Assignment 1: visualization and ranking of protein conformations  (Page 12/5)

Please download files for this assignment from here .

Protein data bank

Your first task is to get familiar with the Protein Data Bank (PDB). Visit the PDB website and perform a site search for CI2 (chymotrypsin inhibitor2). Upon this search, some of the results (in particular those related to the Molybdenum Cofactor) you can disregard. Focus primarily on structures whose PDB name starts with "1C". Find the functional role of CI2 and answer Q1 .Your search will report many different experimentally resolved structures for this protein. Please answer why that is so in Q2 . Focus first on the resolved structures with PDB codes 1CIQ, 1CIR, and 1COA. Note thatthese structures were resolved from different organisms and with different experimental methods. Please answer Q3 .

Let's focus now on one particular structure, the one with PDB code 1COA. You can view an image of the structure of 1COA from the PDB website with the"Images and Visualization" frame to the right. You can either cycle through different images of the protein or download files for different programs and browser plug-ins. You can download the coordinates of the native conformation of 1COAat the "Download Files" option in the left frame. Download the structure file in PDB format. Please get familiar with the PDB file format . For the purpose of this assignment, only the lines starting with the "ATOM" header are meaningful to us. Notethat the x, y, z cartesian coordinates of each atom are stored in columns 7, 8, and 9. These coordinates specify the location of eachatom of 1COA in 3D space. You will use such information in the future to visualize protein conformations.

Visualizing protein conformations

For this section, you will need access to the VMD molecular visualization package. At the end of this assignment there are short instructions on installing VMD.

If you want to install VMD on a computer yourself, you can download a copy from its developers' website . We recommend using the latest version. Installation varies with your platform. Windows versions are distributed as self-installing archives, and should work "out of the box." The MacOS-X version is distributed as a disk image that you simply unpack and move to the location of your choice. Linux and Unix versions will require you to compile the source code, but in most cases, this consists of switching into the correct directory and typing a couple of commands. For specific instructions on how to install the version for your machine, see the README file distributed with the installation archive, which includes a "Quick Installation Instructions" section.

Your next task is to visualize the conformation specified in the PDB file for 1COA through VMD. VMD is a flexible visualizer that allows you to display, manipulation, animate, and analyze biomolecules in full-color, three-dimensional renditions. It also provides a built-in Tcl/Tk interpreter, allowing you to customize its behavior and add functionality.