Howard university presentation ver3

Lourdes Alemán, Ph.D.

Stacie Bumgarner, Ph.D.

April 8-9th, 2010

Howard University STAR Workshop

Office of Educational Innovation and Technology (OEIT)Biology Department

170 liters

Nobel Prize website

Aquaporin structural model

10% of what they hear30% of what they see60% of what they hear & see80% of what they hear, see, & do100% of what they hear, see, do, smell, feel, taste…& purchase on credit

By Ronald A. BerkProfessors are from Mars. Students are from Snickers.

Students learn…

ChallengeBridging the divide between research & the classroom using

interactive technology.

Professor Graham Walker

Professor Graham Walker

Who we are

MIT Biology DepartmentOffice of Educational Innovation & Technology (OEIT)

What we are doing

Designing interactive teaching software toolsto be used IN & OUTSIDE class

Software Tools for Academics & Researchers (STAR) biology tools

1 Educational goals

2 Design process

3 Access & outreach

Educational goals

ChallengeTeaching protein structure in a traditional classroom setting

StarBiochem: protein 3D viewer

ChallengeTeaching experimental design & data interpretation outside of

a genetics lab

StarGenetics: virtual genetics lab

Design process

Collaboration between MIT faculty & OEIT

StarBiochem Professor Graham WalkerIntroductory Biology Series

StarGeneticsProfessor Chris KaiserGeneticsGraduate Student Bridge Program

Access & outreachSoftware & curriculum materials -> freely accessible online

StarBiochem http://web.mit.edu/star/biochem

StarGenetics http://web.mit.edu/star/genetics

Create curriculum modules.

Conduct workshops.

Collaborate with wide range of educational institutions.

Assess how software tools impact different populations of students.

Access & outreach

StarBiochem usage beyond MIT

Visits9881

Countries82

StarBiochem Workshop – Day 1

1 Introduction to StarBiochem

2 StarBiochem hands-on activity

3 StarBiochem educational applications (Part I)Classroom applications

4 StarBiochem educational applications (Part II)Lab applications

5 Designing & writing new StarBiochem curriculum activities







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

ChallengeTeaching protein structure in a traditional classroom setting.

Traditional methods for teaching about protein structure and function

CartoonsCan introduce misconceptions

2-D representationsLimits student exploration

Protein Structure & Function (2007)

Using 3-D protein viewers for teaching about protein structure & function

Research PyMol, KING, Rasmol, Chimera, First Glance in Jmol, Webmol

Educational Protein Explorer, BioMolecular Explorer, other guided tutorials

Limitations of existing 3-D proteins viewers forteaching about proteins structure & function

Research

Educational

uses crystallography jargon

not user-friendly

ability to scale-up not known

windows functionality only

tutorials with limited views/manipulations

StarBiochem: protein 3-D viewer

StarBiochem is a protein 3-D viewer designed for educational purposes

Website: http://web.mit.edu/star/biochem/

Platform independent.

Interface is designed with students in mind.

Parallels how proteins are taught in introductory biology.

Can upload >54,000 Protein Data Bank structures.

StarBiochem hands-on guided tour

http://web.mit.edu/star/biochem/







How mutations in DNA can result in diseasesickle cell anemia: hemoglobin

Hemoglobin

Highly expressed in red blood cells

Responsible for oxygen transport

Contains four protein subunits -> each one binds to a O2 molecule

Protein Data Bank website

Hemoglobin

heme

heme

Protein Data Bank websiteHighly expressed in red blood cells

Responsible for oxygen transport

Contains four protein subunits -> each one binds to a O2 molecule

severe bone pain & necrosis

stroke

enlarged heart

bloodstream infections and pneumonia

www.commercialappeal.com

Sickle cell anemia

A mutation in hemoglobin causes sickle cell anemia

University of Utah Learn Genetics website

How does a mutation in the hemoglobin gene causes the protein to become sticky?

normal hemoglobin vs. sickle hemoglobin (2HBS)(1A3N)

Structure of sickle hemoglobin:

DNA sequenceA -> T

proteinhemoglobin becomes sticky

amino acid sequence Glu6 -> Val6

diseasesickle cell anemia







GoalTo illustrate how StarBiochem can be implemented into an

existing class curriculum.

