Proteopedia - User contributions [en]

Anderson Sandbox

2009-07-20T14:09:42Z

Savannah Anderson:

----
==What is a SMART Team?==

'''S'''- Students
'''M'''- Modeling
'''A'''
'''R'''- Research
'''T'''- Topic

This is a program currently run by the Center for Biomolecular Modeling headed by Shannon Colton. We at the CBM do not do any of the research it's all the students that research and study what it is that their molecule does. These students are any where from Jr.High students to Seniors graduating from High School. Our job at the CBM is to put them in contact with a researcher that is interested in participating in the program and to help in making a physical model for the students to use when demonstrating what it is their molecule does.
[http://www.rpc.msoe.edu/cbm/smartteams/ www.rpc.msoe.edu/cbm/smartteams/]

'''''Why Should I join a SMART team?'''''

*It's a great way to be introduced to modern research
*Looks good on a College application
*Good way to meet new people that are interested in the same things you are
*Most Importantly it's '''FUN!!'''

----
==Center for Biomolecular Modeling Physical Models==
The MSOE Center for Biomolecular Modeling has created various physical models of Hemoglobin. Posted is a video displaying one such model and a discussion of some of the properites of Hemoglobin it exhibits. For more information about the CBM and the models we create, visit our site at [http://cbm.msoe.edu http://cbm.msoe.edu].

----

==Different CBM Slogans==

[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models displayed on this webpage have been designed and build by the MSOE Center for BioMolecular Modeling. To learn more about the CBM and see more examples of protein models, please visit the CBM site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm].

[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models displayed here are examples of models designed and built by the MSOE Center for BioMolecular Modeling. To see more modeling possibilities and learn more about the CBM, please visit our site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm].

----

==Physical Models==

[[Image:Zf_rpmodel.jpg|thumb|250px|left|Model Image 1: Rapid Prototype Model]]
[[Image:Zf_toober.jpg|thumb|250px|right|Model Image 2: Mini-Toober Model]]
The model shown in Model Image 1 to the left is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.

The model in Model Image 2 shown to the right is an example of a 'mini-toober' model. The side chains are again displayed in CPK color format. The zinc atom in this example is displayed in green.

==MSOE Center for BioMolecular Modeling==
[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

----

==MSOE Center for BioMolecular Modeling==
[[Image:Zf_rpmodel.jpg|thumb|300px|left|The model shown above is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.]]

[[Image:Zf_toober.jpg|thumb|300px|left|This model is an example of a 'Mini-Toober' model. The backbone is created by the folding of a 'Mini-Toober,' the sidechains are depicted in CPK color format, and the zinc atom is shown in green.]]

[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

==MSOE Center for BioMolecular Modeling==
[[Image:Zf_rpmodel.jpg|thumb|300px|left|The model shown above is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.]]
[[Image:Center for BioMolecular Modeling Logo.jpg|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

----

==MSOE Center for BioMolecular Modeling==
[[Image:Zf_rpmodel.jpg|thumb|300px|left|The model shown above is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.]]
[[Image:Zf_toober.jpg|thumb|300px|center|This model is an example of a 'Mini-Toober' model. The backbone is created by the folding of a 'Mini-Toober,' the sidechains are depicted in CPK color format, and the zinc atom is shown in green.]]

[[Image:Center for BioMolecular Modeling Logo.jpg|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

----

==MSOE Center for BioMolecular Modeling==
[[Image:Zf_rpmodel.jpg|thumb|300px|left|The model shown above is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.]]

[[Image:Zf_toober.jpg|300px|This model is an example of a 'Mini-Toober' model. The backbone is created by the folding of a 'Mini-Toober,' the sidechains are depicted in CPK color format, and the zinc atom is shown in green.]]

[[Image:Center for BioMolecular Modeling Logo.jpg|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

----

==Physical Models==

[[Image:Zf_rpmodel.jpg|250px|Model Image 1: Rapid Prototype Model]]
[[Image:Zf_toober.jpg|250px|Model Image 2: Mini-Toober Model]]
[[Image:Zf_assort.jpg|250px|Model Image 3: Assorted Representations]]

The model shown in Model Image 1 to the left is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.

The model in Model Image 2, shown in the center, is an example of a 'mini-toober' model. The side chains are again displayed in CPK color format. The zinc atom in this example is displayed in green.

The models in Model Image 3 are a variety of different representations for the zinc finger molecule. These representations include backbone, wireframe, and spacefill model types.

