Dimer Interaction Research Articles

The machine learning pipeline to unravel the functional effects of interactions between sodium channels.

Recent reports obtained using patch clamp approach in Na+ channel (NaV) pairs have suggested cooperative gating of two NaVs, which has been linked to their homodimerization. Yet, the existing methods of the cooperative gating analysis are not effective in unraveling alterations in kinetics of individual NaVs result from their interactions in dimers. To address this issue, we developed a machine learning pipeline to remove capacitance drift and noise within the signal, and detect channel activity in order to infer Markov models parameters from single and multi-channel recordings.

Promotion of protein assembly by nanoparticles: From in vitro to in-cell.

Engineered nanomaterials are increasingly being studied for biomedical applications such as in diagnosis and therapeutics, due to their similarity in size to subcellular scales, and their tunable physico-chemical properties. Nanomaterials acquire a biomolecular corona upon introduction to biological media, which can influence their biological identity and subsequently, their interactions within the cell. Nanoparticle-protein interactions at the nano-bio interface also affect proteins in the corona, leading to biological transformations such as a change in protein function, unmasking new epitopes, and fibrilization. Silica nanoparticles - one of the most widely studied nanomaterials in biomedical applications - were reported to show a dose-dependent or surface ligand-dependent effect on the kinetics and morphology of protein self-assembly in systems like amyloid-β fibrils, α-synuclein and lysozyme. The interaction of silica nanoparticles with polymerizing cytoskeletal proteins, specifically tubulin proteins, has not been investigated quantitatively. BtubA and BtubB are a pair of bacterial tubulin proteins identified in Prosthecobacter strains, acquired by bacteria from eukaryotic cells via horizontal gene transfer. BtubAB dimers are known to self-assemble like eukaryotic tubulin, forming four-stranded microtubules in vitro as well as five-stranded microtubules in vivo. FRET-labeling of each of the Btub monomers with a donor (mEGFP) and acceptor (mRuby3) fluorescent protein provides a quantitative tool to measure the binding interactions of BtubAB dimers in the presence of silica nanoparticles in vitro and in cell using fluorescence spectroscopy and microscopy. We show that silica nanoparticles enhance BtubAB dimerization in vitro, whereas they appear to have little effect on bacterial tubulin self-assembly in the complex mammalian cellular environment.

Visualizing both nucleosome disassembly and reassembly during FACT chaperone activity.

The histone chaperone FACT (FAcilitates Chromatin Transcription) enhances transcription in eukaryotic cells, targeting DNA-protein interactions. FACT, a heterodimer in humans, comprises SPT16 and SSRP1 subunits. We measure nucleosome stability and dynamics in the presence of FACT and critical component domains. Optical tweezers quantify FACT/subdomain binding to nucleosomes, displacing the outer wrap of DNA, disrupting direct DNA-histone (strong site) interactions, altering the energy landscape of unwrapping and increasing the kinetics of DNA-histone disruption. Atomic force microscopy reveals nucleosome remodeling and DNA unwinding. Single molecule multi-channel fluorescence observes component histones as they disassemble under tension and are lost. Yet if tension is released, reassembly is also observed and surprisingly both loss and reassembly are accelerated by key domains of FACT. We resolve this ambiguity, noting that all histone-DNA kinetics are faster with FACT. Of the individual domains we studied, two were shown to influence nucleosome structure and dynamics with distinctly contradictory functions; while the SSRP1 HMGB domain displaces DNA, SPT16 MD/CTD stabilizes DNA-H2A/H2B dimer interactions. However, only intact FACT tethers disrupted DNA to the histones, and supports rapid nucleosome reformation over several cycles of force disruption/release. These results demonstrate how key FACT domains combine to catalyze nucleosome disassembly and reassembly.

