Pingry S.M.A.R.T. Team Website

  • The S.M.A.R.T. Team project is organized and supported by the Center for Biomolecular Modeling at The Milwaukee School of Engineering (Director, Dr. Tim Herman). 
     

  • This website was maintained by Tommie Hata from 2002 to 2010 while teaching at The Pingry School. The projects here reflect the work and efforts of Pingry S.M.A.R.T. Team students and Pingry teacher Deirdre O'Mara.
     

  • JMol Tutorials created by Pingry S.M.A.R.T. Team students

Supported by:

MSOE Center for BioMolecular Modeling


Great teaching kits for educators!  Teaching kits come with standards-based lessons!

Current Pingry S.M.A.R.T. Team, cooperating scientist, and project tutorials

 

2009-2010 Pingry SMART Team

Protein Engineering: AKR's for Biofuel Cells

 

Cooperating Scientist: Dr. Scott Banta (Columbia University, Department of Chemical Engineering)

The 2010 Pingry SMART Team Students: (listed alphabetically by last name) Caryn Ha, Ed Kong, Flo Ma, Doug Ober, Mai-Lee Picard, David Sukhin, Dylan Sun, Ricardo Vollbrechthausen, Connie Wang, and Ed Xiao
Supervising teacher
: Tommie Hata

 

The 2009-2010 Pingry S.M.A.R.T. Team JMol tutorials was developed and is hosted on the Proteopedia website.  Click on the image below to navigate to the Proteopedia site.

 

Rapid prototyping models developed by Pingry
Click on thumbnails to view full-size image. 
Some are large files to show the details of these models; please be patient while it downloads.

2009-2010 


2008-2009 


PhoB regulatory and effector domains with target DNA

ZCorp Plaster Model


PhoB regulatory domain, inactive and active forms

ZCorp Plaster Model


PhoB regulatory domain, dimerized active form

ZCorp Plaster Model


PhoB effector domain with target DNA

ZCorp Plaster Model


MtrA, regulatory and effector domains

ZCorp Plaster Model


MtrA, regulatory and effector domains, separated

ZCorp Plaster Model


2007-2008

PlyB Lysin-Spacefill model

ZCorp Plaster Model


PlyB Lysin-Backbone model

ZCorp Plaster Model


Epimerase-Substrate in active site

ZCorp Plaster Model


Epimerase-No substrate in active site

ZCorp Plaster Model



More models from past years

RNA Polymerase Holoenzyme-Open Promoter Complex

Nylon Model

RNA Polymerase Core Enzyme with Sigma removed

Nylon Model

RNA Polymerase Holoenzyme

Nylon Model

RNA Polymerase Holoenzyme: separated to expose active site and to remove nucleic acids/sigma factor

Nylon Model

RNA Polymerase Ternary Elongation Complex

RNA transcript colored red. Nylon Model

RNA Polymerase Ternary Elongation Complex

Active site amino acids (seven conserved residues, NADFDGD) shown with sidechains. Mg2+ ion colored purple. Nylon Model

RNA Polymerase Ternary Elongation Complex: model separated to expose active site

Nylon Model

RNA Polymerase Ternary Elongation Complex: Nucleic acids removed from RNAP core enzyme

Nylon Model

Prokaryotic RNA Polymerase Activation Complex

ZCorp plaster model. Part of beta subunit removed to expose transcription bubble.

Sigma factor (promoter recognition subunit) complexed with promoter DNA

ZCorp plaster model. Colors on sigma show various domains. Grey is part of core RNAP. Green on DNA are promoter regions.

Cyclic AMP Receptor Protein (CRP) or Catabolite Activator Protein (CAP)

Nylon model. Cyclic AMP colored Red. Dimer interacts with UP-element (region upstream of the promoter DNA) and plays a role in increasing transcription levels.

T7 phage RNA Polymerase elongation complex

Nylon model. Based on PDB ID: 1MSW.

T7 phage RNA Polymerase Initiation (Promoter) complex

ZCorp plaster model. Based on PDB ID: 1CEZ.

T7 phage RNA Polymerase elongation complex

ZCorp plaster model. Based on PDB ID: 1MSW.

Contact Information

Tommie Shintaro Hata

EMail: tshata@gmail.com   

 

Comments and ideas expressed on this site do not necessarily reflect that of the teacher (Tommie Hata) or The Pingry School. This website is maintained by Tommie Hata and the contents of the site is not a responsibility of The Pingry School.

Please send email to tshata@gmail.com with questions or comments about this web site.

Website maintained by Tommie Hata
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