Proteopedia - User contributions [en]

Molecular Playground/Human mtRNA pol

2012-01-08T22:01:47Z

Ketan Mathavan:

<Structure load='3SPA' size='370' frame='true' align='right' caption='Human mitochondrial RNA polymerase (PDB: 3SPA) scene='Molecular_Playground/Human_mtRNA_pol/All/1'/>

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].

=== Transcription and the human mitochondrial RNA polymerase ===

The central dogma of biology in which genetic information is transferred from DNA to RNA, and subsequently into protein, is fundamental to life. A key player in this process is the DNA-dependent RNA polymerase. RNA polymerase produces RNA in the presence of a DNA template under tight control by the cell. In the Martin lab, our goal is to elucidate the energetics and thermodynamics of this complicated process. As a model, we use T7 bacteriophage RNA polymerase (PDB:1QLN). This single-subunit polymerase can transcribe DNA without assistance from other proteins, making it an ideal model to understand transcription. Likewise, it is representative of all other known RNA polymerases in that it initiates at unique positions along the DNA, undergoes abortive cycling, transitions to a stable elongation complex, and terminates transcription at specific sequences.

Related to the T7 RNA polymerase is the human mitochondrial RNA polymerase <scene name='Molecular_Playground/Human_mtRNA_pol/All/1'>(PDB: 3SPA)</scene>. Recent crystallization of this enzyme by [http://www.ncbi.nlm.nih.gov/pubmed/21947009 Temiakov et al.] has revealed structural similarity between the two polymerases. The C-terminal 
<scene name='Molecular_Playground/Human_mtRNA_pol/Ctd/2'>domain</scene> contains the active site for RNA synthesis. The N-terminal <scene name='Molecular_Playground/Human_mtRNA_pol/Ntd/2'>domain</scene>,(NTD) contains the promoter-binding domain (PBD) essential for DNA binding and start site specificity. Key structures of the NTD include the specificity loop <scene name='Molecular_Playground/Human_mtRNA_pol/Specloop/1'> (unresolved)</scene>, intercalating <scene name='Molecular_Playground/Human_mtRNA_pol/Intercalloop/1'>loop</scene> , and AT-recognition <scene name='Molecular_Playground/Human_mtRNA_pol/Atloop/2'>loop</scene>. One feature that is unique to the human mtRNA polymerase is the helical <scene name='Molecular_Playground/Human_mtRNA_pol/Ppr/3'>domain</scene> before the NTD. This domain is believed to play a role in RNA processing.

One very big difference between the two polymerases is in the form of two transcription factors, TFB2M and TFAM. Human mtRNA polymerase requires these two proteins for binding and melting of promoter DNA. TFAM binds 15-40 base pairs upstream while TFB2M binds more proximal to the transcription start site (1-3). The requirement of these transcription factors coupled with the discrepancy of PBD orientation between T7 and human mtRNA polymerase suggests a role in enzyme remodeling for the transcription factors, namely, TFB2M. By studying the structural changes and differences between the two polymerases, we can better under the energetics that governed transcription.

== References ==

#Ekstrand, M. I. Mitochondrial transcription factor A regulates mtDNA copy number in mammals. Hum. Mol. Genet. 13, 935-944 (2004). [http://www.ncbi.nlm.nih.gov/pubmed/15016765 Pubmed]
#Dairaghi, D. J., Shadel, G. S., Clayton, D. A. Human mitochondrial transcription factor A and promoter spacing integrity are required for transcription initiation. Biochim. Biophys. Acta 1271, 127-134 (1995). [http://www.ncbi.nlm.nih.gov/pubmed/7599198 Pubmed]
#Sologub, M., Litonin, D., Anikin, M., Mustaev, A., Temiakov, D. TFB2 is a transient component of the catalytic site of the human mitochondrial RNA polymerase. Cell 139, 934-944 (2009).ﾠ[http://www.ncbi.nlm.nih.gov/pubmed/19945377 Pubmed]

== Helpful Tips ==

1) Avoid using Safari and Google Chrome while making molecular scenes.

2) If presented with a "java.security.AccessControlException: access denied" problem while creating a molecular scene, try accessing your workspace using www.proteopedia.org instead of www.proteopedia.COM

Molecular Playground/Human mtRNA pol

2012-01-08T00:10:08Z

Ketan Mathavan:

<Structure load='3SPA' size='370' frame='true' align='right' caption='Human mitochondrial RNA polymerase (PDB: 3SPA) scene='Molecular_Playground/Human_mtRNA_pol/All/1'/>

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].

=== Transcription and the human mitochondrial RNA polymerase ===

The central dogma of biology in which genetic information is transferred from DNA to RNA, and subsequently into protein, is fundamental to life. A key player in this process is the DNA-dependent RNA polymerase. RNA polymerase produces RNA in the presence of a DNA template under tight control by the cell. In the Martin lab, our goal is to elucidate the energetics and thermodynamics of this complicated process. As a model, we use T7 bacteriophage RNA polymerase (PDB:1QLN). This single-subunit polymerase can transcribe DNA without assistance from other proteins, making it an ideal model to understand transcription. Likewise, it is representative of all other known RNA polymerases in that it initiates at unique positions along the DNA, undergoes abortive cycling, transitions to a stable elongation complex, and terminates transcription at specific sequences.

Related to the T7 RNA polymerase is the human mitochondrial RNA polymerase <scene name='Molecular_Playground/Human_mtRNA_pol/All/1'>(PDB: 3SPA)</scene>. Recent crystallization of this enzyme by [http://www.ncbi.nlm.nih.gov/pubmed/21947009 Temiakov et al.] has revealed structural similarity between the two polymerases. The C-terminal 
<scene name='Molecular_Playground/Human_mtRNA_pol/Ctd/2'>domain</scene> contains the active site for RNA synthesis. The N-terminal <scene name='Molecular_Playground/Human_mtRNA_pol/Ntd/2'>domain</scene>,(NTD) contains the promoter-binding domain (PBD) essential for DNA binding and start site specificity. Key structures of the NTD include the specificity loop <scene name='Molecular_Playground/Human_mtRNA_pol/Specloop/1'> (unresolved)</scene>, intercalating <scene name='Molecular_Playground/Human_mtRNA_pol/Intercalloop/1'>loop</scene> , and AT-recognition <scene name='Molecular_Playground/Human_mtRNA_pol/Atloop/2'>loop</scene>. One feature that is unique to the human mtRNA polymerase is the helical <scene name='Molecular_Playground/Human_mtRNA_pol/Ppr/3'>domain</scene> (cyan) before the NTD. This domain is believed to play a role in RNA processing.

