Proteopedia - User contributions [en]

CBI Molecules

2010-05-11T19:46:08Z

Shiela M. Jones:

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 (which is alphabetical by CBI research mentor); follow the instructions below the list.

Bhatia Lab
: '''[[Molecular Playground/Alginate]]''', David Griffin

[http://chamberslab.com/wp/ Chambers Lab]

: '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano

Forbes Lab

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

[http://www.biochem.umass.edu/garman/index.html Garman Lab]

: '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon

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

[http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]

: '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy

[http://people.chem.umass.edu/jhardy/ Hardy Lab]

: '''[[Molecular Playground/Caspase-7 Dynamics]]''', Daniel Seeman

: '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber

: '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls

Hebert Lab

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

Kaltashov Lab

: '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita

Knapp lab

:'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin

: '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky

[http://www.chem.umass.edu/~cmartin/ Martin Lab]

: '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia
: '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia

[http://robertsgroup.ecs.umass.edu/ Roberts Lab]

: '''[[Molecular Playground/Taxol]]''', Rohan Patil

: '''[[Molecular Playground/Insulin]]''', Whitney Stoppel

[http://www.umass.edu/rotellogroup/ Rotello Lab]

: '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino

: '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang

: '''[[Molecular playground/Chymotrypsin]]''', Brad

: '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell

Schnarr Lab

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

Thayumanavan Lab

: '''[[Molecular Playground/Lysozime ]]''', Daniella Gonzalez

: '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura

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

: '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy

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

: '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang

: ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo

: '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko

Thayumanavan & Vachet Labs

: '''[[Molecular Playground/Trypsin]]''', Gladys Murage

[http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs

: '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones

Vachet Lab

: '''[[Molecular playground/beta 2 microglobulin]]''', Nick

Other UMass labs

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

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.

CBI Molecules

2010-05-11T19:45:36Z

Shiela M. Jones:

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 (which is alphabetical by CBI research mentor); follow the instructions below the list.

Bhatia Lab
: '''[[Molecular Playground/Alginate]]''', David Griffin

[http://chamberslab.com/wp/ Chambers Lab]

: '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano

Forbes Lab

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

[http://www.biochem.umass.edu/garman/index.html Garman Lab]

: '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon

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

[http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]

: '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy

[http://people.chem.umass.edu/jhardy/ Hardy Lab]

: '''[[Molecular Playground/Caspase-7 Dynamics]]''', Daniel Seeman

: '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber

: '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls

Hebert Lab

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

Kaltashov Lab

: '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita

Knapp lab

:'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin

: '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky

[http://www.chem.umass.edu/~cmartin/ Martin Lab]

: '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia
: '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia

[http://robertsgroup.ecs.umass.edu/ Roberts Lab]

: '''[[Molecular Playground/Taxol]]''', Rohan Patil

: '''[[Molecular Playground/Insulin]]''', Whitney Stoppel

[http://www.umass.edu/rotellogroup/ Rotello Lab]

: '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino

: '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang

: '''[[Molecular playground/Chymotrypsin]]''', Brad

: '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell

Schnarr Lab

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

Thayumanavan Lab

: '''[[Molecular Playground/Lysozime ]]''', Daniella Gonzalez

: '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura

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

: '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy

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

: '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang

: ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo

: '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko

Thayumanavan & Vachet Labs

: '''[[Molecular Playground/Trypsin]]''', Gladys Murage

[http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs

: '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Shiela M. Jones

Vachet Lab

: '''[[Molecular playground/beta 2 microglobulin]]''', Nick

Other UMass labs

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

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/Bacterial Chemotaxis Receptors

2010-05-11T19:44:25Z

Shiela M. Jones:

[[Image:intactModelLargeText.jpg|frame|Bacterial chemotaxis receptor]]

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].

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 ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment.

