PDIviz: analysis and visualization of protein–DNA binding interfaces

Abstract

Summary: Specific recognition of DNA by proteins is a crucial step of many biological processes. PDIviz is a plugin for the PyMOL molecular visualization system that analyzes protein–DNA binding interfaces by comparing the solvent accessible surface area of the complex against the free protein and free DNA. The plugin provides three distinct three-dimensional visualization modes to highlight interactions with DNA bases and backbone, major and minor groove, and with atoms of different pharmacophoric type (hydrogen bond donors/acceptors, hydrophobic and thymine methyl). Each mode comes in three styles to focus the visual analysis on the protein or DNA side of the interface, or on the nucleotide sequence. PDIviz allows for the generation of publication quality images, all calculated data can be written to disk, and a command line interface is provided for automating tasks. The plugin may be helpful for the detailed identification of regions involved in DNA base and shape readout, and can be particularly useful in rapidly pinpointing the overall mode of interaction.Availability and implementation: Freely available at http://melolab.org/pdiviz/ as a PyMOL plugin. Tested with incentive, educational, and open source versions of PyMOL on Windows, Mac and Linux systems.Contact: aschueller@bio.puc.clSupplementary Information: Supplementary data are available at Bioinformatics online.

Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions

“…For aligning and comparing the profiles with the respective profiles for FOXO1, FOXI1 and ETS members we matched HT-SELEX k-mers to the respective composite k-mers reported for FOXO1 and ELK3 (ETS1 paralog), using the individual core motif for alignment, respectively. FOXO1:ETS1 crystal structure is visualized in PyMOL 62 from PDB ID:4LG0 24 , and enhanced with the PDIviz software 63 . Conservation of positive charge in the ETS1 residue 409 is calculated from the Pfam ID PF00178 (Ets-domain).…”

“…ETS1 residue R409 interacting with DNA minor groove is highlighted in a red box (PDB ID: 4LG0). Visualization was enhanced using PDIViz 63 . f Dissociation constant measurements using ITC for FOXO1 binding to ω DNA sequence upon addition of ETS1 wild type and selected mutants (Asterisk (*) indicate adjusted p-values obtained using two sided t-test).…”

Crystal structure of an engineered, HIV-specific recombinase for removal of integrated proviral DNA

“…Figures of molecular structures were made using PyMOL (The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, Limited Liability Company). Figures of protein–DNA interaction surface areas were calculated using the PyMol plugin PDVis1.2 ( 30 ). Superpositions of structures were performed using the program ALIGN within PyMOL, SSM and LSQ within Coot.…”

Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein

“…Whereas in TtgV, the N-terminal domains bind only to one face of the DNA, in TrmBL2, owing to their staggered arrangement; they make a larger fraction of the DNA inaccessible to macromolecules. On the other hand, the 19-bp dsDNA in the TrmBL2 complex is more accessible to small solvent molecules than the 42-bp dsDNA in the TtgV complex as in both complexes calculations [21] show that 20% of the DNA is inaccessible to water. This is quite in agreement with the fact that TtgV is a specific binder and therefore contacts the DNA more intimately than TrmBL2, which is a nonspecific binder and forms very few contacts with the DNA bases.…”