Influence of hydroxyl group in stabilizing the Schiff base crystal structure: Crystal structure, computational and molecular docking studies

To investigate the synergetic effect in the formation of crystal structure having two independent molecules in the asymmetric unit and the structure-property relationship of the molecule, we have synthesized the Schiff base compound (E)-4-(((4-chlorobenzyl)imino)methyl)benzene-1,2,3-triol. The formation of the desired compound was confirmed by the FTIR and single-crystal X-ray studies. The enriched hydroxyl group exhibits more intra and inter-strong hydrogen bonds. The chlorine-hydrogen and C6-H6‧‧‧π interaction along with other interactions form a supramolecular architecture. The Hirshfeld surface analysis and 2D fingerprint analysis provide valuable information about the intermolecular interaction present in the crystal structure. The likelihood of occurrence of intermolecular contacts present in the crystal structure was analyzed using enrichment ratio. The visualization of the interaction topology along with interaction energy between the molecules are carried out using an energy framework. QTAIM, NCI, ELF and LOL studies provide information about electron charge density distribution and the nature of intramolecular and dimeric interaction. The DFT studies provide ground state energy of the optimized structure and the HOMO-LUMO energy gap. The molecular electrostatic potential provides the reactive site and anisotropy of charge distribution of chlorine atom. The NBO studies provide stabilization energy associated with the delocalization of orbitals. The docking studies were also carried out for SARS COVID-19 and the effect of hydroxyl group substitution on binding interaction was investigated.

Stable Organic Radicals Participation in Charge Transfer: A New Strategy toward Molecular Functional Materials.

Charge-transfer (CT) engineering with inter-/intramolecular CT interactions by simple compositions has emerged as a universal and efficient way to construct organic functional materials. Stable organic radicals with unique physicochemical properties that cannot be realized in closed-shell molecules, have been widely demonstrated to be ideal building blocks to construct versatile organic CT materials. This concept article provides a brief overview of the advances in the design, structure and property of stable organic radicals-based CT molecular functional materials, and the strategy for the generation of these materials is also highlighted. First, radicals are introduced as open-shell donors or acceptors, with a focus on their importance and uniqueness in improving electrical, magnetic and optical properties of CT functional materials. Additionally, CT interactions in stable radical dimers and trimers are further discussed systematically. Finally, the challenges are summarized and perspectives for future development of stable organic radicals-based CT functional materials are provided.

Domain motions, dimerization, and membrane interactions of the murine guanylate binding protein 2

Guanylate-binding proteins (GBPs) are a group of GTPases that are induced by interferon-gamma and are crucial components of cell-autonomous immunity against intracellular pathogens. Here, we examine murine GBP2 (mGBP2), which we have previously shown to be an essential effector protein for the control of Toxoplasma gondii replication, with its recruitment through the membrane of the parasitophorous vacuole and its involvement in the destruction of this membrane likely playing a role. The overall aim of our work is to provide a molecular-level understanding of the mutual influences of mGBP2 and the parasitophorous vacuole membrane. To this end, we performed lipid-binding assays which revealed that mGBP2 has a particular affinity for cardiolipin. This observation was confirmed by fluorescence microscopy using giant unilamellar vesicles of different lipid compositions. To obtain an understanding of the protein dynamics and how this is affected by GTP binding, mGBP2 dimerization, and membrane binding, assuming that each of these steps are relevant for the function of the protein, we carried out standard as well as replica exchange molecular dynamics simulations with an accumulated simulation time of more than 30 μs. The main findings from these simulations are that mGBP2 features a large-scale hinge motion in its M/E domain, which is present in each of the studied protein states. When bound to a cardiolipin-containing membrane, this hinge motion is particularly pronounced, leading to an up and down motion of the M/E domain on the membrane, which did not occur on a membrane without cardiolipin. Our prognosis is that this up and down motion has the potential to destroy the membrane following the formation of supramolecular mGBP2 complexes on the membrane surface.

