Proteopedia - User contributions [en]

Molecular Playground/YKL-40

2010-05-01T01:18:32Z

Ralph A. Francescone III:

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].

[[Image:YKL-40.jpg|frame|Crystal Structure of YKL-40]]

===YKL-40, a Secreted Glycoprotein===

YKL-40 is named for its first three amino acid residues--tyrosine, lysine, and leucine-- and its molecular weight, 40 kDa. It is a member of the chitinase family of proteins, although it has no chitinase activity. It has been implicated in the progession of inflammatory diseases, diabetes, and many cancers. It is one of the most up-regulated genes in glioblastoma multiform (GBM), the most common malignacy of the brain and central nervous system. High YKL-40 serum levels correlate with the worst prognosis for many cancers, especially in GBM. It is thought to increase tumor angiogenesis and endothelial cell migration into tumors.

{{STRUCTURE_1hjx | PDB=1hjx | SCENE= }}

Click here for a stick representation of the ligands bound to YKL-40 (Glycerol, N-ACETYL-D-GLUCOSAMINE, SULFATE ION):
<scene name='Ralph_A._Francescone_III/sandbox_1/Ligand_bound_state/1'>Ligand Bound State</scene>

===References===

1.) Houston, D.R., Recklies, A.D., Krupa, J.C.,Van Aalten, D.M.F. Structure and ligand-induced conformational change of the 39-kDa glycoprotein from human articular chondrocytes.(2003) J.Biol.Chem. 278: 30206.

2.) Shao et al. YKL-40, a secreted glycoprotein, promotes tumor angiogenesis. Oncogene (2009) 28, 4456–4468.

Molecular Playground banner: YKL-40, A New Cancer Biomarker

Molecular Playground/Human Galactosamine-6-sulfatase

2010-05-01T01:18:08Z

Ralph A. Francescone III:

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].

===Human Lysosomal Protective Protein Cathepsin A (PPCA)===
[[Image:PPCA.jpg|frame|Human Lysosomal Protective Protein Cathepsin A]]

The human protective protein cathepsin A forms a multi-enzyme complex with beta-galactosidase and neuraminidase in lysosomes. PPCA has so far two functions:a catalytic activity overlapping with that of Cathepsin A and a protective function towards lysosomal beta-galactosidase and neuraminidase. The stability and activity of the latter glycosidases depend on their interaction with PPCA [1].

{{Clear}}
<applet load='1ivy' size='[450,338]' frame='true' align='right'
caption='Human Lysosomal Protective Protein Cathepsin A (1ivy)' scene=''User:Yadilette_Rivera-Colon/Sandbox1/Loadedfrompdb/4'/>

=== PPCA Glycosylation sites ===

PPCA, is synthesized as a 542 amino acid precursor with a molecular weight of 54kDa. and it dimerizes soon after synthesis. The sequence contains two glycosylation sites, Asn 117 and Asn 305. It also contains nine cysteines. The spinning protein (<scene name='User:Yadilette_Rivera-Colon/Sandbox1/Glycosylation_sites_ppca/1'>PPCA Glycosylation sites</scene> ) is human protective protein with the glycosylation sites represented in stick model colored by atom.

===References: ===
[1] Jackman, H. L., Morris, P. W., Deddish, P. A., Skidgel, R. A. and Erdos, E. G. (1992) J. Biol. Chem. 267, 2872-2875

Molecular Playground banner: Lysosomal Human Protective Protein Cathepsin A, a lysosomal chaperone, Nobody chaperones the chaperone. That's why it is so right for this job.

Molecular Playground/YKL-40

2010-05-01T01:17:13Z

Ralph A. Francescone III:

Molecular Playground/YKL-40

2010-04-29T20:40:56Z

Ralph A. Francescone III:

Ralph A. Francescone III/sandbox 1

2010-04-29T20:40:20Z

Ralph A. Francescone III:

A CBI Molecule being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.
[[Image:YKL-40.jpg|frame|Crystal Structure of YKL-40]]

===YKL-40, a Secreted Glycoprotein===

YKL-40 is named for its first three amino acid residues--tyrosine, lysine, and leucine-- and its molecular weight, 40 kDa. It is a member of the chitinase family of proteins, although it has no chitinase activity. It has been implicated in the progession of inflammatory diseases, diabetes, and many cancers. It is one of the most up-regulated genes in glioblastoma multiform (GBM), the most common malignacy of the brain and central nervous system. High YKL-40 serum levels correlate with the worst prognosis for many cancers, especially in GBM. It is thought to increase tumor angiogenesis and endothelial cell migration into tumors.

