Proteopedia - User contributions [en]

Molecular playground/Chymotrypsin

2010-05-10T21:59:20Z

Bradley Duncan: d

{{STRUCTURE_4cha | PDB=4cha| SCENE=User:Bradley_Duncan/Sandbox_1/Scene_1/2 }}

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

Chymotrypsin (<scene name='User:Bradley_Duncan/Sandbox_1/Scene_1/2'>Alpha-Chymotrypsin Dimer</scene>) is a proteolytic enzyme which cleaves peptide bonds. The enzyme shows selectively to peptides with aromatic sidechains on the carboxyl side of the peptide bond. This is due to a “hydrophobic pocket” near the active site of the enzyme. The protein also contains a large number of cationic residues.

In this depiction, <scene name='User:Bradley_Duncan/Sandbox_1/Cbi/1'>Cationic Residues</scene>, the cationic amino acid residues on the protein (blue) can interact with anionic, functionalized nanoparticles. After the nanoparticle-protein complex is formed, chymotrypsin then displays a preference for cationic substrates due to interaction with the anionic nanoparticle. The active site of chymotrypsin is shown in red.

Molecular Playground banner: Chymotrypsin is a digestive enzyme that breaks down proteins

===References===

You C-C, Agasti SS, De M, Knapp MJ, Rotello VM. Modulation of the Catalytic Behavior of α-Chymotrypsin at Monolayer-Protected Nanoparticle Surfaces. Journal of the American Chemical Society 2006; 128:14612-14618.

User:Bradley Duncan/Sandbox 1

2010-05-10T21:58:28Z

Bradley Duncan: k

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

Chymotrypsin (<scene name='User:Bradley_Duncan/Sandbox_1/Scene_1/2'>Alpha-Chymotrypsin Dimer</scene>) is a proteolytic enzyme which cleaves peptide bonds. The enzyme shows selectively to peptides with aromatic sidechains on the carboxyl side of the peptide bond. This is due to a “hydrophobic pocket” near the active site of the enzyme. The protein also contains a large number of cationic residues.

In this depiction, <scene name='User:Bradley_Duncan/Sandbox_1/Cbi/1'>Cationic Residues</scene>, the cationic amino acid residues on the protein (blue) can interact with anionic, functionalized nanoparticles. After the nanoparticle-protein complex is formed, chymotrypsin then displays a preference for cationic substrates due to interaction with the anionic nanoparticle. The active site of chymotrypsin is shown in red.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Structure of Alpha-Chymotrypsin (4cha)' scene='User:Bradley_Duncan/Sandbox_1/Scene_1/2'/>

Molecular Playground banner: Chymotrypsin is a digestive enzyme that breaks down proteins

===References===

You C-C, Agasti SS, De M, Knapp MJ, Rotello VM. Modulation of the Catalytic Behavior of α-Chymotrypsin at Monolayer-Protected Nanoparticle Surfaces. Journal of the American Chemical Society 2006; 128:14612-14618.

Molecular playground/Chymotrypsin

2010-05-10T21:52:52Z

Bradley Duncan: d

{{STRUCTURE_4cha | PDB=4cha| SCENE=User:Bradley_Duncan/Sandbox_1/Scene_1/2 }}

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

Chymotrypsin (<scene name='User:Bradley_Duncan/Sandbox_1/Scene_1/2'>Alpha-Chymotrypsin Dimer</scene>) is a proteolytic enzyme which cleaves peptide bonds. The enzyme shows selectively to peptides with aromatic sidechains on the carboxyl side of the peptide bond. This is due to a “hydrophobic pocket” near the active site of the enzyme. The protein also contains a large number of cationic residues.

In this depiction <scene name='User:Bradley_Duncan/Sandbox_1/Cationic_residues/1'>Cationic Residues</scene>, the cationic amino acid residues on the protein (blue) can interact with anionic, functionalized nanoparticles. After the nanoparticle-protein complex is formed, chymotrypsin then displays a preference for cationic substrates due to interaction with the anionic nanoparticle. The active site of chymotrypsin is shown in red.

