged regions that bind to negatively charged phosphoglycerides and others contain covalently attached fatty acyl groups or prenyl groups that anchor them to membranes. Another example is Annexin shows Ca2+ dependent binding to the cytosolic surfaces of cell membranes. Ca2+ ions bind to the iface of each annexin and this promote protein–lipid interactions through a combination of electrostatic and hydrophobic mechanisms. The same result has been shown by crystallographic studies with phosphoglyceride analogs, suggested that some of the bound Ca2+ ions may bind directly to the oxygens of phospholipid head groups. Addition to this, adjacent membrane lipids that do not bind proteins directly may modulate the protein–lipid interactions, the binding of proteins to membrane surfaces may promote further changes in the structure and function of the proteins, and groups of proteins that bind to the same membrane surface may interact with each other to produce complex membrane
4- Tools for simulation and analysis of variouschemical structures such as polymers and nucleotides, example is AmberTools.
... focusing is placed horizontally on an SDS gel , the electric field is applied and the protein macromolecules are separated acrodo with the isoelectric point and in terms of its molecular mass , providing a electrophoretogram that enables viewing and identification of many proteins at once .
Molecular pharmacology deals with the biochemical and biophysical characteristics of interactions between molecules of different substances and those of the cell. In other words, it is molecular biology applied to pharmacologic and toxicologic questions. The methods of molecular pharmacology include precise mathematical, physical, chemical and molecular biological techniques to understand how cells respond to hormones or pharmacologic agents, and how chemical structure correlates with biological activity of various