Protein Bioinformatics
260.655
Computer lab #1 (of 3)
Friday, April 7, 2006
Sean Prigge, Jonathan Pevsner, Ingo Ruczinski
Goals:
[1] Use the NCBI website.
Find the RefSeq accession number(s) for proteins from any given organism.
[2] Use the Protein Data Bank (PDB) website.
Find entries for myoglobin. Use WebMol.
[3] Use the UniProt website.
[4] Use the ExPASy site including DeepView, the Swiss-Pdb Viewer.
[1] Use the NCBI website. (http://www.ncbi.nlm.nih.gov/)
1a. Find the RefSeq accession number(s) for proteins from any given organism.
Find myoglobin. Strategy #1: enter myoglobin as a search term at the front page
of NCBI using the Entrez search engine. Limit to RefSeq.
1b. NCBI strategy #2. Use the taxonomy browser; select Homo sapiens
(alternative problem for advanced students: find whale myoglobin); link to all
human Entrez proteins; limit to RefSeq.
1c. Optional: explain why there are multiple human myoglobin RefSeq entries.
1d. Go to the human entry at TaxBrowser and link to Structures. How many
human structures are there? ________ How many human structures are under
the heading “myoglobin”? _______ What is the “best” myoglobin accession
number (with four characters)? _______
1e. View structure 2MM1 with Cn3D. A screen capture is shown here:
1f. Highlight an alpha helix in the primary amino acid sequence
(shown below) and view the corresponding structure.
Approx. Time
25 minutes
25 minutes
5 minutes
20 minutes
1g. View the side chains and find the
distal histidine (binds to
the iron of the heme group). Use ‘Edit
global style’ under ‘style’.
1h. Find the conserved proline in the sequence ‘HPE’ (after the second helix).
Highlight this proline in the sequence window and find it in the myoglobin
structure. Think of a structural reason why this proline is conserved in
myoglobin and hemoglobin sequences.
1i. If there is time, try to reproduce this space-filling model using the ‘Edit global
style’ menu under ‘style’. Hint: to color the heme purple, select ‘object’ under
‘color scheme’ for heterogens.
[2] Use the Protein Data Bank (PDB) website.
[2a] Go to www.pdb.org. Find entries for myoglobin.
[2b] Enter a search for 2MM1.
_Note the option on the left sidebar to view this structure with the Swiss PDB viewer
(last exercise for today) and WebMol.
_Download the fasta sequence to a text file
_What angstrom resolution is this structure? _________
_What is the space group? ________
[2c] Use WebMol to study the structure of 2MM1. Use the tools on the right
sidebar, from the top down. Repeat this exercise by exploring ubiquitin (1UBQ)
_Try color by secondary structure. Compare this to Cn3D.
_Use the select tool; find the N-terminal and C-terminal atoms.
_Use the Msure dist (measure distance) tool; what is the distance in angstroms
between the N-terminal and C-terminal atoms?
_Explore the DMat tool.
_Try the Ramachandran plot. Which of the bottom two is from 2MM1, and which
is from 1UBQ?
_Try the Trace tool (simply click).
_If there is time, explore the surface tool. What is the difference between
‘SASA’ and ‘vDW’?
[3] Use the UniProt website (www.uniprot.org).
[3a] Do a text search for myoglobin. How many entries are there? _________
[3a] Do a text search for human myoglobin. How many entries are there? _________
What is the number of amino acids of human myoglobin here?
[4] Use the ExPASy website
_ do a text search: myoglobin
_ search a pdb accession: 2mm1
_ download Swiss-Pdb Viewer here
_ explore a variety of these web-based tools for
primary, secondary, and tertiary structure analysis
[4] Use DeepView, the Swiss-Pdb Viewer
[4a] Download DeepView from ExPASy (onto PC, Mac, Linux)
[4b] Save 2MM1.pdf onto your hard drive; open in DeepView.
[4c] Use each of the tools below.
1
2
3
4
5
6
1
center
2
3
4
move (translate)
zoom in/out
rotate
7
8
9 10 11 12 13
5
6
7
click, select two atoms, determine distance in angstroms
measure bond angles (pick center atom, then two more atoms)
measure dihedral angles (ω, φ, ϕ)(omega, phi, psi) from a
selected atom.
8 identify an atom (and the group to which it belongs).
Type: CA, CB, O
Group: LYS116, etc.
x,y,z atom coordinates
9 display groups within a particular distance (e.g. 10A) from a
selected atom. Note the selection on the control and
graphics panels.
10 center display on a selected atom
11-13 advanced tools
[4d] Use the pull-down menu options such as the following:
-- Select  Group property  non-polar (and visualize this)
-- Select  Secondary structure  helices
_ Go to window  control panel.
_Shift/click to select the first five amino acid residues of myoglobin.
They should appear red.
_ Click “labl” (i.e. label)(see arrow, above right). Those five residues
now have a “v”.
_Inspect the display panel; those five residues are labeled.