StarBiochem educational applications (Part I) Classroom applications

1 Current StarBiochem applications

2 In-class activities

3 Outside-class activities

4 Assessment & testing






Current StarBiochem educational applications

• Undergraduate settingIntroductory Biology (MIT)

Introductory Biology Lab (Brandeis)

• High school settingMIT Museum/Environmental Health Sciences Outreach Program (MIT)

Outreach HS program (Broad Institute)

HS fieldtrips (Biology Department, MIT)

Introductory Biology Courses (7.01 series)

StarBiochem modules core topics

StarBiochem case study: MIT

biochemistry molecular biology

recombinant DNA technology

signalingimmunology

cancer biologyneurobiology genetics

PAH amyloid GFP BCR-Abl Herceptin DNA pol Ras HemoglobinPFKcrystallin

Diviya Sinha

StarBiochem case study: Brandeis University

Introductory Biology Lab Course (Bio118)

crystallin protein cataracts

• explore the structure of crystallin using StarBiochem

• design mutation in crystallin based on structure

• test mutant crystallin for in vitro cataract formation

Melissa Kosinski-Collins






StarBiochem in-class activities

Short (2-5 min)

Intermediate (10-20 min)

Long (40-60 min)

StarBiochem in-class activitiesShort

Example: snapshot of a structure or a concept

use StarBiochem live

create video using StarBiochem

create images of a particular structural snapshot

StarBiochem in-class activitiesShort

Example: snapshot of a structure or a concept

use StarBiochem live

create video using StarBiochem (ex: hemoglobin)

create images of a particular structural snapshot

StarBiochem in-class activitiesIntermediate

Example: interactive building protein activity

Protein 1 Protein 2cell membrane protein cytoplasmic protein

StarBiochem in-class activitiesIntermediate

Example: interactive building protein activity

Protein 1 Protein 2cell membrane protein cytoplasmic protein

1 Students are asked to consider what would be necessary to build proteins: location & function.

2 Students answers are compared with actual protein structures in StarBiochem.

StarBiochem in-class activitiesLong

Example: basics of protein structure lecture using StarBiochem (Dr. Chia-Yung Wu)

Example 1 Example 2Potassium channel GFP

Protein structure lecture using StarBiochem Introductory Biology

The live demos using StarBiochem helped me gain a better understanding of the relationship between a

protein's structure and its function.

The live demos on the potassium channel protein in StarBiochem helped me understand how this channel

allows for the passage of potassium ions ONLY.

The live demos using StarBiochem helped me understand the four levels of protein structure:

primary, secondary, tertiary & quaternary.

The live demos using StarBiochem helped me understand what protein structures look like in 3D.

I enjoyed today’s lecture on protein structure. Howard University (2009)






http://web.mit.edu/star/biochem/problemsets

Review available curriculum modules online (exercises).

Modify current modules or develop your own.

Students download software from web.

Each module contains full step-by-step instructions forstudents to use software.

Outside-class activities






Goal

Assess effectiveness of the software in illustrating a concept

Assess implementation of StarBiochem activity

Assessment & testing

Example: open-ended exam question

Introductory Biology (MIT)

Aquaporin exercise (homework)•basics of protein structure•aquaporin specificity for passage of water only

Aquaporin question (exam)•assess both protein structure basics and aquaporin structure -> function relationships•could not be completed without doing the aquaporin exercise

Assessment of software’s ability to illustrate concept

Assessment of software’s curriculum implementationUse simple sample survey provided

1 Survey Monkey (http://www.surveymonkey.com/)• best for remote assessment• data is automatically analyzed• basic membership (free), Pro membership ($300/year)

2 Paper survey• best for direct assessment• manual data manipulation• free

2 Quality of exercise

3 Technical difficulties












GoalTo illustrate how to implement StarBiochem lab activity.

10, 000

DNA mutations

neutral

positive -> evolution

negative -> disease

Effects

Consequences of DNA mutations

Consequences of DNA mutations

DNA mutations

neutral

positive -> evolution

negative -> disease

Effects

What causes DNA mutations?

DNA mutations can be caused by various agents

DNA mutations can be caused by various agents

man-made agents(X-rays, smoking, toxic chemicals)

environmental agents(UV rays, toxic chemicals)

foreign biological agents(viruses, transposons)

cellular processes(DNA replication, cell division, respiration)

respiration

radiation

smoking

Each agent is associated with a particular type of DNA mutations

oxidation

agent mutation type

respiration

radiation

smoking

Each mutation type is fixed by a different cellular mechanism

oxidation

agent mutation type

DNAglycosylase

How our cells try to fix DNA mutationsDNA glycosylase

StarBiochem educational applications (Part II) Lab activity

1 Pre-assignment

2 Hands-on activity: DNA glycosylase exercise

3 Post-assignment


1 Pre-assignment


3 Post-assignment

Lab activity: pre-assignment

Goal

1 Illustrate basic science research -> medical applications

2 Understand relevance of lab activity

Lab activity: pre-assignment

Reading“Mapping the Cancer Genome”

by Francis S. Collins and Anna D. BarkerScientific American Magazine, March 2007: 50-5

Questions• usefulness of the genomic cancer atlas for studying & treating cancer.

