PROTEIN
STRUCTURE
There are a number of
molecular imaging programs that can be downloaded as
stand-alone programs or as programs allowing visualization in
a web browser. These programs convert atomic coordinate
information generated from X-ray crystallographic and other
protein, polynucleotide and small molecule structural analyses
into rotatable images with a
variety of display options. Tutorials for this course were
developed in the mid 1990's, initially using the program
RasMol, and then with Chime, a web browser plug-in.
Chime unfortunately had compatibility issues with
web browsers and is pretty much phased out. A Java-based
program, Jmol, that is platform independent
(Microsoft, Apple, and Linux all work) replaced Chime, but is
now being phased out as web browsers, which run Jmol as a Java
applet, are increasingly restrictive of Java applications. In
the recent past, I've
personally used Firefox, Chrome, IE and SeaMonkey on a PC
for all the tutorials below. Currently, only older
versions of Firefox will work for the Hb and IgG
tutorials below. The latest Chrome will not run any Java,
and the latest IE will not run the applets for these
particular sites. JSmol is replacing Jmol and works in
all the above browsers, but runs very slowly in IE. The
Proteopedia links, which include the HIV protease tutorial
below, use JSmol.
The computer lab
in FSC216 currently has an older Firefox browser that
will work for all the tutorials below.
Java must be enabled
in your browser. Security blocks for sites running
Java scripts will interfere with Jmol. Firefox
should be fine as is, but if not select Enable Javascript under the
options>content in menu. For IE (not recommended
at this time), high security setting in IE will block
Java but medium-high is OK.
More information
about Jmol, Chime and other
imaging programs, as well as links to more tutorials, can be
found at http://www.molviz.org , a site maintained by Eric Martz, Professor
Emeritus at University of Massachusetts. He is the
author of both the Hb and IgG tutorials.
Jmol
also exists as a downloadable desktop program that allows you
to open up pdb files if you have
Java installed. Features include the ability to export
images, web pages, and scripts. The download link can be
obtained at http://jmol.sourceforge.net/
.
Basic
Jmol controls
Toggle spinning (button at bottom of image frame) allows you to
start/stop spinning of the molecule
Rotate the molecule by holding down the left mouse
button and moving the mouse (or just the mousepad on a laptop)
Translate (move entire molecule to center a partular
view) by holding down ctrl and alt buttons and left mouse button
(or just the
mousepad on a laptop) and moving the mouse.
Zoom
the molecule by
holding the shift key and left mouse button (or just the mousepad on a
laptop)and
moving the mouse away from you or towards you.
Identify amino acid residue/atom by putting the mouse over
the atom of interest. WARNING- in some views
there are atoms in front that aren't visible: they are
present, but have been rendered invisible in the script.
If that is the case you may misidentify an amino acid.
Be sure it makes sense. In a specific example you
may encounter in the hemoglobin tutorial, the amino acid Val
(branched hydrocarbon side chain) is very different in
structure from His (5-membered ring structure with 2 N atoms).
Menu - right-click the mouse
with the cursor in the jmol
frame. This will open up the jmol
menu. The menu allows you to select, change color
schemes, turn on and off H bonds etc. For more advanced
users you can also open the console which allows youn enter
and execute specific script commands.
Jmol Tutorials for this lab
Basic Protein Structure and Hemoglobin http://www.umass.edu/molvis/tutorials/hemoglobin/
Basic Protein
Structure and IgG http://www.umass.edu/molvis/bme3d/materials/jmoltuts/antibody/contents/contents.htm
HIV-1 protease http://proteopedia.org/wiki/index.php/HIV-1_protease
Link to questions
to be answered for the above three tutorials
http://webspace.ship.edu/wjpatr/protein_structure_questions.html
For protein structure enthusiasts...
The Jmol- based
program FirstGlance, is
nice for viewing structures http://molvis.sdsc.edu/fgij/index.htm. It has a Jmol window with an extensive,
easy-to-use menu for selecting different
views.
Proteopedia ( http://proteopedia.org/wiki/index.php/Main_Page ) is a Wikipedia-like protein encylopedia. Entries are limited, but growing, and include the nicely done HIV-1 protease page above, and the timely influenza neuraminidase.
Other Programs
Cn3D
Cn3D
is an imaging program that can be downloaded from the NCBI web
site http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml.
This is a downloadable program that will interface
with your web browser. It allows easy visualization
of MMDB database files, but not pdb
files. It is the default viewer for CDD, the
Conserved Domain Database. Its primary strength is that it has
a sequence line that allows easy correspondence of structure
and sequence. It also integrates with CDTree for
protein sequence alignments and to create relationship
trees.
DeepView (Swiss-PDBViewer)
This is a self-standing program http://spdbv.vital-it.ch/index.html
with numerous modeling tools that include "mutations"-
changing amino acid residues to ascertain affects on
structure, add amino acid loops, and alter bond angles.
It also interfaces with Swiss-Model http://swissmodel.expasy.org/workspace/index.php?func=modelling_simple1
, a structure homology-modeling server that will attempt to
model a polypeptide sequence to a 3D model.
Phyre and 3D-PSSM
These are protein structure homology-modeling servers similar to
Swiss-Model that attempt to model a polypeptide sequence to a 3D
model, esssentially threading a sequence onto existing 3D
structures. Phyre2 http://www.sbg.bio.ic.ac.uk/phyre2/
is the latest version; 3D-PSSM is being phased out, and
its fold library database is no longer updated.
Chimera
A versatile
self-standing program with numerous options and
specialized plug-ins
available,
including 3D
RNA modeling.
http://www.cgl.ucsf.edu/chimera/