Eutectic Mixture Formation and Relaxation Dynamics of Coamorphous Mixtures of Two Benzodiazepine Drugs

The formation of coamorphous mixtures of pharmaceuticals is an interesting strategy to improve the solubility and bioavailability of drugs, while at the same time enhancing the kinetic stability of the resulting binary glass and allowing the simultaneous administration of two active principles. In this contribution, we describe kinetically stable amorphous binary mixtures of two commercial active pharmaceutical ingredients, diazepam and nordazepam, of which the latter, besides being administered as a drug on its own, is also the main active metabolite of the other in the human body. We report the eutectic equilibrium-phase diagram of the binary mixture, which is found to be characterized by an experimental eutectic composition of 0.18 molar fraction of nordazepam, with a eutectic melting point of Te = 395.4 ± 1.2 K. The two compounds are barely miscible in the crystalline phase. The mechanically obtained mixtures were melted and supercooled to study the glass-transition and molecular-relaxation dynamics of amorphous mixtures at the corresponding concentration. The glass-transition temperature was always higher than room temperature and varied linearly with composition. The Te was lower than the onset of thermal decomposition of either compound (pure nordazepam decomposes upon melting and pure diazepam well above its melting point), thus implying that the eutectic liquid and glass can be obtained without any degradation of the drugs. The eutectic glass was kinetically stable against crystallization for at least a few months. The relaxation processes of the amorphous mixtures were studied by dielectric spectroscopy, which provided evidence for a single structural (α) relaxation, a single Johari-Goldstein (β) relaxation, and a ring-inversion conformational relaxation of the diazepinic ring, occurring on the same timescale in both drugs. We further characterized both the binary mixtures and pure compounds by FTIR spectroscopy and first-principles density functional theory (DFT) simulations to analyze intermolecular interactions. The DFT calculations confirm the presence of strong attractive forces within the heteromolecular dimer, leading to large dimer interaction energies of the order of -0.1 eV.

Nature and Strength of Weak O⋅⋅⋅O Interactions in Nitryl Halide Dimers.

The use of real space functions and molecular graphs has pushed some chemists to wonder: Are interactions between negatively charged oxygen atoms possible? In this contribution we analyze whether there is a real interaction between oxygen atoms in nitryl halide dimers (XNO2 )2 (X=F, Cl, Br and I) and in tetranitromethane and derivatives. Based on ab-initio and density functional theories (DFT) methods, we show these complexes are weakly stabilized. Energy decomposition analyses based on local molecular orbitals (LMOEDA) and interacting quantum atoms (IQA) reveal both dispersion and exchange play a crucial role in the stabilization of these complexes. Electron charge density and IQA analyses indicate that the oxygen atoms are connected by privileged exchange channels. In addition, electrostatic interactions between O and N atoms are also vital for the stabilization of the complexes. Finally, a reasonable explanation is given for the dynamic behavior of nitryl groups in tetranitromethane and derivatives.

Towards control of excitonic coupling in DNA-templated Cy5 aggregates: the principal role of chemical substituent hydrophobicity and steric interactions.

Understanding and controlling exciton coupling in dye aggregates has become a greater focus as potential applications such as coherent exciton devices, nanophotonics, and biosensing have been proposed. DNA nanostructure templates allow for a powerful modular approach. Using DNA Holliday junction (HJ) templates variations of dye combinations and precision dye positions can be rapidly assayed, as well as creating aggregates of dyes that could not be prepared (either due to excess or lack of solubility) through alternative means. Indodicarbocyanines (Cy5) have been studied in coupled systems due to their large transition dipole moment, which contributes to strong coupling. Cy5-R dyes were recently prepared by chemically modifying the 5,5'-substituents of indole rings, resulting in varying dye hydrophobicity/hydrophilicity, steric considerations, and electron-donating/withdrawing character. We utilized Cy5-R dyes to examine the formation and properties of 30 unique DNA templated homodimers. We find that in our system the sterics of Cy5-R dyes play the determining factor in orientation and coupling strength of dimers, with coupling strengths ranging from 50-138 meV. The hydrophobic properties of the Cy5-R modify the percentage of dimers formed, and have a secondary role in determining the packing characteristics of the dimers when sterics are equivalent. Similar to other reports, we find that positioning of the Cy5-R within the HJ template can favor particular dimer interactions, specifically oblique or H-type dimers.

A critical comparison of CH⋯π versus π⋯π interactions in the benzene dimer: obtaining benchmarks at the CCSD(T) level and assessing the accuracy of lower scaling methods.

