Molecular dynamics of DNA: comparison of force fields and terminal nucleotide definitions

Comparison of interaction between antimiR and microRNA versus HDO-antimiR and microRNA by molecular dynamics simulation

Recently, we found DNA/RNA heteroduplex oligonucleotide-based antimiR (HDO-antimiR) can more efficiently inhibit the target miRNA than conventional antimiR after its cellular uptake. But the mechanism of HDO-antimiR about the target-silencing is unknown. We here tried to elucidate the interaction mechanism of HDO-antimiR to miRNA using molecular dynamics (MD) simulation. When interaction of the conventional antimiR or HDO-antimiR and the target miRNA was simulated, they combined with each other in various forms. In the hydrogen bond analyses, base site of the antimiR formed hydrogen bond with miRNA. On the other hand, phosphate site of the HDO-antimiR formed hydrogen bond with miRNA. These results suggested that there were differences about the binding mechanisms between antimiR and HDO-antimiR to the target miRNA. In particular, there was a difference in the binding site between antimiR and HDO-antimiR. Additionally, it was found that guanine in the miRNA is mainly involved in the binding to the antimiR or HDO-antimiR. MD simulation method is useful in understanding the mechanism of oligonucleotide therapeutics.

Peptidic Compound as DNA Binding Agent: In Silico Fragment-based Design, Machine Learning, Molecular Modeling, Synthesis, and DNA Binding Evaluation

BACKGROUND

Cancer remains a global burden, with increasing mortality rates. Current cancer treatments involve controlling the transcription of malignant DNA genes, either directly or indirectly. DNA exhibits various structural forms, including the G-quadruplex (G4), a secondary structure in guanine-rich regions. G4 plays a crucial role in cellular processes by regulating gene expression and telomerase function. Researchers have recently identified G4-stabilizing binding agents as promising anti-cancer compounds. Additionally, peptides have emerged as effective anticancer pharmaceuticals due to their ability to form multiple hydrogen bonds, electrostatic interactions, and van der Waals forces. These properties enable peptides to bind to specific areas of DNA chains selectively. However, despite these advancements, designing G4-binding peptides remains challenging due to a lack of comprehensive information.

OBJECTIVE

In our present study, we employed an in silico fragment-based approach to design G4- binding peptides. This innovative method combines machine learning classification, molecular docking, and dynamics simulation.

METHODS

AutoDock Vina and Gromacs performed molecular docking and MD simulation, respectively. The machine learning algorithm was implemented by Scikit-learn. Peptide synthesis was performed using the SPPS method. The DNA binding affinity was measured by applying spectrophotometric titration.

RESULTS

As a result of this approach, we identified a high-scoring peptide (p10; sequence: YWRWR). The association constant (Ka) between p10 and the ctDNA double helix chain was 4.45 × 105 M-1. Molecular modeling studies revealed that p10 could form a stable complex with the G4 surface.

CONCLUSION

The obtained Ka value of 4.45 × 105 M-1 indicates favorable interactions. Our findings highlight the role of machine learning and molecular modeling approaches in designing new G4-binding peptides. Further research in this field could lead to targeted treatments that exploit the unique properties of G4 structures.

Exploring the Interaction of Curaxin CBL0137 with G-Quadruplex DNA Oligomers

Curaxins and especially the second-generation derivative curaxin CBL0137 have important antitumor activities in multiple cancers such as glioblastoma, melanoma and others. Although most of the authors suggest that their mechanism of action comes from the activation of p53 and inactivation of NF-kB by targeting FACT, there is evidence supporting the involvement of DNA binding in their antitumor activity. In this work, the DNA binding properties of curaxin CBL0137 with model quadruplex DNA oligomers were studied by ¹H NMR, CD, fluorescence and molecular modeling. We provided molecular details of the interaction of curaxin with two G-quadruplex structures, the single repeat of human telomere d(TTAGGGT)₄ and the c-myc promoter Pu22 sequence. We also performed ¹H and ³¹P NMR experiments were also performed in order to investigate the interaction with duplex DNA models. Our data support the hypothesis that the interaction of curaxin with G-quadruplex may provide a novel insight into the DNA-binding properties of CBL0137, and it will be helpful for the design of novel selective DNA-targeting curaxin analogues.

Establishing the allosteric mechanism in CRISPR-Cas9

Allostery is a fundamental property of proteins, which regulates biochemical information transfer between spatially distant sites. Here, we report on the critical role of molecular dynamics (MD) simulations in discovering the mechanism of allosteric communication within CRISPR-Cas9, a leading genome editing machinery with enormous promises for medicine and biotechnology. MD revealed how allostery intervenes during at least three steps of the CRISPR-Cas9 function: affecting DNA recognition, mediating the cleavage and interfering with the off-target activity. An allosteric communication that activates concerted DNA cleavages was found to led through the L1/L2 loops, which connect the HNH and RuvC catalytic domains. The identification of these "allosteric transducers" inspired the development of novel variants of the Cas9 protein with improved specificity, opening a new avenue for controlling the CRISPR-Cas9 activity. Discussed studies also highlight the critical role of the recognition lobe in the conformational activation of the catalytic HNH domain. Specifically, the REC3 region was found to modulate the dynamics of HNH by sensing the formation of the RNA:DNA hybrid. The role of REC3 was revealed to be particularly relevant in the presence of DNA mismatches. Indeed, interference of REC3 with the RNA:DNA hybrid containing mismatched pairs at specific positions resulted in locking HNH in an inactive "conformational checkpoint" conformation, thereby hampering off-target cleavages. Overall, MD simulations established the fundamental mechanisms underlying the allosterism of CRISPR-Cas9, aiding engineering strategies to develop new CRISPR-Cas9 variants for improved genome editing.

