Student Projects for UMass Chemistry 423 Spring 2011
From Proteopedia
Instruction and signup page (below) were posted in Sandbox423 for all students to edit.
This sandbox is in use for UMass Chemistry 423. Others please do not edit this page. Thanks!
Spring 2011 Chem423 Team Projects: Understanding Drug Mechanisms
Contents |
Project Instructions
1. Team & Structure selection, due 4/1/11: All projects & names must be posted on the list below, linking to sandbox pages displaying initial structure.
- Form teams of 4 people; include both chemistry and chemical engineering majors on each team. Start by finding a protein-drug or nucleic acid-drug complex with a known structure in the pdb that interests your team. Check the list below to see if another team has already chosen this complex. If not, start a new sandbox page (just try sandbox## in the search box to find an unused number) and add a link for your team/protein to our class list below (use editing button above (Ab) or follow my model).
- Copy the message at the top of this page into your sandbox page to "reserve" your sandbox for this course.
- Find the pdb id for your protein-drug complex in the Protein Data Bank. In your sandbox page click"edit this page" (top) and follow the directions to insert your rotating structure on your page.
2. Project completion, due 4/22/11. Your proteopedia page should be organized into the following 5 required sections, with each team member responsible for one of these sections of the team project.
a. Introduction
- Introduce the protein function and the disease treated by the drug. This must be written in your own words with citations to your sources.You cannot include a copyrighted figure unless you request permission to use it.
b. Overall structure
- Describe the overall structure of your protein in words and make "green scenes" to illustrate your points. What elements of secondary structure are present (ie 5 alpha helices and 2 beta strands) and how are they organized? Below I illustrate the start of an "overall structure" section on GFP. Additional description and green scenes could illustrate the polar/nonpolar distrubution of amino acids (is the inside of the barrel polar or nonpolar?), packing of amphipathic elements, etc.
c. Drug binding site
- Describe features of the drug binding site in words and make "green scenes" to illustrate your points. Show the interactions that stabilize binding of this molecule to the protein (ie H bonds).
d. Additional features
- Describe and use green scenes to illustrate additional features of the protein. What you do here depends on what information is available. If a structure of the protein-substrate complex is available, you could compare protein interactions with the substrate vs. with the drug. If the drug is a transition state inhibitor, explain and illustrate that (eg include a reaction scheme with structures of the substrate, transition state and product).
e. Credits -- at the end list who did which portion of the project:
- Introduction -- name of team member
- Overall structure -- name of team member
- Drug binding site -- name of team member
- Additional features -- name of team member
f. References This will include the published paper that describes your structure (the reference associated with your pdb code). You will get much of your information about specific interactions to look for and highlight in the structure from this reference (which is much easier than trying to find these on your own with no guidance!).
3. In-class presentations, to be announced
Example
This is a complex between a macromolecule and its ligand (but this ligand is not a drug) that illlustrates the use of green scenes:
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Asp Receptor Ligand-binding domain
Overall structure
The ligand binding domain of the aspartate receptor () ) is a dimer of two 4-helix bundles that is shown here with the bound.[1] In this the N and C termini are at the bottom of the structure; this is where the connections to the transmembrane helices have been truncated.
Ligand binding site
Interactions that stabilize ligand binding[2] include hydrogen bonding from Tyr149 and Gln152 backbone carbonyls and Thr154 sidechain OH to the and hydrogen bonding from the sidechain nitrogens of Arg64, Arg69, and Arg73 to the two .
References
- ↑ Yeh JI, Biemann HP, Pandit J, Koshland DE, Kim SH. The three-dimensional structure of the ligand-binding domain of a wild-type bacterial chemotaxis receptor. Structural comparison to the cross-linked mutant forms and conformational changes upon ligand binding. J Biol Chem. 1993 May 5;268(13):9787-92. PMID:8486661
- ↑ Milburn MV, Prive GG, Milligan DL, Scott WG, Yeh J, Jancarik J, Koshland DE Jr, Kim SH. Three-dimensional structures of the ligand-binding domain of the bacterial aspartate receptor with and without a ligand. Science. 1991 Nov 29;254(5036):1342-7. PMID:1660187
Project Teams, Topics, Links, and Presentation Dates
C See comment on your page.