{{STRUCTURE_1hjx | PDB=1hjx | SCENE= }}

Click here for a stick representation of the ligands bound to YKL-40 (Glycerol, N-ACETYL-D-GLUCOSAMINE, SULFATE ION):
<scene name='Ralph_A._Francescone_III/sandbox_1/Ligand_bound_state/1'>Ligand Bound State</scene>

===References===

1.) Houston, D.R., Recklies, A.D., Krupa, J.C.,Van Aalten, D.M.F. Structure and ligand-induced conformational change of the 39-kDa glycoprotein from human articular chondrocytes.(2003) J.Biol.Chem. 278: 30206.

2.) Shao et al. YKL-40, a secreted glycoprotein, promotes tumor angiogenesis. Oncogene (2009) 28, 4456–4468.

Ralph A. Francescone III/sandbox 1

2010-04-29T20:39:43Z

Ralph A. Francescone III:

A CBI Molecule being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.
[[Image:YKL-40.jpg|frame|Crystal Structure of YKL-40]]

===YKL-40, a Secreted Glycoprotein===

YKL-40 is named for its first three amino acid residues--tyrosine, lysine, and leucine-- and its molecular weight, 40 kDa. It is a member of the chitinase family of proteins, although it has no chitinase activity. It has been implicated in the progession of inflammatory diseases, diabetes, and many cancers. It is one of the most up-regulated genes in glioblastoma multiform (GBM), the most common malignacy of the brain and central nervous system. High YKL-40 serum levels correlate with the worst prognosis for many cancers, especially in GBM. It is thought to increase tumor angiogenesis and endothelial cell migration into tumors.

{{STRUCTURE_1hjx | PDB=1hjx | SCENE= }}

Click here for a stick representation of the ligands bound to YKL-40 (Glycerol, N-ACETYL-D-GLUCOSAMINE, SULFATE ION):
<scene name='Ralph_A._Francescone_III/sandbox_1/Ligand_bound_state/1'>Ligand Bound State</scene>

===References===

1.) Houston, D.R., Recklies, A.D., Krupa, J.C.,Van Aalten, D.M.F. Structure and ligand-induced conformational change of the 39-kDa glycoprotein from human articular chondrocytes.(2003) J.Biol.Chem. 278: 30206.
2.) Shao et al. YKL-40, a secreted glycoprotein, promotes tumor angiogenesis. Oncogene (2009) 28, 4456–4468.

Molecular Playground/YKL-40

2010-04-29T03:55:51Z

Ralph A. Francescone III: New page: A CBI Molecule being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground. [[Image:YKL-40.jpg|...

CBI Molecules

2010-04-29T03:55:08Z

Ralph A. Francescone III:

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]]''', Thompson & Weis laboratories

'''[[User:Tsung-Yi_Lin/6-deoxyerythronolide_B_synthase|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin

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

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

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

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

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

'''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III

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).

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. Once this link is there, your scene is considered done, and someone will capture the state script for display on the Molecular Playground.

Ralph A. Francescone III/sandbox 1

2010-04-29T03:53:44Z

Ralph A. Francescone III:

Ralph A. Francescone III/sandbox 1

2010-04-29T03:51:47Z

Ralph A. Francescone III:

A CBI Molecule being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.
[[Image:YKL-40.jpg|frame|Crystal Structure of YKL-40]]

===YKL-40, a Secreted Glycoprotein===

YKL-40 is named for its first three amino acid residues--tyrosine, lysine, and leucine-- and its molecular weight, 40 kDa. It is a member of the chitinase family of proteins, although it has no chitinase activity. It has been implicated in the progession of inflammatory diseases, diabetes, and many cancers. It is one of the most up-regulated genes in glioblastoma multiform (GBM), the most common malignacy of the brain and central nervous system. High YKL-40 serum levels correlate with the worst prognosis for many cancers, especially in GBM. It is thought to increase tumor angiogenesis and endothelial cell migration into tumors.