We have established CCSD(T)/CBS (Complete Basis Set) limits for 3 stationary points on the benzene dimer potential energy surface, corresponding to the π⋯π (parallel displaced or PD(C2h), minimum) and CH⋯π (T-shaped or T(C2v), transition state) and tilted T-shaped (or TT(Cs), minimum) bonding scenarios considering both the structure and binding energy. The CCSD(T)/CBS binding energies are -2.65 ± 0.02 (PD), -2.74 ± 0.03 (T), and -2.83 ± 0.01 kcal mol-1 (TT). To this end, the CH⋯π is ∼0.2 kcal mol-1 stronger than the π⋯π interaction, whereas the tilting of the CH donating benzene molecule with respect to the other benzene is worth 0.1 kcal mol-1. As previously discussed in the literature, the MP2 level of theory does not provide a close match for either the energy or structure, yet the SCS-MP2 yields structures in excellent agreement with respect to the CCSD(T) result. It is found that the SCS-MI-MP2 also gives optimized structures very close to SCS-MP2 (within ∼0.01 Å of the benchmark). Despite the closer match in structure, the spin-biased MP2 methods (SCS-, SCS-MI-, and SOS-MP2) incorrectly predict the relative stabilities of the isomers. That said, none of the spin biased MP2 methods offers a good compromise between energy and structure for the systems examined. Finally, the CCSD(T)/CBS benchmarks were used to assess the performance of 13 DFT functionals selected from different rungs of Jacob's ladder. Several functionals such as TPSS-D3, B3LYP-D3, B97-D, B97-D3, and B2PLYP-D3 provided a good description of the binding energies for both CH⋯π and π⋯π interactions, yielding values within 6% of the CCSD(T)/CBS benchmark values. Unlike the MP2 methods, these functionals correctly predict the relative stability of the PD(C2h) and T(C2v) dimers. Further, we find that there is no systematic improvement as Jacob's ladder is ascended (increased complexity of functional). The best functionals that result in a good compromise between structure and energy accuracy are B97-D3 and B2PLYP-D3 for both the CH⋯π and π⋯π interaction. Despite the impressive performance of these functionals, a challenge that remains is ensuring the transferability of these density functionals in accurately describing the interaction between dimers of larger aromatic molecules, the latter requiring high-level benchmarks for these systems.

Characterization of non-covalent contacts in mono- and di-halo substituted acetaldehydes: probing the substitution effects of electron donating and withdrawing groups.

In the current work, a systematic evaluation of the different types of non-covalent interactions (NCIs) in acetaldehyde dimers, including dimers of mono-halo (XCH2CHO)2, di-halo (X2CHCHO)2 and tri-halo substituted (X3CCHO)2 acetaldehydes via the associated stabilization energy of these dimers has been performed. Furthermore, a topological analysis of the electron density based on the quantum theory of atoms in molecules (QTAIM) and non-covalent interaction reduced density gradient (NCI-RDG) isosurfaces has also been performed to evaluate the nature of these NCIs. The geometrical and electronic characteristics have been evaluated via the presence of different electron-donating groups (EDGs) and electron-withdrawing groups (EWGs) or substituents in dimers of these molecules, namely, XCH(Y)CHO and X2C(Y)CHO (wherein X = -F, -Cl, and -Br and Y = -SO3H, -CN, -NO2, -NH2, -CH3, -OCH3, and -SMe3). The C-H⋯O, C-H⋯X, X⋯X, X⋯O and C⋯O tetrel bonded contacts have been recognized to play an important role in the stabilization of the formed dimers. This study also establishes the fact that the overall stability of the dimeric assemblies is governed by the contributions from the mutual and complex interplay of a variety of interactions in the investigated dimers. Hence considerations based on strong H-bond donor-acceptor characteristics hold relevance for simple systems only, but slight alteration in the electronic environment can affect the overall stabilization energies of the system being investigated and the nature of the interactions that contribute towards the same.

Brave new surfactant world revisited by thermoalkalophilic lipases: computational insights into the role of SDS as a substrate analog.