Example (but not a drug complex): Lynmarie Thompson, ..., ..., ... - Asp receptor in complex with Asp (above)
Monday 4/25/11
Nick DeGraan-Weber, Jackie Dorhout, Rachael Jayne, Mike Reardon - flu neuraminidase in complex with tamiflu sandbox45 flu neuraminidase in complex with tamiflu
John Hickey, Josh Drolet, Josephine Harrington, Andrea Simoni - influenza M2 proton channel sandbox 111
Wednesday 4/27/11
Brittany Forkus, Katie Geldart, Elizabeth Schutsky, Breanna Zerfas - beta adrenergic GPCR sandbox226
Lucia Tringali, Shaina Boyle, Jaclyn Somadelis , Dany Mbakop -- HIV Protease Sandbox17
Andy Kim, Zach Brentzel, Tyler Vlass, Zach Hitzig -- Acetylcholinesterase sandbox11
Friday 4/29/11
Varun Chalupadi, Anthony Laviola, Tiffany Brucker, Alan Stebbins - cyclooxygenase sandbox25
Inna Brockman, Robert Nathan, Sarena Horava, Nick Cadirov - p38 kinase sandbox713
David Peltier, Donald Einck, Ethan Leighton, Chris Coakley - Rituximab Fab sandbox99
Monday 5/2/11
Max Moulton, Sally Stras, Jordan Schleeweis, Anh Huynh -- HIV reverse transcription Sandbox77
Chris Brueckner, Daniel Roy, John Clarkson, Justin Srodulski -- Ketamine in binding complex with NMDA receptor sandbox42
Lyes Khendek, Paul Breslin, William Rowley, Joe Perito, Ashley Rivera - G-Quadruplex sandbox888
Students looking for group members
Each group should contain at least one person from a different primary major (typically Chemistry or Chemical Engineering) than the rest.
List yourself + your major, list partial groups looking for members, list your complex if you have chosen one. Contact others to form a group.
4/1/11 update by Prof Thompson: The remaining students can go ahead and form teams regardless of major.
Luis Cristian, Chem major, lcristia@student.umass.edu - looking to be in a group with chem eng
Help Editing
Hint: Ctl-click or right-click on links below and select "Open Link in New Window"
Start with Help in the navigation box on the left. Some things I've found useful:
- Follow the step-by-step written Primer.
- For step-by-step instructions on creating example scenes, try Proteopedia:DIY:Scenes.
- For editing help, try Help:Editing. Guidelines for avoiding plagiarism are listed here: Proteopedia:Guidelines for Ethical Writing.
- You can use the edit button on any page to find out how other users created effects that you see in the text (not the scenes).
[General help with Wiki editing], plus more [Wiki Text examples]
Some of the above are for help editing Wikipedia pages, but the syntax is mostly the same. Proteopedia ADDS protein stuff to the WikiMedia markup language, which powers both WEB sites.
Questions & Answers
Here is a place to post questions and answers for each other about how to do things in Proteopedia:
A very useful color scheme is "chain" which colors separate proteins or DNA strands in different colors (first select all protein or DNA).
Anyone know what format we should be putting our references in?
For references, follow the format used in the example on the Asp receptor and they will be put in automatically. You just find out the PMID code (listed in pubmed for example) and insert it into the following, at the place where you want the reference cited (click edit to see what is actually inserted here). [1] You also need to add the section:
References
- ↑ Yeh JI, Biemann HP, Pandit J, Koshland DE, Kim SH. The three-dimensional structure of the ligand-binding domain of a wild-type bacterial chemotaxis receptor. Structural comparison to the cross-linked mutant forms and conformational changes upon ligand binding. J Biol Chem. 1993 May 5;268(13):9787-92. PMID:8486661
Hey guys this is just a useful tip:
If you get an xml error after you try to save your changes it is due to the green scene coding. Our group experienced this issue and it would not let us access our sandbox. In order to fix this go back (or find the page to edit in your history) and delete the green scene code that was just entered. Then save the page and you should be back to your sandbox. This may be trivial to many, but just throwing it out there.
To highlight some interesting portion of your protein: Under the selections tab, you can "limit to residue numbers." So for example enter in 60-65, then click "replace selection" below. Then if you go to the colors tab you can pick a color for just the residues you have selected. If it is a loop or if they are hard to see you can go to the representation tab and set selection to ball and stick or spacefill.
It is also useful to click the "selection halos:" box under the picture. That shows you what you have in your selection.
Flu Neuraminidase
Introduction
Neuraminidase protein is one of two glycoproteins that coats the envelope of the influenza virus. Neuraminidase's particular function is the removal of sialic acid from the host cell, allowing the replicated influenza viruses to escape the host cell and spread to other cells.
Tamiflu, a drug designed to combat influenza, binds to and inhibits the function of neuraminidase, disabling its function and consequently disallowing the influenza virus to spread between cells.
Influenza is a disease caused by the various species and genera of the influenza RNA virus. The disease, commonly referred to as "the Flu," is highly contagious and travels around the world in seasonal epidemics. It is responsible for the deaths of between 250,000 and 500,000 people each year, and these numbers can sometimes reach the millions in particularly pandemic years. The virus is particularly lethal to people with weakened immune systems, since the virus can enable the spread of dangerous secondary infections such as pneumonias within the host.
The typical symptoms of the Flu include chills, fever, a sore throat, muscle pains, severe headache, coughing, and weakness or fatigue, as well as general discomfort.
Overall Structure
Influenza (flu) Neuraminidase is a homotetramer, with four identical subunits. Each subunit consists mostly of antiparallel beta sheets and three alpha helices, with a beta-propeller folding pattern (). As shown, the alpha helices lie toward the center of the protein.
The is a pocket on the surface of the protein, lined with highly conserved residues. Shown is the ligand Oseltamivir (Tamiflu) bound to one of the four subunits. When Tamiflu is bound, it tightly blocks the virus release sites on nonresistant strains of flu neuraminidase because it binds with the hydrophilic residues exposed on the surface.