Molecular Playground banner: Chymotrypsin is a digestive enzyme that breaks down proteins

===References===

You C-C, Agasti SS, De M, Knapp MJ, Rotello VM. Modulation of the Catalytic Behavior of α-Chymotrypsin at Monolayer-Protected Nanoparticle Surfaces. Journal of the American Chemical Society 2006; 128:14612-14618.

Molecular playground/Chymotrypsin

2010-04-30T21:33:04Z

Bradley Duncan:

{{STRUCTURE_4cha | PDB=4cha| SCENE=User:Bradley_Duncan/Sandbox_1/Scene_1/2 }}

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

Chymotrypsin (<scene name='User:Bradley_Duncan/Sandbox_1/Scene_1/2'>Alpha-Chymotrypsin Dimer</scene>) is a proteolytic enzyme which cleaves peptide bonds. The enzyme shows selectively to peptides with aromatic sidechains on the carboxyl side of the peptide bond. This is due to a “hydrophobic pocket” near the active site of the enzyme. The protein also contains a large number of cationic residues.

In this depiction of the monomer <scene name='User:Bradley_Duncan/Sandbox_1/Cationic_residues/1'>Cationic Residues</scene>, the cationic amino acid residues on the protein (blue) can interact with anionic, functionalized nanoparticles. After the nanoparticle-protein complex is formed, chymotrypsin then displays a preference for cationic substrates due to interaction with the anionic nanoparticle. The active site of chymotrypsin is shown in red.

Molecular Playground banner: Chymotrypsin is a digestive enzyme that breaks down proteins

===References===

You C-C, Agasti SS, De M, Knapp MJ, Rotello VM. Modulation of the Catalytic Behavior of α-Chymotrypsin at Monolayer-Protected Nanoparticle Surfaces. Journal of the American Chemical Society 2006; 128:14612-14618.

Molecular playground/Chymotrypsin

2010-04-30T21:32:06Z

Bradley Duncan: d

{{STRUCTURE_4cha | PDB=4cha| SCENE=User:Bradley_Duncan/Sandbox_1/Scene_1/2 }}

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

Chymotrypsin (<scene name='User:Bradley_Duncan/Sandbox_1/Scene_1/2'>Alpha-Chymotrypsin Dimer</scene>) is a proteolytic enzyme which cleaves peptide bonds. The enzyme shows selectively to peptides with aromatic sidechains on the carboxyl side of the peptide bond. This is due to a “hydrophobic pocket” near the active site of the enzyme. The protein also contains a large number of cationic residues.

In this depiction of the monomer <scene name='User:Bradley_Duncan/Sandbox_1/Cationic_residues/1'>Cationic Residues</scene>, the cationic amino acid residues on the protein (blue) can interact with anionic, functionalized nanoparticles. After the nanoparticle-protein complex is formed, chymotrypsin then displays a preference for cationic substrates due to interaction with the anionic nanoparticle. The active site of chymotrypsin is shown in red.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Structure of Alpha-Chymotrypsin (4cha)' scene='User:Bradley_Duncan/Sandbox_1/Scene_1/2'/>

Molecular Playground banner: Chymotrypsin is a digestive enzyme that breaks down proteins

===References===

You C-C, Agasti SS, De M, Knapp MJ, Rotello VM. Modulation of the Catalytic Behavior of α-Chymotrypsin at Monolayer-Protected Nanoparticle Surfaces. Journal of the American Chemical Society 2006; 128:14612-14618.

CBI Molecules

2010-04-30T21:29:30Z

Bradley Duncan: a

These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].
Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground]. Follow the links below to read nontechnical descriptions in Proteopedia.

UMass CBI Members, add your molecules to the list; follow the instructions below the list.

