1d42 - Revision history

OCA at 11:42, 22 November 2023

OCA — Wed, 22 Nov 2023 11:42:43 GMT

←Older revision		Revision as of 11:42, 22 November 2023
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	==SOLUTION STRUCTURE OF [D(GTATATAC)]2 VIA RESTRAINED MOLECULAR DYNAMICS SIMULATIONS WITH NUCLEAR MAGNETIC RESONANCE CONSTRAINTS DERIVED FROM RELAXATION MATRIX ANALYSIS OF TWO-DIMENSIONAL NUCLEAR OVERHAUSER EFFECT EXPERIMENTS==		==SOLUTION STRUCTURE OF [D(GTATATAC)]2 VIA RESTRAINED MOLECULAR DYNAMICS SIMULATIONS WITH NUCLEAR MAGNETIC RESONANCE CONSTRAINTS DERIVED FROM RELAXATION MATRIX ANALYSIS OF TWO-DIMENSIONAL NUCLEAR OVERHAUSER EFFECT EXPERIMENTS==
-	<StructureSection load='1d42' size='340' side='right'caption='[[1d42~~]], [[NMR_Ensembles_of_Models \| 5 NMR models~~]]' scene=''>	+	<StructureSection load='1d42' size='340' side='right'caption='[[1d42]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1d42]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D42 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1d42]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D42 FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d42 OCA], [https://pdbe.org/1d42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d42 RCSB], [https://www.ebi.ac.uk/pdbsum/1d42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d42 ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d42 OCA], [https://pdbe.org/1d42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d42 RCSB], [https://www.ebi.ac.uk/pdbsum/1d42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d42 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: James~~, T L~~]]	+	[[Category: James TL]]
-	[[Category: Schmitz, U]]	+	[[Category: Schmitz U]]
-	~~[[Category: Dna~~]]	+

OCA at 18:18, 10 March 2021

OCA — Wed, 10 Mar 2021 18:18:27 GMT

←Older revision		Revision as of 18:18, 10 March 2021
Line 3:		Line 3:
	<StructureSection load='1d42' size='340' side='right'caption='[[1d42]], [[NMR_Ensembles_of_Models \| 5 NMR models]]' scene=''>		<StructureSection load='1d42' size='340' side='right'caption='[[1d42]], [[NMR_Ensembles_of_Models \| 5 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1d42]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D42 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1D42 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1d42]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D42 FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1d42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d42 OCA], [~~http~~://pdbe.org/1d42 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1d42 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1d42 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1d42 ProSAT]</span></td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d42 OCA], [https://pdbe.org/1d42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d42 RCSB], [https://www.ebi.ac.uk/pdbsum/1d42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d42 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:37, 5 June 2019

OCA — Wed, 05 Jun 2019 23:37:05 GMT

←Older revision		Revision as of 23:37, 5 June 2019
Line 1:		Line 1:

	==SOLUTION STRUCTURE OF [D(GTATATAC)]2 VIA RESTRAINED MOLECULAR DYNAMICS SIMULATIONS WITH NUCLEAR MAGNETIC RESONANCE CONSTRAINTS DERIVED FROM RELAXATION MATRIX ANALYSIS OF TWO-DIMENSIONAL NUCLEAR OVERHAUSER EFFECT EXPERIMENTS==		==SOLUTION STRUCTURE OF [D(GTATATAC)]2 VIA RESTRAINED MOLECULAR DYNAMICS SIMULATIONS WITH NUCLEAR MAGNETIC RESONANCE CONSTRAINTS DERIVED FROM RELAXATION MATRIX ANALYSIS OF TWO-DIMENSIONAL NUCLEAR OVERHAUSER EFFECT EXPERIMENTS==
-	<StructureSection load='1d42' size='340' side='right' caption='[[1d42]], [[NMR_Ensembles_of_Models \| 5 NMR models]]' scene=''>	+	<StructureSection load='1d42' size='340' side='right'caption='[[1d42]], [[NMR_Ensembles_of_Models \| 5 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1d42]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D42 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1d42]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D42 FirstGlance]. <br>
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: James, T L]]		[[Category: James, T L]]
	[[Category: Schmitz, U]]		[[Category: Schmitz, U]]
	[[Category: Dna]]		[[Category: Dna]]