Non-ionic surfactants were shown to stabilize the active conformation of thermoalkalophilic lipases by mimicking the lipid substrate while the catalytic interactions formed by anionic surfactants have not been well characterized. In this study, we combined μs-scale molecular dynamics (MD) simulations and lipase activity assays to analyze the effect of ionic surfactant, sodium dodecyl sulfate (SDS), on the structure and activity of thermoalkalophilic lipases. Both the open and closed lipase conformations that differ in geometry were recruited to the MD analysis to provide a broader understanding of the molecular effect of SDS on the lipase structure. Simulations at 298 K showed the potential of SDS for maintaining the active lipase through binding to the sn-1 acyl-chain binding pocket in the open conformation or transforming the closed conformation to an open-like state. Consistent with MD findings, experimental analysis showed increased lipase activity upon SDS incubation at ambient temperature. Notably, the lipase cores stayed intact throughout 2 μs regardless of an increase in the simulation temperature or SDS concentration. However, the surface structures were unfolded in the presence of SDS and at elevated temperature for both conformations. Simulations of the dimeric lipase were also carried out and showed reduced flexibility of the surface structures which were unfolded in the monomer, indicating the insulating role of dimer interactions against SDS. Taken together, this study provides insights into the possible substrate mimicry by the ionic surfactant SDS for the thermoalkalophilic lipases without temperature elevation, underscoring SDS's potential for interfacial activation at ambient temperatures.

Atom-economic access to cationic magnesium complexes.

Cationic alkaline-earth complexes attract interest for their enhanced Lewis acidity and reactivity compared with their neutral counterparts. Synthetic protocols to these complexes generally utilize expensive specialized reagents in reactions generating multiple by-products. We have studied a simple ligand transfer approach to these complexes using (NacNac)MgR and ER3 (NacNac = β-diketiminate anion; E = group 13 element; R = aryl/amido anion) which demonstrates high atom economy, opening up the ability to target these species in a more sustainable manner. The success of this methodology is dependent on the identity of the group 13 element with the heavier elements facilitating faster ligand exchange. Furthermore, while this reaction is successful with aromatic ligands such as phenyl and pyrrolyl, the secondary amide piperidide (pip) fails to transfer, which we attribute to the stronger 3-centre-4-electron dimerization interaction of Al2(pip)6.

In Ukrainian

Metal composites modified with various heteroatoms, such as N, B, Si, are used to obtain matrix composites with specified parameters with the strongest adhesive-cohesive bonds between metal atoms and a carbon nanoparticle. Such carbon nanoparticles functionalized with heteroatoms are promising for many metal composites. One of the interesting and promising metals as a matrix for such research work is iron. To predict the specifics of the interaction of iron with the surface of carbon nanomaterials supplemented with heteroatoms of different chemical structure, it is advisable to model such processes using quantum chemistry methods. The aim of the work was to find out the effect of temperature on the chemical interaction of iron clusters with native, boron-, silicon-, and nitrogen-containing graphene-like planes (GLP). The results of the calculations show that the highest value of the energy effect of the chemical interaction for the native graphene-like plane is +204.3 kJ/mol, in the case of calculations both by the B3LYP/6-31G(d,p) method and by the MP2/6-31G(d, p) (+370.7 kJ/mol). The lower value of the energy effect is found in the presence of nitrogen atoms in the composition of the graphene-like plane. This value is even lower for the interaction of iron dimers with a silicon-containing carbon nanocluster. The lowest values of the energy effect, calculated by both methods, are characteristic of the boron-containing graphene-like plane. In particular, for the B3LYP/6-31G(d,p) method, the value of the energy effect of the reaction is ‑210.5 kJ/mol, and for the MP2/6-31G(d,p) method this value is +16.6 kJ/mol. The presence of boron atoms in the composition of the nanocarbon matrix best contributes to the interaction with the iron nanocluster, regardless of the chosen research method. The dependence curves of the Gibbs free energy of the interaction of iron dimers with a graphene-like plane and its derivatives in all cases qualitatively correlate with similar energy effects. In addition, in all cases, the values of the Gibbs free energy increase with increasing temperature.