'''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', [http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] laboratories

'''[[6-deoxyerythronolide B synthase (DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Schnarr lab (Tsung-Yi Lin)

'''[[Molecular Playground/Lysozime ]]''', Daniella Gonzalez, Thayumanavan Research Group

'''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura, Thayumanavan Research group

'''[[Molecular Playground/TRAIL]]''', Charley Swofford

'''[[Molecular Playground/Taxol]]''', [http://robertsgroup.ecs.umass.edu/ Roberts Research Group] (Rohan Patil)

'''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon, [http://www.biochem.umass.edu/garman/index.html Garman Research Group]

'''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]

'''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Rotello lab (Daniel Moyano-Marino)

'''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Thai lab (Krishna Reddy Raghupathi)

'''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Thai lab (Rami Rajasekar Reddy)

'''[[Molecular_Playground/ERMan1]]''', Johan Sunryd

'''[[Molecular Playground/Insulin]]''', [http://robertsgroup.ecs.umass.edu/ Roberts Research Group] (Whitney Stoppel)

'''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia ([http://www.chem.umass.edu/~cmartin/ Martin] lab)

'''[[Molecular Playground/Human PPCA]]''', Nilima Kolli

'''[[Molecular Playground/Alginate]]''', David Griffin

'''[[Molecular Playground/Glutamate Receptor]]''', [http://chamberslab.com/wp/ Chambers Lab] (Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano)

'''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado

'''[[Molecular Playground/FIH]]''', Knapp Lab, (Cornelius Taabazuing, Breanne Holmes, John Hangasky)

'''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Thai lab (Jiaming Zhuang)

'''[[Molecular Playground/Pancreatic Lipase]]''', [http://www.umass.edu/rotellogroup/ Rotello lab] (Rui Tang)

'''[[Molecular Playground/Trypsin]]''', Thai-Vachet lab (Murage, Gladys)

'''[[Molecular playground/beta 2 microglobulin]]''', Vachet lab (Nick)

''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Thai lab (Jing Guo)

'''[[Molecular playground/Chymotrypsin]]''', Rotello lab (Brad)

Instructions:

'''We plan to award a prize for the best CBI Molecules page and/or scene!'''

Choose a molecule that is part of your research project.

1. If you don't already have one, request a Proteopedia account and log in. If you are new to Proteopedia, click Help in the navigation box on the left to get started.

2. Make yourself a sandbox page in which you will develop your CBI Molecule scene and description (Enter "User:your name/sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. See example [[User:Lynmarie K Thompson/Sandbox 1]]).

3. Follow the format of the sample CBI molecule page [[Molecular Playground/Bacterial Chemotaxis Receptors]]. Easiest way to do this is to copy this page (in editing mode), paste it into your sandbox page, keep the first paragraph about CBI molecules, and then edit to describe and display your molecule. Your goal is to make this an interesting, nontechnical description of the molecule. If multiple people in one group work on the same molecule, you can each make different scenes for the same CBI molecule and each describe them on the same proteopedia page. Talk with each other about your plans so you are not duplicating efforts.

4. Create an attractive scene for your molecule: use the scene authoring tools in the edit mode to create the view you like, then copy the wiki text into your window.

5. Follow instructions at [[Molecular Playground/Procedures]] as well. But don't "capture the state script for your scene"; that will be done for you (see #7). With your chosen Jmol scene for the Molecular Playground, specify a "banner", which will be projected with the molecule on the Molecular Playground. This should be a short, one-line headline for your scene that includes the name of the molecule and what is important about the scene or the molecule. Remember to design this for the general public, including non-scientists. My example is: "Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment."

6. When you are happy with your sandbox page, make yourself a permanent Proteopedia page, which will be editable by others. Enter "Molecular Playground/your molecule" (omit quotes) in the search box, then follow the instructions to create a new page with this title. Copy the content of your sandbox to this new page.

7. When you have finished the final version of your page and scene, edit this CBI Molecules page to add a listing and link for your molecule, following the "Bacterial chemotaxis receptors" example above. Please list your lab group, with your name in parentheses. That way more than one name can be associated with a Molecular Playground page (if there are several students on the Molecular Playground page, please indicate your scene with your initials). It would be great to link the lab names to web pages too. Once this link is there, your scene is considered done, and someone will capture the state script for display on the Molecular Playground.

