Teaching Resources in Biochemistry:

Jason Kahn, University of Maryland College Park.
Disclaimer: I know this area could be better organized. I know some of the content is out of date. It will gradually improve. Let me know if specific things that you need are broken.

Nucleic Acid Sequence, Stability, Structure, and Dynamics

Tools and Tutorials for Molecular Structure

Excel spreadsheets for modeling simple chemical and biochemical principles.

Matlab programs for modeling simple chemical and biochemical principles.

Protein domains and (mis)folding overheads.

Student posters (very old)

Rasmol/Chime/Jmol installation and use

Biochem 461/463-oriented materials (protein structure and allostery)

PDB files of nucleic acids and protein-nucleic acid complexes

Biochemistry 465 and 661/662 and the old 674

Collection of exams

Literature Searching and EndNote/Papers Hints (Biochemistry 677)

TEDxUMD talk on teaching philosophy

Nucleic Acid Sequence, Stability, Structure, Dynamics, Enzymology

Tools and Tutorials for Molecular Structure:

This file links to a variety of small tutorials/examples focusing on visualization of biomolecules in three dimensions, using the program RasMol.

A very brief note on philosophy

These pages are intended to help the user learn to use RasMol as a research tool, not just to look at pictures of molecules. For this reason, I have decided to provide lists of commands rather than Rasmol scripts (these are very different) and to use RasMol rather than Chime, so that the user has access to the process (indeed, cannot avoid the process) by which these pictures were all created. Once methods for viewing and integrating Rasmol scripts into Chime presentations become more robust, maybe I will switch over. The teach a person to fish paradigm.

Note: perhaps I flatter myself, but if you link to this page or otherwise make substantive use of the content, please let me know and/or link/give credit appropriately. Suggestions are always welcome. The creation of this content was part of the educational part of an NSF Career Award Proposal.

Rasmol/Chime/Jmol installation and use

Update 2005: The free Jmol viewer appears to be a viable replacement for most of Rasmol and especially Chime.

To view structures in PDB (= Protein Data Bank) format you need a program which understands PDB. The free options in most common use are RasMol and Chime. Rasmol is a stand-alone program available for Mac, Windows, and Unix platforms. Chime is a plug-in which as of this writing works only with recent versions of Netscape. The Protein Explorer is essentially an environment used to run Chime more intuitively, with a lot of typical commands pre-loaded. It makes extensive use of javascripts for communication between Chime and the user.

To view structures on/from the Web, you have to configure your browser to launch a PDB viewer program. To do this, you have several options. This server (www.biochem.umd.edu) supports the experimental mime type chemical/x-pdb. If you configure your browser correctly (see below), you can bring up a pdb viewer (either Rasmol or Chime) directly upon clicking on a PDB file link. Otherwise, you will be asked to save the file and can then read it in to a viewer (Rasmol) from outside your browser. On some platforms (e.g. Silicon Graphics, probably other X-windows), you need to tell Netwscape to open a shell window which then in turn runs Rasmol, otherwise the command window will not appear (Netscape intercepts the application's desire to open a window). One option that should always work is to launch Rasmol on its own, save the pdb file as text (download by holding the mouse down on the link (Mac) or using the alt key (SGI)), and then open the pdb file from within Rasmol.

There is an excellent resource on Rasmol and Chime, including pointers to download locations and many examples, at U Mass. This site showcases much more sophisticated presentations than are provided here, but at some cost to simplicity and interactivity. The Protein Explorer is emphasized at the site.

You can get the Chime plug-in to display structures from within Netscape from MDLI . IMHO (= in my humble opinion, for "newbies"), Rasmol is better, especially if you have a pre-1994 computer. Nothing can crash a computer like Netscape, esp. w/ plug-ins, and Chime doesn't seem to provide a user-accessible command line, although it can read more file formats and is apparently better for advanced scripting within Web pages. Rasmol can be run on its own after you have quit Netscape or whatever and re-connected your phone line, and the command line gives you more control and immediate feedback. You can even just ftp the pdb file and run Rasmol without running a browser at all, but any computer that can't run Netscape will probably choke on any complicated Rasmol work.

For more rasmol, other PDB viewers, and a great deal more, see The NIH Guide to Molecular Modeling . It's difficult navigating but there's a wealth of information there.