G-quadruplex binding properties of a potent PARP-1 inhibitor derived from 7-azaindole-1-carboxamide

Poly ADP-ribose polymerases (PARP) are key proteins involved in DNA repair, maintenance as well as regulation of programmed cell death. For this reason they are important therapeutic targets for cancer treatment. Recent studies have revealed a close interplay between PARP1 recruitment and G-quadruplex stabilization, showing that PARP enzymes are activated upon treatment with a G4 ligand. In this work the DNA binding properties of a PARP-1 inhibitor derived from 7-azaindole-1-carboxamide, (2-[6-(4-pyrrolidin-1-ylmethyl-phenyl)-pyrrolo[2,3-b]pyridin-1-yl]-acetamide, compound 1) with model duplex and quadruplex DNA oligomers were studied by NMR, CD, fluorescence and molecular modelling. We provide evidence that compound 1 is a strong G-quadruplex binder. In addition we provide molecular details of the interaction of compound 1 with two model G-quadruplex structures: the single repeat of human telomeres, d(TTAGGGT)₄, and the c-MYC promoter Pu22 sequence. The formation of defined and strong complexes with G-quadruplex models suggests a dual G4 stabilization/PARP inhibition mechanism of action for compound 1 and provides the molecular bases of its therapeutic potential.

Effect of Charge Distribution in a Modified tRNA Substrate on Pre-Reaction Protein-tRNA Complex Geometry

An important aspect of molecular mechanics simulations of a protein structure and ligand binding often involves the generation of reliable force fields for nonstandard residues and ligands. We consider the aminoacyl-tRNA synthetase (AaRS) system that involves nucleic acid and amino acid derivatives, obtaining force field atomic charges using the restrained electrostatic potential (RESP) approach. These charges are shown to predict observed properties of the post-transfer editing reaction in this system, in contrast to simulations performed using approximate charges conceived based upon standard charges for related systems present in force field databases. In particular, the simulations predicted key properties induced by mutation. The approach taken for generating the RESP charges retains established charges for known fragments, defining new charges only for the novel chemical features present in the modified residues. This approach is of general relevance for the design of force fields for pharmacological applications, and indeed the AaRS target system is itself relevant to antibiotics development.

Assessment of the Wolf method using the Stillinger-Lovett sum rules: From strong electrolytes to weakly charged colloidal dispersions

The Ewald method has been the cornerstone in molecular simulations for modeling electrostatic interactions of charge-stabilized many-body systems. In the late 1990s, Wolf and collaborators developed an alternative route to describe the long-range nature of electrostatic interactions; from a computational perspective, this method provides a more efficient and straightforward way to implement long-range electrostatic interactions than the Ewald method. Despite these advantages, the validity of the Wolf potential to account for the electrostatic contribution in charged fluids remains controversial. To alleviate this situation, in this contribution, we implement the Wolf summation method to both electrolyte solutions and charged colloids with moderate size and charge asymmetries in order to assess the accuracy and validity of the method. To this end, we verify that the proper selection of parameters within the Wolf method leads to results that are in good agreement with those obtained through the standard Ewald method and the theory of integral equations of simple liquids within the so-called hypernetted chain approximation. Furthermore, we show that the results obtained with the original Wolf method do satisfy the moment conditions described by the Stillinger-Lovett sum rules, which are directly related to the local electroneutrality condition and the electrostatic screening in the Debye-Hückel regime. Hence, the fact that the solution provided by the Wolf method satisfies the first and second moments of Stillinger-Lovett proves, for the first time, the reliability of the method to correctly incorporate the electrostatic contribution in charge-stabilized fluids. This makes the Wolf method a powerful alternative compared to more demanding computational approaches.

Investigation of nanotubes as the smart carriers for targeted delivery of mercaptopurine anticancer drug

Mercaptopurine (MCP) is an anticancer drug that is used to treat acute lymphoblastic leukemia. The therapeutic effect of the mercaptopurine limits its severe side effects like other cytotoxic (anti-cancer) drugs. Nanostructures or nanoparticles can be widely used as potential drug carriers for diagnosis and treatment of cancer. In the current study, the boron nitride nanotube (BNNT) and carbon nanotube (CNT) were studied as the delivery carriers of MCP using the density functional theory (DFT) calculations and molecular dynamics (MDs) simulation studies. To further understand the electronic properties of mercaptopurine, the partial density of states (PDOS) was calculated. The PDOS results depicted that the electronic features of the MCP do not change after the adsorption on the surface of the nanotubes. More stability of the MCP/BNNT complexes may be attributed to the existence of the intermolecular hydrogen bonds (H-bonds) between the hydrogen atoms of the MCP molecule and the N atoms of the BNNT. The results of the quantum theory of atoms in molecules (QTAIM) confirmed the presence of H-bonds in these complexes. Moreover, MD simulation studies were done in the presence of five drug molecules. The results revealed that the strongest van der Waals (vdW) interaction energy was found between the BNNT and MCP among the studied nanotubes, indicating the BNNT is a better nanocarrier than carbon nanotube for delivery of the MCP drug within the biological systems. In general, the obtained results may present helpful information on the nature of the interactions between mercaptopurine anticancer drug with BNNT and/or CNT.Communicated by Ramaswamy H. Sarma.