Molecular Playground/Chymotrypsin

2010-04-30T21:27:58Z

Bradley Duncan: s

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

Chymotrypsin (<scene name='User:Bradley_Duncan/Sandbox_1/Scene_1/2'>Alpha-Chymotrypsin Dimer</scene>) is a proteolytic enzyme which cleaves peptide bonds. The enzyme shows selectively to peptides with aromatic sidechains on the carboxyl side of the peptide bond. This is due to a “hydrophobic pocket” near the active site of the enzyme. The protein also contains a large number of cationic residues.

In this depiction of the monomer <scene name='User:Bradley_Duncan/Sandbox_1/Cationic_residues/1'>Cationic Residues</scene>, the cationic amino acid residues on the protein (blue) can interact with anionic, functionalized nanoparticles. After the nanoparticle-protein complex is formed, chymotrypsin then displays a preference for cationic substrates due to interaction with the anionic nanoparticle. The active site of chymotrypsin is shown in red.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Structure of Alpha-Chymotrypsin (4cha)' scene='User:Bradley_Duncan/Sandbox_1/Scene_1/2'/>

Molecular Playground banner: Chymotrypsin is a digestive enzyme that breaks down proteins

===References===

You C-C, Agasti SS, De M, Knapp MJ, Rotello VM. Modulation of the Catalytic Behavior of α-Chymotrypsin at Monolayer-Protected Nanoparticle Surfaces. Journal of the American Chemical Society 2006; 128:14612-14618.

User:Bradley Duncan/Sandbox 1

2010-04-30T21:25:43Z

Bradley Duncan: s

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

Chymotrypsin (<scene name='User:Bradley_Duncan/Sandbox_1/Scene_1/2'>Alpha-Chymotrypsin Dimer</scene>) is a proteolytic enzyme which cleaves peptide bonds. The enzyme shows selectively to peptides with aromatic sidechains on the carboxyl side of the peptide bond. This is due to a “hydrophobic pocket” near the active site of the enzyme. The protein also contains a large number of cationic residues.

In this depiction of the monomer <scene name='User:Bradley_Duncan/Sandbox_1/Cationic_residues/1'>Cationic Residues</scene>, the cationic amino acid residues on the protein (blue) can interact with anionic, functionalized nanoparticles. After the nanoparticle-protein complex is formed, chymotrypsin then displays a preference for cationic substrates due to interaction with the anionic nanoparticle. The active site of chymotrypsin is shown in red.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Structure of Alpha-Chymotrypsin (4cha)' scene='User:Bradley_Duncan/Sandbox_1/Scene_1/2'/>

Molecular Playground banner: Chymotrypsin is a digestive enzyme that breaks down proteins

===References===

You C-C, Agasti SS, De M, Knapp MJ, Rotello VM. Modulation of the Catalytic Behavior of α-Chymotrypsin at Monolayer-Protected Nanoparticle Surfaces. Journal of the American Chemical Society 2006; 128:14612-14618.

User:Bradley Duncan/Sandbox 1

2010-04-30T21:24:30Z

Bradley Duncan: x

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

Chymotrypsin (<scene name='User:Bradley_Duncan/Sandbox_1/Scene_1/2'>Alpha-Chymotrypsin Dimer</scene>) is a proteolytic enzyme which cleaves peptide bonds. The enzyme shows selectively to peptides with aromatic sidechains on the carboxyl side of the peptide bond. This is due to a “hydrophobic pocket” near the active site of the enzyme. The protein also contains a large number of cationic residues.

In this depiction of the monomer <scene name='User:Bradley_Duncan/Sandbox_1/Cationic_residues/1'>Cationic Residues</scene>, the cationic amino acid residues on the protein (blue) can interact with anionic, functionalized nanoparticles. After the nanoparticle-protein complex is formed, chymotrypsin then displays a preference for cationic substrates due to interaction with the anionic nanoparticle. The active site of chymotrypsin is shown in red.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Structure of Alpha-Chymotrypsin (4cha)' scene='User:Bradley_Duncan/Sandbox_1/Scene_1/2'/>

Molecular Playground banner: Chymotrypsin is a digestive enzyme that breaks down proteins

===References===

You C-C, Agasti SS, De M, Knapp MJ, Rotello VM. Modulation of the Catalytic Behavior of Î±-Chymotrypsin at Monolayer-Protected Nanoparticle Surfaces. Journal of the American Chemical Society 2006; 128:14612-14618.

