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The overall goal of this event will be to enhance scientific appreciation and enthusiasm by high school students for protein structure and function. The high school classroom often lacks connections to authentic science and how it is applied in a research lab. We plan to use our skills and experience as undergraduate researchers to go into a local high school classroom and share our knowledge and passion about the proteins we are investigating.

We will engage students in a hands-on activity that is tied to a computer-based exercise to visualize protein structure. Initially, we will give a brief overview of our individual research projects in order to provide students with a context explaining how the concepts discussed in the activity can be applied outside of the classroom. Groups of 2-3 students will be assigned to work on a single protein for the duration of the activity. The groups will be asked to access a model of their protein from the PDB and visualize it in PyMOL. We will help students manipulate their structure to define the active site and examine ligand interactions within the active site. The students will create images of their proteins as a basic introduction to protein visualization.

Using "Modeling Mini Toobers” the students will physically recreate their protein’s active site, specifying the amino acids involved in ligand interactions. Groups will be assigned a physical set of possible inhibitory compounds, and asked to rank compounds from most likely to bind, to least likely to bind. In order to make accurate predictions, students will need to think critically about the possible interactions between active site amino acids and the various compounds. At the conclusion of the activity, students will be shown the predicted virtual screening scores corresponding to each ligands. Groups will then be able to compare their own predictions to the predictions made by the virtual screening software.

Equipment & Supplies
3D Molecular Designs: Amino Acid Starter Kit© (6-Group Set)
3D Molecular Designs: Potassium Channel Bound with Scorpion Toxin Mini Model



The Protein Society: Member Mini Grants
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The goal of this program is to enable members to hold protein science-reltaed events in their communities. These events could be meetings, seminars, workshops, experiments, networking or other small gatherings that bring groups together to learn, collaborate, share perspectives and make professional connections. Also encouraged are outreach events intended to communicate the unique appeal and fascinating potential of research involving proteins to junior investigators, students and under-represented minorities. Among members is VDSer Tony Garcia who sponsors an outreach program in the Austin area. For more information on this program go this the Protein Society's website below.

http://www.proteinsociety.org/join/benefits/minigrants/







Science Olympiad

2016 - Ashley C, Lisa S, Simone M. will coordinate the event.

2015 - Tony, Alberto, Cidia and Dr. B helped run the Protein Modeling event for the UT Science Olympiad.

Science Olympiad page for UT:

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NOTES

February 20, 2016
Protein Modeling Event
40 points - prebuild
30 points - onsite build
30 points - exam

LINK TO THE BUILD ENVIRONMENT
Pre-Build for 1sep.pdb.

OnSite Build Model
Link to Jmol
Link to Environment Site

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ScienceOlympiadMar2015_VDSers (3).jpgScienceOlympiadMar2015_VDSers (1).jpg




Shadow a Scientist
The Shadow a Scientist program matches two middle school students with a scientist for a two-hour tour of the scientist’s lab and experiments in progress. Shadowing a scientist gives middle school students the opportunity to visit laboratories on a university campus and meet and interact with scientists. The middle school students visit one scientist, selected based on their personal interests, and the student participants have included those from private, public and home-schools. On a typical visit, the students meet with the scientist, and are introduced to their research. The students ask questions about research, do hands-on tasks in the lab and are shown lab equipment. There is flexibility in each tour and the experience necessarily varies depending on the scientist’s particular research discipline.
The goals of the program are to provide the opportunity for young students to cultivate their interest in science and allow them to experience first-hand what a scientist does on a daily basis and to provide graduate students and scientists the opportunity to explain their research and to practice and improve their scientific communication skills.
http://cns.utexas.edu/fri/outreach/164-freshman-research-initiative/outreach/633-shadow-a-scientist-program.



High School Research Academy (Summer Research Academy - SRA)
The College of Natural Sciences Summer High School Research Academy offers high school students the chance to experience research and mentorship opportunities during the summer.
The participants will see how research works by being directly involved in research projects on the UT-Austin campus. They will learn advanced techniques and interact with students and faculty at UT. By being involved in research, the students will experience the joy of discovery that is central to being a scientist. This is a unique opportunity that will give high school students a real taste of life as a researcher. For Summer 2015 we have two programs available for high school students entering their junior or senior year in the 2015-16 academic year.
https://cns.utexas.edu/tides/students/summer-research-academy


PyMol Session for Research Methods/SIAD classes
PyMOL Software

CHEAT SHEET: access pyMOL cheatsheet here
You can download their own Educational version of PyMol from the Schroedinger website. You must be on campus (have an ip on campus) for it to recognize you are academic.

http://pymol.org/educational/

Mac Version:
https://www.dropbox.com/s/a2pnuyhjk0tx0fo/MacPyMOL-v1.3r2-edu.tar.bz2?dl=0
PC Version:
https://www.dropbox.com/s/oiwk79ke4w8mksb/pymol-v1.3r1-edu-Win32.msi?dl=0
If those links don't work - here is a Google Drive link for the software:
https://drive.google.com/folderview?id=0B_Gl3lMyhDsoNDJiYzI4N2UtMWExNS00YjcyLThmYjktZjI1ZmJmNzNiMzgy&usp=sharing

Show a pretty PyMol image of your protein – as a good example of what can be done
Then show 4V5D – pymol of a Ribosome - very pretty. RNA + Protein

Starting with PyMol - a few structures:
Alpha Helix: Here is the link to the helix.pdb
https://drive.google.com/file/d/0B_Gl3lMyhDsoSVZWcW5JN0hmbXc/view?usp=sharing
Here is the link to the Beta sheet.pdb
https://drive.google.com/file/d/0B_Gl3lMyhDsoX3Rfc29ocFJYN1k/view?usp=sharing

A CANCER TARGET PROTEIN
Then have them them load (or fetch) 1U72 and select the NADPH and MTX and show as sticks
Walk through all the features (sticks, lines, show water as spheres, surface, mesh, etc)
A RIBOSOME
Then go to the PDB to download the Ribosome PDB (4V5D) and have them use Action à Preset à Publication. To show a pretty image

DISEASE & DRUG PAIR
Go into PDB and search for a disease name and find a structure that matches (e.g. cancer, heart disease, diabetes).
They can then read a little bit about the target and download it to PyMol to view.

TOP 10 DRUGS
Then do a google search for Top 10 drugs
  • go to Wikipedia to get the scientific name of the drug.
  • go back to PDB and enter the scientific drug name to get a structure