{{Clear}}
<applet load='2ho9' size='[450,338]' frame='true' align='right'
caption='E. coli chemotaxis adaptor protein CheW (2ho9)' scene='User:Shiela_M._Jones/Sandbox_1/Chew_suppressionmutants/1'/>

=== Chemotaxis adaptor protein CheW ===

CheW is a chemotaxis adaptor protein, and part of the tertiary complex formed by the chemotaxis receptor, histidine kinase protein CheA, and CheW. As an adaptor protein, CheW mediates the interaction between the chemotaxis receptor and CheA, and is necessary for the formation of kinase active complexes. CheW has been found to bind to the P5 domain of CheA through crystallographic studies.

At right, CheW is shown with suppression mutants (blue)that have been measured to decrease receptor binding and chemotaxis.

User:Shiela M. Jones/Sandbox 1

2010-05-11T19:42:59Z

Shiela M. Jones:

User:Shiela M. Jones/Sandbox 1

2010-05-11T19:41:20Z

Shiela M. Jones: /* Chemotaxis adaptor protein CheW */

[[Image:intactModelLargeText.jpg|frame|Bacterial chemotaxis receptor]]

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].

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 ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment.

{{Clear}}
<applet load='2ho9' size='[450,338]' frame='true' align='right'
caption='E. coli chemotaxis adaptor protein CheW (2ho9)' />

=== Chemotaxis adaptor protein CheW ===

CheW is a chemotaxis adaptor protein, and part of the tertiary complex formed by the chemotaxis receptor, histidine kinase protein CheA, and CheW. As an adaptor protein, CheW mediates the interaction between the chemotaxis receptor and CheA, and is necessary for the formation of kinase active complexes. CheW has been found to bind to the P5 domain of CheA through crystallographic studies.

At right, CheW is shown with suppression mutants (blue)that have been measured to decrease receptor binding and chemotaxis.

User:Shiela M. Jones/Sandbox 1

2010-05-11T19:21:45Z

Shiela M. Jones:

[[Image:intactModelLargeText.jpg|frame|Bacterial chemotaxis receptor]]

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].

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 ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment.

{{Clear}}
<applet load='2ho9' size='[450,338]' frame='true' align='right'
caption='E. coli chemotaxis adaptor protein CheW (2ho9)' />

=== Chemotaxis adaptor protein CheW ===

CheW is a chemotaxis adaptor protein, and part of the tertiary complex formed by the chemotaxis receptor, histidine kinase protein CheA, and CheW. As an adaptor protein, CheW mediates the interaction between the chemotaxis receptor and CheA, and is necessary for the formation of kinase active complexes.

User:Shiela M. Jones/Sandbox 1

2010-05-11T19:15:19Z

Shiela M. Jones: New page: Bacterial chemotaxis receptor One of the CBI Molecules being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Ch...

[[Image:intactModelLargeText.jpg|frame|Bacterial chemotaxis receptor]]

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].

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 ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment.

=== Chemotaxis adaptor protein CheW ===
<applet load='2ho9' size='[450,338]' frame='true' align='right'
caption='E. coli chemotaxis adaptor protein CheW (2ho9)' />

Kinesin-5

2008-12-09T10:13:24Z

Shiela M. Jones: New page: {{STRUCTURE_1yrs | PDB=1yrs | SCENE= }} ==Function== Kinesins are an [http://en.wikipedia.org/wiki/ATPase ATPase] motor protein found in Eukaryotic cells. Kinesins support [http://en...

{{STRUCTURE_1yrs | PDB=1yrs | SCENE= }}
==Function==

Kinesins are an [http://en.wikipedia.org/wiki/ATPase ATPase] motor protein found in Eukaryotic cells. Kinesins support [http://en.wikipedia.org/wiki/Mitosis mitosis], [http://en.wikipedia.org/wiki/Meiosis meiosis] and transport cellular cargo along microtubule cables inside the cell. Kinesin-5 is a dimer-of-dimers with two motor domains, located at the end of a four-stranded stalk.

