proteins in 3d, nmc 2009
DESCRIPTION
Lourdes Aleman & Molly Ruggles from MIT's Office of Educational Innovation and Technology present on the 3d protein viewer, StarBiochem.TRANSCRIPT
Proteins in 3DViewing Biological Molecules in the
Classroom
OEIT | MIT | Star
Lourdes Aleman | Molly Ruggles
Presentation Outline1 What is STAR?
– Purpose, focus, impact– Unique qualities
2 StarBiochem 3D protein viewer
– Comparison
3 History
4 Demo (hands-on)
5 Case Studies
6 Looking into the future
What is STAR?Software Tools for Academics & Researchers
Purpose:– Enhance learning/improve educational experience– Created in response to MIT faculty – Freely available
Focus: – biology, computer science, environmental engineering &
materials science.
Importance to Learning:– real case applications, using valid scientific data.– Subject matter is more interesting and engaging.– Understand concepts, see relationships
User-centered tools faithful to the science foundations of the domains they represent.
dilemma:
intuitive/accessible versus comprehensive/scholarly
Star tools:fully leverage research data and UI that is ultra-intuitive
What makes Star Tools Unique
StarBiochem• Features:
– Exposes molecular structure– Extensive deployment in higher ed and high school – Platform independent– Shallow learning curve
• Impact:– Students see all facets– Can’t see 3D in 2D space– Pre-requisite to deeper study– Embraces language of biology
• Protein Databank (pdb.org)– Free access– Over 50,000 records - updated regularly
Download: web.mit.edu/star/biochem
Handout for downloading and installing StarBiochem
StarBiochem embraces qualities of both educational & research tools• Educational Category
– Protein Explorer, BioMolecular Explorer• Research Category
– Type A easy & intuitive but not comprehensive• web-based: WebMol, Jmol, • Java applet: Protein Workshop• mobile: iMole.
– Type B Comprehensive but steep learning curve. • Rasmol, PyMol, Chimera
– Type AB StarBioChem
StarBiochem History
TEALSim suite (John Belcher)Physics visualizations for electromagnetism.
Transform physics education– Studio Physics classroom– Hands-on exercises: small groups– Visualizations: pre-lab prep and in-class labs
Created from open-source componentsSupports all the requirements of the TEALSim
visualization suite.
•UI controls: L2Fprod.com•Graphing: Ptolemny (Berkeley) •Rendering: engine is Java 3D•Computational engine: scratch
TEALSim is an open-source java-based framework
TealSim visualization: Helmholtz Coil
TEALSim --> Star Biochem
Physics
data: not much
computation: lots
Biology
data: lots
computation: not much
Parser to interpret data from PDB
Specs to render data visually
Schubert & Ceraj: adapt TEALSim to other disciplines.
Graham Walker: improve comprehension (Biology)
DNA GLYCOSYLASE(1EBM)
ChallengeTeaching protein structure in a traditional classroom setting.
Proteins perform many important biological functions
hemoglobincarry oxygen in the blood
F1 ATPasegenerate energy
antibodyprotect against
infections
aquaporinwater transport
microtubulescell division
Protein Data Bank website
The function of a protein is determined by its structure
structure function
Understanding how proteins work
Understanding the basis of disease
Designing drugs that act specifically
StarBiochem can be used to understand biology concepts & their medical implications
Understanding how proteins work
Understanding the basis of disease
Designing drugs that act specifically
StarBiochem can be used to understand biology concepts & their medical implications
Understanding how proteins workDNA repair proteins
10,000,000,000,000,000
Mutations often result in disease
mutations cancer
Where do mutations come from?
DNA mutations can be caused by various agents
cancer mutations
DNA mutations can be caused by various agents
UV rays(sun) oxidation
(respiration, radiation, smoking)
toxic chemicals(industrial & environmental) X-rays
(clinic)
viruses(HPV)
cancer mutations
endogenous(DNA replication)
DNA mutations can be caused by various agents
UV rays(sun) oxidation
(respiration, radiation, smoking)
toxic chemicals(industrial & environmental) X-rays
(clinic)
viruses(HPV)
cancer mutations
endogenous(DNA replication)
DNA glycosylases
StarBiochem: human DNA glycosylase (1EBM)
How does DNA glycosylase recognize oxidated DNA bases?
Structure of human DNA glycosylase
structurehuman DNA glycosylase & DNA
functionrecognition of damaged DNA bases
Understanding the basis of diseaseSickle cell anemia
Sickle cell anemia
severe bone pain and death
stroke
enlarged heart
bloodstream infections and pneumonia
www.commercialappeal.com
A mutation in hemoblogin causes sickle cell anemia
University of Utah Learn Genetics website
StarBiochem: sickle hemoglobin (2HBS)
Why is hemoglobin sticky in sickle cell anemia patients?
Structure of sickle hemoglobin
structuremutated amino acid in hemoglobin
DiseaseVal 6 location in hemoglobin
makes it sticky
Conclusion
Deepen understanding
Engage interactive learning
Spark curiosity
structure function health/disease
Current StarBiochem classroom applications
• Undergraduate settingIntroductory biology (MIT)
Introductory biology lab (Brandeis University)
• High school settingOutreach HS program (Broad Institute of MIT & Harvard)
MIT Museum/Center for Environmental Health Sciences Outreach (MIT)
HS fieldtrips (Biology Department, MIT)
Educational benefits
• Make visible what is invisible– Understand concepts; see relationships
• Intuitive user interface– No help files– Encourage exploration
• Fills a pedagogical need– Learn essential concepts quicker– More engaging and interesting
What next?
• From same simulation engine• StarHydro – hydrology visualization
• User centered tools: different architecture• StarBiogene – genomics data visualization• StarGenetics – genetic cross simulator• StarORF – gene finder• StarHPC – parallel programming• StarMolsim – materials modeling
Thank you!Star Team:
Chuck Shubert
Ivan Ceraj
Rocklyn Clarke
Justin Riley
Sara Bonner
TeamSim Team:
Andrew McKinney
Kirky DeLong
Other Supporters:
John Belcher
Graham Walker
Megan Rokop
Kathy Vandiver
Phil Bailey
Vikay Kumar
Peter Wilkins
Dr. Lourdes Aleman [email protected] | Molly Ruggles [email protected]