{{STRUCTURE_1hjx | PDB=1hjx | SCENE= }}

Click here for a stick representation of the ligands bound to YKL-40:
<scene name='Ralph_A._Francescone_III/sandbox_1/Ligand_bound_state/1'>Ligand Bound State</scene>

Ralph A. Francescone III/sandbox 1

2010-04-29T03:36:21Z

Ralph A. Francescone III:

Ralph A. Francescone III/sandbox 1

2010-04-29T03:31:31Z

Ralph A. Francescone III:

[[Image:YKL-40.jpg|frame|Crystal Structure of YKL-40]]

===YKL-40 is the best===

{{STRUCTURE_1hjx | PDB=1hjx | SCENE= }}

<scene name='Ralph_A._Francescone_III/sandbox_1/Ligand_bound_state/1'>Ligand Bound State</scene>

Ralph A. Francescone III/sandbox 1

2010-04-29T03:13:19Z

Ralph A. Francescone III:

[[Image:YKL-40.jpg|frame|Crystal Structure of YKL-40]]

===YKL-40 is the best===

{{STRUCTURE_1hjx | PDB=1hjx | SCENE= }}

The spinning protein (<scene name='User:Ralph_A_Francescone_III/sandbox_1/Loadedfrompdb/4'>Initial view</scene>)

Ralph A. Francescone III/sandbox 1

2010-04-29T03:12:44Z

Ralph A. Francescone III:

Ralph A. Francescone III/sandbox 1

2010-04-29T03:11:21Z

Ralph A. Francescone III: /* Ligand-binding domain */

Ralph A. Francescone III/sandbox 1

2010-04-29T03:11:05Z

Ralph A. Francescone III:

Ralph A. Francescone III/sandbox 1

2010-04-29T03:10:34Z

Ralph A. Francescone III:

[[Image:YKL-40.jpg|frame|Crystal Structure of YKL-40]]

===YKL-40 is the best===

{{STRUCTURE_1hjx | PDB=1hjx | SCENE= }}

{{Clear}}
<applet load='1hjx' size='[450,338]' frame='true' align='right'
caption='Crystal structure of human cartilage gp39 (1hjx)' scene='User:Ralph_A_Francescone_III/sandbox_1/Loadedfrompdb/4'/>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Ralph_A_Francescone_III/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 receptor protein used by bacteria to "smell" their environment.

Ralph A. Francescone III/sandbox 1

2010-04-29T03:08:08Z

Ralph A. Francescone III:

[[Image:YKL-40.jpg|frame|Crystal Structure of YKL-40]]

===YKL-40 is the best===

{{STRUCTURE_1hjx | PDB=1hjx | SCENE= }}

{{Clear}}
<applet load='1hjx' size='[450,338]' frame='true' align='right'
caption='Crystal structure of human cartilage gp39 (1nwr)' scene='User:Ralph_A_Francescone_III/sandbox_1/Loadedfrompdb/4'/>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Ralph_A._Francescone_III/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 receptor protein used by bacteria to "smell" their environment.

Ralph A. Francescone III/sandbox 1

2010-04-29T03:05:18Z

Ralph A. Francescone III:

[[Image:YKL-40.jpg|frame|Crystal Structure of YKL-40]]

===YKL-40 is the best===

{{STRUCTURE_1nwr | PDB=1nwr | SCENE= }}

{{Clear}}
<applet load='1nwr' size='[450,338]' frame='true' align='right'
caption='Crystal structure of human cartilage gp39 (1nwr)' scene='User:Ralph_A_Francescone_III/sandbox_1/Loadedfrompdb/4'/>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Ralph_A._Francescone_III/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 receptor protein used by bacteria to "smell" their environment.

Ralph A. Francescone III/sandbox 1

2010-04-29T03:01:59Z

Ralph A. Francescone III:

[[Image:YKL-40.jpg|frame|Crystal Structure of YKL-40]]

===YKL-40 is the best===

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Crystal structure of human cartilage gp39 (1nwr)' scene='User:Ralph_A_Francescone_III/sandbox_1/Loadedfrompdb/4'/>

=== Ligand-binding domain ===

{{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'/>

The spinning protein (<scene name='User:Ralph_A._Francescone_III/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 receptor protein used by bacteria to "smell" their environment.

Ralph A. Francescone III/sandbox 1

2010-04-29T02:59:39Z

Ralph A. Francescone III:

[[Image:YKL-40.jpg|frame|Crystal Structure of YKL-40]]

===YKL-40 is the best.===

{{Clear}}
<applet load='1nwr' size='[450,338]' frame='true' align='right'
caption='Crystal structure of human cartilage gp39 (1nwr)' scene='User:Ralph_A._Francescone_III/sandbox_1/Loadedfrompdb/4'/>

=== Ligand-binding domain ===

{{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'/>

The spinning protein (<scene name='User:Ralph_A._Francescone_III/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 receptor protein used by bacteria to "smell" their environment.