One very big difference between the two polymerases is in the form of two transcription factors, TFB2M and TFAM. Human mtRNA polymerase requires these two proteins for binding and melting of promoter DNA. TFAM binds 15-40 base pairs upstream while TFB2M binds more proximal to the transcription start site (1-3). The requirement of these transcription factors coupled with the discrepancy of PBD orientation between T7 and human mtRNA polymerase suggests a role in enzyme remodeling for the transcription factors, namely, TFB2M. By studying the structural changes and differences between the two polymerases, we can better under the energetics that governed transcription.

== References ==

#Ekstrand, M. I. Mitochondrial transcription factor A regulates mtDNA copy number in mammals. Hum. Mol. Genet. 13, 935-944 (2004). [http://www.ncbi.nlm.nih.gov/pubmed/15016765 Pubmed]
#Dairaghi, D. J., Shadel, G. S., Clayton, D. A. Human mitochondrial transcription factor A and promoter spacing integrity are required for transcription initiation. Biochim. Biophys. Acta 1271, 127-134 (1995). [http://www.ncbi.nlm.nih.gov/pubmed/7599198 Pubmed]
#Sologub, M., Litonin, D., Anikin, M., Mustaev, A., Temiakov, D. TFB2 is a transient component of the catalytic site of the human mitochondrial RNA polymerase. Cell 139, 934-944 (2009).ﾠ[http://www.ncbi.nlm.nih.gov/pubmed/19945377 Pubmed]

== Helpful Tips ==

1) To make scenes with your own molecules, avoid using Safari and Google Chrome.

2) If presented with a "java.security.AccessControlException: access denied" problem while creating a molecular scene, try accessing your workspace using www.proteopedia.org. You may using proteopedia.com.

Molecular Playground/Human mtRNA pol

2012-01-07T23:59:52Z

Ketan Mathavan:

<Structure load='3SPA' size='370' frame='true' align='right' caption='Human mitochondrial RNA polymerase (PDB: 3SPA) scene='Molecular_Playground/Human_mtRNA_pol/All/1'>

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].

=== Transcription and the human mitochondrial RNA polymerase ===

The central dogma of biology in which genetic information is transferred from DNA to RNA, and subsequently into protein, is fundamental to life. A key player in this process is the DNA-dependent RNA polymerase. RNA polymerase produces RNA in the presence of a DNA template under tight control by the cell. In the Martin lab, our goal is to elucidate the energetics and thermodynamics of this complicated process. As a model, we use T7 bacteriophage RNA polymerase (PDB:1QLN). This single-subunit polymerase can transcribe DNA without assistance from other proteins, making it an ideal model to understand transcription. Likewise, it is representative of all other known RNA polymerases in that it initiates at unique positions along the DNA, undergoes abortive cycling, transitions to a stable elongation complex, and terminates transcription at specific sequences.

Related to the T7 RNA polymerase is the human mitochondrial RNA polymerase <scene name='Molecular_Playground/Human_mtRNA_pol/All/1'>(PDB: 3SPA)</scene>. Recent crystallization of this enzyme by [http://www.ncbi.nlm.nih.gov/pubmed/21947009 Temiakov et al.] has revealed structural similarity between the two polymerases. The C-terminal 
<scene name='Molecular_Playground/Human_mtRNA_pol/Ctd/2'>domain</scene> contains the active site for RNA synthesis. The N-terminal <scene name='Molecular_Playground/Human_mtRNA_pol/Ntd/2'>domain</scene>,(NTD) contains the promoter-binding domain (PBD) essential for DNA binding and start site specificity. Key structures of the NTD include the specificity loop <scene name='Molecular_Playground/Human_mtRNA_pol/Specloop/1'> (unresolved)</scene>, intercalating <scene name='Molecular_Playground/Human_mtRNA_pol/Intercalloop/1'>loop</scene> , and AT-recognition <scene name='Molecular_Playground/Human_mtRNA_pol/Atloop/2'>loop</scene>. One feature that is unique to the human mtRNA polymerase is the helical <scene name='Molecular_Playground/Human_mtRNA_pol/Ppr/3'>domain</scene> (cyan) before the NTD. This domain is believed to play a role in RNA processing.

One very big difference between the two polymerases is in the form of two transcription factors, TFB2M and TFAM. Human mtRNA polymerase requires these two proteins for binding and melting of promoter DNA. TFAM binds 15-40 base pairs upstream while TFB2M binds more proximal to the transcription start site (1-3). The requirement of these transcription factors coupled with the discrepancy of PBD orientation between T7 and human mtRNA polymerase suggests a role in enzyme remodeling for the transcription factors, namely, TFB2M. By studying the structural changes and differences between the two polymerases, we can better under the energetics that governed transcription.

== References ==

#Ekstrand, M. I. Mitochondrial transcription factor A regulates mtDNA copy number in mammals. Hum. Mol. Genet. 13, 935-944 (2004). [http://www.ncbi.nlm.nih.gov/pubmed/15016765 Pubmed]
#Dairaghi, D. J., Shadel, G. S., Clayton, D. A. Human mitochondrial transcription factor A and promoter spacing integrity are required for transcription initiation. Biochim. Biophys. Acta 1271, 127-134 (1995). [http://www.ncbi.nlm.nih.gov/pubmed/7599198 Pubmed]
#Sologub, M., Litonin, D., Anikin, M., Mustaev, A., Temiakov, D. TFB2 is a transient component of the catalytic site of the human mitochondrial RNA polymerase. Cell 139, 934-944 (2009).ﾠ[http://www.ncbi.nlm.nih.gov/pubmed/19945377 Pubmed]

== Helpful Tips ==

1) To make scenes with your own molecules, avoid using Safari and Google Chrome.

2) If presented with a "java.security.AccessControlException: access denied" problem while creating a molecular scene, try accessing your workspace using www.proteopedia.org. You may using proteopedia.com.

Molecular Playground/Human mtRNA pol

2012-01-07T23:57:32Z

Ketan Mathavan:

<Structure load='3SPA' size='370' frame='true' align='right' caption='Human mitochondrial RNA polymerase (PDB: 3SPA) scene='Insert optional scene name here' />

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].

=== Transcription and the human mitochondrial RNA polymerase ===

The central dogma of biology in which genetic information is transferred from DNA to RNA, and subsequently into protein, is fundamental to life. A key player in this process is the DNA-dependent RNA polymerase. RNA polymerase produces RNA in the presence of a DNA template under tight control by the cell. In the Martin lab, our goal is to elucidate the energetics and thermodynamics of this complicated process. As a model, we use T7 bacteriophage RNA polymerase (PDB:1QLN). This single-subunit polymerase can transcribe DNA without assistance from other proteins, making it an ideal model to understand transcription. Likewise, it is representative of all other known RNA polymerases in that it initiates at unique positions along the DNA, undergoes abortive cycling, transitions to a stable elongation complex, and terminates transcription at specific sequences.

