proteins in 3d, nmc 2009

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 laleman@mit.edu | Molly Ruggles ruggles@mit.edu