User:Bradley Duncan/Sandbox 1

2010-04-30T21:23:46Z

Bradley Duncan: d

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

Chymotrypsin (<scene name='User:Bradley_Duncan/Sandbox_1/Scene_1/2'>Alpha-Chymotrypsin Dimer</scene>) is a proteolytic enzyme which cleaves peptide bonds. The enzyme shows selectively to peptides with aromatic sidechains on the carboxyl side of the peptide bond. This is due to a “hydrophobic pocket” near the active site of the enzyme. The protein also contains a large number of cationic residues.

In this depiction of the monomer <scene name='User:Bradley_Duncan/Sandbox_1/Cationic_residues/1'>Cationic Residues</scene>, the cationic amino acid residues on the protein (blue) can interact with anionic, functionalized nanoparticles. After the nanoparticle-protein complex is formed, chymotrypsin then displays a preference for cationic substrates due to interaction with the anionic nanoparticle. The active site of chymotrypsin is shown in red.

===References===

You C-C, Agasti SS, De M, Knapp MJ, Rotello VM. Modulation of the Catalytic Behavior of Î±-Chymotrypsin at Monolayer-Protected Nanoparticle Surfaces. Journal of the American Chemical Society 2006; 128:14612-14618.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Structure of Alpha-Chymotrypsin (4cha)' scene='User:Bradley_Duncan/Sandbox_1/Scene_1/2'/>

Molecular Playground banner: Chymotrypsin is a digestive enzyme that breaks down proteins

User:Bradley Duncan/Sandbox 1

2010-04-30T21:19:01Z

Bradley Duncan: d

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

Chymotrypsin (<scene name='User:Bradley_Duncan/Sandbox_1/Scene_1/2'>Alpha-Chymotrypsin Dimer</scene>) is a proteolytic enzyme which cleaves peptide bonds. The enzyme shows selectively to peptides with aromatic sidechains on the carboxyl side of the peptide bond. This is due to a “hydrophobic pocket” near the active site of the enzyme. The protein also contains a large number of cationic residues.

In this depiction of the monomer <scene name='User:Bradley_Duncan/Sandbox_1/Cationic_residues/1'>Cationic Residues</scene>, the cationic amino acid residues on the protein (blue) can interact with anionic, functionalized nanoparticles. After the nanoparticle-protein complex is formed, chymotrypsin then displays a preference for cationic substrates due to interaction with the anionic nanoparticle. The active site of chymotrypsin is shown in red.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Structure of Alpha-Chymotrypsin (4cha)' scene='User:Bradley_Duncan/Sandbox_1/Scene_1/2'/>

Molecular Playground banner: Chymotrypsin is a digestive enzyme that breaks down proteins

User:Bradley Duncan/Sandbox 1

2010-04-30T21:18:13Z

Bradley Duncan:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

Chymotrypsin (<scene name='User:Bradley_Duncan/Sandbox_1/Scene_1/2'>Alpha-Chymotrypsin Dimer</scene>) is a proteolytic enzyme which cleaves peptide bonds. The enzyme shows selectively to peptides with aromatic sidechains on the carboxyl side of the peptide bond. This is due to a “hydrophobic pocket” near the active site of the enzyme. The protein also contains a large number of cationic residues.

