Group:USC-LCHS - Revision history

Remo Rohs: /* The Rohs Lab at USC and the Protein-DNA Institute at La Cañada High School */

Remo Rohs — Fri, 22 Jul 2011 03:33:49 GMT

The Rohs Lab at USC and the Protein-DNA Institute at La Cañada High School

←Older revision		Revision as of 03:33, 22 July 2011
Line 1:		Line 1:
-	= The Rohs Lab at USC and ~~the~~ Protein-DNA Institute at La Cañada High School=	+	= The Rohs Lab at USC and Protein-DNA Institute at La Cañada High School=

	Welcome, students, fellow researchers and educators! Welcome to your home page for the joint structural biology initiative between the [http://rohslab.cmb.usc.edu/ Rohs Lab] at the [http://www.usc.edu University of Southern California] (USC) and the Protein-DNA Institute at [http://www.lcusd.net/lchs/site/ La Cañada High School] (LCHS), hosted on the [[Main Page\|Proteopedia]] web resource. The goal of this website is to provide a cyber-infrastructure for the use of graphic visualization tools in integrated educational and research activities focused at structural aspects of proteins and nucleic acids. You will notice that this is not a regular webpage. If you scroll down a bit, you will find that there are interactive 3D structures of protein-DNA complexes on this page. You can even trigger animations by clicking on green hyperlinks in the text when you find them. These green hyperlinks will change the orientation and representation of the 3D structure in order to illustrate a point made in the related scientific publication. The best part is that it is easy to create your own page with an interactive 3D structure and green links, and that is what you will be doing to present your findings! Feel free to also explore other pages in Proteopedia that are not related to USC-LCHS. Proteopedia is a collaborative 3D encyclopedia of proteins and other biomolecules, and you will find many interesting molecules described in interactive detail.		Welcome, students, fellow researchers and educators! Welcome to your home page for the joint structural biology initiative between the [http://rohslab.cmb.usc.edu/ Rohs Lab] at the [http://www.usc.edu University of Southern California] (USC) and the Protein-DNA Institute at [http://www.lcusd.net/lchs/site/ La Cañada High School] (LCHS), hosted on the [[Main Page\|Proteopedia]] web resource. The goal of this website is to provide a cyber-infrastructure for the use of graphic visualization tools in integrated educational and research activities focused at structural aspects of proteins and nucleic acids. You will notice that this is not a regular webpage. If you scroll down a bit, you will find that there are interactive 3D structures of protein-DNA complexes on this page. You can even trigger animations by clicking on green hyperlinks in the text when you find them. These green hyperlinks will change the orientation and representation of the 3D structure in order to illustrate a point made in the related scientific publication. The best part is that it is easy to create your own page with an interactive 3D structure and green links, and that is what you will be doing to present your findings! Feel free to also explore other pages in Proteopedia that are not related to USC-LCHS. Proteopedia is a collaborative 3D encyclopedia of proteins and other biomolecules, and you will find many interesting molecules described in interactive detail.

Remo Rohs: /* The Rohs Lab at USC and Protein-DNA Institute at La Cañada High School */

Remo Rohs — Fri, 22 Jul 2011 03:33:04 GMT

The Rohs Lab at USC and Protein-DNA Institute at La Cañada High School

←Older revision		Revision as of 03:33, 22 July 2011
Line 1:		Line 1:
-	= The Rohs Lab at USC and Protein-DNA Institute at La Cañada High School=	+	= The Rohs Lab at USC and the Protein-DNA Institute at La Cañada High School=