Related to the T7 RNA polymerase is the human mitochondrial RNA polymerase <scene name='Molecular_Playground/Human_mtRNA_pol/All/1'>(PDB: 3SPA)</scene>. Recent crystallization of this enzyme by [http://www.ncbi.nlm.nih.gov/pubmed/21947009 Temiakov et al.] has revealed structural similarity between the two polymerases. The C-terminal 
<scene name='Molecular_Playground/Human_mtRNA_pol/Ctd/2'>domain</scene> contains the active site for RNA synthesis. The N-terminal <scene name='Molecular_Playground/Human_mtRNA_pol/Ntd/2'>domain</scene>,(NTD) contains the promoter-binding domain (PBD) essential for DNA binding and start site specificity. Key structures of the NTD include the specificity loop <scene name='Molecular_Playground/Human_mtRNA_pol/Specloop/1'> (unresolved)</scene>, intercalating <scene name='Molecular_Playground/Human_mtRNA_pol/Intercalloop/1'>loop</scene> , and AT-recognition <scene name='Molecular_Playground/Human_mtRNA_pol/Atloop/2'>loop</scene>. One feature that is unique to the human mtRNA polymerase is the helical <scene name='Molecular_Playground/Human_mtRNA_pol/Ppr/3'>domain</scene> (cyan) before the NTD. This domain is believed to play a role in RNA processing.

One very big difference between the two polymerases is in the form of two transcription factors, TFB2M and TFAM. Human mtRNA polymerase requires these two proteins for binding and melting of promoter DNA. TFAM binds 15-40 base pairs upstream while TFB2M binds more proximal to the transcription start site (1-3). The requirement of these transcription factors coupled with the discrepancy of PBD orientation between T7 and human mtRNA polymerase suggests a role in enzyme remodeling for the transcription factors, namely, TFB2M. By studying the structural changes and differences between the two polymerases, we can better under the energetics that governed transcription.

== References ==

#Ekstrand, M. I. Mitochondrial transcription factor A regulates mtDNA copy number in mammals. Hum. Mol. Genet. 13, 935-944 (2004). [http://www.ncbi.nlm.nih.gov/pubmed/15016765 Pubmed]
#Dairaghi, D. J., Shadel, G. S., Clayton, D. A. Human mitochondrial transcription factor A and promoter spacing integrity are required for transcription initiation. Biochim. Biophys. Acta 1271, 127-134 (1995). [http://www.ncbi.nlm.nih.gov/pubmed/7599198 Pubmed]
#Sologub, M., Litonin, D., Anikin, M., Mustaev, A., Temiakov, D. TFB2 is a transient component of the catalytic site of the human mitochondrial RNA polymerase. Cell 139, 934-944 (2009).ﾠ[http://www.ncbi.nlm.nih.gov/pubmed/19945377 Pubmed]

== Helpful Tips ==

1) To make scenes with your own molecules, avoid using Safari and Google Chrome.

2) If presented with a "java.security.AccessControlException: access denied" problem while creating a molecular scene, try accessing your workspace using www.proteopedia.org. You may using proteopedia.com.

Molecular Playground/Human mtRNA pol

2012-01-07T23:40:22Z

Ketan Mathavan:

<Structure load='3SPA' size='370' frame='true' align='right' caption='Human mitochondrial RNA polymerase (PDB: 3SPA) scene='Insert optional scene name here' />

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].

=== Transcription and the human mitochondrial RNA polymerase ===

The central dogma of biology in which genetic information is transferred from DNA to RNA, and subsequently into protein, is fundamental to life. A key player in this process is the DNA-dependent RNA polymerase. RNA polymerase produces RNA in the presence of a DNA template under tight control by the cell. In the Martin lab, our goal is to elucidate the energetics and thermodynamics of this complicated process. As a model, we use T7 bacteriophage RNA polymerase (PDB:1QLN). This single-subunit polymerase can transcribe DNA without assistance from other proteins, making it an ideal model to understand transcription. Likewise, it is representative of all other known RNA polymerases in that it initiates at unique positions along the DNA, undergoes abortive cycling, transitions to a stable elongation complex, and terminates transcription at specific sequences.

Related to the T7 RNA polymerase is the human mitochondrial RNA polymerase <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'> (PDB: 3SPA)</scene>. Recent crystallization of this enzyme by [http://www.ncbi.nlm.nih.gov/pubmed/21947009 Temiakov et al.] has revealed structural similarity between the two polymerases. The C-terminal 
<scene name='Molecular_Playground/Human_mtRNA_pol/Ctd/2'>domain</scene> contains the active site for RNA synthesis. The N-terminal <scene name='Molecular_Playground/Human_mtRNA_pol/Ntd/2'>domain</scene>,(NTD) contains the promoter-binding domain (PBD) essential for DNA binding and start site specificity. Key structures of the NTD include the specificity loop <scene name='Molecular_Playground/Human_mtRNA_pol/Specloop/1'> (unresolved)</scene>, intercalating <scene name='Molecular_Playground/Human_mtRNA_pol/Intercalloop/1'>loop</scene> , and AT-recognition <scene name='Molecular_Playground/Human_mtRNA_pol/Atloop/2'>loop</scene>. One feature that is unique to the human mtRNA polymerase is the helical <scene name='Molecular_Playground/Human_mtRNA_pol/Ppr/2'>domain</scene> (light purple) before the NTD. This domain is believed to play a role in RNA processing.

One very big difference between the two polymerases is in the form of two transcription factors, TFB2M and TFAM. Human mtRNA polymerase requires these two proteins for binding and melting of promoter DNA. TFAM binds 15-40 base pairs upstream while TFB2M binds more proximal to the transcription start site (1-3). The requirement of these transcription factors coupled with the discrepancy of PBD orientation between T7 and human mtRNA polymerase suggests a role in enzyme remodeling for the transcription factors, namely, TFB2M. By studying the structural changes and differences between the two polymerases, we can better under the energetics that governed transcription.