==MSOE Center for BioMolecular Modeling==
[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

Anderson Sandbox

2009-07-20T14:08:04Z

Savannah Anderson: /* Center for Biomolecular Modeling Physical Models */

===A SMART Team Modeling Project from the CBM===

[[Image:(image info)|thumb|(Caption)]]

<ref name="G. Gidwani">[http://www.faqs.org/nutrition/Kwa-Men/Lactose-Intolerance.html]</ref>

<applet load='1pv7' size='350' frame='true' align='right' caption='Image of Lac-y Permease' />

----
Replace the PDB id after the STRUCTURE_ and after PDB= to load
and display another structure.

{{STRUCTURE_ | PDB= | SCENE= }}

----
==What is a SMART Team?==

'''S'''- Students
'''M'''- Modeling
'''A'''
'''R'''- Research
'''T'''- Topic

This is a program currently run by the Center for Biomolecular Modeling headed by Shannon Colton. We at the CBM do not do any of the research it's all the students that research and study what it is that their molecule does. These students are any where from Jr.High students to Seniors graduating from High School. Our job at the CBM is to put them in contact with a researcher that is interested in participating in the program and to help in making a physical model for the students to use when demonstrating what it is their molecule does.
[http://www.rpc.msoe.edu/cbm/smartteams/ www.rpc.msoe.edu/cbm/smartteams/]

'''''Why Should I join a SMART team?'''''

*It's a great way to be introduced to modern research
*Looks good on a College application
*Good way to meet new people that are interested in the same things you are
*Most Importantly it's '''FUN!!'''

----
==Center for Biomolecular Modeling Physical Models==
The MSOE Center for Biomolecular Modeling has created various physical models of Hemoglobin. Posted is a video displaying one such model and a discussion of some of the properites of Hemoglobin it exhibits. For more information about the CBM and the models we create, visit our site at [http://cbm.msoe.edu http://cbm.msoe.edu].

----

==Different CBM Slogans==

[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models displayed on this webpage have been designed and build by the MSOE Center for BioMolecular Modeling. To learn more about the CBM and see more examples of protein models, please visit the CBM site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm].

[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models displayed here are examples of models designed and built by the MSOE Center for BioMolecular Modeling. To see more modeling possibilities and learn more about the CBM, please visit our site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm].

----

==Physical Models==

[[Image:Zf_rpmodel.jpg|thumb|250px|left|Model Image 1: Rapid Prototype Model]]
[[Image:Zf_toober.jpg|thumb|250px|right|Model Image 2: Mini-Toober Model]]
The model shown in Model Image 1 to the left is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.

The model in Model Image 2 shown to the right is an example of a 'mini-toober' model. The side chains are again displayed in CPK color format. The zinc atom in this example is displayed in green.

==MSOE Center for BioMolecular Modeling==
[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

----

==MSOE Center for BioMolecular Modeling==
[[Image:Zf_rpmodel.jpg|thumb|300px|left|The model shown above is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.]]

[[Image:Zf_toober.jpg|thumb|300px|left|This model is an example of a 'Mini-Toober' model. The backbone is created by the folding of a 'Mini-Toober,' the sidechains are depicted in CPK color format, and the zinc atom is shown in green.]]

[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

==MSOE Center for BioMolecular Modeling==
[[Image:Zf_rpmodel.jpg|thumb|300px|left|The model shown above is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.]]
[[Image:Center for BioMolecular Modeling Logo.jpg|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

----

==MSOE Center for BioMolecular Modeling==
[[Image:Zf_rpmodel.jpg|thumb|300px|left|The model shown above is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.]]
[[Image:Zf_toober.jpg|thumb|300px|center|This model is an example of a 'Mini-Toober' model. The backbone is created by the folding of a 'Mini-Toober,' the sidechains are depicted in CPK color format, and the zinc atom is shown in green.]]

[[Image:Center for BioMolecular Modeling Logo.jpg|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

----

==MSOE Center for BioMolecular Modeling==
[[Image:Zf_rpmodel.jpg|thumb|300px|left|The model shown above is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.]]

[[Image:Zf_toober.jpg|300px|This model is an example of a 'Mini-Toober' model. The backbone is created by the folding of a 'Mini-Toober,' the sidechains are depicted in CPK color format, and the zinc atom is shown in green.]]

[[Image:Center for BioMolecular Modeling Logo.jpg|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

----

==Physical Models==

[[Image:Zf_rpmodel.jpg|250px|Model Image 1: Rapid Prototype Model]]
[[Image:Zf_toober.jpg|250px|Model Image 2: Mini-Toober Model]]
[[Image:Zf_assort.jpg|250px|Model Image 3: Assorted Representations]]

The model shown in Model Image 1 to the left is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.

