Lac repressor morph methods - Revision history

Eric Martz: /* DNA sequence and alignment */

Eric Martz — Sat, 19 Mar 2011 21:22:16 GMT

DNA sequence and alignment

←Older revision		Revision as of 21:22, 19 March 2011
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	The morph is a linear interpolation of atomic coordinates. The empirical start and finish models are taken from ensembles obtained by NMR. The animation begins with model 9 of [[1osl]], and ends with model 14 of [[1l1m]]. '''Model 14''' of 1L1M was chosen because it is the most representative (according to [http://www.ebi.ac.uk/msd-srv/olderado/ Olderado]). '''Model 9''' of 1OSL was chosen because the flexible carboxy termini are in the vicinity of those in 1L1M. The final morph PDB file is available within Proteopedia as [[Image:1osl_19_1l1m_9_morph.pdb]].		The morph is a linear interpolation of atomic coordinates. The empirical start and finish models are taken from ensembles obtained by NMR. The animation begins with model 9 of [[1osl]], and ends with model 14 of [[1l1m]]. '''Model 14''' of 1L1M was chosen because it is the most representative (according to [http://www.ebi.ac.uk/msd-srv/olderado/ Olderado]). '''Model 9''' of 1OSL was chosen because the flexible carboxy termini are in the vicinity of those in 1L1M. The final morph PDB file is available within Proteopedia as [[Image:1osl_19_1l1m_9_morph.pdb]].

-	===DNA sequence and alignment===	+	===DNA sequence and structural alignment===

	The straight, near-B-form nonspecific 18-mer DNA in 1OSL model 9 was replaced with a straight B-form model of the specific 23-mer DNA sequence in 1LIM (GAATT GTGAG CGGAT AACAA TTT). This theoretical model was generated by Model It (see instructions at [http://molvisindex.org molvisindex.org] under Molecules, Sources of PDB Files, under DNA Tools). (Some of the hydrogen atom names in the PDB file generated by Model It were misaligned so that [[Swiss-PDBViewer_%3D_DeepView\|DeepView]] did not include them; these were corrected with a text editor by shifting one character position to the right.) The specific DNA model was [[Structural alignment tools\|structurally aligned]] to the nonspecific DNA in 1OSL at three points (phosphorus atoms) using DeepView's "Fit molecules from selection". The alignment points were chosen by inspection of 1OSL model 9 to represent contacts of the DNA backbone with the protein. Both T3's of 1OSL were aligned with both T4's in the theoretical model, and one T11 with A14. The RMS deviation was 1.57 Ångstroms for the three phosphorus atom pairs, and 7.22 Å for 18 phosphorus atom pairs. (Better alignments were possible but were not explored further.)		The straight, near-B-form nonspecific 18-mer DNA in 1OSL model 9 was replaced with a straight B-form model of the specific 23-mer DNA sequence in 1LIM (GAATT GTGAG CGGAT AACAA TTT). This theoretical model was generated by Model It (see instructions at [http://molvisindex.org molvisindex.org] under Molecules, Sources of PDB Files, under DNA Tools). (Some of the hydrogen atom names in the PDB file generated by Model It were misaligned so that [[Swiss-PDBViewer_%3D_DeepView\|DeepView]] did not include them; these were corrected with a text editor by shifting one character position to the right.) The specific DNA model was [[Structural alignment tools\|structurally aligned]] to the nonspecific DNA in 1OSL at three points (phosphorus atoms) using DeepView's "Fit molecules from selection". The alignment points were chosen by inspection of 1OSL model 9 to represent contacts of the DNA backbone with the protein. Both T3's of 1OSL were aligned with both T4's in the theoretical model, and one T11 with A14. The RMS deviation was 1.57 Ångstroms for the three phosphorus atom pairs, and 7.22 Å for 18 phosphorus atom pairs. (Better alignments were possible but were not explored further.)

