Molecular modeling study of binding site selectivity of TQMP to G-quadruplex DNA

DockSurf: A Molecular Modeling Software for the Prediction of Protein/Surface Adhesion

The elucidation of structural interfaces between proteins and inorganic surfaces is a crucial aspect of bionanotechnology development. Despite its significance, the interfacial structures between proteins and metallic surfaces are yet to be fully understood, and the lack of experimental investigation has impeded the development of many devices. To overcome this limitation, we suggest considering the generation of protein/surface structures as a molecular docking problem with a homogenous plan as the target. To this extent, we propose a new software, DockSurf, which aims to quickly propose reliable protein/surface structures. Our approach considers the conformational exploration with Euler's angles, which provide a cartography instead of a unique structure. Interaction energies were derived from quantum mechanics computations for a set of small molecules that describe protein atom types and implemented in a Derjaguin, Landau, Verwey, and Overbeek potential for the consideration of large systems such as proteins. The validation of DockSurf software was conducted with molecular dynamics for corona proteins with gold surfaces and provided enthusiastic results. This software is implemented in the RPBS platform to facilitate widespread access to the scientific community.

Theoretical and Experimental Elucidation of the Adsorption Process of a Bioinspired Peptide on Mineral Surfaces

Inorganic materials used for biomedical applications such as implants generally induce the adsorption of proteins on their surface. To control this phenomenon, the bioinspired peptidomimetic polymer 1 (PMP1), which aims to reproduce the adhesion of mussel foot proteins, is commonly used to graft specific proteins on various surfaces and to regulate the interfacial mechanism. To date and despite its wide application, the elucidation at the atomic scale of the PMP1 mechanism of adsorption on surfaces is still unknown. The purpose of the present work was thus to unravel this process through experimental and computational investigations of adsorption of PMP1 on gold, TiO₂, and SiO₂ surfaces. A common mechanism of adsorption is identified for the adsorption of PMP1 which emphasizes the role of electrostatics to approach the peptide onto the surface followed by a full adhesion process where the entropic desolvation step plays a key role. Besides, according to the fact that mussel naturally controls the oxidation states of its proteins, further investigations were performed for two distinct redox states of PMP1, and we conclude that even if both states are able to allow interaction of PMP1 with the surfaces, the oxidation of PMP1 leads to a stronger interaction.

Computational Studies of a DNA-Based Aptasensor: toward Theory-Driven Transduction Improvement

Aptamers are a class of bioreceptors intensively used in current analytical tools dedicated to molecular diagnostics due to their ability to perform large structural reorganization upon target binding. However, there is a lack of methodologies allowing us to rationalize their structure in order to improve the transduction efficiency in aptamer sensors. We choose here, as a model system, a three-strand DNA structure as the probe, composed of two DNA strands anchored on a gold surface and partially hybridized with an aptamer sequence sensitive to ampicillin (AMP). The DNA structure has been designed to show strong structural change upon AMP binding to its aptamer. Using a set of computational techniques including molecular dynamics simulations, we deeply investigated the structure change upon analyte binding, taking into account the grafting on the surface. Original analyses of ion distributions along the trajectories unveil a distinct pattern between both states which can be related to changes in capacitance of the interface between these states. To our knowledge, this work demonstrates the ability of computational investigations for the first time to drive, in silico, the design of aptasensors.

In Vitro interaction between yeast frataxin and superoxide dismutases: Influence of mitochondrial metals

BACKGROUND

Friedreich's ataxia results from a decreased expression of the nuclear gene encoding the mitochondrial protein, frataxin. Frataxin participates in the biosynthesis of iron-sulfur clusters and heme cofactors, as well as in iron storage and protection against oxidative stress. How frataxin interacts with the antioxidant defence components is poorly understood.

METHODS

Therefore, we have investigated by kinetic, thermodynamic and modelling approaches the molecular interactions between yeast frataxin (Yfh1) and superoxide dismutases, Sod1 and Sod2, and the influence of Yfh1 on their enzymatic activities.

RESULTS

Yfh1 interacts with cytosolic Sod1 with a dissociation constant, Kd = 1.3 ± 0.3 μM, in two kinetic steps. The first step occurs in the 200 ms range and corresponds to the Yfh1-Sod1 interaction, whereas the second is slow and is assumed to be a change in the conformation of the protein-protein adduct. Furthermore, computational investigations confirm the stability of the Yfh1-Sod1 complex. Yfh1 forms two protein complexes with mitochondrial Sod2 with 1:1 and 2:1 Yfh1/Sod2 stoichiometry (Kd1 = 1.05 ± 0.05 and Kd2 = 6.6 ± 0.1 μM). Furthermore, Yfh1 increases the enzymatic activity of Sod1 while slightly affecting that of Sod2. Finally, the stabilities of the protein-protein adducts and the effect of Yfh1 on superoxide dismutase activities depend on the nature of the mitochondrial metal.

CONCLUSIONS

This work confirms the participation of Yfh1 in cellular defence against oxidative stress.

Molecular Dynamics Simulation of a RNA Aptasensor

Single-stranded RNA aptamers have emerged as novel biosensor tools. However, the immobilization procedure of the aptamer onto a surface generally induces a loss of affinity. To understand this molecular process, we conducted a complete simulation study for the Flavin mononucleotide aptamer for which experimental data are available. Several molecular dynamics simulations (MD) of the Flavin in complex with its RNA aptamer were conducted in solution, linked with six thymidines (T6) and, finally, immobilized on an hexanol-thiol-functionalized gold surface. First, we demonstrated that our MD computations were able to reproduce the experimental solution structure and to provide a meaningful estimation of the Flavin free energy of binding. We also demonstrated that the T6 linkage, by itself, does not generate a perturbation of the Flavin recognition process. From the simulation of the complete biosensor system, we observed that the aptamer stays oriented parallel to the surface at a distance around 36 Å avoiding, this way, interaction with the surface. We evidenced a structural reorganization of the Flavin aptamer binding mode related to the loss of affinity and induced by an anisotropic distribution of sodium cationic densities. This means that ionic diffusion is different between the surface and the aptamer than above this last one. We suggest that these findings might be extrapolated to other nucleic acids systems for the future design of biosensors with higher efficiency and selectivity.

