Protein Bioinformatics Computer lab #1 Friday, April 11, 2008 Sean Prigge and Ingo Ruczinski
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1 Protein Bioinformatics Computer lab #1 Friday, April 11, 2008 Sean Prigge and Ingo Ruczinski Goals: Approx. Time [1] Use the Protein Data Bank PDB website. 10 minutes [2] Use the WebMol Viewer. 20 minutes [3] Use the Cn3D on the NCBI website. 20 minutes [4] Use the ExPASy site including DeepView, the Swiss-Pdb Viewer. 15 minutes [1] Use the PDB website ( 1a. Find a structures of human myoglobin: Strategy 1. type myoglobin in the search box - how many structures are there? Strategy 2 type human myoglobin or sapiens myoglobin -do these searches yield the same results? 1b. Click on structure 2MM1 What information is displayed on the top page for this structure? What is the resolution of the structure? What is the R-factor? Are there any other molecules bound to this protein?
2 1c. Now look at the tools on the left hand side How can you get the amino acid sequence of this protein? - Advanced: Use the sequence for an advanced sequence search. Look at Download Original Files and Display Files - This is how you can save a full PDB record to your computer for later use Now look at the Display Molecule tab and click on WebMol Viewer
![[2] Experiment with the WebMol viewer Use the top right tool to show mainchain or backbone Use the color tool to color by: secondary struct, B-factor, or buried/exposed atoms Use the surface tool.](/docs-images/83/88577785/images/3-0.jpg "What is the difference between SASA and VDW? - solvent available surface area, Van der Waals What do the HetAt and HOH tools do?")
3 [2] Experiment with the WebMol viewer Use the top right tool to show mainchain or backbone Use the color tool to color by: secondary struct, B-factor, or buried/exposed atoms Use the surface tool. What is the difference between SASA and VDW? - solvent available surface area, Van der Waals What do the HetAt and HOH tools do? -HeteroAtom, Water Use the Select and Focus tools to explore the heme group. What atom is in the center of the heme? Use the Msure (measure) tool to look at distances and angles in the heme. what is the distance in angstroms between the N-terminal and C-terminal atoms? What is the Dmat tool and what does it tell us? What is the Rama tool? Click on alpha-helical and non-helical residues. Advanced: Experiment with the tools on the bottom of the screen.
![[3] Use the NCBI website. (http://www.ncbi.nlm.nih.gov/) 3a. Find myoglobin. Strategy #1: enter myoglobin as a search term at the front page of NCBI. 3b.](/docs-images/83/88577785/images/4-0.jpg "NCBI strategy #2. Use the taxonomy browser; select Homo sapiens ; click on the protein link. Now add the word myoglobin in the search box. 3c.")
4 [3] Use the NCBI website. ( 3a. Find myoglobin. Strategy #1: enter myoglobin as a search term at the front page of NCBI. 3b. NCBI strategy #2. Use the taxonomy browser; select Homo sapiens ; click on the protein link. Now add the word myoglobin in the search box. 3c. NCBI strategy #3: Do the same as in 3b, but select Structure links in the Display box. This should yield 6 hits including 2MM1. 3d. Click on 2MM1 and view structure 2MM1 with Cn3D. A screen capture is shown here: 3e. Highlight an alpha helix in the primary amino acid sequence (shown below) and view the corresponding structure.
5 3f View the side chains and find the distal histidine (binds to the iron of the heme group). Use Edit global style under style. 3g. 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. 3h. 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.
![[4] Use the ExPASy website do a text search: myoglobin search a pdb accession: 2mm1 download Swiss-Pdb](/docs-images/83/88577785/images/6-0.jpg "Viewer here explore a variety of these web-based tools for primary, secondary, and tertiary structure")
6 [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
7 [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 center 2 move (translate) 3 zoom in/out 4 rotate 5 click, select two atoms, determine distance in angstroms 6 measure bond angles (pick center atom, then two more atoms) 7 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 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
8 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.
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