Eric Martz: /* DNA sequence and alignment */

Eric Martz — Sat, 19 Mar 2011 21:01:13 GMT

DNA sequence and alignment

←Older revision		Revision as of 21:01, 19 March 2011
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	===DNA sequence and alignment===		===DNA sequence and alignment===

-	The straight, near-B-form nonspecific 18-mer DNA in 1OSL model 9 was replaced with a straight B-form model of the specific 23-mer DNA sequence in 1LIM (GAATT GTGAG CGGAT AACAA TTT). This theoretical model was generated by Model It (see instructions at [http://molvisindex.org molvisindex.org] under Molecules, Sources of PDB Files, under DNA Tools). (Some of the hydrogen atom names in the PDB file generated by Model It were misaligned so that [[Swiss-PDBViewer_%3D_DeepView\|DeepView]] did not include them; these were corrected with a text editor by shifting one character position to the right.) The specific DNA model was aligned to the nonspecific DNA in 1OSL at three points (phosphorus atoms) using DeepView's "Fit molecules from selection". The alignment points were chosen by inspection of 1OSL model 9 to represent contacts of the DNA backbone with the protein. Both T3's of 1OSL were aligned with both T4's in the theoretical model, and one T11 with A14. The RMS deviation was 1.57 Ångstroms for the three phosphorus atom pairs, and 7.22 Å for 18 phosphorus atom pairs. (Better alignments were possible but were not explored further.)	+	The straight, near-B-form nonspecific 18-mer DNA in 1OSL model 9 was replaced with a straight B-form model of the specific 23-mer DNA sequence in 1LIM (GAATT GTGAG CGGAT AACAA TTT). This theoretical model was generated by Model It (see instructions at [http://molvisindex.org molvisindex.org] under Molecules, Sources of PDB Files, under DNA Tools). (Some of the hydrogen atom names in the PDB file generated by Model It were misaligned so that [[Swiss-PDBViewer_%3D_DeepView\|DeepView]] did not include them; these were corrected with a text editor by shifting one character position to the right.) The specific DNA model was [[Structural alignment tools\|structurally aligned]] to the nonspecific DNA in 1OSL at three points (phosphorus atoms) using DeepView's "Fit molecules from selection". The alignment points were chosen by inspection of 1OSL model 9 to represent contacts of the DNA backbone with the protein. Both T3's of 1OSL were aligned with both T4's in the theoretical model, and one T11 with A14. The RMS deviation was 1.57 Ångstroms for the three phosphorus atom pairs, and 7.22 Å for 18 phosphorus atom pairs. (Better alignments were possible but were not explored further.)

	===Linear Interpolation===		===Linear Interpolation===

Eric Martz: /* Overview */ polishing

Eric Martz — Thu, 16 Oct 2008 21:15:20 GMT

Overview - polishing

←Older revision		Revision as of 21:15, 16 October 2008
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	===Overview===		===Overview===

-	The morph is a linear interpolation of atomic coordinates. The empirical start and finish models are taken from ensembles obtained by NMR. The animation begins with model 9 of [[1osl]], and ends with model 14 of [[1l1m]]. '''Model 14''' of 1L1M was chosen because it is the most representative (according to [http://www.ebi.ac.uk/msd-srv/olderado/ Olderado]). '''Model 9''' of 1OSL was chosen because the flexible carboxy termini are in the vicinity of those in 1L1M.	+	The morph is a linear interpolation of atomic coordinates. The empirical start and finish models are taken from ensembles obtained by NMR. The animation begins with model 9 of [[1osl]], and ends with model 14 of [[1l1m]]. '''Model 14''' of 1L1M was chosen because it is the most representative (according to [http://www.ebi.ac.uk/msd-srv/olderado/ Olderado]). '''Model 9''' of 1OSL was chosen because the flexible carboxy termini are in the vicinity of those in 1L1M. The final morph PDB file is available within Proteopedia as [[Image:1osl_19_1l1m_9_morph.pdb]].

