NAR Breakthrough Article Crystal structure of Hop2-Mnd1 and mechanistic insights into its role in meiotic recombination

In meiotic DNA recombination, the Hop2-Mnd1 complex promotes Dmc1-mediated single-stranded DNA (ssDNA) invasion into homologous chromosomes to form a synaptic complex by a yet-unclear mechanism. Here, the crystal structure of Hop2-Mnd1 reveals that it forms a curved rod-like structure consisting of three leucine zippers and two kinked junctions. One end of the rod is linked to two juxtaposed winged-helix domains, and the other end is capped by extra alpha-helices to form a helical bundle-like structure. Deletion analysis shows that the helical bundle-like structure is sufficient for interacting with the Dmc1-ssDNA nucleofilament, and molecular modeling suggests that the curved rod could be accommodated into the helical groove of the nucleofilament. Remarkably, the winged-helix domains are juxtaposed at fixed relative orientation, and their binding to DNA is likely to perturb the base pairing according to molecular simulations. These findings allow us to propose a model explaining how Hop2-Mnd1 juxtaposes Dmc1-bound ssDNA with distorted recipient double-stranded DNA and thus facilitates strand invasion.

Duocarmycins binding to DNA explored by molecular simulation

Paolo Carloni, Ursula Röthlisberger

Duocarmycins are a potent class of antitumor agents. Their activity arises by their covalent binding to adenine nucleobases of DNA. We use classical mol. dynamics and hybrid (QM/MM) Car-Parrinello mol. dynamics simulations to study non-covalent and covalent binding of three duocarmycins with different reactivities, namely DSA, DSI and NBOC-DSA. Reactions in water are explored for NBOC-DSA with adenine and simple model reactants. Our calcns. suggest that: (i) Non-covalent drug binding does not significantly perturb the DNA structure. (ii) The exptl. obsd. DNA catalytic power might be due, at least in part, to a polarization of the biomol. scaffold over the drugs. Instead, our calcns. do not support the "shape induced activation" mechanism, in which the conformational properties of the drug play a pivotal role for catalysis (5). (iii) The chem. nature of the drug influences the structure of the drug-DNA adduct, thus affecting the reactivity of the initial complex. (iv) The functional groups of the drugs affect the intrinsic reactivity of the compd. [on SciFinder (R)]

2005

Cisplatin binding to DNA oligomers from hybrid Car-Parrinello/molecular dynamics simulations

Paolo Carloni, Ursula Röthlisberger

Cisplatin is widely used in clinic treatment against a variety of cancer diseases. It binds to two adjacent guanine residues and induces a bend in the DNA double helix. It is believed that cell death is induced upon binding of proteins, which recognize platinated DNA and impede replication and cell repair processes. Because of the high toxicity of cisplatin, there exists a great interest in new Pt-derivs., which are less toxic but as efficient as cisplatin. Thus, a profound understanding of the structural characteristics of Pt/DNA complexes is needed. NMR and X-Ray structures of cisplatin/DNA adducts share the overall structural features, but disagree in the local structure at the platinated site. In our work we performed hybrid QM/MM Car-Parrinello mol. dynamics on cisplatin/DNA adducts in the free from and complexed to the HMG protein domain A. Since this method allows for a parameter free treatment of the Pt-moiety and includes as well the DNA environment, we gain accurate insight into the structure of the drug/DNA complex. We conclude that the QM/MM approach described here proves to be a valuable tool for metal-DNA models and it can be used in the future to model the interaction of other platinum-based compds. with DNA, for which a valuable force field parametrization has not yet been developed. [on SciFinder (R)]

2004

Molecular Modeling of Bacterial Nanomachineries

Matteo Thomas Degiacomi

Proteins have the ability to assemble in multimeric states to perform their specific biological function. Unfortunately, characterizing experimentally these structures at atomistic resolution is usually difficult. For this reason, in silico methodologies aiming at predicting how multiple protein copies arrange to forma multimeric complex would be desirable. We present Parallel OptimizationWorkbench (POW), a swarm intelligence based optimization framework able to deal, in principle, with any optimization problem. We show that POW can be applied to biologically relevant problems such as prediction of protein assemblies and the parameterization of a Coarse-Grained force field for proteins. By combining POW optimizations, Molecular Dynamics simulations, Poisson-Boltzmann calculations and a variety of experiments, we subsequently study two bacterial nanomachieries: Aeromonas hydrophila's pore-forming toxin aerolysin, and Yersinia enterocolitica injectisome. These structures are challenging both for their size, and for the timescales involved in their functioning. Aerolysin is a pore-forming toxin secreted as an hydrophilic monomer. By means of large conformational changes, the protein heptamerizes on the target cell's surface, and finally inserts β-barrel into its lipid bilayer, causing cell death. The main hurdle in the study of this structure is the complexity of the mode of action, which spans timescales currently unreachable by classical molecular dynamics. We show that aerolysin C-terminal region has the dual role of preventing premature oligomerization and helping the folding of tertiary structure, qualifying therefore as an intramolecular chaperone. We study the transmembrane β-barrel properties and compare them with those of the homologous protein α-hemolysin. We show that aerolysin's barrel is more rigid than α-hemolysin's, and should be anion selective. We present models for aerolysin heptamer both in prepore and, for the first time, in membrane-inserted conformation. Our results are validated experimentally, and are consistent with known biochemical and structural data. The injectisome is an example of a type III secretion system. Its most striking feature is probably its size: hundreds of proteins assemble in a unique structure spanning the Gram-negative bacterial double membrane, and protruding outside the cell as a needle for tenth of nanometers. Obtaining an atomistic representation of this massive structure, and therefore some insights about its mode of action, is one of the greatest challenges. We show that the final length of injectisome's needle is determined by the secondary structure content of a ruler protein located inside its cavity during assembly. Using POW, we also produce the first model for Yersinia injectisome's basal body, highlighting the flexibility of this region in adapting between the inner and outer membranes. As a whole, this work demonstrates that a synergy of dry and wet experiments can provide precious insights into macromolecular structure and function.

EPFL2012

Molecular Modeling of Bacterial Nanomachineries

Matteo Thomas Degiacomi

EPFL2012