Different conformations account for drug resistance of flu neuraminidase. 2hu4 is the “closed” conformation of the wild type 3hu0. For example, a mutation at the site H274Y, on the closed-form wild type, causes a change in the usual binding site for Tamiflu, possibly affecting resistance.
Research on the structures of the different mutants of flu Neuraminidase suggests that the slight change in the binding site affects the drug resistance of the molecule. In a specific case presented by Wang , et al., the H5N1 mutant being observed has a hydrophobic Tyr347 compared to the hydrophilic Asn347 of the wild type and closed form. Since Tamiflu binds to hydrophilic regions of the pore, this change has the potential to greatly affect the binding affinity, hence the mutant’s resistance to oseltamivir.
Drug Binding Site
Flu neuraminidase is a homotetramer, and each of the four protein chains has a catalytic site. The catalytic sites are shown with Tamiflu shown in purple.
Tamiflu was designed specifically to fit to the binding site of neuraminidase by induced fit. The binding site contains a loop of residues 147-152. When it binds at the active site, Tamiflu pulls a loop made of Asp151 and Glu119 closer to the inhibitor, thereby enclosing the Tamiflu inhibitor.
There are five specific residues that are in contact with the Tamiflu substrate - Arg292, Glu276, Arg152, Arg371, and Arg118. They are in the active site.
Tamiflu does not work on all types of the flu virus, and some are becoming immune to it. However, it was recently discovered that one of the subunits has a larger surface-accessible cavity in the substrate binding region. The larger end of this cavity is not in contact with Tamiflu when the substrate is bound. This presents an opportunity to design another drug with greater specificity to this pocket.
Additional Features
Template:STRUCTURE 2hu4 Neuraminidase breaks the groups from glycoproteins. from on the virus attaches to the sialic acid groups. The virus is from the cell and is released when neuraminidase breaks the sialic acid groups. This will allow flu replication to happen and a neuraminidase inhibitor, such as Tamiflu, is required to stop neuraminidase. The interaction of Tamiflu with N1 neuraminidase is shown with this (1). Tamiflu in this model is bound when it is visible and the loop in moved in towards the drug through induced fit.
When neuraminidase breaks the sialic acid groups, the virus (virion) is released. This will allow replication of the virus. The inhibitor prevents the breaking of the sialic acid groups, so no virion is released and replicated.
Credits
Introduction - Mike Reardon
Overall Structure - Rachael Jayne
Drug Binding Site - Jackie Dorhout
Additional Features - Nick DeGraan-Weber
References
(1) Martz, E.; Hodis, E.; Canner, D.; Samish, I.; Prilusky, J.; Goodsell, D. S.; Strong, M. Avian Influenza Neuraminidase, Tamiflu and Relenza. http://www.proteopedia.org/wiki/index.php/Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza 2011.
(2) Influenza (Seasonal). World Health Organization. http://www.who.int/mediacentre/factsheets/fs211/en/ 2011
(3) "Influenza: Viral Infections: Merck Manual Home Edition". http://www.merck.com/mmhe/sec17/ch198/ch198d.html 2011
(2) OCA 7nn9 - Native Influenza Virus Neuraminidase Subtype N9. http://www.proteopedia.org/wiki/index.php/7nn9 2011.
(3) OCA 2hu4 - N1 Neuraminidase in Complex with Oseltamivir 2. http://www.proteopedia.org/wiki/index.php/2hu4 2011.
(4) Goodsell, David. Molecule of the Month: Influenza Neuraminidase- RCSB PDB. http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb113_1.html 2009.
(5) Russell, R.J.; Haire, L.F.; Stevens, D.J.; Collins, P.J.; Lin, Y.P.; Blackburn, G.M.; Hay, A.J.; Gamblin, S.J.; Skehel, J.J. N1 neuraminidase in complex with oseltamivir 2. http://www.rcsb.org/pdb/explore.do?structureId=2hu4.
(6) Garcia-Sosa, Alfonso; Sild, Sulev; Maran, Uko. Design of Multi-Binding-Site Inhibitors, Ligand Efficiency, and Consensus Screening of Avian Influenza H5N1 Wild-Type Neuraminidase and of the Oseltamivir-Resistant H274Y Variant. Journal of Chemical Information and Modeling. http://pubs.acs.org/doi/full/10.1021/ci800242z. 2009.
(7) Wang, Shu-Qing; Dub, Qi-Shi; Huang, Ri-Bo; Zhang, Da-Wei; Chou, Kuo-Chen. Insights from investigating the interaction of oseltamivir (Tamiflu) with neuraminidase of the 2009 H1N1 swine flu virus. http://www.scirp.org/kcchou/papers/BBRC_2009_H1N1_Tamiflu.pdf. 2009.
(8) Neuraminidase Inhibitors. http://www.fluwiki.info/pmwiki.php?n=Consequences.NeuraminidaseInhibitors. 2009.
(9) Investor Update. http://www.roche.com/investors/ir_update/inv-update-2009-09-13.htm. 2009.