OCA at 04:09, 30 August 2017

OCA — Wed, 30 Aug 2017 04:09:25 GMT

←Older revision		Revision as of 04:09, 30 August 2017
Line 1:		Line 1:
		+
	==SOLUTION STRUCTURE OF [D(GTATATAC)]2 VIA RESTRAINED MOLECULAR DYNAMICS SIMULATIONS WITH NUCLEAR MAGNETIC RESONANCE CONSTRAINTS DERIVED FROM RELAXATION MATRIX ANALYSIS OF TWO-DIMENSIONAL NUCLEAR OVERHAUSER EFFECT EXPERIMENTS==		==SOLUTION STRUCTURE OF [D(GTATATAC)]2 VIA RESTRAINED MOLECULAR DYNAMICS SIMULATIONS WITH NUCLEAR MAGNETIC RESONANCE CONSTRAINTS DERIVED FROM RELAXATION MATRIX ANALYSIS OF TWO-DIMENSIONAL NUCLEAR OVERHAUSER EFFECT EXPERIMENTS==
	<StructureSection load='1d42' size='340' side='right' caption='[[1d42]], [[NMR_Ensembles_of_Models \| 5 NMR models]]' scene=''>		<StructureSection load='1d42' size='340' side='right' caption='[[1d42]], [[NMR_Ensembles_of_Models \| 5 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1d42]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D42 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1d42]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D42 FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d42 OCA], [http://pdbe.org/1d42 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d42 RCSB], [http://www.ebi.ac.uk/pdbsum/1d42 PDBsum]</span></td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d42 OCA], [http://pdbe.org/1d42 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d42 RCSB], [http://www.ebi.ac.uk/pdbsum/1d42 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1d42 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:27, 10 September 2015

OCA — Thu, 10 Sep 2015 08:27:37 GMT

←Older revision		Revision as of 08:27, 10 September 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1d42]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D42 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1d42]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D42 FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d42 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d42 RCSB], [http://www.ebi.ac.uk/pdbsum/1d42 PDBsum]</span></td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d42 OCA], [http://pdbe.org/1d42 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d42 RCSB], [http://www.ebi.ac.uk/pdbsum/1d42 PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 13:		Line 13:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1d42" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:30, 22 December 2014

OCA — Mon, 22 Dec 2014 23:30:45 GMT

←Older revision		Revision as of 23:30, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1d42]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D42 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1d42]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D42 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d42 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d42 RCSB], [http://www.ebi.ac.uk/pdbsum/1d42 PDBsum]</span></td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d42 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d42 RCSB], [http://www.ebi.ac.uk/pdbsum/1d42 PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: James, T L.]]	+	[[Category: James, T L]]
-	[[Category: Schmitz, U.]]	+	[[Category: Schmitz, U]]
	[[Category: Dna]]		[[Category: Dna]]

OCA at 09:17, 27 August 2014

OCA — Wed, 27 Aug 2014 09:17:54 GMT

←Older revision		Revision as of 09:17, 27 August 2014
Line 1:		Line 1:
-	[[~~Image~~:1d42.~~png\|left\|200px~~]]	+	==SOLUTION STRUCTURE OF [D(GTATATAC)]2 VIA RESTRAINED MOLECULAR DYNAMICS SIMULATIONS WITH NUCLEAR MAGNETIC RESONANCE CONSTRAINTS DERIVED FROM RELAXATION MATRIX ANALYSIS OF TWO-DIMENSIONAL NUCLEAR OVERHAUSER EFFECT EXPERIMENTS==
		+	<StructureSection load='1d42' size='340' side='right' caption='[[1d42]], [[NMR_Ensembles_of_Models \| 5 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1d42]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D42 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d42 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d42 RCSB], [http://www.ebi.ac.uk/pdbsum/1d42 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Two-dimensional nuclear Overhauser effect (2D NOE) spectra have been used as the experimental basis for determining the solution structure of the duplex [d(GTATATAC)]2 employing restrained molecular dynamics (rMD) simulations. The MARDIGRAS algorithm has been employed to construct a set of 233 interproton distance constraints via iterative complete relaxation matrix analysis utilizing the peak intensities from the 2D NOE spectra obtained for different mixing times and model structures. The upper and lower bounds for each of the constraints, defining size of a flat-well potential function term used in the rMD simulations, were conservatively chosen as the largest or smallest value calculated by MARDIGRAS. Three different starting models were utilized in several rMD calculations: energy-minimized A-DNA, B-DNA, and a structure containing wrinkled D-DNA in the interior. Considerable effort was made to define the appropriate force constants to be employed with the NOE terms in the AMBER force field, using as criteria the average constraints deviation, the constraints violation energy and the total energy. Of the 233 constraints, one was generated indirectly, but proved to be crucial in defining the structure: the cross-strand A5-H2 A5-H2 distance. As those two protons resonate isochronously for the self-complementary duplex, the distance cannot be determined directly. However, the general pattern of 2D NOE peak intensities, spin-lattice relaxation time (T1) values, and 31P nuclear magnetic resonance spectra lead to use of the A3-H2 A7-H2 distance for A5-H2 A5-H2 as well. Five rMD runs, with different random number seeds, were made for each of the three starting structures with the full distance constraint set. The average structure from all 15 runs and the five-structure averages from each starting structure were all quite similar. Two rMD runs for each starting structure were made with the A5-H2 A5-H2 constraint missing. The average of these six rMD runs revealed differences in structure, compared to that with the full set of constraints, primarily for the middle two base-pairs involving the missing cross-strand constraint but global deviations also were found. Conformational analysis of the resulting structures revealed that the inner four to six base-pairs differed in structure from the termini. Furthermore, an alternating structure was suggested with features alternating for the A-T and T-A steps.