Benchmark assessment of molecular geometries and energies from small molecule force fields

Background: Force fields are used in a wide variety of contexts for classical molecular simulation, including studies on protein-ligand binding, membrane permeation, and thermophysical property prediction. The quality of these studies relies on the quality of the force fields used to represent the systems. Methods: Focusing on small molecules of fewer than 50 heavy atoms, our aim in this work is to compare nine force fields: GAFF, GAFF2, MMFF94, MMFF94S, OPLS3e, SMIRNOFF99Frosst, and the Open Force Field Parsley, versions 1.0, 1.1, and 1.2. On a dataset comprising 22,675 molecular structures of 3,271 molecules, we analyzed force field-optimized geometries and conformer energies compared to reference quantum mechanical (QM) data. Results: We show that while OPLS3e performs best, the latest Open Force Field Parsley release is approaching a comparable level of accuracy in reproducing QM geometries and energetics for this set of molecules. Meanwhile, the performance of established force fields such as MMFF94S and GAFF2 is generally somewhat worse. We also find that the series of recent Open Force Field versions provide significant increases in accuracy. Conclusions: This study provides an extensive test of the performance of different molecular mechanics force fields on a diverse molecule set, and highlights two (OPLS3e and OpenFF 1.2) that perform better than the others tested on the present comparison. Our molecule set and results are available for other researchers to use in testing.

Molecular mechanism for the encapsulation of the doxorubicin in the cucurbit[n]urils cavity and the effects of diameter, protonation on loading and releasing of the anticancer drug:Mixed quantum mechanical/ molecular dynamics simulations

BACKGROUND AND OBJECTIVES

Doxorubicin is a common apoptotic chemotherapeutic which has shown an obvious inhibitory effect in cancer chemotherapy. Here, cucurbit[n]urils (n = 7,10) have been proposed as a doxorubicin carrier, and the effects of diameter, protonation on loading and releasing of the anticancer drug doxorubicin has been studied.

METHODS

The Density Functional Theory (DFT) calculation and Molecular Dynamics (MD) simulation are performed to study the adsorption process of the (guest) Doxorubicin molecule in the neutral and protonated states within the (host) cucurbit[n]urils (n = 7,10).

RESULTS

DFT results show that the adsorption process in water is thermodynamically favorable. It is found that the binding energies for protonated drug encapsulation in cucurbit[n]urils are weaker than those of the neutral drug, implying the protonation of doxorubicin can promote the drug release from the adsorption situation. The electron density values and their Laplacian are evaluated to identify the nature of the intermolecular interactions through the topological parameters using the Bader's theory of atoms in molecules. Furthermore, the natural bond orbital analysis shows that the electrons aretransferred from cucurbit[n]urils to drug in all complexes. MD simulation results indicate that value of drug diffusion coefficient is small, therefore, we expect DOX to be slowly released from the CB cavity.

CONCLUSIONS

Based on obtained results, cucurbit[n]urils may be a prominent nano-carrier to loading and release drug on to target cells.

The assessment of three dimensional modelling design for single strand DNA aptamers for computational chemistry application

Aptamers are oligonucleotides and peptides around 15-100 bases in length and are suitable as detection probes or as therapeutics molecules. There are growing interests in the aptamer screening approach through computational simulation methods. DNA and RNA modelling lacks of validation on their predicted 3D structures due to less number of validation tools, unlike protein structures. We suggest an approach to design the stem-loop/hairpin for the three dimensional structure of DNA aptamers through serial applications of computational prediction methods by comparing the simulated structures with the experimental data deposited in PDB Data bank, followed by MD simulations. The result shows minimal structural differences were observed between the designed and the original NMR aptamers, and the stem-loop conformational structures were also retained during the MD thus suggesting the proposed aptamers designing methods are able to synthesize a high quality molecular structure of hairpin aptamers, comparable to the NMR structures.

Multispectroscopic analysis, atomic force microscopy, molecular docking and molecular dynamic simulation studies of the interaction between [SnMe2Cl2(Me2phen)] complex and ct-DNA in the presence of glucose

In this study, the spectroscopic methods (UV-vis, fluorimetric), Atomic force microscopy, and computational studies (molecular docking and molecular dynamic simulation) were used to investigate the interaction of [SnMe₂Cl₂(Me₂phen)] complex with CT-DNA in the presence of glucose. The results showed the complex in the medium containing glucose has less effect on calf thymus DNA (ct-DNA) than the medium without glucose. Cytotoxicity of [SnMe₂Cl₂(Me₂phen)] complex on MCF-7 cells was examined and showed Sn(IV) complex possesses potential cytotoxicity against this cell line. Molecular docking study showed that Sn(IV) complex interacts with DNA by groove binding mode. Radius of gyration (Rg) was smaller upon binding of the Sn(IV) complex suggesting a more compact structure of DNA in the presence of Sn(IV) complex.Communicated by Ramaswamy H. Sarma.

Unexpected sequence adsorption features of polynucleotide ssDNA on graphene oxide

The sequence features of single-stranded DNA (ssDNA) adsorbed on a graphene oxide (GO) surface are important for applications of the DNA/GO functional structure in biosensors, biomedicine, and materials science. In this study, molecular dynamics (MD) simulations were used to examine the adsorption of polynucleotide ssDNAs (A₁₂, C₁₂, G₁₂, and T₁₂) and single nucleotides (A, C, G, and T) on the GO surface. For the latter case, the nucleotide-GO interaction energy followed the trend G > A > C > T, even though it was influenced by specific adsorption sites. In the case of polynucleotides, unexpectedly polythymidine (T₁₂) had the strongest interaction with the GO surface. The angle distributions of the adsorbed nucleobases indicated that T₁₂ was more likely to form a quasi-parallel structure with GO compared to A₁₂, C₁₂, or G₁₂. This was attributed to the weakest π-stacking interactions of thymine. Weaker intra-molecular base-stacking interactions made it easier to break the structures of pyrimidine bases relative to those of purine bases. Weaker inter-molecular base-stacking interactions between T₁₂ and the GO surface enabled T₁₂ to adjust its structure easily to a more stable one by slipping on the surface. This result provides a new understanding of polynucleotide ssDNA adsorption on GO surfaces, which will help in the design of functional DNA/GO structure-based platforms.