	Welcome, students, fellow researchers and educators! Welcome to your home page for the joint structural biology initiative between the [http://rohslab.cmb.usc.edu/ Rohs Lab] at the [http://www.usc.edu University of Southern California] (USC) and the Protein-DNA Institute at [http://www.lcusd.net/lchs/site/ La Cañada High School] (LCHS), hosted on the [[Main Page\|Proteopedia]] web resource. The goal of this website is to provide a cyber-infrastructure for the use of graphic visualization tools in integrated educational and research activities focused at structural aspects of proteins and nucleic acids. You will notice that this is not a regular webpage. If you scroll down a bit, you will find that there are interactive 3D structures of protein-DNA complexes on this page. You can even trigger animations by clicking on green hyperlinks in the text when you find them. These green hyperlinks will change the orientation and representation of the 3D structure in order to illustrate a point made in the related scientific publication. The best part is that it is easy to create your own page with an interactive 3D structure and green links, and that is what you will be doing to present your findings! Feel free to also explore other pages in Proteopedia that are not related to USC-LCHS. Proteopedia is a collaborative 3D encyclopedia of proteins and other biomolecules, and you will find many interesting molecules described in interactive detail.		Welcome, students, fellow researchers and educators! Welcome to your home page for the joint structural biology initiative between the [http://rohslab.cmb.usc.edu/ Rohs Lab] at the [http://www.usc.edu University of Southern California] (USC) and the Protein-DNA Institute at [http://www.lcusd.net/lchs/site/ La Cañada High School] (LCHS), hosted on the [[Main Page\|Proteopedia]] web resource. The goal of this website is to provide a cyber-infrastructure for the use of graphic visualization tools in integrated educational and research activities focused at structural aspects of proteins and nucleic acids. You will notice that this is not a regular webpage. If you scroll down a bit, you will find that there are interactive 3D structures of protein-DNA complexes on this page. You can even trigger animations by clicking on green hyperlinks in the text when you find them. These green hyperlinks will change the orientation and representation of the 3D structure in order to illustrate a point made in the related scientific publication. The best part is that it is easy to create your own page with an interactive 3D structure and green links, and that is what you will be doing to present your findings! Feel free to also explore other pages in Proteopedia that are not related to USC-LCHS. Proteopedia is a collaborative 3D encyclopedia of proteins and other biomolecules, and you will find many interesting molecules described in interactive detail.

Remo Rohs: /* Example: Readout of DNA minor groove shape is the molecular basis for Hox specificity */

Remo Rohs — Wed, 20 Jul 2011 19:13:59 GMT

Example: Readout of DNA minor groove shape is the molecular basis for Hox specificity

←Older revision		Revision as of 19:13, 20 July 2011
Line 8:		Line 8:
	<StructureSection load='2r5z' size='500' side='right' caption='Hox protein Scr (blue) and its cofactor Exd (green) bind to the Scr-specific DNA target (PDB entry [[2r5z]])' scene=''>		<StructureSection load='2r5z' size='500' side='right' caption='Hox protein Scr (blue) and its cofactor Exd (green) bind to the Scr-specific DNA target (PDB entry [[2r5z]])' scene=''>
	<!-- Publication Abstract from PubMed -->		<!-- Publication Abstract from PubMed -->
-	The recognition of specific DNA-binding sites by transcription factors is a critical yet poorly understood step in the control of gene expression. Members of the Hox family of transcription factors bind DNA by making nearly identical major groove contacts via the recognition helices of their homeodomains. In vivo specificity, however, often depends on extended and unstructured regions that link Hox homeodomains to a DNA-bound cofactor, Extradenticle (Exd). Using a combination of structure determination, computational analysis, and in vitro and in vivo assays, we show that Hox proteins recognize specific Hox-Exd binding sites via <scene name='Group:USC-LCHS/2r5z_his-12arg3arg5_closeup/3'>residues located in these extended regions that insert into the minor groove</scene> ~~insert into the minor groove~~ but only when presented with the correct DNA sequence. Our results suggest that these residues, which are conserved in a paralog-specific manner, confer specificity by recognizing a sequence-dependent DNA structure instead of directly reading a specific DNA sequence.	+	The recognition of specific DNA-binding sites by transcription factors is a critical yet poorly understood step in the control of gene expression. Members of the Hox family of transcription factors bind DNA by making nearly identical major groove contacts via the recognition helices of their homeodomains. In vivo specificity, however, often depends on extended and unstructured regions that link Hox homeodomains to a DNA-bound cofactor, Extradenticle (Exd). Using a combination of structure determination, computational analysis, and in vitro and in vivo assays, we show that Hox proteins recognize specific Hox-Exd binding sites via <scene name='Group:USC-LCHS/2r5z_his-12arg3arg5_closeup/3'>residues located in these extended regions that insert into the minor groove</scene> but only when presented with the correct DNA sequence. Our results suggest that these residues, which are conserved in a paralog-specific manner, confer specificity by recognizing a sequence-dependent DNA structure instead of directly reading a specific DNA sequence.