-	~~{{STRUCTURE_1d42\| PDB=1d42 \| SCENE= }}~~	+	Solution structure of [d(GTATATAC)]2 via restrained molecular dynamics simulations with nuclear magnetic resonance constraints derived from relaxation matrix analysis of two-dimensional nuclear Overhauser effect experiments.,Schmitz U, Pearlman DA, James TL J Mol Biol. 1991 Sep 5;221(1):271-92. PMID:1920410<ref>PMID:1920410</ref>

-	===SOLUTION STRUCTURE OF [D(GTATATAC)]2 VIA RESTRAINED MOLECULAR DYNAMICS SIMULATIONS WITH NUCLEAR MAGNETIC RESONANCE CONSTRAINTS DERIVED FROM RELAXATION MATRIX ANALYSIS OF TWO-DIMENSIONAL NUCLEAR OVERHAUSER EFFECT EXPERIMENTS===	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_1920410}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[1d42]] is a 2 chain structure. Full experimental information is available from [http:~~//~~oca.weizmann.ac.il/oca-bin/ocashort?id=1D42 OCA].~~	+	</StructureSection>
	[[Category: James, T L.]]		[[Category: James, T L.]]
	[[Category: Schmitz, U.]]		[[Category: Schmitz, U.]]
	[[Category: Dna]]		[[Category: Dna]]

OCA: Protected "1d42" [edit=sysop:move=sysop]

OCA — Sun, 21 Oct 2012 20:12:06 GMT

Protected "1d42" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:12, 21 October 2012

OCA at 20:12, 21 October 2012

OCA — Sun, 21 Oct 2012 20:12:03 GMT

←Older revision		Revision as of 20:12, 21 October 2012
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-	{{Seed}}
	[[Image:1d42.png\|left\|200px]]		[[Image:1d42.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1d42", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1d42\| PDB=1d42 \| SCENE= }}		{{STRUCTURE_1d42\| PDB=1d42 \| SCENE= }}

	===SOLUTION STRUCTURE OF [D(GTATATAC)]2 VIA RESTRAINED MOLECULAR DYNAMICS SIMULATIONS WITH NUCLEAR MAGNETIC RESONANCE CONSTRAINTS DERIVED FROM RELAXATION MATRIX ANALYSIS OF TWO-DIMENSIONAL NUCLEAR OVERHAUSER EFFECT EXPERIMENTS===		===SOLUTION STRUCTURE OF [D(GTATATAC)]2 VIA RESTRAINED MOLECULAR DYNAMICS SIMULATIONS WITH NUCLEAR MAGNETIC RESONANCE CONSTRAINTS DERIVED FROM RELAXATION MATRIX ANALYSIS OF TWO-DIMENSIONAL NUCLEAR OVERHAUSER EFFECT EXPERIMENTS===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_1920410}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 1920410 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_1920410}}		{{ABSTRACT_PUBMED_1920410}}