Study of G-quadruplexes in the STAT3 gene using electrospray ionization mass spectrometry

RATIONALE

As a key signal transducer and transcription activator, STAT3 plays a very important role in many cell processes. We found that there were many G-rich sequences existing in the STAT3 gene including its promoter, intron, exon and 3'-flanking regions. These G-rich tracts can form G-quadruplexes under near physiological conditions. In this research, we systemically studied the G-quadruplexes in the STAT3 gene at a whole gene scale for the first time.

METHODS

In this research, the formation of G-quadruplexes in the STAT3 gene was probed by electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD). Their structures were constructed and refined by a molecular modeling method. We also used ESI-MS to study the recognition of the G-quadruplexes in the promoter of the STAT3 gene by flexible molecules which do not have a planar core like the other common quadruplex ligands.

RESULTS

The results based on ESI-MS suggested that the G-quadruplexes in the promoter of the STAT3 gene formed and were further recognized by some small molecules.

CONCLUSION

Our research proved that the G-rich sequences in the STAT3 gene could form G-quadruplexes under near physiological conditions. This provides a promising target to study the regulation of cell signal transduction in vivo and drug design that aims to target STAT3 G-quadruplexes. Copyright © 2016 John Wiley & Sons, Ltd.

All-atomic simulations on human telomeric G-quadruplex DNA binding with thioflavin T

Ligand-stabilized human telomeric G-quadruplex DNA is believed to be an anticancer agent, as it can impede the continuous elongation of telomeres by telomerase in cancer cells. In this study, five well-established human telomeric G-quadruplex DNA models were probed on their binding behaviors with thioflavin T (ThT) via both conventional molecular dynamics (MD) and well-tempered metadynamics (WT-MetaD) simulations. Novel dynamics and characteristic binding patterns were disclosed by the MD simulations. It was observed that the K(+) promoted parallel and hybridized human telomeric G-quadruplex conformations pose higher binding affinities to ThT than the Na(+) and K(+) promoted basket conformations. It is the end, sandwich, and base stacking driven by π-π interactions that are identified as the major binding mechanisms. As the most energy favorable binding mode, the sandwich stacking observed in (3 + 1) hybridized form 1 G-quadruplex conformation is triggered by reversible conformational change of the G-quadruplex. To further examine the free energy landscapes, WT-MetaD simulations were utilized on G-quadruplex-ThT systems. It is found that all of the major binding modes predicted by the MD simulations are confirmed by the WT-MetaD simulations. The results in this work not only accord with existing experimental findings, but also reinforce our understanding on the dynamics of G-quadruplexes and aid future drug developments for G-quadruplex stabilization ligands.

Investigations on the mechanisms of interactions between matrix metalloproteinase 9 and its flavonoid inhibitors using a combination of molecular docking, hybrid quantum mechanical/molecular mechanical calculations, and molecular dynamics simulations

Many experimental studies have found that flavonoids can inhibit the activities of matrix metalloproteinases (MMPs), but the relevant mechanisms are still unclear. In this paper, the interaction mechanisms of MMP-9 with its five flavonoid inhibitors are investigated using a combination of molecular docking, hybrid quantum mechanical and molecular mechanical (QM/MM) calculations, and molecular dynamics simulations. The molecular dynamics simulation results show a good linear correlation between the calculated binding free energies of QM/MM−Poisson–Boltzmann surface area (PBSA) and the experimental −log(EC50) regarding the studied five flavonoids on MMP-9 inhibition in explicit solvent. It is found that compared with the MM−PBSA method, the QM/MM−PBSA method can obviously improve the accuracy for the calculated binding free energies. The predicted binding modes of the five flavonoid−MMP-9 complexes reveal that the different hydrogen bond networks can form besides producing the Zn−O coordination bonds, which can reasonably explain previous experimental results. The agreement between our calculated results and the previous experimental facts indicates that the force field parameters used here are effective and reliable for investigating the systems of flavonoid−MMP-9 interactions, and thus, these simulations and analyses could be reproduced for the other related systems involving protein−ligand interactions. This paper may be helpful for designing the new MMP-9 inhibitors having higher biological activities by carrying out the structural modifications of flavonoid molecules.

Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures

The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids.

Is inhibition process better described with MD(QM/MM) simulations? The case of urokinase type plasminogen activator inhibitors

Urokinase plasminogen activator (uPA) is an enzyme involved in cancer growth and metastasis. Therefore, the design of inhibitors of uPA is of high therapeutic value, and several chemical families have been explored, even if none has still emerged, emphasizing the need of a rationalized approach. This work represents a complete computational study of uPA complexed with five inhibitors, which present weak similarities. Molecular dynamics simulations in explicit solvent were conducted, and structural analyses, along with molecular mechanics (MM)/Poisson-Boltzmann surface area free energies estimations, yield precious structure-activity relationships of these inhibitors. Besides, we realized supplemental QM/MM computations that improved drastically the quality of our models providing original information on the hydrogen bonds and charge transfer effects, which are, most often, neglected in other studies. We suggest that these simulations and analyses could be reproduced for other systems involving protein/ligand molecular recognitions.