• hallmarks of cancer cells such as abnormalities in self-control and repair mechanisms.

• complexity of assembly a genomic cancer atlas.


1 Pre-assignment


3 Post-assignment

Oxidation can cause mutations in DNA


1

2


1

2

1a

1b

2a

2b

DNA glycosylase proteins help repair DNA damage caused by oxidation

DNA glycosylases

1

2

1a

1b

2a

2b

How does DNA glycosylase fix DNA oxidation damage?

DNA glycosylase: human 8-oxoguanine glycosylase (hOGG1)

Structure of DNA glycosylase:

structurehuman DNA glycosylase &

DNA substrate

mechanismrotating DNA bases outside of

double helix to check for mutations

Personalized medicine for treating cancer

Rebecca Henretta (2007)


Non-responders

Responders



Non-responders

Responders

alternative treatment

conventional treatment


Personalized medicine for treating cancer: hOGG1 levels & lung cancer

low cancer risk

high

low

high

hOGG1 levelsCleveland Clinic website


1 Pre-assignment


3 Post-assignment

Lab activity: post-assignment

GoalSynthesis of pre-assignment & DNA glycosylase exercise

Lab activity: post-assignment

Questions

• understand how the genomic cancer atlas can be used to uncover potential new roles of hOGG1 in cancer.

• understand how new cancer treatments can be design based on hOGG1.


1 Pre-assignment


3 Post-assignment







GoalEmpower you to build your own StarBiochem exercises by

illustrating the design and building process.

Designing & writing StarBiochem curriculum activities

1 Design & building process

What is the goal of the activity?

What type of activity accomplishes goal?

How to select a structure that accomplishes goal?

How to structure the activity?

2 Interactive exercise creating a StarBiochem activity









structure -> function

structure -> function -> disease

structure -> medical therapies

protein regulation

evolution of protein structure


1 Course

• Introductory Biology• Biochemistry• Cell/Molecular Biology• Pharmacology• Etc.

2 Course curriculum

• format• duration of activity


Example 1

Structure -> function

Course Introductory BiologyCurriculum central concept of the course

Activity

StarBiochem protein structure lecture + StarBiochem exercise (homework/lab activity)


Example 2

Structure -> medical therapies

Course Cell BiologyCurriculum minor point within a lecture

Activity

StarBiochem video or in class-demo illustrating structure –> targeted therapies


1 Goal

Is the structure suitable for illustrating goal?

2 Course/format of activity

Is the structure accessible to your students?

Is the activity format suitable for explaining the structure?

Schneider, T.L. and Linton, B. (2008) Introduction to Protein Structure through Genetics Diseases. Journal of Chemical Education 85: 663-665


Schneider, T.L. and Linton, B. (2008) Introduction to Protein Structure through Genetics Diseases. Journal of Chemical Education 85: 663-665


Researching & finding the appropriate structure

Protein Data Bank http://www.pdb.org/pdb/home/home.do

Search:• keyword• four digit PDB ID• title of paper


Researching & finding the appropriate structure

Hemoglobin: exercise with a well defined activity

structure -> function -> diseaseGlu6 -> Val6 in hemoglobin leads to sickle cell anemia

DNA glycosylase: exercise with less well defined activity

structure -> functionillustrate how DNA glycosylase repairs DNA



1 Format/duration

Short activity straight to the the point

ex: DNA glycosylase video

Long activity framework for building complexity

ex: DNA glycosylase exercise


1 Format/duration






1 Format/duration






References

Structure: 1EBMBruner, S. et al. (2000) Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA. Nature 403:

859-866.

Structures: 1YQK, 1YQRBanerjee, A. et al. (2005) Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA.

Nature 434: 612-618.

How to structure the activity?Structure: 1EBMBruner, S. et al. (2000) Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA. Nature 403: 859-866.

How hOGG1 repairs oxidized guanines:

1.Extrusion of oxoG from the double helix

1.Recognition of oxoG by Gly 42




“The structure of the hOGG1-DNA complex provides a clear solution to the long-standing puzzle of how the cellular repair machinery recognizes oxoG in DNA amidst the vast excess of guanine, a close structural relative. The oxoG residue is fully extruded from the DNA helix and inserted into an extrahelical active-site pocket on the enzyme, consistent with structure-based predictions made for other members of the HhH-GPD superfamily.”