Length feature of ssDNA adsorption onto graphene oxide with both large unoxidized and oxidized regions

DNA/GO functional structures have been widely used in biosensors, biomedicine and materials science. However, most studies about DNA/GO functional structures do not take into account the coexistence of both large unoxidized and oxidized regions on GO sheets. This special local structure provides the boundary region, which is the junction area between unoxidized and oxidized regions, and exhibits a special amphiphilic property of the GO sheets. Here based on molecular dynamics simulations, our results predict that the adsorption efficiency of long strand ssDNA molecules adsorbed on GO is 43%. Further analysis has shown that the ssDNA adsorption behaviors on the GO surface are more likely to start in the boundary region, even for 20 mer ssDNA molecules. Looking into the adsorption dynamic process we can see that the hydrogen bonds between ssDNA and GO are very active and easily broken and formed, especially for the boundary region of the GO surface, resulting in easy capture and adsorption of the ssDNA molecules on this region. The result provides insightful understanding of the adsorption behavior of ssDNA molecules on this amphiphilic GO surface and is helpful in the design of DNA/GO functional structure-based biosensors.

Spontaneous Embedding of DNA Mismatches Within the RNA:DNA Hybrid of CRISPR-Cas9

CRISPR-Cas9 is the forefront technology for editing the genome. In this system, the Cas9 protein is programmed with guide RNAs to process DNA sequences that match the guide RNA forming an RNA:DNA hybrid structure. However, the binding of DNA sequences that do not fully match the guide RNA can limit the applicability of CRISPR-Cas9 for genome editing, resulting in the so-called off-target effects. Here, molecular dynamics is used to probe the effect of DNA base pair mismatches within the RNA:DNA hybrid in CRISPR-Cas9. Molecular simulations revealed that the presence of mismatched pairs in the DNA at distal sites with respect to the Protospacer Adjacent Motif (PAM) recognition sequence induces an extended opening of the RNA:DNA hybrid, leading to novel interactions established by the unwound nucleic acids and the protein counterpart. On the contrary, mismatched pairs upstream of the RNA:DNA hybrid are rapidly incorporated within the heteroduplex, with minor effect on the protein-nucleic acid interactions. As a result, mismatched pairs at PAM distal ends interfere with the activation of the catalytic HNH domain, while mismatches fully embedded in the RNA:DNA do not affect the HNH dynamics and enable its activation to cleave the DNA. These findings provide a mechanistic understanding to the intriguing experimental evidence that PAM distal mismatches hamper a proper function of HNH, explaining also why mismatches within the heteroduplex are much more tolerated. This constitutes a step forward in understanding off-target effects in CRISPR-Cas9, which encourages novel structure-based engineering efforts aimed at preventing the onset of off-target effects.

Dynamical aspects of supercooled TIP3P-water in the grooves of DNA

We investigate by molecular dynamics simulations the mobility of the water located at the DNA minor and major grooves. We employ the TIP3P water model, and our system is analyzed for a range of temperatures 190-300 K. For high temperatures, the water at the grooves shows an Arrhenius behavior similar to that observed in the bulk water. At lower temperatures, a departure from the bulk behavior is observed. This slowing down in the dynamics is compared with the dynamics of the hydrogen of the DNA at the grooves and with the autocorrelation functions of the water hydrogen bonds. Our results indicate that the hydrogen bonds of the water at the minor grooves are highly correlated, which suggests that this is the mechanism for the slow dynamics at this high confinement.

Single-stranded DNA structural diversity: TAGGGT from monomers to dimers to tetramer formation

RATIONALE

DNA quadruplex structures have emerged as novel drug targets due to their role in preventing abnormal gene transcription and maintaining telomere stability. Trapped Ion Mobility Spectrometry-Mass Spectrometry (TIMS-MS), combined with theoretical modeling, is a powerful tool for studying the kinetic intermediates of DNA complexes formed in solution and interrogated in the gas phase after desolvation.

METHODS

A TAGGGT ssDNA sequence was purchased and studied in 10 mM ammonium acetate using nanospray electrospray ionization (nESI)-TIMS-MS in positive and negative ion mode. Collisional cross section (CCS) profiles were measured using internal calibration (Tune Mix). Theoretical structures were proposed based on molecular dynamics, charge location and geometry optimization for the most intense IMS bands based on the number of TAGGGT units, adduct form and charge states.

RESULTS

A distribution of monomeric, dimeric and tetrameric TAGGGT structures were formed in solution and separated in the gas phase based on their mobility and m/z value (e.g., [M + 2H]⁺² , [2M + 3H]⁺³ , [M - 2H]^-2 , [2M - 3H]^-3 , [4M + 4H]⁺⁴ , [4M + 3H + NH₄ ]⁺⁴ , [4M + 2H + 2NH₄ ]⁺⁴ and [4M + H + 3NH₄ ]⁺⁴ ). The high mobility resolution of the TIMS-MS analyzer permitted the observation of multiple CCS bands per molecular ion form. Comparison with theoretical candidate structures suggests that monomeric TAGGGT species are stabilized by A-T and G⁺ -G interactions, with the size of the conformer influenced by the proton location. In the case of the TAGGGT quadruplex, the protonated species displayed a broad CCS distribution, while six discrete conformers were stabilized by the presence of ammonium ions (n = 1-3).