In this depiction of the monomer <scene name='User:Bradley_Duncan/Sandbox_1/Cationic_residues/1'>Cationic Residues</scene>, the cationic amino acid residues on the protein (blue) can interact with anionic, functionalized nanoparticles. After the nanoparticle-protein complex is formed chymotrypsin then displays a preference for cationic substrates due to interaction with the anionic nanoparticle. The active site of chymotrypsin is shown in red.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Structure of Alpha-Chymotrypsin (4cha)' scene='User:Bradley_Duncan/Sandbox_1/Scene_1/2'/>

Molecular Playground banner: Chymotrypsin is a digestive enzyme that breaks down proteins

User:Bradley Duncan/Sandbox 1

2010-04-30T21:17:59Z

Bradley Duncan: d

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

Chymotrypsin (<scene name='User:Bradley_Duncan/Sandbox_1/Scene_1/2'>Alpha-Chymotrypsin Dimer</scene>) is a proteolytic enzyme which cleaves peptide bonds. The enzyme shows selectively to peptides with aromatic sidechains on the carboxyl side of the peptide bond. This is due to a “hydrophobic pocket” near the active site of the enzyme. The protein also contains a large number of cationic residues.

In this depiction of the monomer<scene name='User:Bradley_Duncan/Sandbox_1/Cationic_residues/1'>Cationic Residues</scene>, the cationic amino acid residues on the protein (blue) can interact with anionic, functionalized nanoparticles. After the nanoparticle-protein complex is formed chymotrypsin then displays a preference for cationic substrates due to interaction with the anionic nanoparticle. The active site of chymotrypsin is shown in red.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Structure of Alpha-Chymotrypsin (4cha)' scene='User:Bradley_Duncan/Sandbox_1/Scene_1/2'/>

Molecular Playground banner: Chymotrypsin is a digestive enzyme that breaks down proteins

User:Bradley Duncan/Sandbox 1

2010-04-30T21:16:41Z

Bradley Duncan: df

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

Chymotrypsin (<scene name='User:Bradley_Duncan/Sandbox_1/Scene_1/2'>Alpha-Chymotrypsin Dimer</scene>) is a proteolytic enzyme which cleaves peptide bonds. The enzyme shows selectively to peptides with aromatic sidechains on the carboxyl side of the peptide bond. This is due to a “hydrophobic pocket” near the active site of the enzyme. The protein also contains a large number of cationic residues.

In the this depiction <scene name='User:Bradley_Duncan/Sandbox_1/Cationic_residues/1'>Cationic Residues</scene>, these cationic amino acid residues on the protein (blue) can interact with anionic, functionalized nanoparticles. After the nanoparticle-protein complex is formed chymotrypsin then displays a preference for cationic substrates due to interaction with the anionic nanoparticle. The active site of chymotrypsin is shown in red.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Structure of Alpha-Chymotrypsin (4cha)' scene='User:Bradley_Duncan/Sandbox_1/Scene_1/2'/>

Molecular Playground banner: Chymotrypsin is a digestive enzyme that breaks down proteins

User:Bradley Duncan/Sandbox 1

2010-04-30T20:02:09Z

Bradley Duncan: fv

<scene name='User:Bradley_Duncan/Sandbox_1/Scene_1/2'>Alpha-Chymotrypsin</scene>

<scene name='User:Bradley_Duncan/Sandbox_1/Cationic_residues/1'>Cationic Residues</scene>

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

The dimer form of the protein (<scene name='User:Bradley_Duncan/Sandbox_1/Scene_1/2'>Alpha-Chymotrypsin</scene>) ).

Many bacteria can "smell" their surroundings and "choose" where to go. They detect molecules such as amino acids or sugars using receptors that bind these molecules and transmit a signal into the cell. This signal controls several proteins which ultimately control the direction of rotation of the motors that rotate the flagella. One direction causes the cell to continue swimming; the other direction causes the cell to tumble. When an attractant molecule binds, the receptor signals: "Things look good, keep swimming!" The opposite signal occurs when bacteria sense a repellant or less attractant molecules: "Time to tumble and try a new swimming direction."