	''Functional specificity of a Hox protein mediated by the recognition of minor groove structure., Joshi R, Passner JM, [[User:Remo Rohs\|Rohs R]], Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS, Cell. 2007 Nov 2;131(3):530-43. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17981120 17981120]''		''Functional specificity of a Hox protein mediated by the recognition of minor groove structure., Joshi R, Passner JM, [[User:Remo Rohs\|Rohs R]], Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS, Cell. 2007 Nov 2;131(3):530-43. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17981120 17981120]''

Remo Rohs: /* The Rohs Lab at USC and the Protein-DNA Institute at La Cañada High School */

Remo Rohs — Wed, 20 Jul 2011 04:05:25 GMT

The Rohs Lab at USC and the Protein-DNA Institute at La Cañada High School

←Older revision		Revision as of 04:05, 20 July 2011
Line 1:		Line 1:
-	= The Rohs Lab at USC and ~~the~~ Protein-DNA Institute at La Cañada High School=	+	= The Rohs Lab at USC and Protein-DNA Institute at La Cañada High School=

	Welcome, students, fellow researchers and educators! Welcome to your home page for the joint structural biology initiative between the [http://rohslab.cmb.usc.edu/ Rohs Lab] at the [http://www.usc.edu University of Southern California] (USC) and the Protein-DNA Institute at [http://www.lcusd.net/lchs/site/ La Cañada High School] (LCHS), hosted on the [[Main Page\|Proteopedia]] web resource. The goal of this website is to provide a cyber-infrastructure for the use of graphic visualization tools in integrated educational and research activities focused at structural aspects of proteins and nucleic acids. You will notice that this is not a regular webpage. If you scroll down a bit, you will find that there are interactive 3D structures of protein-DNA complexes on this page. You can even trigger animations by clicking on green hyperlinks in the text when you find them. These green hyperlinks will change the orientation and representation of the 3D structure in order to illustrate a point made in the related scientific publication. The best part is that it is easy to create your own page with an interactive 3D structure and green links, and that is what you will be doing to present your findings! Feel free to also explore other pages in Proteopedia that are not related to USC-LCHS. Proteopedia is a collaborative 3D encyclopedia of proteins and other biomolecules, and you will find many interesting molecules described in interactive detail.		Welcome, students, fellow researchers and educators! Welcome to your home page for the joint structural biology initiative between the [http://rohslab.cmb.usc.edu/ Rohs Lab] at the [http://www.usc.edu University of Southern California] (USC) and the Protein-DNA Institute at [http://www.lcusd.net/lchs/site/ La Cañada High School] (LCHS), hosted on the [[Main Page\|Proteopedia]] web resource. The goal of this website is to provide a cyber-infrastructure for the use of graphic visualization tools in integrated educational and research activities focused at structural aspects of proteins and nucleic acids. You will notice that this is not a regular webpage. If you scroll down a bit, you will find that there are interactive 3D structures of protein-DNA complexes on this page. You can even trigger animations by clicking on green hyperlinks in the text when you find them. These green hyperlinks will change the orientation and representation of the 3D structure in order to illustrate a point made in the related scientific publication. The best part is that it is easy to create your own page with an interactive 3D structure and green links, and that is what you will be doing to present your findings! Feel free to also explore other pages in Proteopedia that are not related to USC-LCHS. Proteopedia is a collaborative 3D encyclopedia of proteins and other biomolecules, and you will find many interesting molecules described in interactive detail.

Remo Rohs: /* USC-LCHS: An integrated educational and research initiative at USC and La Cañada High School */

Remo Rohs — Wed, 20 Jul 2011 04:04:27 GMT

USC-LCHS: An integrated educational and research initiative at USC and La Cañada High School

←Older revision		Revision as of 04:04, 20 July 2011
Line 1:		Line 1:
-	=USC-~~LCHS: An integrated educational and research initiative~~ at ~~USC and~~ La Cañada High School=	+	= The Rohs Lab at USC and the Protein-DNA Institute at La Cañada High School=