== References ==

#Ekstrand, M. I. Mitochondrial transcription factor A regulates mtDNA copy number in mammals. Hum. Mol. Genet. 13, 935-944 (2004). [http://www.ncbi.nlm.nih.gov/pubmed/15016765 Pubmed]
#Dairaghi, D. J., Shadel, G. S., Clayton, D. A. Human mitochondrial transcription factor A and promoter spacing integrity are required for transcription initiation. Biochim. Biophys. Acta 1271, 127-134 (1995). [http://www.ncbi.nlm.nih.gov/pubmed/7599198 Pubmed]
#Sologub, M., Litonin, D., Anikin, M., Mustaev, A., Temiakov, D. TFB2 is a transient component of the catalytic site of the human mitochondrial RNA polymerase. Cell 139, 934-944 (2009).ﾠ[http://www.ncbi.nlm.nih.gov/pubmed/19945377 Pubmed]
== HELP! ==

I was unable to create Jmol scenes to illustrate structures of the human mitochondrial RNA polymerase due to a "java.security.AccessControlException: access denied" problem regardless of the computer or web browser I use.

If there is anyone that may know a remedy for this problem, please contact kmathavan@mcb.umass.edu. Thank you!

Molecular Playground/Human mtRNA pol

2012-01-07T22:14:47Z

Ketan Mathavan:

<Structure load='3SPA' size='370' frame='true' align='right' caption='Human mitochondrial RNA polymerase (PDB: 3SPA) scene='Insert optional scene name here' />

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].

=== Transcription and the human mitochondrial RNA polymerase ===

The central dogma of biology in which genetic information is transferred from DNA to RNA, and subsequently into protein, is fundamental to life. A key player in this process is the DNA-dependent RNA polymerase. RNA polymerase produces RNA in the presence of a DNA template under tight control by the cell. In the Martin lab, our goal is to elucidate the energetics and thermodynamics of this complicated process. As a model, we use T7 bacteriophage RNA polymerase (PDB:1QLN). This single-subunit polymerase can transcribe DNA without assistance from other proteins, making it an ideal model to understand transcription. Likewise, it is representative of all other known RNA polymerases in that it initiates at unique positions along the DNA, undergoes abortive cycling, transitions to a stable elongation complex, and terminates transcription at specific sequences.

Related to the T7 RNA polymerase is the human mitochondrial RNA polymerase <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'> (PDB: 3SPA)</scene>. Recent crystallization of this enzyme by [http://www.ncbi.nlm.nih.gov/pubmed/21947009 Temiakov et al.] has revealed structural similarity between the two polymerases. The C-terminal <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>domain</scene> contains the active site for RNA synthesis. The N-terminal <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'> domain, </scene>(NTD) contains the promoter-binding domain (PBD) essential for DNA binding and start site specificity. Key structures of the NTD include the specificity <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene>, intercalating <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene> , and AT-recognition <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene>. One feature that is unique to the human mtRNA polymerase is the helical <scene name='Molecular_Playground/Human_mtRNA_pol/Ppr/1'>domain</scene> helical before the NTD. This domain is believed to play a role in RNA processing.

One very big difference between the two polymerases is in the form of two transcription factors, TFB2M and TFAM. Human mtRNA polymerase requires these two proteins for binding and melting of promoter DNA. TFAM binds 15-40 base pairs upstream while TFB2M binds more proximal to the transcription start site (1-3). The requirement of these transcription factors coupled with the discrepancy of PBD orientation between T7 and human mtRNA polymerase suggests a role in enzyme remodeling for the transcription factors, namely, TFB2M. By studying the structural changes and differences between the two polymerases, we can better under the energetics that governed transcription.

== References ==

#Ekstrand, M. I. Mitochondrial transcription factor A regulates mtDNA copy number in mammals. Hum. Mol. Genet. 13, 935-944 (2004). [http://www.ncbi.nlm.nih.gov/pubmed/15016765 Pubmed]
#Dairaghi, D. J., Shadel, G. S., Clayton, D. A. Human mitochondrial transcription factor A and promoter spacing integrity are required for transcription initiation. Biochim. Biophys. Acta 1271, 127-134 (1995). [http://www.ncbi.nlm.nih.gov/pubmed/7599198 Pubmed]
#Sologub, M., Litonin, D., Anikin, M., Mustaev, A., Temiakov, D. TFB2 is a transient component of the catalytic site of the human mitochondrial RNA polymerase. Cell 139, 934-944 (2009).ﾠ[http://www.ncbi.nlm.nih.gov/pubmed/19945377 Pubmed]

== HELP! ==

I was unable to create Jmol scenes to illustrate structures of the human mitochondrial RNA polymerase due to a "java.security.AccessControlException: access denied" problem regardless of the computer or web browser I use.

If there is anyone that may know a remedy for this problem, please contact kmathavan@mcb.umass.edu. Thank you!

CBI Molecules

2011-12-15T04:29:09Z

Ketan Mathavan:

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] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.

UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.

It's great to build on a previous entry, but you must leave the earlier one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.

Fall 2011: New entries are due 12/16/11. Please append the designation (new Fall 2011) to your new entries.

==Molecules==
Bhatia Lab

: '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin

: '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin

: '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer

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

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

[http://openwetware.org/wiki/Chien Chien Lab]

: '''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau
:: Best CBI Molecule 2011

Forbes Lab

: '''[[Molecular Playground/CheR]]''', Miaomin Zhang

: '''[[Molecular Playground/RBP]]''', Jan Panteli

: '''[[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
:: Best Overall CBI Molecule 2010

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

: '''[[Molecular Playground/Caspase-7 Dynamics]]'''

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

: '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez

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

: '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz

Hebert Lab

: '''[[Molecular Playground/Saposin C]]''', Abla Tannous
: '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd

[http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]

: '''[[Molecular_Playground/Pcr H]]''', Fabian Romano

Kaltashov Lab

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

Knapp lab

:'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin
:: Best CBI Molecule Proteopedia Page 2010

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

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

: '''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia
:: Best CBI Molecule 2011
: '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia

: NEW Fall 2011! '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan

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

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

: '''[[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, Jon Amoroso

: '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad

Thayumanavan Lab

: '''[[Molecular Playground/Lysozyme ]]''', 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

: '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang

[http://www.chem.umass.edu/~vachet/index.html Vachet Lab]

: '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto
:: Best CBI Molecule Jmol scenes 2010

: '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou

:'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne

Other Molecules of interest

: '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]

Other Laboratories

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

: '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab

: '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab

==Instructions==

'''Congratulations to the prize-winning CBI molecules noted above! These also provide great examples to follow. Another prize for best CBI Molecule page and/or scene will be awarded in summer 2012!'''

Fall 2011: Complete steps 1-4 by 12/1/11, in preparation for the CBI Molecule Workshop.

Choose a molecule that is part of your research project. If someone in your group has already made a page for your research molecule, you can improve on that previous entry. You must leave the previously created page intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.

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. Add a link to your sandbox page at [[Sandbox_CBI]] (CBI Molecules in Progress).

5. 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.