CONCLUSIONS

This is the first observation of multiple conformations of TAGGGT complexes (n = 1, 2 and 4) in 10 mM ammonium acetate. Candidate structures with intramolecular interactions of the form of G⁺ -G and traditional A-T base pairing agreed with the experimental trends. Our results demonstrate the structural diversity of TAGGGT monomers, dimers and tetramers in the gas phase beyond the previously reported solution structure, using 10 mM ammonium acetate to replicate biological conditions.

Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics

CRISPR-Cas9 is the state-of-the-art technology for editing and manipulating nucleic acids. However, the occurrence of off-target mutations can limit its applicability. Here, all-atom enhanced molecular dynamics (MD) simulations-using Gaussian accelerated MD (GaMD)-are used to decipher the mechanism of off-target binding at the molecular level. GaMD reveals that base pair mismatches in the target DNA at distal sites with respect to the protospacer adjacent motif (PAM) can induce an extended opening of the RNA:DNA heteroduplex, which leads to newly formed interactions between the unwound DNA and the L2 loop of the catalytic HNH domain. These conserved interactions constitute a "lock" effectively decreasing the conformational freedom of the HNH domain and hampering its activation for cleavage. Remarkably, depending on their positions at PAM distal sites, DNA mismatches responsible for off-target cleavages are unable to "lock" the HNH domain, thereby leading to the unselective cleavage of DNA sequences. In consistency with the available experimental data, the ability to "lock" the catalytic HNH domain in an inactive "conformational checkpoint" is shown to be a key determinant in the onset of off-target effects. This mechanistic rationale contributes in clarifying a long lasting open issue in the CRISPR-Cas9 function and poses the foundation for designing novel and more specific Cas9 variants, which could be obtained by magnifying the "locking" interactions between HNH and the target DNA in the presence of any incorrect off-target sequence, thus preventing undesired cleavages.

Carbon and boron nanotubes as a template material for adsorption of 6-Thioguanine chemotherapeutic: a molecular dynamics and density functional approach

The interaction of 6-Thioguanine molecule, an antitumor drug with carbon nanotube and boron nitride nanotube (BNNT) is investigated using molecular dynamics simulations. Based on the obtained results, the strongest negative van der Waals interaction is found between 6-TG and BNNT among the studied nanotubes, which indicated BNNT is a better nanocarrier of the 6-TG drug than CNT within biological systems. Moreover, the adsorption and electronic properties of the 6-Thioguanine interacted with boron-nitride nanotube has been studied within the framework of density functional theory calculations. The negative binding energy values denote that there is the favorable interaction between 6-TG drug and BNNT at the studied 6-TG/BNNT complexes. Also, the amounts of the binding energies indicated that the 6-Thioguanine molecule physically interacts with the surface of BNNT. The values of electron densities and their Laplacian have been analyzed using the Bader's theory of atoms in molecules to characterize the nature of the intermolecular interactions through the topological parameters. We hope that the results of this work may provide useful information about the nature of the nanotube-drug molecule interactions and highlight the ability of these materials to be used as an adsorbent enhancing delivery of drug to cancer cells. Communicated by Ramaswamy H. Sarma.

Predicting the mechanism and rate of H-NS binding to AT-rich DNA

Bacteria contain several nucleoid-associated proteins that organize their genomic DNA into the nucleoid by bending, wrapping or bridging DNA. The Histone-like Nucleoid Structuring protein H-NS found in many Gram-negative bacteria is a DNA bridging protein and can structure DNA by binding to two separate DNA duplexes or to adjacent sites on the same duplex, depending on external conditions. Several nucleotide sequences have been identified to which H-NS binds with high affinity, indicating H-NS prefers AT-rich DNA. To date, highly detailed structural information of the H-NS DNA complex remains elusive. Molecular simulation can complement experiments by modelling structures and their time evolution in atomistic detail. In this paper we report an exploration of the different binding modes of H-NS to a high affinity nucleotide sequence and an estimate of the associated rate constant. By means of molecular dynamics simulations, we identified three types of binding for H-NS to AT-rich DNA. To further sample the transitions between these binding modes, we performed Replica Exchange Transition Interface Sampling, providing predictions of the mechanism and rate constant of H-NS binding to DNA. H-NS interacts with the DNA through a conserved QGR motif, aided by a conserved arginine at position 93. The QGR motif interacts first with phosphate groups, followed by the formation of hydrogen bonds between acceptors in the DNA minor groove and the sidechains of either Q112 or R114. After R114 inserts into the minor groove, the rest of the QGR motif follows. Full insertion of the QGR motif in the minor groove is stable over several tens of nanoseconds, and involves hydrogen bonds between the bases and both backbone and sidechains of the QGR motif. The rate constant for the process of H-NS binding to AT-rich DNA resulting in full insertion of the QGR motif is in the order of 10⁶ M⁻¹s⁻¹, which is rate limiting compared to the non-specific association of H-NS to the DNA backbone at a rate of 10⁸ M⁻¹s⁻¹.