	Welcome, students, fellow researchers and educators! Welcome to your home page for the joint structural biology initiative between the [http://rohslab.cmb.usc.edu/ Rohs Lab] at the [http://www.usc.edu University of Southern California] (USC) and the Protein-DNA Institute at [http://www.lcusd.net/lchs/site/ La Cañada High School] (LCHS), hosted on the [[Main Page\|Proteopedia]] web resource. The goal of this website is to provide a cyber-infrastructure for the use of graphic visualization tools in integrated educational and research activities focused at structural aspects of proteins and nucleic acids. You will notice that this is not a regular webpage. If you scroll down a bit, you will find that there are interactive 3D structures of protein-DNA complexes on this page. You can even trigger animations by clicking on green hyperlinks in the text when you find them. These green hyperlinks will change the orientation and representation of the 3D structure in order to illustrate a point made in the related scientific publication. The best part is that it is easy to create your own page with an interactive 3D structure and green links, and that is what you will be doing to present your findings! Feel free to also explore other pages in Proteopedia that are not related to USC-LCHS. Proteopedia is a collaborative 3D encyclopedia of proteins and other biomolecules, and you will find many interesting molecules described in interactive detail.		Welcome, students, fellow researchers and educators! Welcome to your home page for the joint structural biology initiative between the [http://rohslab.cmb.usc.edu/ Rohs Lab] at the [http://www.usc.edu University of Southern California] (USC) and the Protein-DNA Institute at [http://www.lcusd.net/lchs/site/ La Cañada High School] (LCHS), hosted on the [[Main Page\|Proteopedia]] web resource. The goal of this website is to provide a cyber-infrastructure for the use of graphic visualization tools in integrated educational and research activities focused at structural aspects of proteins and nucleic acids. You will notice that this is not a regular webpage. If you scroll down a bit, you will find that there are interactive 3D structures of protein-DNA complexes on this page. You can even trigger animations by clicking on green hyperlinks in the text when you find them. These green hyperlinks will change the orientation and representation of the 3D structure in order to illustrate a point made in the related scientific publication. The best part is that it is easy to create your own page with an interactive 3D structure and green links, and that is what you will be doing to present your findings! Feel free to also explore other pages in Proteopedia that are not related to USC-LCHS. Proteopedia is a collaborative 3D encyclopedia of proteins and other biomolecules, and you will find many interesting molecules described in interactive detail.

Remo Rohs: /* USC-LCHS: The Protein-DNA Institute - An integrated educational and research initiative of the Rohs Lab at USC and La Cañada High School */

Remo Rohs — Wed, 20 Jul 2011 04:02:47 GMT

USC-LCHS: The Protein-DNA Institute - An integrated educational and research initiative of the Rohs Lab at USC and La Cañada High School

←Older revision		Revision as of 04:02, 20 July 2011
Line 1:		Line 1:
-	=USC-LCHS: ~~The Protein-DNA Institute -~~ An integrated educational and research initiative ~~of the Rohs Lab~~ at USC and La Cañada High School=	+	=USC-LCHS: An integrated educational and research initiative at USC and La Cañada High School=

	Welcome, students, fellow researchers and educators! Welcome to your home page for the joint structural biology initiative between the [http://rohslab.cmb.usc.edu/ Rohs Lab] at the [http://www.usc.edu University of Southern California] (USC) and the Protein-DNA Institute at [http://www.lcusd.net/lchs/site/ La Cañada High School] (LCHS), hosted on the [[Main Page\|Proteopedia]] web resource. The goal of this website is to provide a cyber-infrastructure for the use of graphic visualization tools in integrated educational and research activities focused at structural aspects of proteins and nucleic acids. You will notice that this is not a regular webpage. If you scroll down a bit, you will find that there are interactive 3D structures of protein-DNA complexes on this page. You can even trigger animations by clicking on green hyperlinks in the text when you find them. These green hyperlinks will change the orientation and representation of the 3D structure in order to illustrate a point made in the related scientific publication. The best part is that it is easy to create your own page with an interactive 3D structure and green links, and that is what you will be doing to present your findings! Feel free to also explore other pages in Proteopedia that are not related to USC-LCHS. Proteopedia is a collaborative 3D encyclopedia of proteins and other biomolecules, and you will find many interesting molecules described in interactive detail.		Welcome, students, fellow researchers and educators! Welcome to your home page for the joint structural biology initiative between the [http://rohslab.cmb.usc.edu/ Rohs Lab] at the [http://www.usc.edu University of Southern California] (USC) and the Protein-DNA Institute at [http://www.lcusd.net/lchs/site/ La Cañada High School] (LCHS), hosted on the [[Main Page\|Proteopedia]] web resource. The goal of this website is to provide a cyber-infrastructure for the use of graphic visualization tools in integrated educational and research activities focused at structural aspects of proteins and nucleic acids. You will notice that this is not a regular webpage. If you scroll down a bit, you will find that there are interactive 3D structures of protein-DNA complexes on this page. You can even trigger animations by clicking on green hyperlinks in the text when you find them. These green hyperlinks will change the orientation and representation of the 3D structure in order to illustrate a point made in the related scientific publication. The best part is that it is easy to create your own page with an interactive 3D structure and green links, and that is what you will be doing to present your findings! Feel free to also explore other pages in Proteopedia that are not related to USC-LCHS. Proteopedia is a collaborative 3D encyclopedia of proteins and other biomolecules, and you will find many interesting molecules described in interactive detail.