Simplified Y6-Based Nonfullerene Acceptors: In-Depth Study on Molecular Structure-Property Relation, Molecular Dynamics Simulation, and Charge Dynamics.

Two new Y6 derivatives of symmetrical YBO-2O and asymmetrical YBO-FO nonfullerene acceptors (NFAs) are prepared with a simplified synthetic procedure by incorporating octyl and fluorine substituents onto the terminal 2-(3-oxo-2,3-dihydro-1H-inden-1-ylidene)malononitrile (INCN) moiety. By moving the alkyl substituents on the Y6 core to the terminal INCN moiety, the lowest unoccupied molecular orbital of the YBO NFAs increases without decreasing solubility, resulting in high open-circuit voltages of the devices. Molecular dynamics simulation shows that YBO-2O/-FO preferentially form core-core and terminal-terminal dimeric interactions, demonstrating their tighter packing structure and higher electron mobility than Y6, which is consistent with 2D grazing incidence X-ray scattering and space charge limited current measurements. In blend films, the hole transfer (HT) from YBO-2O/-FO to the polymer donor PM6 is studied in detail by transient absorption spectroscopy, demonstrating efficient HT from YBO-FO to PM6 with their suitable energy level alignment. Despite the simplified synthesis, YBO-FO demonstrates photovoltaic performance similar to that of Y6, exhibiting a power conversion efficiency of 15.01%. Overall, this design strategy not only simplifies the synthetic procedures but also adjusts the electrical properties by modifying the intermolecular packing and energy level alignment, suggesting a novel simplified molecular design of Y6 derivatives.

Activity of EGFR transmembrane region variants indicates specific transmembrane dimers are not required for EGFR activity.

The Epidermal Growth Factor Receptor (EGFR) is a Receptor Tyrosine Kinase that mediates cell proliferation and differentiation events during development and maintenance of complex organisms. Formation of specific, ligand-dependent EGFR dimers is a key step in stimulating EGFR signaling, and crystal structures of active, dimeric forms of isolated EGFR extracellular regions and kinase domains have revealed much about how dimer interactions regulate EGFR activity. The nature and role of the transmembrane region in regulating EGFR activity remains less clear, however. Proposed roles for the transmembrane region range from nonspecific but energetically favorable interactions to specific transmembrane dimer conformations being associated with active, inactive, or activity-modulated states of EGFR. To investigate the role of specific transmembrane dimers in modulating EGFR activity we generated thirteen EGFR variants with altered transmembrane sequences designed to favor or disfavor specific types of transmembrane region interactions. We show using FRET microscopy that EGFR transmembrane regions have an intrinsic propensity to associate in mammalian cell membranes that is counteracted by the extracellular region. We show using cell-based assays that each of the EGFR transmembrane variants except the Neu variant, which results in constitutive receptor phosphorylation, is able to autophosphorylate and stimulate phosphorylation of downstream effectors Erk and Akt. Our results indicate that many transmembrane sequences, including polyleucine, are compatible with EGFR activity and provide no evidence for specific transmembrane dimers regulating EGFR function.

Insights into molecular cluster materials with adamantane-like core structures by considering dimer interactions.

A class of adamantane-like molecular materials attracts attention because they exhibit an extreme non-linear optical response and emit a broad white-light spectrum after illumination with a continuous-wave infrared laser source. According to recent studies, not only the nature of the cluster molecules, but also the macroscopic structure of the materials determines their non-linear optical properties. Here we present a systematic study of cluster dimers of the compounds AdR4 and [(RT)4 S6 ] (T=Si, Ge, Sn) with R=methyl, phenyl or 1-naphthyl to gain fundamental knowledge about the interactions in the materials. For all compounds, a similar type of dimer structures with a staggered arrangement of substituents was determined as the energetically most favorable configuration. The binding energy between the dimers, determined by including London dispersion interactions, increases with the size of the core and the substituents. The cluster interactions can be classified as substituent-substituent-dominated (small cores, large substituents) or core-core-dominated (large cores, small substituents). Among various possible dimer conformers, those with small core-core distances are energetically preferred. Trimer and tetramer clusters display similar trends regarding the minimal core-core distances and binding energies. The much lower energy barrier determined for the rotation of substituents as compared to the rotation of the cluster dimers past each other indicates that the rotation of substituents more easily leads to different conformers in the material. Thus, understanding the interaction of the cluster dimers allows an initial assessment of the interactions in the materials.

