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Bridges to Structure
Peter Woodruff
Stacey Kiser
Joyce Cadwallader
Traditional “Systems Biology”
Organ Systems
…
Dissection
Form
Function
…
Building Investigations at
Different Levels of Structure
http://www.nsf.gov/od/lpa/forum/colwell/rc03norwaycsis/sld011.htm
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ontogeny
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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
Integumentary
Skeletal
Muscular
Digestive
Circulatory
Respiratory
Sensory
Nervous
Reproductive
Endocrine
Image
(Structure)
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
Integumentary Keratin
Image
(Structure)
No
Skeletal
collagen
Muscular
tropomyosin
1IC2
Sensory
Crysallin
Nervous
Ach E
Reproductive
E Rece
Endocrine
Insulin
IA5D
2ACK
*
IEV6
Digestive
Circulatory
Respiratory
Interleukin 1
484
251
196
743
Yes(41)
Yes(9)
Yes(22)
Yes(161)
Respiratory: CFTR
QuickTi me™ a nd a
TIFF (Uncompre ssed ) decomp resso r
are need ed to se e th is p icture.
http://www.people.virginia.edu/~rjh9u/gif/cftr.gif
QuickTime™ and a
TIFF (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 a
TIFF (Uncompressed) decompressor
are needed to see this picture.
Human surfactant protein D (pdb entry:1b08)
http://ashtoret.tau.ac.il/~sharon/hspd.jpg
Reproductive: Estrogen receptor
1ERE
QuickTime™ and a
TIFF (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 Beta
Cn3D of cd00099.3, IGv
Cn#D of2MIB
Skeletal: Collagen
Cn3D of 1CGD
Muscular: Tropomyosin
Cn3D of 1IC2
http://202.20.99.18/~jjkim/Lecture/Animalphy/Ap10muscle/actin-ca.gif
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/