Remo Rohs: /* USC-LCHS: The Rohs Lab at the University of Southern California - The Protein-DNA Institute at La Cañada High School */

Remo Rohs — Wed, 20 Jul 2011 04:01:56 GMT

USC-LCHS: The Rohs Lab at the University of Southern California - The Protein-DNA Institute at La Cañada High School

←Older revision		Revision as of 04:01, 20 July 2011
Line 1:		Line 1:
-	=USC-LCHS: ~~The Rohs Lab at the University of Southern California -~~ The Protein-DNA Institute at La Cañada High School=	+	=USC-LCHS: The Protein-DNA Institute - An integrated educational and research initiative of the Rohs Lab at USC and La Cañada High School=

	Welcome, students, fellow researchers and educators! Welcome to your home page for the joint structural biology initiative between the [http://rohslab.cmb.usc.edu/ Rohs Lab] at the [http://www.usc.edu University of Southern California] (USC) and the Protein-DNA Institute at [http://www.lcusd.net/lchs/site/ La Cañada High School] (LCHS), hosted on the [[Main Page\|Proteopedia]] web resource. The goal of this website is to provide a cyber-infrastructure for the use of graphic visualization tools in integrated educational and research activities focused at structural aspects of proteins and nucleic acids. You will notice that this is not a regular webpage. If you scroll down a bit, you will find that there are interactive 3D structures of protein-DNA complexes on this page. You can even trigger animations by clicking on green hyperlinks in the text when you find them. These green hyperlinks will change the orientation and representation of the 3D structure in order to illustrate a point made in the related scientific publication. The best part is that it is easy to create your own page with an interactive 3D structure and green links, and that is what you will be doing to present your findings! Feel free to also explore other pages in Proteopedia that are not related to USC-LCHS. Proteopedia is a collaborative 3D encyclopedia of proteins and other biomolecules, and you will find many interesting molecules described in interactive detail.		Welcome, students, fellow researchers and educators! Welcome to your home page for the joint structural biology initiative between the [http://rohslab.cmb.usc.edu/ Rohs Lab] at the [http://www.usc.edu University of Southern California] (USC) and the Protein-DNA Institute at [http://www.lcusd.net/lchs/site/ La Cañada High School] (LCHS), hosted on the [[Main Page\|Proteopedia]] web resource. The goal of this website is to provide a cyber-infrastructure for the use of graphic visualization tools in integrated educational and research activities focused at structural aspects of proteins and nucleic acids. You will notice that this is not a regular webpage. If you scroll down a bit, you will find that there are interactive 3D structures of protein-DNA complexes on this page. You can even trigger animations by clicking on green hyperlinks in the text when you find them. These green hyperlinks will change the orientation and representation of the 3D structure in order to illustrate a point made in the related scientific publication. The best part is that it is easy to create your own page with an interactive 3D structure and green links, and that is what you will be doing to present your findings! Feel free to also explore other pages in Proteopedia that are not related to USC-LCHS. Proteopedia is a collaborative 3D encyclopedia of proteins and other biomolecules, and you will find many interesting molecules described in interactive detail.

Remo Rohs: /* Example: Readout of DNA minor groove shape is the molecular basis for Hox specificity */

Remo Rohs — Wed, 20 Jul 2011 03:43:39 GMT

Example: Readout of DNA minor groove shape is the molecular basis for Hox specificity

←Older revision		Revision as of 03:43, 20 July 2011
Line 6:		Line 6:

	==Example: Readout of DNA minor groove shape is the molecular basis for Hox specificity==		==Example: Readout of DNA minor groove shape is the molecular basis for Hox specificity==
-	<StructureSection load='2r5z' size='500' side='right' caption='Hox protein Scr and its cofactor Exd bind to DNA target (PDB entry [[2r5z]])' scene=''>	+	<StructureSection load='2r5z' size='500' side='right' caption='Hox protein Scr (blue) and its cofactor Exd (green) bind to the Scr-specific DNA target (PDB entry [[2r5z]])' scene=''>
	<!-- Publication Abstract from PubMed -->		<!-- Publication Abstract from PubMed -->
	The recognition of specific DNA-binding sites by transcription factors is a critical yet poorly understood step in the control of gene expression. Members of the Hox family of transcription factors bind DNA by making nearly identical major groove contacts via the recognition helices of their homeodomains. In vivo specificity, however, often depends on extended and unstructured regions that link Hox homeodomains to a DNA-bound cofactor, Extradenticle (Exd). Using a combination of structure determination, computational analysis, and in vitro and in vivo assays, we show that Hox proteins recognize specific Hox-Exd binding sites via <scene name='Group:USC-LCHS/2r5z_his-12arg3arg5_closeup/3'>residues located in these extended regions that insert into the minor groove</scene> insert into the minor groove but only when presented with the correct DNA sequence. Our results suggest that these residues, which are conserved in a paralog-specific manner, confer specificity by recognizing a sequence-dependent DNA structure instead of directly reading a specific DNA sequence.		The recognition of specific DNA-binding sites by transcription factors is a critical yet poorly understood step in the control of gene expression. Members of the Hox family of transcription factors bind DNA by making nearly identical major groove contacts via the recognition helices of their homeodomains. In vivo specificity, however, often depends on extended and unstructured regions that link Hox homeodomains to a DNA-bound cofactor, Extradenticle (Exd). Using a combination of structure determination, computational analysis, and in vitro and in vivo assays, we show that Hox proteins recognize specific Hox-Exd binding sites via <scene name='Group:USC-LCHS/2r5z_his-12arg3arg5_closeup/3'>residues located in these extended regions that insert into the minor groove</scene> insert into the minor groove but only when presented with the correct DNA sequence. Our results suggest that these residues, which are conserved in a paralog-specific manner, confer specificity by recognizing a sequence-dependent DNA structure instead of directly reading a specific DNA sequence.

Remo Rohs: /* Example: Hoogsteen base pairs modulate shape of p53-DNA binding site */

Remo Rohs — Wed, 20 Jul 2011 03:42:09 GMT

Example: Hoogsteen base pairs modulate shape of p53-DNA binding site

←Older revision		Revision as of 03:42, 20 July 2011
Line 17:		Line 17:
	==Example: Hoogsteen base pairs modulate shape of p53-DNA binding site==		==Example: Hoogsteen base pairs modulate shape of p53-DNA binding site==
	{{Clear}}		{{Clear}}
-	<StructureSection load='3kz8_BioFromPDB2.pdb' size='500' side='left' caption='p53 binds as a tetramer to DNA targets (Biological Assembly of PDB entry [[3kz8]])' scene='Group:USC-LCHS/3kz8_ba_initialscene/2'>	+	<StructureSection load='3kz8_BioFromPDB2.pdb' size='500' side='left' caption='Tumor suppressor p53 binds as a tetramer to DNA targets (Biological Assembly of PDB entry [[3kz8]])' scene='Group:USC-LCHS/3kz8_ba_initialscene/2'>
	<!-- Publication Abstract from PubMed -->		<!-- Publication Abstract from PubMed -->
	p53 binds as a tetramer to DNA targets consisting of two decameric half-sites separated by a variable spacer. Here we present high-resolution crystal structures of complexes between p53 core-domain tetramers and DNA targets consisting of contiguous half-sites. In contrast to previously reported p53-DNA complexes that show <scene name='Group:USC-LCHS/3kmd_wcbp_closeup/1'>standard Watson-Crick base pairs</scene>, the newly reported structures show <scene name='Group:USC-LCHS/3kz8_ba_hoogsteen/1'>noncanonical Hoogsteen base-pairing geometry at the central A-T doublet of each half-site</scene>. Structural and computational analyses show that the <scene name='Group:USC-LCHS/3kz8_ba_hoogsteencloseup/2'>Hoogsteen geometry</scene> distinctly modulates the B-DNA helix in terms of local shape and electrostatic potential, which, together with the contiguous DNA configuration, results in enhanced protein-DNA and protein-protein interactions compared to noncontiguous half-sites. Our results suggest a mechanism relating spacer length to protein-DNA binding affinity. Our findings also expand the current understanding of protein-DNA recognition and establish the structural and chemical properties of <scene name='Group:USC-LCHS/3kz8_ba_hoogsteencloseup/2'>Hoogsteen base pairs</scene> as the basis for a novel mode of sequence readout.		p53 binds as a tetramer to DNA targets consisting of two decameric half-sites separated by a variable spacer. Here we present high-resolution crystal structures of complexes between p53 core-domain tetramers and DNA targets consisting of contiguous half-sites. In contrast to previously reported p53-DNA complexes that show <scene name='Group:USC-LCHS/3kmd_wcbp_closeup/1'>standard Watson-Crick base pairs</scene>, the newly reported structures show <scene name='Group:USC-LCHS/3kz8_ba_hoogsteen/1'>noncanonical Hoogsteen base-pairing geometry at the central A-T doublet of each half-site</scene>. Structural and computational analyses show that the <scene name='Group:USC-LCHS/3kz8_ba_hoogsteencloseup/2'>Hoogsteen geometry</scene> distinctly modulates the B-DNA helix in terms of local shape and electrostatic potential, which, together with the contiguous DNA configuration, results in enhanced protein-DNA and protein-protein interactions compared to noncontiguous half-sites. Our results suggest a mechanism relating spacer length to protein-DNA binding affinity. Our findings also expand the current understanding of protein-DNA recognition and establish the structural and chemical properties of <scene name='Group:USC-LCHS/3kz8_ba_hoogsteencloseup/2'>Hoogsteen base pairs</scene> as the basis for a novel mode of sequence readout.

