Description of protein-DNA complexes in terms of electron-density topological features.
This paper presents a computer-modelling approach for the generation of low-resolution representations of two protein-DNA complexes, NF-kappaB and HIF-1. The representation is obtained by topological analysis of electron-density maps at 2.85 A crystallographic resolution, which leads to a set containing a limited number of critical points (CP). Analyses of the structure and properties of the CP graphs (density at peak position, volume and ellipticity), as well as comparisons with other reduced representations, are performed in order to assess the usefulness of such representations in molecular-docking applications at medium resolution.
Becue
Andy
A
Laboratoire de Physico-Chimie Informatique, Facultés Universitaires Notre-Dame de la Paix, Rue de Bruxelles 61, B-5000 Namur, Belgium.
Meurice
Nathalie
N
Leherte
Laurence
L
Vercauteren
Daniel P
DP
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D019281:Dimerization; D051793:Hypoxia-Inducible Factor 1; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016328:NF-kappa B / Q000737:chemistry*; D009687:Nuclear Proteins / Q000737:chemistry*; D009705:Nucleosides / Q000737:chemistry; D009711:Nucleotides / Q000737:chemistry; D021122:Protein Subunits; D055672:Static Electricity; D014157:Transcription Factors
D000596:Amino Acids; D004268:DNA-Binding Proteins; D051793:Hypoxia-Inducible Factor 1; D016328:NF-kappa B; D009687:Nuclear Proteins; D009705:Nucleosides; D009711:Nucleotides; D021122:Protein Subunits; D014157:Transcription Factors; D004247:DNA