6. Choose a "green scene" on your Proteopedia page to suggest for display at the Molecular Playground and specify a "banner" which will be projected with the molecule. 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."

7. 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.

8. 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 examples above, and be sure to mark it as NEW FALL 2011. If you are improving a previously created page, leave the old one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list. When multiple authors contribute to a Molecular Playground page, please indicate your scene with your initials. Please link the lab names to web pages too.

==Links to HELP pages==
Videos showing how to use Proteopedia:
[[Proteopedia:Video_Guide]]
(Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)

[[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]
gives succinct step by step instructions on how to create a molecular scene.

A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.
[http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]

[[Proteopedia:Guidelines for Ethical Writing]].
Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.

For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.

Molecular Playground/Human mtRNA pol

2011-12-15T04:24:54Z

Ketan Mathavan: New page: <Structure load='3SPA' size='370' frame='true' align='right' caption='Human mitochondrial RNA polymerase (PDB: 3SPA) scene='Insert optional scene name here' /> One of the [[CBI Molecules]...

<Structure load='3SPA' size='370' frame='true' align='right' caption='Human mitochondrial RNA polymerase (PDB: 3SPA) scene='Insert optional scene name here' />

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].

=== Transcription and the human mitochondrial RNA polymerase ===

The central dogma of biology in which genetic information is transferred from DNA to RNA, and subsequently into protein, is fundamental to life. A key player in this process is the DNA-dependent RNA polymerase. RNA polymerase produces RNA in the presence of a DNA template under tight control by the cell. In the Martin lab, our goal is to elucidate the energetics and thermodynamics of this complicated process. As a model, we use T7 bacteriophage RNA polymerase (PDB:1QLN). This single-subunit polymerase can transcribe DNA without assistance from other proteins, making it an ideal model to understand transcription. Likewise, it is representative of all other known RNA polymerases in that it initiates at unique positions along the DNA, undergoes abortive cycling, transitions to a stable elongation complex, and terminates transcription at specific sequences.

Related to the T7 RNA polymerase is the human mitochondrial RNA polymerase <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'> (PDB: 3SPA)</scene>. Recent crystallization of this enzyme by [http://www.ncbi.nlm.nih.gov/pubmed/21947009 Temiakov et al.] has revealed structural similarity between the two polymerases. The C-terminal <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>domain</scene> contains the active site for RNA synthesis. The N-terminal <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'> domain, </scene>(NTD) contains the promoter-binding domain (PBD) essential for DNA binding and start site specificity. Key structures of the NTD include the specificity <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene>, intercalating <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene> , and AT-recognition <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene>.

One very big difference between the two polymerases is in the form of two transcription factors, TFB2M and TFAM. Human mtRNA polymerase requires these two proteins for binding and melting of promoter DNA. TFAM binds 15-40 base pairs upstream while TFB2M binds more proximal to the transcription start site (1-3). The requirement of these transcription factors coupled with the discrepancy of PBD orientation between T7 and human mtRNA polymerase suggests a role in enzyme remodeling for the transcription factors, namely, TFB2M. By studying the structural changes and differences between the two polymerases, we can better under the energetics that governed transcription.

== References ==

#Ekstrand, M. I. Mitochondrial transcription factor A regulates mtDNA copy number in mammals. Hum. Mol. Genet. 13, 935-944 (2004). [http://www.ncbi.nlm.nih.gov/pubmed/15016765 Pubmed]
#Dairaghi, D. J., Shadel, G. S., Clayton, D. A. Human mitochondrial transcription factor A and promoter spacing integrity are required for transcription initiation. Biochim. Biophys. Acta 1271, 127-134 (1995). [http://www.ncbi.nlm.nih.gov/pubmed/7599198 Pubmed]
#Sologub, M., Litonin, D., Anikin, M., Mustaev, A., Temiakov, D. TFB2 is a transient component of the catalytic site of the human mitochondrial RNA polymerase. Cell 139, 934-944 (2009).ﾠ[http://www.ncbi.nlm.nih.gov/pubmed/19945377 Pubmed]

== HELP! ==

I was unable to create Jmol scenes to illustrate structures of the human mitochondrial RNA polymerase due to a "java.security.AccessControlException: access denied" problem regardless of the computer or web browser I use.

If there is anyone that may know a remedy for this problem, please contact kmathavan@mcb.umass.edu. Thank you!

User:Ketan Mathavan/Sandbox 1

2011-12-15T04:08:46Z

Ketan Mathavan:

<Structure load='3SPA' size='370' frame='true' align='right' caption='Human mitochondrial RNA polymerase (PDB: 3SPA) scene='Insert optional scene name here' />

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].

=== Transcription and the human mitochondrial RNA polymerase ===

The central dogma of biology in which genetic information is transferred from DNA to RNA, and subsequently into protein, is fundamental to life. A key player in this process is the DNA-dependent RNA polymerase. RNA polymerase produces RNA in the presence of a DNA template under tight control by the cell. In the Martin lab, our goal is to elucidate the energetics and thermodynamics of this complicated process. As a model, we use T7 bacteriophage RNA polymerase (PDB:1QLN). This single-subunit polymerase can transcribe DNA without assistance from other proteins, making it an ideal model to understand transcription. Likewise, it is representative of all other known RNA polymerases in that it initiates at unique positions along the DNA, undergoes abortive cycling, transitions to a stable elongation complex, and terminates transcription at specific sequences.

Related to the T7 RNA polymerase is the human mitochondrial RNA polymerase <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'> (PDB: 3SPA)</scene>. Recent crystallization of this enzyme by [http://www.ncbi.nlm.nih.gov/pubmed/21947009 Temiakov et al.] has revealed structural similarity between the two polymerases. The C-terminal <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>domain</scene> contains the active site for RNA synthesis. The N-terminal <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'> domain, </scene>(NTD) contains the promoter-binding domain (PBD) essential for DNA binding and start site specificity. Key structures of the NTD include the specificity <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene>, intercalating <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene> , and AT-recognition <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene>.

One very big difference between the two polymerases is in the form of two transcription factors, TFB2M and TFAM. Human mtRNA polymerase requires these two proteins for binding and melting of promoter DNA. TFAM binds 15-40 base pairs upstream while TFB2M binds more proximal to the transcription start site (1-3). The requirement of these transcription factors coupled with the discrepancy of PBD orientation between T7 (Fig. 2; salmon) and human mtRNA polymerase (Fig. 2; grey) suggests a role in enzyme remodeling for the transcription factors, namely, TFB2M. By studying the structural changes and differences between the two polymerases, we can better under the energetics that governed transcription.

