Advances in Human-Protein Interaction - Interactive and Immersive Molecular Simulations

International audienc

How Cations Can Assist DNase I in DNA Binding and Hydrolysis

DNase I requires Ca2+ and Mg2+ for hydrolyzing double-stranded DNA. However, the number and the location of DNase I ion-binding sites remain unclear, as well as the role of these counter-ions. Using molecular dynamics simulations, we show that bovine pancreatic (bp) DNase I contains four ion-binding pockets. Two of them strongly bind Ca2+ while the other two sites coordinate Mg2+. These theoretical results are strongly supported by revisiting crystallographic structures that contain bpDNase I. One Ca2+ stabilizes the functional DNase I structure. The presence of Mg2+ in close vicinity to the catalytic pocket of bpDNase I reinforces the idea of a cation-assisted hydrolytic mechanism. Importantly, Poisson-Boltzmann-type electrostatic potential calculations demonstrate that the divalent cations collectively control the electrostatic fit between bpDNase I and DNA. These results improve our understanding of the essential role of cations in the biological function of bpDNase I. The high degree of conservation of the amino acids involved in the identified cation-binding sites across DNase I and DNase I-like proteins from various species suggests that our findings generally apply to all DNase I-DNA interactions

Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments

Homologous recombination is a fundamental process enabling the repair of double-strand breaks with a high degree of fidelity. In prokaryotes, it is carried out by RecA nucleofilaments formed on single-stranded DNA (ssDNA). These filaments incorporate genomic sequences that are homologous to the ssDNA and exchange the homologous strands. Due to the highly dynamic character of this process and its rapid propagation along the filament, the sequence recognition and strand exchange mechanism remains unknown at the structural level. The recently published structure of the RecA/DNA filament active for recombination (Chen et al., Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structure, Nature 2008, 453, 489) provides a starting point for new exploration of the system. Here, we investigate the possible geometries of association of the early encounter complex between RecA/ssDNA filament and double-stranded DNA (dsDNA). Due to the huge size of the system and its dense packing, we use a reduced representation for protein and DNA together with state-of-the-art molecular modeling methods, including systematic docking and virtual reality simulations. The results indicate that it is possible for the double-stranded DNA to access the RecA-bound ssDNA while initially retaining its Watson–Crick pairing. They emphasize the importance of RecA L2 loop mobility for both recognition and strand exchange

Multi-resolution approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device.

International audienceMetal ions drive important parts of biology, yet it remains experimentally challenging to locate their binding sites. Here we present an innovative computational approach. We use interactive steering of charged ions or small molecules in an electrostatic potential map in order to identify potential binding sites. The user interacts with a haptic device and experiences tactile feedback related to the strength of binding at a given site. The potential field is the first level of resolution used in this model. Any type of potential field can be used, implicitly taking into account various conditions such as ionic strength, dielectric constants or the presence of a membrane. At a second level, we represent the accessibility of all binding sites by modelling the shape of the target macromolecule via non-bonded van der Waals interactions between its static atomic or coarse-grained structure and the probe molecule(s). The third independent level concerns the representation of the molecular probe itself. Ion selectivity can be assessed by using multiple interacting ions as probes. This method was successfully applied to the DNase I enzyme, where we recently identified two new cation binding sites by computationally expensive extended molecular dynamics simulations