	===DNA sequence and alignment===		===DNA sequence and alignment===

Eric Martz: polishing

Eric Martz — Thu, 16 Oct 2008 21:11:27 GMT

polishing

←Older revision		Revision as of 21:11, 16 October 2008
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-	This page describes the methods used to create the morph displayed at:	+	<big>This page describes the methods used to create the morph displayed at:

	* [[Lac repressor#Morph of Conversion]]		* [[Lac repressor#Morph of Conversion]]
	* [[Morphs]]		* [[Morphs]]

		+	</big><br>
	==Methods==		==Methods==

Eric Martz: /* Content Attribution */ polishing

Eric Martz — Thu, 16 Oct 2008 21:10:36 GMT

Content Attribution - polishing

←Older revision		Revision as of 21:10, 16 October 2008
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	==Content Attribution==		==Content Attribution==
-	The methods on this page were first described in 2004 on the original [Lac Repressor Binding to DNA] page by [[User:Eric Martz\|Eric Martz]], who adapted them to this Proteopedia page.	+	The methods on this page were first described in 2004 on the original [http://atlas.proteinexplorer.org/morphs/lacrep Lac Repressor Binding to DNA] page within [http://proteinexplorer.org ProteinExplorer.Org] by [[User:Eric Martz\|Eric Martz]], who adapted them to this Proteopedia page.

	==References==		==References==
	<references />		<references />

Eric Martz: /* Salt Bridges */ polishing

Eric Martz — Thu, 16 Oct 2008 21:09:07 GMT

Salt Bridges - polishing

←Older revision		Revision as of 21:09, 16 October 2008
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	===Salt Bridges===		===Salt Bridges===
-	In the nonspecific interaction, Kalodimos et al. report salt bridges to the DNA backbone phosphates involving Arg22, Arg35, Lys33, Lys37, and His29. In model 9 of 1OSL, the only two of these I could see were Arg22B.NH1 3.0 Å from A3D.O2P, and His29B.ND1 2.8 Å from G2D.O2P. Therefore I did not make an animation showing the nonspecific salt bridges. Presumably the salt bridges are more prominent in NMR models other than 9, but I did not explore this.	+	In the nonspecific interaction, Kalodimos et al.<ref name='kalodimos' /> report salt bridges to the DNA backbone phosphates involving Arg22, Arg35, Lys33, Lys37, and His29. In model 9 of 1OSL, the only two of these I could see were Arg22B.NH1 3.0 Å from A3D.O2P, and His29B.ND1 2.8 Å from G2D.O2P. Therefore I did not make an animation showing the nonspecific salt bridges. Presumably the salt bridges are more prominent in NMR models other than 9, but I did not explore this.

	==Content Attribution==		==Content Attribution==

Eric Martz: /* Hydrogen Bonds */ polishing

Eric Martz — Thu, 16 Oct 2008 21:08:43 GMT

Hydrogen Bonds - polishing

←Older revision		Revision as of 21:08, 16 October 2008
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	===Hydrogen Bonds===		===Hydrogen Bonds===
-	There are five hydrogen-bonded donor-acceptor pairs of atoms spacefilled in the "Specific contacts" animation: 1 pair in the minor groove, 2 pairs in the major groove for each protein chain. Three of these five pairs were selected from among those listed by Kalodimos ''et al.''<ref>Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Kalodimos CG, Biris N, Bonvin AM, Levandoski MM, Guennuegues M, Boelens R, Kaptein R. Science 305:386-9, 2004. [http://www.ncbi.nlm.nih.gov/pubmed/15256668 PubMed 15256668]</ref> in Fig. 2C after correcting the DNA sequence numbers in Fig. 2C to agree with those in 1L1M. All of these 3 hydrogen bonds involved protein chain A. The two hydrogen bonds shown for chain B involve the same donor-acceptor pairs on the other side of 1L1M, verified to be probable hydrogen bonds by inspection of interatomic distances.	+	There are five hydrogen-bonded donor-acceptor pairs of atoms spacefilled in the "Specific contacts" animation: 1 pair in the minor groove, 2 pairs in the major groove for each protein chain. Three of these five pairs were selected from among those listed by Kalodimos ''et al.''<ref name='kalodimos'>Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Kalodimos CG, Biris N, Bonvin AM, Levandoski MM, Guennuegues M, Boelens R, Kaptein R. Science 305:386-9, 2004. [http://www.ncbi.nlm.nih.gov/pubmed/15256668 PubMed 15256668]</ref> in Fig. 2C after correcting the DNA sequence numbers in Fig. 2C to agree with those in 1L1M. All of these 3 hydrogen bonds involved protein chain A. The two hydrogen bonds shown for chain B involve the same donor-acceptor pairs on the other side of 1L1M, verified to be probable hydrogen bonds by inspection of interatomic distances.