Ralph A. Francescone III/sandbox 1

2010-04-29T02:57:57Z

Ralph A. Francescone III:

[[Image:YKL-40.jpg|frame|Crystal Structure of YKL-40]]

===YKL-40 is the best.===

{{Clear}}
<applet load='1nwr' size='[450,338]' frame='true' align='right'
caption='Crystal structure of human cartilage gp39 (HC-gp39)(1nwr)' scene='User:Ralph_A._Francescone_III/sandbox_1/Loadedfrompdb/4'/>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Ralph_A._Francescone_III/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 receptor protein used by bacteria to "smell" their environment.

Ralph A. Francescone III/sandbox 1

2010-04-29T02:57:12Z

Ralph A. Francescone III:

[[Image:YKL-40.jpg|frame|Crystal Structure of YKL-40]]

===YKL-40 is the best.===

{{Clear}}
<applet load='1nwr' size='[450,338]' frame='true' align='right'
caption='Crystal structure of human cartilage gp39 (HC-gp39)(1nwr)' scene='User:Ralph_A_Francescone_III/sandbox_1/Loadedfrompdb/4'/>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Ralph_A_Francescone_III/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 receptor protein used by bacteria to "smell" their environment.

Ralph A. Francescone III/sandbox 1

2010-04-29T02:56:06Z

Ralph A. Francescone III:

[[Image:YKL-40.jpg|frame|Crystal Structure of YKL-40]]

===YKL-40 is the best.===

{{Clear}}
<applet load='1nwr' size='[450,338]' frame='true' align='right'
caption='Crystal structure of human cartilage gp39 (HC-gp39)(1nwr)' scene='User:Ralph_A_Francescone_III/sandbox_1/Loadedfrompdb/4'/>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Ralph_A._Francescone_III/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 receptor protein used by bacteria to "smell" their environment.

Ralph A. Francescone III/sandbox 1

2010-04-29T02:54:16Z

Ralph A. Francescone III:

[[Image:YKL-40.jpg|frame|Crystal Structure of YKL-40]]

===YKL-40 is the best.===

{{Clear}}
<applet load='1nwr' size='[450,338]' frame='true' align='right'
caption='Crystal structure of human cartilage gp39 (HC-gp39) (1nwr)' scene='User:Ralph_A._Francescone_III/sandbox_1/Loadedfrompdb/4'/>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Ralph_A._Francescone_III/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 receptor protein used by bacteria to "smell" their environment.

Ralph A. Francescone III/sandbox 1

2010-04-29T02:53:20Z

Ralph A. Francescone III: /* Ligand-binding domain */

[[Image:YKL-40.jpg|frame|Crystal Structure of YKL-40]]

===YKL-40 is the best.===

{{Clear}}
<applet load='1nwr' size='[450,338]' frame='true' align='right'
caption=' Crystal structure of human cartilage gp39 (HC-gp39) (1nwr)' scene='User:Ralph_A._Francescone_III/sandbox_1/Loadedfrompdb/4'/>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Ralph_A._Francescone_III/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 receptor protein used by bacteria to "smell" their environment.

Ralph A. Francescone III/sandbox 1

2010-04-29T02:52:51Z

Ralph A. Francescone III:

[[Image:YKL-40.jpg|frame|Crystal Structure of YKL-40]]

===YKL-40 is the best.===

{{Clear}}
<applet load='1nwr' size='[450,338]' frame='true' align='right'
caption=' Crystal structure of human cartilage gp39 (HC-gp39) (1nwr)' scene='User:Ralph_A._Francescone_III/sandbox_1/Loadedfrompdb/4'/>

=== Ligand-binding domain ===

The spinning protein (<scene name='Ralph_A._Francescone_III/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 receptor protein used by bacteria to "smell" their environment.

File:YKL-40.jpg

2010-04-29T02:51:11Z

Ralph A. Francescone III:

Ralph A. Francescone III/sandbox 1

2010-04-29T02:50:38Z

Ralph A. Francescone III: New page: Crystal Structure of YKL-40 ===YKL-40 is the best.=== {{Clear}} <applet load='1nwr' size='[450,338]' frame='true' align='right' caption=' Crystal structure o...

[[Image:YKL-40.jpg|frame|Crystal Structure of YKL-40]]

===YKL-40 is the best.===

{{Clear}}
<applet load='1nwr' size='[450,338]' frame='true' align='right'
caption=' Crystal structure of human cartilage gp39 (HC-gp39) (1nwr)' scene='User:Ralph_A._Francescone_III/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 receptor protein used by bacteria to "smell" their environment.

User:Ralph A. Francescone III/sandbox 1

2010-04-22T23:47:01Z

Ralph A. Francescone III: New page: YKL-40

YKL-40