The Histone-like Nucleoid Structuring protein (H-NS) occurs in enterobacteria, such as Salmonella typhimurium and Escherichia coli, and structures DNA by forming filaments along DNA duplexes. Several nucleotide sequences have been identified to which H-NS binds with high affinity. Yet, obtaining highly detailed structural information of the H-NS DNA complex has proven to be a major challenge, which has not been yet resolved. By employing molecular dynamics simulations we were able to provide high resolution insights into the mechanism of DNA binding by H-NS. We identified various ways in which H-NS can bind to DNA. In all binding events, a conserved region in the protein initiates the association of H-NS to DNA. Our results show that H-NS binds in the minor groove of AT-rich DNA via a series of intermediate steps. Using advanced molecular simulation methods we predicted that the process of H-NS binding to the DNA backbone to full insertion into the minor groove occurs in the order of a million times per second, which is slower than the non-specific association of H-NS to the DNA backbone.

Toward realistic computer modeling of paraffin-based composite materials: critical assessment of atomic-scale models of paraffins

Paraffin-based composites represent a promising class of materials with numerous practical applications such as e.g. heat storage. Computer modeling of these complex multicomponent systems requires a proper theoretical description of both the n-alkane matrix and the non-alkane filler molecules. The latter can be modeled with the use of a state-of-the-art general-purpose force field such as GAFF, CHARMM, OPLS-AA and GROMOS, while the paraffin matrix is traditionally described in the frame of relatively old, alkane-specific force fields (TraPPE, NERD, and PYS). In this paper we link these two types of models and evaluate the performance of several general-purpose force fields in computer modeling of paraffin by their systematic comparison with earlier alkane-specific models as well as with experimental data. To this end, we have performed molecular dynamics simulations of n-eicosane bulk samples with the use of 10 different force fields: TraPPE, NERD, PYS, OPLS-UA, GROMOS, GAFF, GAFF2, OPLS-AA, L-OPLS-AA, and CHARMM36. For each force field we calculated several thermal, structural and dynamic characteristics of n-eicosane over a wide temperature range. Overall, our findings show that the general-purpose force fields such as CHARMM36, L-OPLS-AA and GAFF/GAFF2 are able to provide a realistic description of n-eicosane samples. While alkane-specific models outperform most general-purpose force fields as far as the temperature dependence of mass density, the coefficient of volumetric thermal expansion in the liquid state, and the crystallization temperature are concerned, L-OPLS-AA, CHARMM36 and GAFF2 force fields provide a better match with experiment for the shear viscosity and the diffusion coefficient in melt. Furthermore, we show that most general-purpose force fields are able to reproduce qualitatively the experimental triclinic crystal structure of n-eicosane at low temperatures.

Atomic-scale computational models of paraffins are critically assessed and compared.

Assessment of the chitosan-functionalized graphene oxide as a carrier for loading thioguanine, an antitumor drug and effect of urea on adsorption process: Combination of DFT computational and molecular dynamics simulation studies

In this study, the interaction thioguanine (TG) anticancer drug with the functionalized graphene oxide (GO) nanosheet surface is theoretically studied in both gas phase and separately in physiological media using the density functional theory (DFT) calculations. DFT calculations indicated the adsorption and solvation energies are negative for f-GONS/TG complexes which propose the adsorption process of TG molecule onto the f-GONS surface is possible from the energetic viewpoint. QTAIM calculations confirm the nature of partially covalent-partially electrostatic between drug and nanosheet. These results are sorely relevant that an approach for loading of TG molecule is the chemical modification of GO using covalent functionalization which can serve as a nanocarrier to load drug molecules. Moreover, to understand the effect of urea on the nature of the interaction between TG and f-GONS, molecular dynamics (MD) simulation was employed. The results indicated that in the presence of urea the adsorption process gets affected and leads to instability of system, while the affinity of the TG for adsorption onto GO surface is increased in pure water. Communicated by Ramaswamy H. Sarma.

In silico and in vitro study of magnetic niosomes for gene delivery: The effect of ergosterol and cholesterol

A low transfection efficiency and failure to deliver therapeutic genes to target organs limit the use of vesicular systems in gene therapy. In this study, magnetic niosomes were used to improve transfection efficiency and overcome limitations. In this light, Tween 60 and Span 60 molecules were employed as the bilayer component and ergosterol and/or cholesterol as membrane-stabilizing agents. We studied the structural and dynamical properties of cholesterol-containing niosomes (ST60/Chol) and ergosterol-containing vesicles (ST60/Ergo) using the molecular dynamics (MD) simulation technique. In in vitro experiments, the protamine-condensed DNA along with magnetic nanoparticles were prepared and incorporated into the niosome to form magnetic niosome-entrapped protamine-condensed DNA (M-NPD). The MD simulation comparison of two bilayers showed that the ST60/Ergo vesicles have better properties for gene delivery. Our in vitro results confirmed the in silico results and revealed that Ergo-niosomes have smaller size, better polydispersity, and slower release of plasmid than Chol-niosome. Moreover, M-NPD-Ergo showed higher cellular uptake and gene expresssion in HEK-293T cell line compared to M-NPD-Chol vesicles.

Validation and Comparison of Force Fields for Native Cyclodextrins in Aqueous Solution

Molecular dynamics simulations of native α-, β-, and γ-cyclodextrin in aqueous solution have been conducted with the goal to investigate the performance of the CHARMM36 force field, the AMBER-compatible q4md-CD force field, and five variants of the GROMOS force field. The properties analyzed are structural parameters derived from X-ray diffraction and NMR experiments as well as hydrogen bonds and hydration patterns, including hydration free enthalpies. Recent revisions of the torsional-angle parameters for carbohydrate systems within the GROMOS family of force fields lead to a significant improvement of the agreement between simulated and experimental NMR data. Therefore, we recommend using the variant 53A6_GLYC instead of 53A6 and 56A6_{CARBO_R} or 2016H66 instead of 56A6_CARBO to simulate cyclodextrins in solution. The CHARMM36 and q4md-CD force fields show a similar performance as the three recommended GROMOS parameter sets. A significant difference is the more flexible nature of the cyclodextrins modeled with the CHARMM36 and q4md-CD force fields compared to the three recommended GROMOS parameter sets.