Remo Rohs: /* Example: Readout of DNA minor groove shape is the molecular basis for Hox specificity */

Remo Rohs — Wed, 20 Jul 2011 03:41:07 GMT

Example: Readout of DNA minor groove shape is the molecular basis for Hox specificity

←Older revision		Revision as of 03:41, 20 July 2011
Line 6:		Line 6:

	==Example: Readout of DNA minor groove shape is the molecular basis for Hox specificity==		==Example: Readout of DNA minor groove shape is the molecular basis for Hox specificity==
-	<StructureSection load='2r5z' size='500' side='right' caption='Hox protein Scr ~~with~~ its ~~co-factor~~ Exd ~~recognizes~~ DNA (PDB entry [[2r5z]])' scene=''>	+	<StructureSection load='2r5z' size='500' side='right' caption='Hox protein Scr and its cofactor Exd bind to DNA target (PDB entry [[2r5z]])' scene=''>
	<!-- Publication Abstract from PubMed -->		<!-- Publication Abstract from PubMed -->
	The recognition of specific DNA-binding sites by transcription factors is a critical yet poorly understood step in the control of gene expression. Members of the Hox family of transcription factors bind DNA by making nearly identical major groove contacts via the recognition helices of their homeodomains. In vivo specificity, however, often depends on extended and unstructured regions that link Hox homeodomains to a DNA-bound cofactor, Extradenticle (Exd). Using a combination of structure determination, computational analysis, and in vitro and in vivo assays, we show that Hox proteins recognize specific Hox-Exd binding sites via <scene name='Group:USC-LCHS/2r5z_his-12arg3arg5_closeup/3'>residues located in these extended regions that insert into the minor groove</scene> insert into the minor groove but only when presented with the correct DNA sequence. Our results suggest that these residues, which are conserved in a paralog-specific manner, confer specificity by recognizing a sequence-dependent DNA structure instead of directly reading a specific DNA sequence.		The recognition of specific DNA-binding sites by transcription factors is a critical yet poorly understood step in the control of gene expression. Members of the Hox family of transcription factors bind DNA by making nearly identical major groove contacts via the recognition helices of their homeodomains. In vivo specificity, however, often depends on extended and unstructured regions that link Hox homeodomains to a DNA-bound cofactor, Extradenticle (Exd). Using a combination of structure determination, computational analysis, and in vitro and in vivo assays, we show that Hox proteins recognize specific Hox-Exd binding sites via <scene name='Group:USC-LCHS/2r5z_his-12arg3arg5_closeup/3'>residues located in these extended regions that insert into the minor groove</scene> insert into the minor groove but only when presented with the correct DNA sequence. Our results suggest that these residues, which are conserved in a paralog-specific manner, confer specificity by recognizing a sequence-dependent DNA structure instead of directly reading a specific DNA sequence.