Configuration directions for using Rasmol and Chime:

  1. If it isn't already available, get Rasmol (it's freely downloadable) and install/compile it on your computer.
  2. For Mac/SGI Netscape, set helper applications or plug-in choices under "Options/General/Helpers", such that the chemical/x-pdb file type or any file that ends in ".pdb" is opened by Rasmol. To enable the use of the command window under X-windows, use the line below as the "helper application" (thank you very much to Roger Sayle for this info):
    xterm -e rasmol %s
    For Windoze or Internet Explorer, Microsoft probably lets you do something similar but you're on your own as to exactly how.

    If you install the Chime plug-in, you choose to launch the plug-in essentially as above. You can go back and forth if you wish -- I have both installed but usually use RasMol.

    Some UNIX setups may require you to change your .mailcap file. Include the line:
    chemical/x-pdb ; rasmol %s
    If you install Chime, it will modify the .mailcap file or otherwise take over.

For Jmol: Download, install as plugin (more later if necessry).

Biochem 461/463-oriented materials:

If you are using Netscape/Rasmol as above, download the pdb file first and thereby launch Rasmol. Then go to the appropriate command file and cut and paste line by line or larger chunks from Netscape to the command line in Rasmol (you may be able to choose "Paste" even when the structure window is uppermost).

Here is a rather arcane spreadsheet rationalizing why irreversible steps in a pathway are the right places to control flux.

Structures of amino acids and proteins

Loren Williams' teaching pages at Georgia Tech have a wealth of material in a vein similar to what you will find here.

Protein conformational analysis: the Ramachandran plot

The Ramachandran plot is used to illustrate the conformational space accessible to proteins, the energetics of different choices of phi/psi angles. This page contains an illustrated version with links to pdb files. Note that this is an example of the fact that just because you have a pdb file doesn't mean the structure shown can actually form. Here is a short explanation of why proline breaks alpha helices, which is not due to its restricted accessible area on the Ramachandran plot.

Alpha helix and beta sheet structures

The files below are provided as examples of idealized secondary structures.

NEW: These little tutorials have been recoeed for jmol but may not have been fully debugged.
Here is the alpha helix.
Here is the same alpha helix in reality in the GCN4-DNA co-crystal.
Here is the beta sheet.
Here is the beta sheet in the protein tendamistat .

The .txt files below are lists of Rasmol commands. On a Mac or SGI, you can cut-and-paste commands into the command window as I do in class -- take chunks delimited by # signs or pause statements, or go line-by-line. Pasting also works in newer versions of Jmol, and it uses essentially the same command language. On Windows, pasting doesn't work and you will have to save the file as a script and then "script file_name" to run it. You will need to give the complete path.

The .scr file is a Rasmol script which recreates a particular view. The .pdb files are the actual molecular data files, essentially xyz coordinates of the atoms. These are just text files -- go ahead and look.

Protein supersecondary and tertiary structure example: TIM et al.

"TIM" is triose phosphate isomerase, a key enzyme in glycolysis. Our interest is in TIM as a prototype alpha/beta barrel protein and an example of protein tertiary structure. Myohemerythrin is an oxygen-binding protein, of interest to us an an example of a four-helix bundle. The transthyretin dimer (the protein formerly known as prealbumin), has two beta sheets packed against each other. Hexokinase is a famous enzyme which clamps down on glucose in order to phosphorylate it in the first step of glycolysis. Mathews and van Holde show the bottom half of this protein (Fig. 6.16c) as an example of mixed alpha helix/beta sheet structure. Note that Rasmol's (and Insight's) structure analysis algorithms don't find quite as much beta sheet as the text.

Quaternary structure and allostery

Hemoglobin is the most studied protein in the world. Biochemical, biophysical, and crystallographic studies have illuminated many of the tertiary and quaternary changes accompanying cooperative oxygen binding.

PDB files of nucleic acids and protein-nucleic acid complexes

I've made available a large collection of PDB files, mainly of RNA, DNA, RNA/DNA binding proteins, and protein-RNA/DNA complexes. These were downloaded from the Brookhaven Protein Data Bank Web site some time ago, so there may have been some evolution of the files after they moved to the new PDB.

Biochemistry 465, 661/662, and old 674:

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