A combined molecular dynamics simulation and quantum mechanics study on mercaptopurine interaction with the cucurbit [6,7] urils: Analysis of electronic structure

In the current study, the probability of complex formation between mercaptopurine drug with cucurbit[6]urils and cucurbit[7]urils has been investigated. The calculations for geometry optimization of complexes have been carried out by means of DFT (B3LYP), DFT-D (B3LYP-D) and M06-2X methods. The Atoms In Molecules (AIM), Natural Bond Orbital (NBO), NMR, the density of states (DOSs) and frontier molecular orbital (MO) analyses have been done on the inclusion complexes. In addition, the UV-Vis spectra of the first eight states have been obtained by CAM-B3LYP/TD-DFT calculation. The obtained results of the complexation process reveal that CB[7]-DRG complexes are more favorable than that of CB[6]-DRG interactions. Furthermore, our theoretical results show that configurations III and I are the most stable configurations related to the CB[6]/DRG and CB[7]/DRG interactions, respectively. The positive ∇²_ρ(r) and HC values at the bond critical points indicate that exist the weak H-bonds between CB[6] and CB[7] with H atoms of the drug molecule. The obtained negative binding energy values of CB[7]-DRG interaction in solution phase show the stability of these complexes in the aqueous medium. Also, all of the observed parameters of molecular dynamics simulation such as the number of contacts, hydrogen bonding, center-of-mass distance and van der Waals energy values confirm the encapsulation of mercaptopurine molecule inside the cucurbit[7]urils cavity at about 3.2ns.

Enhanced basepair dynamics pre-disposes protein-assisted flips of key bases in DNA strand separation during transcription initiation

Localized separation of strands of duplex DNA is a necessary step in many DNA-dependent processes, including transcription and replication.

Adaptive resolution simulation of oligonucleotides

Nucleic acids are characterized by a complex hierarchical structure and a variety of interaction mechanisms with other molecules. These features suggest the need of multiscale simulation methods in order to grasp the relevant physical properties of deoxyribonucleic acid (DNA) and RNA using in silico experiments. Here we report an implementation of a dual-resolution modeling of a DNA oligonucleotide in physiological conditions; in the presented setup only the nucleotide molecule and the solvent and ions in its proximity are described at the atomistic level; in contrast, the water molecules and ions far from the DNA are represented as computationally less expensive coarse-grained particles. Through the analysis of several structural and dynamical parameters, we show that this setup reliably reproduces the physical properties of the DNA molecule as observed in reference atomistic simulations. These results represent a first step towards a realistic multiscale modeling of nucleic acids and provide a quantitatively solid ground for their simulation using dual-resolution methods.

Systematic hierarchical coarse-graining with the inverse Monte Carlo method

We outline our coarse-graining strategy for linking micro- and mesoscales of soft matter and biological systems. The method is based on effective pairwise interaction potentials obtained in detailed ab initio or classical atomistic Molecular Dynamics (MD) simulations, which can be used in simulations at less accurate level after scaling up the size. The effective potentials are obtained by applying the inverse Monte Carlo (IMC) method [A. P. Lyubartsev and A. Laaksonen, Phys. Rev. E 52(4), 3730-3737 (1995)] on a chosen subset of degrees of freedom described in terms of radial distribution functions. An in-house software package MagiC is developed to obtain the effective potentials for arbitrary molecular systems. In this work we compute effective potentials to model DNA-protein interactions (bacterial LiaR regulator bound to a 26 base pairs DNA fragment) at physiological salt concentration at a coarse-grained (CG) level. Normally the IMC CG pair-potentials are used directly as look-up tables but here we have fitted them to five Gaussians and a repulsive wall. Results show stable association between DNA and the model protein as well as similar position fluctuation profile.

General Force-Field Parametrization Scheme for Molecular Dynamics Simulations of Conjugated Materials in Solution

We describe a general scheme to obtain force-field parameters for classical molecular dynamics simulations of conjugated polymers. We identify a computationally inexpensive methodology for calculation of accurate intermonomer dihedral potentials and partial charges. Our findings indicate that the use of a two-step methodology of geometry optimization and single-point energy calculations using DFT methods produces potentials which compare favorably to high level theory calculation. We also report the effects of varying the conjugated backbone length and alkyl side-chain lengths on the dihedral profiles and partial charge distributions and determine the existence of converged lengths above which convergence is achieved in the force-field parameter sets. We thus determine which calculations are required for accurate parametrization and the scope of a given parameter set for variations to a given molecule. We perform simulations of long oligomers of dioctylfluorene and hexylthiophene in explicit solvent and find peristence lengths and end-length distributions consistent with experimental values.

