Albany 2015:Book of Abstracts
June 9-13 2015
©Adenine Press (2012)
New insights on Nucleic Acids - protein interfaces revealed by VLDM, a geometrical approach
Complexes involving nucleic acids and proteins are ubiquitous and fundamental for cell life. Deciphering the interface between nucleic acids and proteins is crucial for better understanding the stabilities of the complexes and the mechanisms underlying their formation.
To describe the interface between nucleic acids and proteins, we developed a geometrical method, called VLDM (Voronoi Laguerre Delauney for Macromolecules). VLDM is based on the representation of molecules by a collection of polyhedra filling space without overlaps or gaps (Esque & Oguey, 2010). On the basis of this diagram, the topology of complex systems can be explored systematically without any need of empirical or subjective adjustments. In this work, VLDM was applied to two systems of major biological interest.
The nucleocapsid protein NCp7 of HIV-1 is a small basic protein with a chaperone activity on nucleic acids, RNA and DNA. The latter binds to two non equivalent Zn-fingers. A series of NMR structures of RNA and DNA-containing complexes (Darlix et al. 2011) were analyzed by VLDM. The results showed that, in both cases, the same Zn-finger is specialized in the recognition of one guanine. In contrast, the other Zn-finger exhibits various behaviours according to the nucleic acids nature (DNA or RNA) and the presence/absence of double-strand regions. This analysis supplies reliable quantitative basis supporting striking differences in binding properties of the two Zn-fingers and strengthens the proposal of two different functions for the Zn-fingers in NCp7, a view supported by biochemical studies.
The nucleosome, the fundamental building block of packaged DNA in eukaryotic cells, consists in eight histone proteins around which a ~147bp DNA is wrapped in a bit less than two turns. A nucleosome containing the high affinity sequence 601 was simulated using molecular dynamics in explicit solvent and then analyzed with VLDM. The most salient discovery was that the DNA is more strongly maintained around the histone core than expected. In addition to the structured part of histones, the unstructured, flexible histone tails efficiently contribute to the interface. Electrostatic interactions are supplemented by extensive hydrophobic contacts. The identification of such dense interface gives a better understanding of how the marked DNA distortions required by the wrapping are promoted and stabilized, keeping the double helix intact.
Overall, this work demonstrates that an accurate description of interfaces in complexes provides new insights into the interaction mode of nucleic acids-proteins complexes and opens a new way towards the elucidation of molecular recognition processes.
Darlix JL, Godet J, Ivanyi-Nagy R, Fosse P, Mauffret O, and Mély Y. (2011). Flexible nature and specific functions of the HIV-1 nucleocapsid protein. J. Mol. Biol. 410, 565-581.
A. Elbahnsi 1, 2
1 LBPA - UMR 8113 CNRS