	==About this Structure==		==About this Structure==
-	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D42 OCA].	+	[[1d42]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D42 OCA].
-		+
-	~~==Reference==~~	+
-	Solution structure of [d(GTATATAC)]2 via restrained molecular dynamics simulations with nuclear magnetic resonance constraints derived from relaxation matrix analysis of two-dimensional nuclear Overhauser effect experiments., Schmitz U, Pearlman DA, James TL, J Mol Biol. 1991 Sep 5;221(1):271-92. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1920410 1920410]	+
	[[Category: James, T L.]]		[[Category: James, T L.]]
	[[Category: Schmitz, U.]]		[[Category: Schmitz, U.]]
	[[Category: Dna]]		[[Category: Dna]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 22:22:13 2008''

OCA at 19:22, 30 June 2008

OCA — Mon, 30 Jun 2008 19:22:20 GMT

←Older revision		Revision as of 19:22, 30 June 2008
Line 1:		Line 1:
-	[[Image:1d42.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1d42.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_1d42\| PDB=1d42 \| SCENE= }}		{{STRUCTURE_1d42\| PDB=1d42 \| SCENE= }}

-	~~'''~~SOLUTION STRUCTURE OF [D(GTATATAC)]2 VIA RESTRAINED MOLECULAR DYNAMICS SIMULATIONS WITH NUCLEAR MAGNETIC RESONANCE CONSTRAINTS DERIVED FROM RELAXATION MATRIX ANALYSIS OF TWO-DIMENSIONAL NUCLEAR OVERHAUSER EFFECT EXPERIMENTS~~'''~~	+	===SOLUTION STRUCTURE OF [D(GTATATAC)]2 VIA RESTRAINED MOLECULAR DYNAMICS SIMULATIONS WITH NUCLEAR MAGNETIC RESONANCE CONSTRAINTS DERIVED FROM RELAXATION MATRIX ANALYSIS OF TWO-DIMENSIONAL NUCLEAR OVERHAUSER EFFECT EXPERIMENTS===


-	~~==Overview==~~	+	<!--
-	Two-dimensional nuclear Overhauser effect (2D NOE) spectra have been used as the experimental basis for determining the solution structure of the duplex [d(GTATATAC)]2 employing restrained molecular dynamics (rMD) simulations. The MARDIGRAS algorithm has been employed to construct a set of 233 interproton distance constraints via iterative complete relaxation matrix analysis utilizing the peak intensities from the 2D NOE spectra obtained for different mixing times and model structures. The upper and lower bounds for each of the constraints, ~~defining size of a flat-well potential function term used in the rMD simulations~~, ~~were conservatively chosen as~~ the largest or smallest value calculated by MARDIGRAS. Three different starting models were utilized in several rMD calculations: energy-minimized A-DNA, B-DNA, and a structure containing wrinkled D-DNA in the interior. Considerable effort was made to ~~define~~ the ~~appropriate force constants to be employed with the NOE terms in the AMBER force field, using~~ as criteria the average constraints deviation, the constraints violation energy and the total energy. Of the 233 constraints, one was generated indirectly, but proved to be crucial in defining the structure: ~~the cross-strand A5-H2 A5-H2 distance~~. ~~As those two protons resonate isochronously for the self-complementary duplex, the distance cannot be determined directly~~. ~~However, the general pattern of 2D NOE peak intensities, spin-lattice relaxation time (T1~~) ~~values~~, ~~and 31P nuclear magnetic resonance spectra lead to use of~~ the ~~A3-H2 A7-H2 distance for A5-H2 A5-H2 as well. Five rMD runs, with different random~~ number ~~seeds, were made for each of the three starting structures with the full distance constraint set~~. ~~The average structure from all 15 runs and the five~~-~~structure averages from each starting structure were all quite similar. Two rMD runs for each starting structure were made with the A5~~-H2 A5-H2 constraint missing. The average of these six rMD runs revealed differences in structure, compared to that with the full set of constraints, primarily for the middle two base-pairs involving the missing cross-strand constraint but global deviations also were found. Conformational analysis of the resulting structures revealed that the inner four to six base-pairs differed in structure from the termini. Furthermore, an alternating structure was suggested with features alternating for the A-T and T-A steps.	+	The line below this paragraph, {{ABSTRACT_PUBMED_1920410}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 1920410 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_1920410}}

	==About this Structure==		==About this Structure==
-	Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D42 OCA].	+	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D42 OCA].

	==Reference==		==Reference==
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	[[Category: Schmitz, U.]]		[[Category: Schmitz, U.]]
	[[Category: Dna]]		[[Category: Dna]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri May 2 13~~:25:53 2008''	+
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