	===Salt Bridges===		===Salt Bridges===

Eric Martz: /* Hydrogen Bonds */ polishing

Eric Martz — Thu, 16 Oct 2008 21:08:09 GMT

Hydrogen Bonds - polishing

←Older revision		Revision as of 21:08, 16 October 2008
Line 20:		Line 20:

	===Hydrogen Bonds===		===Hydrogen Bonds===
-	There are five hydrogen-bonded donor-acceptor pairs of atoms spacefilled in the "Specific contacts" animation: 1 pair in the minor groove, 2 pairs in the major groove for each protein chain. Three of these five pairs were selected from among those listed by Kalodimos ''et al.''<ref>Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Kalodimos CG, Biris N, Bonvin AM, Levandoski MM, Guennuegues M, Boelens R, Kaptein R. Science 305:386-9, 2004. [http://www.ncbi.nlm.nih.gov/pubmed/15256668 PubMed 15256668]</ref> in Fig. 2C after correcting the DNA sequence numbers in Fig. 2C to agree with those in 1L1M. All of these 3 hydrogen bonds involved protein chain A. The two hydrogen bonds shown for chain B involve the same donor-acceptor pairs on the other side of 1L1M, verified to be ~~engaged in~~ hydrogen ~~bonding~~ by inspection.	+	There are five hydrogen-bonded donor-acceptor pairs of atoms spacefilled in the "Specific contacts" animation: 1 pair in the minor groove, 2 pairs in the major groove for each protein chain. Three of these five pairs were selected from among those listed by Kalodimos ''et al.''<ref>Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Kalodimos CG, Biris N, Bonvin AM, Levandoski MM, Guennuegues M, Boelens R, Kaptein R. Science 305:386-9, 2004. [http://www.ncbi.nlm.nih.gov/pubmed/15256668 PubMed 15256668]</ref> in Fig. 2C after correcting the DNA sequence numbers in Fig. 2C to agree with those in 1L1M. All of these 3 hydrogen bonds involved protein chain A. The two hydrogen bonds shown for chain B involve the same donor-acceptor pairs on the other side of 1L1M, verified to be probable hydrogen bonds by inspection of interatomic distances.

	===Salt Bridges===		===Salt Bridges===

Eric Martz: /* Hydrogen Bonds */ polishing

Eric Martz — Thu, 16 Oct 2008 21:07:08 GMT

Hydrogen Bonds - polishing

←Older revision		Revision as of 21:07, 16 October 2008
Line 20:		Line 20:

	===Hydrogen Bonds===		===Hydrogen Bonds===
-	There are five hydrogen-bonded donor-acceptor pairs of atoms spacefilled in the "Specific contacts" animation: 1 pair in the minor groove, 2 pairs in the major groove for each protein chain. Three of these five pairs were selected from among those listed by Kalodimos ''et al.''<ref>Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Kalodimos CG, Biris N, Bonvin AM, Levandoski MM, Guennuegues M, Boelens R, Kaptein R. Science 305:386-9, 2004. [http://www.ncbi.nlm.nih.gov/pubmed/15256668 PubMed 15256668]</ref> in Fig. 2C after correcting the DNA sequence numbers in Fig. 2C to agree with those in 1L1M. All of these 3 hydrogen bonds involved protein chain A. The two hydrogen bonds shown for chain B involve the same donor-acceptor pairs on the other side of 1L1M, verified to be engaged in hydrogen bonding by inspection. Visualization of the hydrogen atoms in these hydrogen bonds was crucial to confirm a hydrogen-bonded conformation, and required an enhancement to the "Contacts Controls" in Protein Explorer's QuickViews, a checkbox that displays hydrogen atoms for the contacting atoms (to be released in PE version 2.42).	+	There are five hydrogen-bonded donor-acceptor pairs of atoms spacefilled in the "Specific contacts" animation: 1 pair in the minor groove, 2 pairs in the major groove for each protein chain. Three of these five pairs were selected from among those listed by Kalodimos ''et al.''<ref>Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Kalodimos CG, Biris N, Bonvin AM, Levandoski MM, Guennuegues M, Boelens R, Kaptein R. Science 305:386-9, 2004. [http://www.ncbi.nlm.nih.gov/pubmed/15256668 PubMed 15256668]</ref> in Fig. 2C after correcting the DNA sequence numbers in Fig. 2C to agree with those in 1L1M. All of these 3 hydrogen bonds involved protein chain A. The two hydrogen bonds shown for chain B involve the same donor-acceptor pairs on the other side of 1L1M, verified to be engaged in hydrogen bonding by inspection.