The model in Model Image 2, shown in the center, is an example of a 'mini-toober' model. The side chains are again displayed in CPK color format. The zinc atom in this example is displayed in green.

The models in Model Image 3 are a variety of different representations for the zinc finger molecule. These representations include backbone, wireframe, and spacefill model types.

==MSOE Center for BioMolecular Modeling==
[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

Anderson Sandbox

2009-07-20T14:01:46Z

Savannah Anderson:

===A SMART Team Modeling Project from the CBM===

[[Image:(image info)|thumb|(Caption)]]

<ref name="G. Gidwani">[http://www.faqs.org/nutrition/Kwa-Men/Lactose-Intolerance.html]</ref>

<applet load='1pv7' size='350' frame='true' align='right' caption='Image of Lac-y Permease' />

----
Replace the PDB id after the STRUCTURE_ and after PDB= to load
and display another structure.

{{STRUCTURE_ | PDB= | SCENE= }}

----
==What is a SMART Team?==

'''S'''- Students
'''M'''- Modeling
'''A'''
'''R'''- Research
'''T'''- Topic

This is a program currently run by the Center for Biomolecular Modeling headed by Shannon Colton. We at the CBM do not do any of the research it's all the students that research and study what it is that their molecule does. These students are any where from Jr.High students to Seniors graduating from High School. Our job at the CBM is to put them in contact with a researcher that is interested in participating in the program and to help in making a physical model for the students to use when demonstrating what it is their molecule does.
[http://www.rpc.msoe.edu/cbm/smartteams/ www.rpc.msoe.edu/cbm/smartteams/]

'''''Why Should I join a SMART team?'''''

*It's a great way to be introduced to modern research
*Looks good on a College application
*Good way to meet new people that are interested in the same things you are
*Most Importantly it's '''FUN!!'''

----
==Center for Biomolecular Modeling Physical Models==
The MSOE Center for Biomolecular Modeling has created various physical models of Hemoglobin. Posted is a video displaying one such model and discussing some of the properties of Hemoglobin. For more information about the CBM and the models we create, visit our site at [http://cbm.msoe.edu http://cbm.msoe.edu].

----
==Different CBM Slogans==

[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models displayed on this webpage have been designed and build by the MSOE Center for BioMolecular Modeling. To learn more about the CBM and see more examples of protein models, please visit the CBM site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm].

[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models displayed here are examples of models designed and built by the MSOE Center for BioMolecular Modeling. To see more modeling possibilities and learn more about the CBM, please visit our site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm].

----

==Physical Models==

[[Image:Zf_rpmodel.jpg|thumb|250px|left|Model Image 1: Rapid Prototype Model]]
[[Image:Zf_toober.jpg|thumb|250px|right|Model Image 2: Mini-Toober Model]]
The model shown in Model Image 1 to the left is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.

The model in Model Image 2 shown to the right is an example of a 'mini-toober' model. The side chains are again displayed in CPK color format. The zinc atom in this example is displayed in green.

==MSOE Center for BioMolecular Modeling==
[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

----

==MSOE Center for BioMolecular Modeling==
[[Image:Zf_rpmodel.jpg|thumb|300px|left|The model shown above is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.]]

[[Image:Zf_toober.jpg|thumb|300px|left|This model is an example of a 'Mini-Toober' model. The backbone is created by the folding of a 'Mini-Toober,' the sidechains are depicted in CPK color format, and the zinc atom is shown in green.]]

[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

==MSOE Center for BioMolecular Modeling==
[[Image:Zf_rpmodel.jpg|thumb|300px|left|The model shown above is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.]]
[[Image:Center for BioMolecular Modeling Logo.jpg|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

----

==MSOE Center for BioMolecular Modeling==
[[Image:Zf_rpmodel.jpg|thumb|300px|left|The model shown above is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.]]
[[Image:Zf_toober.jpg|thumb|300px|center|This model is an example of a 'Mini-Toober' model. The backbone is created by the folding of a 'Mini-Toober,' the sidechains are depicted in CPK color format, and the zinc atom is shown in green.]]

[[Image:Center for BioMolecular Modeling Logo.jpg|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

----

==MSOE Center for BioMolecular Modeling==
[[Image:Zf_rpmodel.jpg|thumb|300px|left|The model shown above is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.]]

[[Image:Zf_toober.jpg|300px|This model is an example of a 'Mini-Toober' model. The backbone is created by the folding of a 'Mini-Toober,' the sidechains are depicted in CPK color format, and the zinc atom is shown in green.]]