Evaluation of the Gibbs Free Energy Changes and Melting Temperatures of DNA/DNA Duplexes Using Hybridization Enthalpy Calculated by Molecular Dynamics Simulation

A molecular dynamics simulation approach was applied for the prediction of the thermal stability of oligonucleotide duplexes. It was shown that the enthalpy of the DNA/DNA complex formation could be calculated using this approach. We have studied the influence of various simulation parameters on the secondary structure and the hybridization enthalpy value of Dickerson-Drew dodecamer. The optimal simulation parameters for the most reliable prediction of the enthalpy values were determined. The thermodynamic parameters (enthalpy and entropy changes) of a duplex formation were obtained experimentally for 305 oligonucleotides of various lengths and GC-content. The resulting database was studied with molecular dynamics (MD) simulation using the optimized simulation parameters. Gibbs free energy changes and the melting temperatures were evaluated using the experimental correlation between enthalpy and entropy changes of the duplex formation and the enthalpy values calculated by the MD simulation. The average errors in the predictions of enthalpy, the Gibbs free energy change, and the melting temperature of oligonucleotide complexes were 11%, 10%, and 4.4 °C, respectively. We have shown that the molecular dynamics simulation gives a possibility to calculate the thermal stability of native DNA/DNA complexes a priori with an unexpectedly high accuracy.

Recovery of the poisoned topoisomerase II for DNA religation: coordinated motion of the cleavage core revealed with the microsecond atomistic simulation

Type II topoisomerases resolve topological problems of DNA double helices by passing one duplex through the reversible double-stranded break they generated on another duplex. Despite the wealth of information in the cleaving operation, molecular understanding of the enzymatic DNA ligation remains elusive. Topoisomerase poisons are widely used in anti-cancer and anti-bacterial therapy and have been employed to entrap the intermediates of topoisomerase IIβ with religatable DNA substrate. We removed drug molecules from the structure and conducted molecular dynamics simulations to investigate the enzyme-mediated DNA religation. The drug-unbound intermediate displayed transitions toward the resealing-compliant configuration: closing distance between the cleaved DNA termini, B-to-A transformation of the double helix, and restoration of the metal-binding motif. By mapping the contact configurations and the correlated motions between enzyme and DNA, we identified the indispensable role of the linker preceding winged helix domain (WHD) in coordinating the movements of TOPRIM, the nucleotide-binding motifs, and the bound DNA substrate during gate closure. We observed a nearly vectorial transition in the recovery of the enzyme and identified the previously uncharacterized roles of Asn508 and Arg677 in DNA rejoining. Our findings delineate the dynamic mechanism of the DNA religation conducted by type II topoisomerases.

Dynamic hydrogen bonding and DNA flexibility in minor groove binders: molecular dynamics simulation of the polyamide f-ImPyIm bound to the Mlu1 (MCB) sequence 5'-ACGCGT-3' in 2:1 motif

Molecular dynamics simulations of the DNA 10-mer 5'-CCACGCGTGG-3' alone and complexed with the formamido-imidazole-pyrrole-imidazole (f-ImPyIm) polyamide minor groove binder in a 2:1 fashion were conducted for 50 ns using the pbsc0 parameters within the AMBER 12 software package. The change in DNA structure upon binding of f-ImPyIm was evaluated via minor groove width and depth, base pair parameters of Slide, Twist, Roll, Stretch, Stagger, Opening, Propeller, and x-displacement, dihedral angle distributions of ζ, ε, α, and γ determined using the Curves+ software program, and hydrogen bond formation. The dynamic hydrogen bonding between the f-ImPyIm and its cognate DNA sequence was compared to the static image used to predict sequence recognition by polyamide minor groove binders. Many of the predicted hydrogen bonds were present in less than 50% of the simulation; however, persistent hydrogen bonds between G5/15 and the formamido group of f-ImPyIm were observed. It was determined that the DNA is wider in the Complex than without the polyamide binder; however, there is flexibility in this particular sequence, even in the presence of the f-ImPyIm as evidenced by the range of minor groove widths the DNA exhibits and the dynamics of the hydrogen bonding that binds the two f-ImPyIm ions to the minor groove. The Complex consisting of the DNA and the 2 f-ImPyIm binders shows slight fraying of the 5' end of the 10-mer at the end of the simulation, but the portion of the oligomer responsible for recognition and binding is stable throughout the simulation. Several structural changes in the Complex indicate that minor groove binders may have a more active role in inhibiting transcription than just preventing binding of important transcription factors.

Charge-induced instabilities of droplets containing macromolecular complexes

Solvated macromolecular complexes are ubiquitous in nature, notably in biological systems containing proteins and nucleic acids. Studies of the interactions within a macromolecular complex and between the complex and the solvent in droplet environments are critical for understanding the stability of macromolecular complexes in electrospray ionization (ESI) and nanofluidic experiments. In this study, two distinct cases of macromolecular complexes in aqueous nanodrops are examined by using molecular dynamics simulations: (i) a pair of sodiated poly(ethylene) glycol (PEG) macroions and (ii) a double-stranded DNA (dsDNA). PEG represents a case in which the surface energy of the aqueous droplet is larger than the solvent–macromolecule energy. Conversely, in a droplet solvating dsDNA, the solvent–macromolecule interaction energy overcomes the solvent interaction energy. We report that charge-induced instabilities previously identified for single macroions also appear in the case of complexes, but with a higher level of complexity. In the case of a pair of PEG macroions, we found that their conformations on the surface of a droplet “sense” each other. The charged PEGs are each released from a droplet at different times through contiguous extrusion or drying-out mechanisms. In the case of the DNA, the charge-induced instability manifests as a spine droplet morphology. Narrow regions of the spines promote break down of the hydrogen bonds that hold the dsDNA together. The dsDNA separates into two single strands as it is increasingly exposed to vacuum. These findings elucidate charge-induced instabilities of macromolecular complexes in droplets, which are critical intermediates in ESI and nanofluidic experiments.

An α1-adrenergic receptor ligand repurposed as a potent antiproliferative agent for head and neck squamous cell carcinoma

In this study we report the anticancer properties of RN5-Me, an α₁-adrenergic receptor ligand.