Lac repressor morph methods

From Proteopedia

This page describes the methods used to create the morph displayed at:

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 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 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 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 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 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

The interpolation for the morph is linear. No corrections were done to make interatomic distances or angles be 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 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.

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.^[1] 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

In the nonspecific interaction, Kalodimos et al.^[1] 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 within ProteinExplorer.Org by Eric Martz, who adapted them to this Proteopedia page.

References

1. ↑ ^{1.0 1.1} 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. PubMed 15256668