Lac repressor morph methods: Difference between revisions
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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=== | ||