[[Image:Center for BioMolecular Modeling Logo.jpg|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

----

==Physical Models==

[[Image:Zf_rpmodel.jpg|250px|Model Image 1: Rapid Prototype Model]]
[[Image:Zf_toober.jpg|250px|Model Image 2: Mini-Toober Model]]
[[Image:Zf_assort.jpg|250px|Model Image 3: Assorted Representations]]

The model shown in Model Image 1 to the left is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.

The model in Model Image 2, shown in the center, is an example of a 'mini-toober' model. The side chains are again displayed in CPK color format. The zinc atom in this example is displayed in green.

The models in Model Image 3 are a variety of different representations for the zinc finger molecule. These representations include backbone, wireframe, and spacefill model types.

==MSOE Center for BioMolecular Modeling==
[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

Influenza hemagglutinin

2009-07-16T14:34:44Z

Savannah Anderson:

''This page refers to a physical model based on [[5HMG]] from the [http://cbm.msoe.edu/ MSOE Center for BioMolecular Modeling]''

[[Image:HA sfp model.jpg|left]]Influenza Hemagglutinin is one of two proteins found on the surface of an influenza virus. Hemagglutinin plays a key role in both host cell recognition and membrane fusion.

===Structure===

The hemagglutinin protein is initially assembled into a homo-trimer. Each of the three identical proteins consists of 549 amino acids. Later during the maturation of the virus, the monomers are cleaved by a protease to generate two chains known as HA1 and HA2.

<applet load="5HMG" size="300" color="white" frame="true" align="right" caption="Influenza Hemagglutinin Based on 5HMG" />

====HA1====

The <scene name='Influenza_hemagglutinin/Ha1_initial/1'>HA1 protein chain</scene> begins at the base of the structure and forms a globular bulb at the top of the structure. This bulbous structure contains sialic acid receptor binding site. The amino acids that line the receptor binding pocket determine the specificity of the virus, that is, whether it can infect human, bird, or swine cells. As this portion of the protein is the most exposed, it is also the site most targeted by immune responses and the most affected by mutation.

====HA2====

The <scene name='Influenza_hemagglutinin/Ha2_initial/2'>HA2 protein chain</scene> is primarily resposible for facilitating membrane fusion. The C-terminal end of the protein is embedded in the viral membrane. The N-terminal end, known as the "fusion peptide," consists of 10 hydrophobic amino acids. When the protein undergoes pH induced conformational changes, this fusion peptide becomes embedded in the host cell membrane. Additionally, the C-terminus embedded in the viral membrane rearranges, bringing the two membranes closer together and facilitation fusion.

===pH Induced Conformational Changes===

After the virus has bound to the cell membrane, the cell engulfs the viral capsule through the process of endocytosis. Included on the lining of the endosome are ion pumps, were originally used to pump ions out of the cell and maintain a proper pH level. As a part of the endosomal lining, the pumps continue to pump ions, but now into the endsome. This causes the pH surrounding the viral capsule to become acidic.

When the pH level reaches 5.5, the HA1 protein shifts its position, rearranging to allow the HA2 protein to access the endosomal membrane. The HA2 chain begins to rearrange, and the loop shown in blue refolds into a helix at pH5. This causes the HA2 chain to reform into the longest known alpha helix in nature. This allows the fusion peptide to become embedded in the endosomal membrane. The C-terminus of the HA2 also rearranges, positioning the viral membrane in close proximity to the endosomal membrane and allowing membrane fusion to occur. This allows the viral RNA to be released from the capsule and into the host cell cytoplasm.

===Video===
~We hope to have a short video available soon that will display a physical model of this protein and some of the concepts discussed above.

==MSOE Center for BioMolecular Modeling==
[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://cbm.msoe.edu/ http://cbm.msoe.edu/] .

Influenza hemagglutinin

2009-07-16T14:34:30Z

Savannah Anderson:

2009-02-04T16:15:20Z

Savannah Anderson:

===A SMART Team Modeling Project from the CBM===
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====This is a Test Series of scenes for <scene name='Anderson_Sandbox/Orig/1'>Lac-Y Permease</scene>====

To the right is an image representation of Lac-Y permese of E-coli. The Ligand is shown <scene name='Anderson_Sandbox/Ligand/3'>here</scene>, the Sidechains Participating in substrate binding are <scene name='Anderson_Sandbox/Sbu_binding_res/2'>here</scene>, and residues participating in proton translocation are here.