A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Structure of Alpha-Chymotrypsin (4cha)' scene='User:Bradley_Duncan/Sandbox_1/Scene_1/2'/>

Molecular Playground banner: Chymotrypsin is a digestive enzyme that breaks down proteins

User:Bradley Duncan/Sandbox 1

2010-04-30T19:59:29Z

Bradley Duncan: c

<scene name='User:Bradley_Duncan/Sandbox_1/Scene_1/2'>Alpha-Chymotrypsin</scene>

<scene name='User:Bradley_Duncan/Sandbox_1/Cationic_residues/1'>Cationic Residues</scene>

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

The dimer form of the protein (<scene name='User:Bradley_Duncan/Sandbox_1/Scene_1/2'>Alpha-Chymotrypsin</scene>) ).

Many bacteria can "smell" their surroundings and "choose" where to go. They detect molecules such as amino acids or sugars using receptors that bind these molecules and transmit a signal into the cell. This signal controls several proteins which ultimately control the direction of rotation of the motors that rotate the flagella. One direction causes the cell to continue swimming; the other direction causes the cell to tumble. When an attractant molecule binds, the receptor signals: "Things look good, keep swimming!" The opposite signal occurs when bacteria sense a repellant or less attractant molecules: "Time to tumble and try a new swimming direction."

A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Aspartate receptor ligand binding domain (1wat)' scene='User:Bradley_Duncan/Sandbox_1/Scene_1/2'/>

Molecular Playground banner: Chymotrypsin is a digestive enzyme that breaks down proteins

User:Bradley Duncan/Sandbox 1

2010-04-30T19:57:21Z

Bradley Duncan: b

<scene name='User:Bradley_Duncan/Sandbox_1/Scene_1/2'>Alpha-Chymotrypsin</scene>

<scene name='User:Bradley_Duncan/Sandbox_1/Cationic_residues/1'>Cationic Residues</scene>

[[Image:intactModelLargeText.jpg|frame|Chymotrypsin]]

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

The dimer form of the protein (<scene name='User:Bradley_Duncan/Sandbox_1/Scene_1/2'>Alpha-Chymotrypsin</scene>) ).

Many bacteria can "smell" their surroundings and "choose" where to go. They detect molecules such as amino acids or sugars using receptors that bind these molecules and transmit a signal into the cell. This signal controls several proteins which ultimately control the direction of rotation of the motors that rotate the flagella. One direction causes the cell to continue swimming; the other direction causes the cell to tumble. When an attractant molecule binds, the receptor signals: "Things look good, keep swimming!" The opposite signal occurs when bacteria sense a repellant or less attractant molecules: "Time to tumble and try a new swimming direction."

A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Aspartate receptor ligand binding domain (1wat)' scene='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'/>

=== Ligand-binding domain ===

Molecular Playground banner: Chymotrypsin is a digestive enzyme that breaks down proteins

User:Bradley Duncan/Sandbox 1

2010-04-30T18:34:51Z

Bradley Duncan: b

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User:Bradley Duncan/Sandbox 1

2010-04-30T17:03:18Z

Bradley Duncan:

User:Bradley Duncan/Sandbox 1

2010-04-30T06:13:44Z

Bradley Duncan: b

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User:Bradley Duncan/Sandbox 1

2010-04-29T21:02:24Z

Bradley Duncan: b

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User:Bradley Duncan/Sandbox 1

2010-04-29T20:43:46Z

Bradley Duncan: b

User:Bradley Duncan/Sandbox 1

2010-03-16T15:59:26Z

Bradley Duncan:

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User:Bradley Duncan/Sandbox 1

2010-03-16T15:56:50Z

Bradley Duncan:

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User:Bradley Duncan/Sandbox 1

2010-03-16T15:32:35Z

Bradley Duncan: x

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User:Bradley Duncan/Sandbox 1

2010-03-16T15:21:58Z

Bradley Duncan: x

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User:Bradley Duncan/Sandbox 1

2010-03-16T15:19:34Z

Bradley Duncan: x

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User:Bradley Duncan/Sandbox 1

2010-03-16T15:19:15Z

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2010-03-16T15:12:42Z

Bradley Duncan: x

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User:Bradley Duncan/Sandbox 1

2010-03-16T15:11:06Z

Bradley Duncan: x

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User:Bradley Duncan/Sandbox 1

2010-03-16T15:10:27Z

Bradley Duncan: x