== References ==

#Ekstrand, M. I. Mitochondrial transcription factor A regulates mtDNA copy number in mammals. Hum. Mol. Genet. 13, 935-944 (2004). [http://www.ncbi.nlm.nih.gov/pubmed/15016765 Pubmed]
#Dairaghi, D. J., Shadel, G. S., Clayton, D. A. Human mitochondrial transcription factor A and promoter spacing integrity are required for transcription initiation. Biochim. Biophys. Acta 1271, 127-134 (1995). [http://www.ncbi.nlm.nih.gov/pubmed/7599198 Pubmed]
#Sologub, M., Litonin, D., Anikin, M., Mustaev, A., Temiakov, D. TFB2 is a transient component of the catalytic site of the human mitochondrial RNA polymerase. Cell 139, 934-944 (2009).ﾠ[http://www.ncbi.nlm.nih.gov/pubmed/19945377 Pubmed]

== HELP! ==

I was unable to create Jmol scenes to illustrate structures of the human mitochondrial RNA polymerase due to a "java.security.AccessControlException: access denied" problem regardless of the computer or web browser I use.

If there is anyone that may know a remedy for this problem, please contact kmathavan@mcb.umass.edu. Thank you!

User:Ketan Mathavan/Sandbox 1

2011-12-14T18:29:54Z

Ketan Mathavan:

<Structure load='3SPA' size='370' frame='true' align='right' caption='Human mitochondrial RNA polymerase (PDB: 3SPA) scene='Insert optional scene name here' />

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].

=== Transcription and the human mitochondrial RNA polymerase ===

The central dogma of biology in which genetic information is transferred from DNA to RNA, and subsequently into protein, is fundamental to life. A key player in this process is the DNA-dependent RNA polymerase. RNA polymerase produces RNA in the presence of a DNA template under tight control by the cell. In the Martin lab, our goal is to elucidate the energetics and thermodynamics of this complicated process. As a model, we use T7 bacteriophage RNA polymerase (PDB:1QLN). This single-subunit polymerase can transcribe DNA without assistance from other proteins, making it an ideal model to understand transcription. Likewise, it is representative of all other known RNA polymerases in that it initiates at unique positions along the DNA, undergoes abortive cycling, transitions to a stable elongation complex, and terminates transcription at specific sequences.

Related to the T7 RNA polymerase is the human mitochondrial RNA polymerase <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'> (PDB: 3SPA)</scene>. Recent crystallization of this enzyme by [http://www.ncbi.nlm.nih.gov/pubmed/21947009 Temiakov et al.] has revealed structural similarity between the two polymerases. The C-terminal <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>domain</scene> contains the active site for RNA synthesis. The N-terminal <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'> domain, </scene>(NTD) contains the promoter-binding domain (PBD) essential for DNA binding and start site specificity. Key structures of the NTD include the specificity <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene>, intercalating <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene> , and AT-recognition <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene>.

One very big difference between the two polymerases is in the form of two transcription factors, TFB2M and TFAM. Human mtRNA polymerase requires these two proteins for binding and melting of promoter DNA. TFAM binds 15-40 base pairs upstream while TFB2M binds more proximal to the transcription start site (1-3). The requirement of these transcription factors coupled with the discrepancy of PBD orientation between T7 (Fig. 2; salmon) and human mtRNA polymerase (Fig. 2; grey) suggests a role in enzyme remodeling for the transcription factors, namely, TFB2M. By studying the structural changes and differences between the two polymerases, we can better under the energetics that governed transcription.

== References ==

#Ekstrand, M. I. Mitochondrial transcription factor A regulates mtDNA copy number in mammals. Hum. Mol. Genet. 13, 935-944 (2004). [http://www.ncbi.nlm.nih.gov/pubmed/15016765 Pubmed]
#Dairaghi, D. J., Shadel, G. S., Clayton, D. A. Human mitochondrial transcription factor A and promoter spacing integrity are required for transcription initiation. Biochim. Biophys. Acta 1271, 127-134 (1995). [http://www.ncbi.nlm.nih.gov/pubmed/7599198 Pubmed]
#Sologub, M., Litonin, D., Anikin, M., Mustaev, A., Temiakov, D. TFB2 is a transient component of the catalytic site of the human mitochondrial RNA polymerase. Cell 139, 934-944 (2009).ﾠ[http://www.ncbi.nlm.nih.gov/pubmed/19945377 Pubmed]

User:Ketan Mathavan/Sandbox 1

2011-12-14T18:17:32Z

Ketan Mathavan:

<Structure load='3SPA' size='370' frame='true' align='right' caption='Human mitochondrial RNA polymerase (PDB: 3SPA) scene='Insert optional scene name here' />

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].

=== Transcription and the human mitochondrial RNA polymerase ===

The central dogma of biology in which genetic information is transferred from DNA to RNA, and subsequently into protein, is fundamental to life. A key player in this process is the DNA-dependent RNA polymerase. RNA polymerase produces RNA in the presence of a DNA template under tight control by the cell. In the Martin lab, our goal is to elucidate the energetics and thermodynamics of this complicated process. As a model, we use T7 bacteriophage RNA polymerase (PDB:1QLN). This single-subunit polymerase can transcribe DNA without assistance from other proteins, making it an ideal model to understand transcription. Likewise, it is representative of all other known RNA polymerases in that it initiates at unique positions along the DNA, undergoes abortive cycling, transitions to a stable elongation complex, and terminates transcription at specific sequences.

Related to the T7 RNA polymerase is the human mitochondrial RNA polymerase <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'> (PDB: 3SPA)</scene>. Recent crystallization of this enzyme by [http://www.ncbi.nlm.nih.gov/pubmed/21947009 Temiakov et al.] has revealed structural similarity between the two polymerases. The C-terminal <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>domain</scene> contains the active site for RNA synthesis. The N-terminal <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'> domain, </scene>(NTD) contains the promoter-binding domain (PBD) essential for DNA binding and start site specificity. Key structures of the NTD include the specificity <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene>, intercalating <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene> , and AT-recognition <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene>.

One very big difference between the two polymerases is in the form of two transcription factors, TFB2M and TFAM. Human mtRNA polymerase requires these two proteins for binding and melting of promoter DNA. TFAM binds 15-40 base pairs upstream while TFB2M binds more proximal to the transcription start site (Fig.1) (1-3). The requirement of these transcription factors coupled with the discrepancy of PBD orientation between T7 (Fig. 2; salmon) and human mtRNA polymerase (Fig. 2; grey) suggests a role in enzyme remodeling for the transcription factors, namely, TFB2M. By studying the structural changes and differences between the two polymerases, we can better under the energetics that governed transcription.