“The most characteristic feature of oxoG - its8-oxo-carbonyl function - is completely devoid of any interacting partner. Instead, the enzyme recognizes the urea system in oxoG by virtue of its N7-H, which donates a hydrogen bond to the main chain carbonyl of Gly 42… Indeed, of all the contacts made to the oxoG base, that involving Gly 42 is the only one that would clearly be different with oxoG versus guanine; thus, the responsibility for discriminating oxoG from guanine appears to be borne by a single hydrogen bond.”




How to structure the activity?Structures: 1YQK, 1YQRBanerjee, A. et al. (2005) Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA. Nature 434: 612-618.

How hOGG1 distinguishes oxidized guanines from undamaged guanines:

1.oxoG:hOGG1 interaction differs from the G:hOGG1 interaction



“Whereas the oxoG nucleobase inserts itself deeply into the lesion recognition pocket on the enzyme (Figs 2, left, and 3a), G is rejected by the lesion recognition pocket and instead lies against the protein surface at an exo-site some 5A ° outside the pocket (Figs 2, right panel, and 3b). The G base does interact with two active-site residues, Phe 319 and His 270, but the contacts are completely different from those made with oxoG.”



“…a hydrogen bond is apparent between the carbonyl oxygen of Gly 42 and N7 H of oxoG. This attractive interaction would be replaced in the case of G by a strongly repulsive interaction with the N7 lone pair, if G and Gly 42 assumed the same positions as in the oxoG complex.”


Long activity: framework for building complexity

Begin with: simple questionsAllow students to become familiar with protein structure basics

End with: complex questionsAllow students to understand the goal of the activity


Long activity: framework for building complexity

Begin with: simple questionsAllow students to become familiar with protein structure basicsDNA Glycosylase Exercise: questions 1-5

End with: goal of the exercisestructure -> functionDNA Glycosylase Exercise: questions 6-8

DNA Glycosylase Exercise: simple questions

Question 1: overall structureexplore different 3-D models for representing atoms

Question 2: amino acid structureexplore difference between amino acid backbone and side chain

Question 3,4: secondary structureexplore how individual amino acids fold to form secondary structures

Question 5: tertiary structureexplore relationship between a protein’s environment & its tertiary structure

DNA Glycosylase Exercise: complex questions

Question 6: hOGG1 repairs DNA by extruding oxidized bases from double helixlocation of oxoG with respect to the double helix

Question 7: hOGG1 recognizes oxidized bases by contacting the damaged base directly and recognizing a specific modificationcomparison of secondary structures where amino acids that interact with oxoG are likely to be located

Question 8: hOGG1’s specificity for oxidized guanines lies in the inability of guanine to bind to the active site of hOGG1comparison of the oxoG:hOGG1 interaction with that of the G:hOGG1 interaction















Interactive exercise: creating a StarBiochem activity

- Goal of the activity you would like to implement

- Type of activity (length, structure, specifics)

1. Work alone2. Discuss with a partner3. Share ideas with the group







Acknowledgements

Star TeamSara Bonner

Rocklyn ClarkeIvan Ceraj

Justin RileyChuck Shubert

Biology DepartmentChris Kaiser

Graham WalkerDiviya Sinha

OEITVikay Kumar

Molly Ruggles

CollaboratorsStacie Bumgarner

Melissa Kosinski-CollinsMegan Rokop

Kathy Vandiver

Lourdes Aleman [email protected]

Collaborating InstitutionsBrandeis UniversityBroad Institute Outreach ProgramHoward UniversityMIT MuseumSuffolk UniversityTufts University

Outside FundingDavis Educational FoundationHHMI MIT’s Institutional Grant

“The ‘trip’ through the potassium channel protein was AMAZING. I'll explain to Grandma. Refreshing! :)”

“I'm not a bio major but found the interphase fun, easy, and educational. I plan to recommend it to my high school bio teacher.”

“I have found an appreciation for biochemistry almost entirely due to this program.”

“Great Job! Thank you! The StarBiochem program is truly innovative and gives a new perspective on the 2-D images provided by books and overheads.”

StarBiochem feedback

StarGenetics

•test new version (Yeast)

•add visualizers-C. elegans-bacteria

•curriculum modules

•tutorials

•videos: -illustrate use cases

•assessment

•human pedigrees

•association studies

•population genetics

Other genetic tools StarCellBio

•test new version

•curriculum modules

•videos: -illustrate use cases

StarBiochem

Future directions for STAR biology software

StarBiochem & StarGenetics usage beyond MIT

Visits14,963

Documents

Howard university presentation ver3