Protein Structure and Function

Proteins do the work of our cells. Proteins are chains of amino acids that fold in particular ways depending on the sequence of amino acids in each chain.

The keratin protein that makes up our hair has a cable elongated structure and so do the myosins of our muscles. Most proteins are globular or somewhat spherical.

Protein structure has several levels of complexity:

Primary structure is the sequence or order of the amino acids in the chain
Secondary structures are helical coils (a-helix) or folded back stretches (b-sheets)
Tertiary structures are how parts of the chain interact and stick together. Disulfide bonds between cysteine amino acids help stabilize tertiary structures.
Quaternary structures describe the interactions of different subunits in a protein. These interactions may be stabilized by hydrogen bonds between chains, or ionic H-bond interactions with small molecule cofactors.

Dr. Toby's Modeling Protein Structure (.pdf file)

Protein examples

To view these protein structures, you will need to download free, professional software such as CHIME, RasMol, or Cn3D These web sites open as a new web page. Move the page over so you can continue to read this page while you follow the download instructions.

Tell your school system administrator that this software is free and for use by students and professionals alike. Your system administrator might be able to configure the software on your school/media center server so that it can be accessed by many computers in your school.

All the molecule viewers turn the geometric information about the atom placement in the molecules into color coded objects. Try out a tutorial and try different ways of viewing the molecules. You will see that you can learn different things about the molecules depending on which way you view the data. I like to view display: cartoons to show the backbone and color: structure to show the helix/sheet/coil sections, and then view display: space filling and color: CPK which colors the atoms.

A cool movie of an HIV protein unfolding (denaturing) (Quicktime or mpeg, 2.5 Mb)

Using the Structure database at NCBI

Go to http://www.ncbi.nlm.nih.gov/Structure/ (This site opens as a new web page.) Move the page to the side so you can read these instructions as you follow the instructions.
Type in the recommended keywords
Scroll to the bottom of the page (View/Save button)
Under "Options," choose "Launch Viewer" or other as you prefer
Under "Viewer," choose the software application you have downloaded and configured on your computer terminal (choose RasMol if you are using CHIME)
Under "Complexity," choose "All Atom Model"

1ZEH	insulin (keywords used: human insulin hormone)
1DPX	lysozyme (egg white lysozyme)
1EPT	trypsin (porcine trypsin)
1A4E	catalase (YEAST CATALASE)
1A94	HIV protease
1HBB	hemoglobin
1CL7	antibody (monoclonal antibody)
1MEY	zinc finger protein (transcription regulator)
1YCS	p53 anti-oncogene (partial structure)
1LBI	lac repressor protein

National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/Structure/

Protein DataBank http://www.rcsb.org (Check out "Get Educated" for great background articles)

Also, check out the WebMolecules web site http://www.webmolecules.com!