== References ==

#Ekstrand, M. I. Mitochondrial transcription factor A regulates mtDNA copy number in mammals. Hum. Mol. Genet. 13, 935-944 (2004). [http://www.ncbi.nlm.nih.gov/pubmed/15016765 Pubmed]
#Dairaghi, D. J., Shadel, G. S., Clayton, D. A. Human mitochondrial transcription factor A and promoter spacing integrity are required for transcription initiation. Biochim. Biophys. Acta 1271, 127-134 (1995). [http://www.ncbi.nlm.nih.gov/pubmed/7599198 Pubmed]
#Sologub, M., Litonin, D., Anikin, M., Mustaev, A., Temiakov, D. TFB2 is a transient component of the catalytic site of the human mitochondrial RNA polymerase. Cell 139, 934-944 (2009).ﾠ[http://www.ncbi.nlm.nih.gov/pubmed/19945377 Pubmed]

User:Ketan Mathavan/Sandbox 1

2011-12-14T17:04:45Z

Ketan Mathavan:

<Structure load='3SPA' size='400' frame='true' align='right' caption='Human mitochondrial RNA polymerase' scene='Insert optional scene name here' />

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].

=== Transcription and the human mitochondrial RNA polymerase ===

The central dogma of biology in which genetic information is transferred from DNA to RNA, and subsequently into protein, is fundamental to life. A key player in this process is the DNA-dependent RNA polymerase. RNA polymerase produces RNA in the presence of a DNA template under tight control by the cell. In the Martin lab, our goal is to elucidate the energetics and thermodynamics of this complicated process. As a model, we use T7 bacteriophage RNA polymerase (PDB:1QLN). This single-subunit polymerase can transcribe DNA without assistance from other proteins, making it an ideal model to understand transcription. Likewise, it is representative of all other known RNA polymerases in that it initiates at unique positions along the DNA, undergoes abortive cycling, transitions to a stable elongation complex, and terminates transcription at specific sequences.

Related to the T7 RNA polymerase is the human mitochondrial RNA polymerase (PDB:3SPA). Recent crystallization of this enzyme by [http://www.ncbi.nlm.nih.gov/pubmed/21947009 Temiakov et al.] has revealed structural similarity between the two polymerases. C-terminal <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>domain</scene> contains the active site for RNA synthesis. The N-terminal <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'> domain, </scene>(NTD) contains the promoter-binding domain (PBD) essential for DNA binding and start site specificity. Key structures of the NTD include the specificity <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene>, intercalating <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene> , and AT-recognition <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene> .

One very big difference between the two polymerases is in the form of two transcription factors, TFB2M and TFAM. Human mtRNA polymerase requires these two proteins for binding and melting of promoter DNA. TFAM binds 15-40 base pairs upstream while TFB2M binds more proximal to the transcription start site (Figure 1). The requirement of these transcription factors coupled with the discrepancy of PBD orientation between T7 (Figure 2; salmon) and human mtRNA polymerase (Figure 2; grey) suggests a role in enzyme remodeling for the transcription factors, namely, TFB2M. By studying the structural changes and differences between the two polymerases, we can better under the energetics that governed transcription.

<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'/>

== References ==

#Ekstrand, M. I. Mitochondrial transcription factor A regulates mtDNA copy number in mammals. Hum. Mol. Genet. 13, 935-944 (2004). [http://www.ncbi.nlm.nih.gov/pubmed/15016765 Pubmed]
#Dairaghi, D. J., Shadel, G. S., Clayton, D. A. Human mitochondrial transcription factor A and promoter spacing integrity are required for transcription initiation. Biochim. Biophys. Acta 1271, 127-134 (1995). [http://www.ncbi.nlm.nih.gov/pubmed/7599198 Pubmed]
#Sologub, M., Litonin, D., Anikin, M., Mustaev, A., Temiakov, D. TFB2 is a transient component of the catalytic site of the human mitochondrial RNA polymerase. Cell 139, 934-944 (2009).ﾠ[http://www.ncbi.nlm.nih.gov/pubmed/19945377 Pubmed]

User:Ketan Mathavan/Sandbox 1

2011-12-14T16:59:14Z

Ketan Mathavan:

User:Ketan Mathavan/Sandbox 1

2011-12-14T16:58:17Z

Ketan Mathavan:

User:Ketan Mathavan/Sandbox 1

2011-12-14T16:37:12Z

Ketan Mathavan:

<Structure load='3SPA' size='400' frame='true' align='right' caption='Human mitochondrial RNA polymerase' scene='Insert optional scene name here' />

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].

'''Transcription and the human mitochondrial RNA polymerase '''

The central dogma of biology in which genetic information is transferred from DNA to RNA, and subsequently into protein, is fundamental to life. A key player in this process is the DNA-dependent RNA polymerase. RNA polymerase produces RNA in the presence of a DNA template under tight control by the cell. In the Martin lab, our goal is to elucidate the energetics and thermodynamics of this complicated process. As a model, we use T7 bacteriophage RNA polymerase (PDB:1QLN). This single-subunit polymerase can transcribe DNA without assistance from other proteins, making it an ideal model to understand transcription. Likewise, it is representative of all other known RNA polymerases in that it initiates at unique positions along the DNA, undergoes abortive cycling, transitions to a stable elongation complex, and terminates transcription at specific sequences.

Related to the T7 RNA polymerase is the human mitochondrial RNA polymerase (PDB:3SPA). Recent crystallization of this enzyme by [http://www.ncbi.nlm.nih.gov/pubmed/21947009 Temiakov et al.] has revealed structural similarity between the two polymerases. The (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>C-terminal domain view</scene>) C-terminal domain contains the active site for RNA synthesis. The N-terminal domain (NTD) contains the promoter-binding domain (PBD) essential for DNA binding and start site specificity. Key structures of the NTD include the specificity loop (yellow), intercalating loop (orange), and AT-recognition loop (blue).

One very big difference between the two polymerases is in the form of two transcription factors, TFB2M and TFAM. Human mtRNA polymerase requires these two proteins for binding and melting of promoter DNA. TFAM binds 15-40 base pairs upstream while TFB2M binds more proximal to the transcription start site (Figure 1). The requirement of these transcription factors coupled with the discrepancy of PBD orientation between T7 (Figure 2; salmon) and human mtRNA polymerase (Figure 2; grey) suggests a role in enzyme remodeling for the transcription factors, namely, TFB2M. By studying the structural changes and differences between the two polymerases, we can better under the energetics that governed transcription.

<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 ) 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.