Dissecting Bonding Interactions in Cysteine Dimers.

Neutral (n) and zwitterionic (z) forms of cysteine monomers are combined in this work to extensively explore the potential energy surfaces for the formation of cysteine dimers in aqueous environments represented by a continuum. A simulated annealing search followed by optimization and characterization of the candidate structures afforded a total of 746 structurally different dimers held together via 80 different types of intermolecular contacts in 2894 individual non-covalent interactions as concluded from Natural Bond Orbitals (NBO), Quantum Theory of Atoms in Molecules (QTAIM) and Non-Covalent Interactions (NCI) analyses. This large pool of interaction possibilities includes the traditional primary hydrogen bonds and salt bridges which actually dictate the structures of the dimers, as well as the less common secondary hydrogen bonds, exotic X⋯Y (X = C, N, O, S) contacts, and H⋯H dihydrogen bonds. These interactions are not homogeneous but have rather complex distributions of strengths, interfragment distances and overall stabilities. Judging by their Gibbs bonding energies, most of the structures located here are suitable for experimental detection at room conditions.

Protein-Ligand Binding Free-Energy Calculations with ARROW─A Purely First-Principles Parameterized Polarizable Force Field.

Protein-ligand binding free-energy calculations using molecular dynamics (MD) simulations have emerged as a powerful tool for in silico drug design. Here, we present results obtained with the ARROW force field (FF)─a multipolar polarizable and physics-based model with all parameters fitted entirely to high-level ab initio quantum mechanical (QM) calculations. ARROW has already proven its ability to determine solvation free energy of arbitrary neutral compounds with unprecedented accuracy. The ARROW FF parameterization is now extended to include coverage of all amino acids including charged groups, allowing molecular simulations of a series of protein-ligand systems and prediction of their relative binding free energies. We ensure adequate sampling by applying a novel technique that is based on coupling the Hamiltonian Replica exchange (HREX) with a conformation reservoir generated via potential softening and nonequilibrium MD. ARROW provides predictions with near chemical accuracy (mean absolute error of ∼0.5 kcal/mol) for two of the three protein systems studied here (MCL1 and Thrombin). The third protein system (CDK2) reveals the difficulty in accurately describing dimer interaction energies involving polar and charged species. Overall, for all of the three protein systems studied here, ARROW FF predicts relative binding free energies of ligands with a similar accuracy level as leading nonpolarizable force fields.

Human FACT subunits coordinate to catalyze both disassembly and reassembly of nucleosomes

The histone chaperone FACT (facilitates chromatin transcription) enhances transcription in eukaryotic cells, targeting DNA-protein interactions. FACT, a heterodimer in humans, comprises SPT16 and SSRP1 subunits. We measure nucleosome stability and dynamics in the presence of FACT and critical component domains. Optical tweezers quantify FACT/subdomain binding to nucleosomes, displacing the outer wrap of DNA, disrupting direct DNA-histone (core site) interactions, altering the energy landscape of unwrapping, and increasing the kinetics of DNA-histone disruption. Atomic force microscopy reveals nucleosome remodeling, while single-molecule fluorescence quantifies kinetics of histone loss for disrupted nucleosomes, a process accelerated by FACT. Furthermore, two isolated domains exhibit contradictory functions; while the SSRP1 HMGB domain displaces DNA, SPT16 MD/CTD stabilizes DNA-H2A/H2B dimer interactions. However, only intact FACT tethers disrupted DNA to the histones and supports rapid nucleosome reformation over several cycles of force disruption/release. These results demonstrate that key FACT domains combine to catalyze both nucleosome disassembly and reassembly.