==Structure==

Kinesin-5 is a dimer-of-dimers with two major domains; the motor domain, a globular region that binds to the microtubules, and the stalk, a long coiled-coil tail which binds to the cargo.
[[Image:1YRS_Compare.png|center|250px|1YRS.pdb.]]

The concavity of the motor domain, shown below, can be used to determine possible binding spots. The most likely spot, determined with [http://hotpatch.mbi.ucla.edu/ HotPatch],
[[Image:1YRS_Concavity.png|center|250px|Concavity of 1YRS.pdb. Red is very concave, whereas blue is not concave. Produced with HotPatch.]]

It can be noted that immediately surrounding the main binding site of the motor domain are two mobile loops. Coloring the cartoon by occupancy (B-factor) can give a general idea of the mobility of the loops. As expected, the center of the protein is very well defined, shown in a dark to medium blue. The outside edges and loops, shown in red, indicate mobile residues with the possibility of many rotomers.
[[Image:1YRS_occupancy.png|center|250px|Occupancy of 1YRS.pdb. Dark blue residues are well-defined, whereas red are very mobile. Produced with PyMol.]]

Conserved residues for this protein was analyzed with ConSurf. Compared against 200 unique sequences, most conserved residues can be seen as a magenta, and least conserved as blue.
Note: Most of the analysis is derived from 1YRS.pdb.
[[Image:1YRS_consurf.png|center|250px|Conserved residues of 1YRS.pdb evaluated by ConSurf. Red are most conserved, blue least conserved.]]

==References==

[1] Kaseda, K.; Crevel, I.; Hirose, K.; Cross, R. A. “Single-headed mode of kinesin-5.” Euro. Mol. Bio. Org. reports. 2008, 9(8), 761-765.

[2] Kull, F. J.; Sablin, E. P.; Lau, R.; Fletterick, R. J.; Vale, R. D. “Crystal structure of the kinesin motor domain reveals a structural similarity to myosin.” Nature. 1996, 380, 550-555.

[3] Cox, C. D.; Breslin, M. J.; Mariano, B. J.; Coleman, P. J.; Buser, C. A.; et al. “Kinesin spindle protein (KSP) inhibitors. Part 1: The discovery of 3,5-diaryl-4,5-dihydropyrazoles as potent and selective inhibitors of the mitotic kinesin KSP.” Bioorg. & Med. Chem. Letters. 2005, 15, 2041-2045.

[4] Saunders, A. M.; Powers, J.; Strome, S.; Saxton, W. M. “Kinesin-5 acts as a brake in anaphase spindle elongation.” Current Biol. 2007, 17(12), 453-454.

File:1YRS consurf.png

2008-12-09T09:08:54Z

Shiela M. Jones: Conserved residues of 1YRS.pdb evaluated using http://consurf.tau.ac.il/ ConSurf.

Conserved residues of 1YRS.pdb evaluated using [[http://consurf.tau.ac.il/ ConSurf]].

File:1YRS Compare.png

2008-12-09T08:54:25Z

Shiela M. Jones: 1YRS.pdb, produced in PyMol.

1YRS.pdb, produced in PyMol.

File:1YRS Concavity.png

2008-12-09T08:47:46Z

Shiela M. Jones: Concavity study of 1YRS.pdb using [http://hotpatch.mbi.ucla.edu/ HotPatch]. Very concave spots, and thus likely to be binding spots, are depicted red, whereas spots with little concavity are depicted blue.

== Summary ==
Concavity study of 1YRS.pdb using [http://hotpatch.mbi.ucla.edu/ HotPatch]. Very concave spots, and thus likely to be binding spots, are depicted red, whereas spots with little concavity are depicted blue.
== Licensing ==
{{PD-self}}

File:1YRS occupancy.png

2008-12-09T08:28:17Z

Shiela M. Jones: Occupancy of 1YRS.pdb. Dark blue residues are well-defined, red is very mobile residues. Image produced with PyMol.

== Summary ==
Occupancy of 1YRS.pdb. Dark blue residues are well-defined, red is very mobile residues. Image produced with PyMol.
== Licensing ==
{{PD-self}}