<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'/>

== References ==

#
#

User:Ketan Mathavan/Sandbox 1

2011-12-14T16:27:09Z

Ketan Mathavan:

<Structure load='3SPA' size='400' frame='true' align='right' caption='Human mitochondrial RNA polymerase' scene='Insert optional scene name here' />

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].

'''Transcription and the human mitochondrial RNA polymerase '''

The central dogma of biology in which genetic information is transferred from DNA to RNA, and subsequently into protein, is fundamental to life. A key player in this process is the DNA-dependent RNA polymerase. RNA polymerase produces RNA in the presence of a DNA template under tight control by the cell. In the Martin lab, our goal is to elucidate the energetics and thermodynamics of this complicated process. As a model, we use T7 bacteriophage RNA polymerase (PDB:1QLN). This single-subunit polymerase can transcribe DNA without assistance from other proteins, making it an ideal model to understand transcription. Likewise, it is representative of all other known RNA polymerases in that it initiates at unique positions along the DNA, undergoes abortive cycling, transitions to a stable elongation complex, and terminates transcription at specific sequences.
(<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>)

Related to the T7 RNA polymerase is the human mitochondrial RNA polymerase (PDB:3SPA). Recent crystallization of this enzyme by [http://www.ncbi.nlm.nih.gov/pubmed/21947009 Temiakov et al.] has revealed structural similarity between the two polymerases. The C-terminal domain (gray) contains the active site for RNA synthesis. The N-terminal domain (NTD) contains the promoter-binding domain (PBD) essential for DNA binding and start site specificity. Key structures of the NTD include the specificity loop (yellow), intercalating loop (orange), and AT-recognition loop (blue).

One very big difference between the two polymerases is in the form of two transcription factors, TFB2M and TFAM. Human mtRNA polymerase requires these two proteins for binding and melting of promoter DNA. TFAM binds 15-40 base pairs upstream while TFB2M binds more proximal to the transcription start site (Figure 1). The requirement of these transcription factors coupled with the discrepancy of PBD orientation between T7 (Figure 2; salmon) and human mtRNA polymerase (Figure 2; grey) suggests a role in enzyme remodeling for the transcription factors, namely, TFB2M. By studying the structural changes and differences between the two polymerases, we can better under the energetics that governed transcription.

<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 ) 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.

<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'/>

== References ==

#
#

User:Ketan Mathavan/Sandbox 1

2011-12-14T04:33:41Z

Ketan Mathavan:

<Structure load='3SPA' size='250' frame='true' align='right' caption='Human mitochondrial RNA polymerase' scene='Insert optional scene name here' />

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].

'''Transcription and the human mitochondrial RNA polymerase '''

The central dogma of biology in which genetic information is transferred from DNA to RNA, and subsequently into protein, is fundamental to life. A key player in this process is the DNA-dependent RNA polymerase. RNA polymerase produces RNA in the presence of a DNA template under tight control by the cell. In the Martin lab, our goal is to elucidate the energetics and thermodynamics of this complicated process. As a model, we use T7 bacteriophage RNA polymerase. This single-subunit polymerase can transcribe DNA without assistance from other proteins, making it an ideal model to understand transcription. Likewise, it is representative of all other known RNA polymerases in that it initiates at unique positions along the DNA, undergoes abortive cycling, transitions to a stable elongation complex, and terminates transcription at specific sequences.

Initially transcribing complexes are relatively unstable through about the first 8-10 bases of transcription. During this time, short RNA transcripts are made and released in a process known as abortive cycling. Abortive cycling in particular, and promoter-proximal pausing more generally, plays key roles in gene regulation. Thus understanding the mechanism of initial transcription is key to understanding cellular regulation.

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 (SMJ).

User:Ketan Mathavan/Sandbox 1

2011-12-14T04:16:27Z

Ketan Mathavan:

Test <Structure load='1UM8' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

<Structure load='1UM8' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

[['''Bold text'''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 (SMJ).

Ketan Mathavan/Sandbox 1

2011-12-07T17:56:12Z

Ketan Mathavan:

<Structure load='3spa' size='400' frame='true' align='right' caption='Human mitochondrial RNA polymerase (3SPA)' scene='Labelled' />

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

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='3spa' size='[450,338]' frame='true' align='right'
caption='Human mitochondrial RNA polymerase (3spa)' scene='User:Ketan_Mathavan/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.

Ketan Mathavan/Sandbox 1

2011-12-07T17:38:21Z

Ketan Mathavan:

<Structure load='3spa' size='500' frame='true' align='right' caption='Human mitochondrial RNA polymerase (3SPA)' scene='Insert optional scene name here' />

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

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='3spa' size='[450,338]' frame='true' align='right'
caption='Human mitochondrial RNA polymerase (3spa)' scene='User:Ketan_Mathavan/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.

Ketan Mathavan/Sandbox 1

2011-12-07T16:58:56Z

Ketan Mathavan:

Ketan Mathavan/Sandbox 1

2011-12-07T16:38:33Z

Ketan Mathavan: New page: <!-- Please use the "3D" button above this box to insert a Jmol applet (molecule) on this page. Or use the four-green-boxes-button to insert scrollable text adjacent to a Jmol applet. Che...

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

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 motors that rotate the flagella to cause the cell to either continue swimming or to tumble. When an attractant molecule binds, it signals: "Things look good, keep swimming!" The opposite signal occurs when bacteria sense decreasing concentrations of 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 receptor protein used by bacteria to "smell" their environment.

Sandbox CBI

2011-12-07T16:37:02Z

Ketan Mathavan:

This page is for links to CBI Molecules in Progress (user sandbox pages).

http://proteopedia.org/wiki/index.php/Ketan_Mathavan/Sandbox_1

http://proteopedia.org/wiki/index.php/Brittany_deRonde/Sandbox_1

http://proteopedia.org/wiki/index.php/Heidi_Hu/Sandbox_1

http://proteopedia.org/wiki/index.php/User:Xuni_Li/Sandbox_1

http://proteopedia.org/wiki/index.php/Gustavo_Elberto_Epalza_Sanchez/Sandbox_1

http://proteopedia.org/wiki/index.php/Scott_Eron/Sandbox1

http://www.proteopedia.org/wiki/index.php/User:Jing_Liu/Sandbox_1

User:Ketan Mathavan/Sandbox 1

2011-12-07T16:02:16Z

Ketan Mathavan: New page: Bacterial chemotaxis receptor Many bacteria can "smell" their surroundings and "choose" where to go. They detect molecules such as amino acids or ...

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

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 motors that rotate the flagella to cause the cell to either continue swimming or to tumble. When an attractant molecule binds, it signals: "Things look good, keep swimming!" The opposite signal occurs when bacteria sense decreasing concentrations of 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 receptor protein used by bacteria to "smell" their environment.