		+	===Salt Bridges===
	In the nonspecific interaction, Kalodimos et al. report salt bridges to the DNA backbone phosphates involving Arg22, Arg35, Lys33, Lys37, and His29. In model 9 of 1OSL, the only two of these I could see were Arg22B.NH1 3.0 Å from A3D.O2P, and His29B.ND1 2.8 Å from G2D.O2P. Therefore I did not make an animation showing the nonspecific salt bridges. Presumably the salt bridges are more prominent in NMR models other than 9, but I did not explore this.		In the nonspecific interaction, Kalodimos et al. report salt bridges to the DNA backbone phosphates involving Arg22, Arg35, Lys33, Lys37, and His29. In model 9 of 1OSL, the only two of these I could see were Arg22B.NH1 3.0 Å from A3D.O2P, and His29B.ND1 2.8 Å from G2D.O2P. Therefore I did not make an animation showing the nonspecific salt bridges. Presumably the salt bridges are more prominent in NMR models other than 9, but I did not explore this.

Eric Martz: /* Linear Interpolation */ polishing

Eric Martz — Thu, 16 Oct 2008 21:04:54 GMT

Linear Interpolation - polishing

←Older revision		Revision as of 21:04, 16 October 2008
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	===Linear Interpolation===		===Linear Interpolation===
-	The [[Morphs\|interpolation for the morph]] is linear. No corrections were done to make interatomic distances or angles be [[Morphs\|chemically realistic]. Because Jmol assigns covalent bonds based on interatomic distances, and because some of these distances become unrealistically close during linear interpolation, spurious "bonds" appear and then disappear in some regions of the interpolated frames during wireframe animations of the morph. These appear as "wads" of bonds or "cobwebs".	+	The [[Morphs\|interpolation for the morph]] is linear. No corrections were done to make interatomic distances or angles be [[Morphs\|chemically realistic]]. Because Jmol assigns covalent bonds based on interatomic distances, and because some of these distances become unrealistically close during linear interpolation, spurious "bonds" appear and then disappear in some regions of the interpolated frames during wireframe animations of the morph. These appear as "wads" of bonds or "cobwebs".

	The interpolation was done with the [http://www.umass.edu/microbio/rasmol/pdbtools.htm freely available DOS program morph2.exe], inserting 10 (or in some cases 12) frames between the two empirical end points (after all hydrogens were removed with DOS program striph.exe). The resulting 12-model file was 1.6 megabytes, and was gzipped to 0.4 megabytes. For the morph showing specific contacts as hydrogen bonds, 8 carefully selected hydrogen atoms were re-inserted into the start and end models prior to doing the interpolation.		The interpolation was done with the [http://www.umass.edu/microbio/rasmol/pdbtools.htm freely available DOS program morph2.exe], inserting 10 (or in some cases 12) frames between the two empirical end points (after all hydrogens were removed with DOS program striph.exe). The resulting 12-model file was 1.6 megabytes, and was gzipped to 0.4 megabytes. For the morph showing specific contacts as hydrogen bonds, 8 carefully selected hydrogen atoms were re-inserted into the start and end models prior to doing the interpolation.