====Function of Lactose Permease====
[[Image:(image info)|thumb|(Caption)]]

Lactose Permease is a transmembrane protein that facilitates the passage of lactose across the phospholipid bi-layer of the cell membrane. The transport mechanism used is an active co-transport that uses the inwardly directed H+ electrochemical gradient as its driving force. As a result, the lactose is accompanied from the periplasm to the cytoplasm of the cell by an H+ proton.<ref name="A. Green, et. al.">[http://www.jbc.org/cgi/content/full/275/30/23240]</ref>

Lactose is a disaccharide carbohydrate found primarily in mammalian milk. It is a disaccharide composed of the monosaccharides glucose and galactose. When lactose is ingested, it is brought into cells in the digestive system by the protein Lactose Permease. Here it is broken down into its monosaccharide subunits by the enzyme lactase so it may be used in the process of cellular respiration.<ref name="G. Gidwani">[http://www.faqs.org/nutrition/Kwa-Men/Lactose-Intolerance.html]</ref>

<applet load='1pv7' size='300' frame='true' align='right' caption='Image of Lac-y Permease' />

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Replace the PDB id after the STRUCTURE_ and after PDB= to load
and display another structure.

{{STRUCTURE_ | PDB= | SCENE= }}

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==Physical Models==

[[Image:Zf_rpmodel.jpg|thumb|250px|left|Model Image 1: Rapid Prototype Model]]
[[Image:Zf_toober.jpg|thumb|250px|right|Model Image 2: Mini-Toober Model]]
The model shown in Model Image 1 to the left is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.

The model in Model Image 2 shown to the right is an example of a 'mini-toober' model. The side chains are again displayed in CPK color format. The zinc atom in this example is displayed in green.

==MSOE Center for BioMolecular Modeling==
[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

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==MSOE Center for BioMolecular Modeling==
[[Image:Zf_rpmodel.jpg|thumb|300px|left|The model shown above is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.]]

[[Image:Zf_toober.jpg|thumb|300px|left|This model is an example of a 'Mini-Toober' model. The backbone is created by the folding of a 'Mini-Toober,' the sidechains are depicted in CPK color format, and the zinc atom is shown in green.]]

[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

==MSOE Center for BioMolecular Modeling==
[[Image:Zf_rpmodel.jpg|thumb|300px|left|The model shown above is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.]]
[[Image:Center for BioMolecular Modeling Logo.jpg|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

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==MSOE Center for BioMolecular Modeling==
[[Image:Zf_rpmodel.jpg|thumb|300px|left|The model shown above is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.]]

[[Image:Zf_toober.jpg|thumb|300px|center|This model is an example of a 'Mini-Toober' model. The backbone is created by the folding of a 'Mini-Toober,' the sidechains are depicted in CPK color format, and the zinc atom is shown in green.]]

[[Image:Center for BioMolecular Modeling Logo.jpg|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

----

==MSOE Center for BioMolecular Modeling==
[[Image:Zf_rpmodel.jpg|thumb|300px|left|The model shown above is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.]]

[[Image:Zf_toober.jpg|300px|This model is an example of a 'Mini-Toober' model. The backbone is created by the folding of a 'Mini-Toober,' the sidechains are depicted in CPK color format, and the zinc atom is shown in green.]]

[[Image:Center for BioMolecular Modeling Logo.jpg|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

----

==Physical Models==

[[Image:Zf_rpmodel.jpg|250px|Model Image 1: Rapid Prototype Model]]
[[Image:Zf_toober.jpg|250px|Model Image 2: Mini-Toober Model]]

The model shown in Model Image 1 to the left is an example of a physical model of the zinc finger protien. In this representation, the Alpha Helix is shown in Red, the Beta Sheets are displayed in Yellow, and the Residues are represented in CPK color format (O=red, N=blue, C=gray, S=yellow). The Zinc Atom in this structure is colored Red.

The model in Model Image 2 shown to the right is an example of a 'mini-toober' model. The side chains are again displayed in CPK color format. The zinc atom in this example is displayed in green.

==MSOE Center for BioMolecular Modeling==
[[Image:Center for BioMolecular Modeling Logo.jpg|left|200px]]

The physical models shown on this page were designed and built by the MSOE Center for BioMolecular Modeling. For more information about physical protein modeling, visit the CBM web site at [http://www.rpc.msoe.edu/cbm www.rpc.msoe.edu/cbm] .

Anderson Sandbox

2009-02-02T22:27:49Z

Savannah Anderson:

Lactose Permease

2009-02-02T22:23:19Z

2009-02-02T21:56:02Z

Savannah Anderson:

Anderson Sandbox

2009-02-02T21:55:36Z

Savannah Anderson: