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OSI Protein Modeling Challenge. December 2010. Joan Kiely, Stony Brook University joan.kiely@stonybrook.edu Debbie Pelio , Stony Brook University cesame@stonybrook.edu http://www.stonybrook.edu/cesame Linda Padwa , Stony Brook University Kristen La Magna, Stony Brook University - PowerPoint PPT Presentation
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1Fall 2010
OSI Protein Modeling Challenge
December 2010
2Fall 2010
Joan Kiely, Stony Brook Universityjoan.kiely@stonybrook.edu
Debbie Pelio, Stony Brook Universitycesame@stonybrook.edu
http://www.stonybrook.edu/cesame
Linda Padwa, Stony Brook UniversityKristen La Magna, Stony Brook University
Shannon Colton, Ph.D., Technical AdvisorMilwaukee School of Engineering
http://cbm.msoe.edu/
3Fall 2010
• To compete successfully in the Protein Modeling Challenge, you will:
– Meet and get to know Epidermal Growth Factor Receptor (a tyrosine kinase receptor), Tarceva and their roles in Lung Cancer
– Build models that illustrate what you know about EGFR, Tarceva and Lung Cancer.
– Become a maven of protein structure– Enhance your computer skills with Jmol
Protein Modeling Challenge
4Fall 2010
Web-Based Resources• This powerpoint presentation will serve as an interactive
resource for your team to gain the knowledge they need to be successful in the Protein Modeling Challenge
• You will find links distributed throughout this presentation, indicated by the blue underlined text
• Follow these links to the appropriate sources
• Good luck and have fun!
5Fall 20105
Protein Structure Resources
• The following links will serve as tools to help you learn the basic information needed to be successful in this challenge. Please follow these links:
– Basic Introduction to Protein Structure and Modeling– http://cbm.msoe.edu/stupro/so/index.html
– Protein Databank Molecule of the Monthhttp://www.pdb.org/pdb/explore/motm.do
6Fall 2010
• Proteins are macromolecules• Amino acids are the basic building blocks of proteins• Working as a team, make an amino acid
6
Protein Structure
Nitrogen
Amino Group
Carboxyl Group
Alpha-Carbon
Sidechain (R-Group)
• s your amino acid L or D form?
7Fall 2010
D-Alanine L-Alanine
8Fall 20108
Amino Acids Have Unique Chemical Characteristics
• Each amino acid has the same “backbone” structure, but has different chemical groups (R groups or sidechains) attached
• Working with another team, construct an amino acid and a dipeptide with a molymod kit
NH2-CH-COOH R
9Fall 20109
• A linear chain of amino acids is the protein “primary” structure
• A chain of amino acids will spontaneously form stable “secondary structures”, ie: beta-sheet or alpha-helix
• Hydrogen bonds may stabilize these structures
• Science researchers would like to understand what controls this folding.– http://fold.it/portal/
Proteins Have Secondary Structure
Alpha Helix
Beta-sheet
10Fall 201010
• Protein folding is due to the behavior of different chemical groups on amino acids in an aqueous environment
• You can explore amino acid sidechain chemistry and protein structure through the game Fold It: http://fold.it/portal/
Proteins Fold Into a Tertiary Structure
11Fall 201011
• Proteins spontaneously fold into a specific three dimensional “tertiary” structure that governs a protein’s function
Proteins Fold Into a Tertiary Structure
12Fall 201012
Protein Data Bank• The 3-dimensional structure of proteins is often
determined by x-ray diffraction or NMR analysis
• PDB file lists the X, Y, Z coordinates for each atom in a protein
• Protein Data Bank http://www.pdb.org/pdb/home/home.do
• PDB Molecule of the Month features the structure and function of a different protein each monthhttp://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/alphabetical_list.html
13Fall 201013
Molecule of the Month (MOM)
• A monthly PDB feature written by David Goodsellhttp://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/alphabetical_list.html
– Features a specific molecule
– Describes protein function
– Relates structure with function
Epidermal Growth Factor June 2010 David Goodsell
http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb126_1.html
14Fall 201014
Jmol• Jmol is a computer visualization software that displays
data from a PDB file as a “3D” image of the molecule on the computer screen
• Jmol is Java-based and will work on most computers• http://bioportal.weizmann.ac.il/oca-docs/fgij/index.htm• http://cbm.msoe.edu/teachRes/index.html
15Fall 201015
Exploring Protein Structure with Jmol
• Jmol allows you to identify elements of protein structure
– Helix (magenta)
– Sheet (yellow)
– N-terminus (blue)
– C-terminus (red)
– Amino acid sidechains (CPK)
– Alpha-carbon backbone model format
16Fall 201016
Mini-Toober Models (cont.)• Mark location of structures on Mini-Toober
• Fold Mini-Toober into a 3D model representing protein
17Fall 201017
Protein Modeling Challenge
• 2010 Event Rules www.stonybrook.edu/cesame
• Pre-build model (40%)
• On-site build (30%)
• Written exam (30%)
18Fall 201018
EGFR Pre-Built Model 2010• Epidermal Growth Factor and written description based on June
2010 Molecule Of the Month and Protein Databank File 1M17 residues 695-854http://www.pdb.org/pdb/explore/motm.do
– Must arrive at Stony Brook by 4:30 December 1 for judging– 40% team score
19Fall 201019
Written Exam 2010• Exam covers material in:
– PDB file 1M17– Molecule of the Month article on Epidermal Growth Factor– Jmol– Campbell, Biology, will be used a the material base for questions
on protein structure and function and cell communication– Taken as a group– Available at the exam will be:
• PDB file, abstract, • Molecule of the Month
• 30% team score
20Fall 201020
EGFR• On-site build• PDB file will be provided on the day of the exam• Students will build a portion of the EGFR receptor. They will be
given: a toober, selected amino acid side chains, a computer, jmol and the pdb file.
21Fall 201021
Protein Modeling Challenge With National Science Content
Standards• Science and Technology
– Abilities of Technological Design– Understandings about Science and Technology
• Life Science– The Cell– Physiology
• Science as Inquiry– Abilities Necessary to do Scientific Inquiry
• Physical Science– Structure and Properties of Matter– Chemical Reactions
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