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Bridges to Structure

Peter Woodruff

Stacey Kiser

Joyce Cadwallader

Organ Organ SystemsSystems …

Traditional “Systems Biology”

DissectionDissection

FormForm

FunctionFunction

…

Building Investigations at Different Levels of Structure

http://www.nsf.gov/od/lpa/forum/colwell/rc03norwaycsis/sld011.htm

Size

Organs

Tissues

Cells

Macro

molecules

Size

Organs

Tissues

Cells

Macro

molecules

Time

ontogeny

Phylogeny

Multidimensional Systems Space

http://tetraspace.alkaline.org/

Brian White’s Course Web Site

Phylogenetic Tree Instructions

Choosing Organisms

Results

Protein Structure Investigation

• The students will investigate protein structure (Problem Posing) by use of the Biology Workbench and NCBI.

• They will get information from the NCBI web site about a protein they think might be representative of a particular organ system.

• They will then gather the materials from that site to dissect the structure of their protein including a visual representation (Problem Solving).

Protein Structure Comparison

• Either using the NCBI or Workbench sequences,they will use Workbench to do additional trees of representative proteins of a particular organ system

• They will present their findings on the proteins in class.

Organ System Protein NCBI

#

#of Hits in GBVET, MAM, INV

Image

(Structure)

Integumentary

Skeletal

Muscular

Digestive

Circulatory

Respiratory

Sensory

Nervous

Reproductive

Endocrine

Immune

Get NCBI Protein File

Get a List of Similar Molecules

Get Structure

Workbench.sdsc.edu

Work in Progress

• Adding activities from Comparative Genome site would be helpful, but time allowed only a start.

• Although we have provided some ascension numbers for proteins, remember only genomic sequences work in this database (Find them at NCBL.).

Workbench (Organisms Used)

Workbench Alignment Data

Organ System

Protein NCBI

#

#of Hits in GBVET, MAM, INV

Image

(Structure)

Integumentary Keratin NoSkeletal collagenMuscular tropomyosin 1IC2Digestive

Circulatory

Respiratory

Sensory Crysallin IA5D 484 Yes(41)Nervous Ach E 2ACK 251 Yes(9)Reproductive E Rece * 196 Yes(22)Endocrine Insulin IEV6 743 Yes(161)Immune Interleukin 1 1IOB Yes

Respiratory: CFTR

http://www.people.virginia.edu/~rjh9u/gif/cftr.gif

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

http://www.brunel.ac.uk/depts/bl/project/biocomp/sequence/seqanal_guide/pds/cftr.jpg

Respiratory: Surfactant Protein D

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

http://ashtoret.tau.ac.il/~sharon/hspd.jpg

Human surfactant protein D (pdb entry:1b08)

Reproductive: Estrogen receptor1ERE

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

http://www.bch.msu.edu/~kuhn/projects/screening/er.jpg

Immune System:Immunoglobulin, Variable Region

& Interleukin-1 BetaCn3D of cd00099.3, IGv

Cn#D of2MIB

Skeletal: Collagen

Cn3D of 1CGD

Muscular: Tropomyosin

http://202.20.99.18/~jjkim/Lecture/Animalphy/Ap10muscle/actin-ca.gif

Cn3D of 1IC2

Workbench Unrooted Tree

www.dcode.org

Data from search for estrogen receptor

Conservation Information for Estrogen Receptor

Bringing Dissection Up to Date

http://www.activehistory.co.uk/2nds/TudorProject/tudor_medicine_and_health.htm

http://mason.gmu.edu/~dgomez2/