Lac repressor morph methods: Difference between revisions

(5 intermediate revisions by the same user not shown)

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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]]

* [[Morphs]]

</big><br>

==Methods==

===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 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 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===

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Line 24:

===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==

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==

Lac repressor morph methods: Difference between revisions

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@@ Line 1: / Line 1: @@
-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]]
 * [[Morphs]]
+</big><br>
 ==Methods==
 ===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 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 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===
@@ Line 23: / Line 24: @@
 ===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==
-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 />