Dimer Interaction Research Articles

Spiro-fused indoline-quinazoline hybrids as smart bombs against TNF-α-mediated inflammation.

Inflammation is central to numerous diseases, highlighting the need for new anti-inflammatory agents. This study explores the potential of novel spirofused indoline-quinazoline hybrids (4a-p) as anti-inflammatory compounds, inspired by a spiroisatin analogue (VI) that showed modest TNF-α inhibition. We aimed to enhance activity by modifying the isatin scaffold: first, introducing N-alkylation (propyl, butyl, or isobutyl) to improve hydrophobic interactions within the TNF-α dimer active site; second, adding halogens (F, Cl, Br) at the 5-position to increase lipophilicity. Anti-inflammatory activity against TNF-α was confirmed in-vivo for all synthesized analogues, with 4b, 4e, 4 k, and 4n emerging as the top candidates. Further studies on these four compounds assessed their analgesic effects, as well as their impact on PGE2, NF-κB, paw thickness, and paw weight. In-vitro analyses revealed nanomolar TNFR2-TNF-α binding inhibition for the four leads. Safety evaluations included histopathology, ulcerogenic potential, kidney and liver functions, and acute hemotoxicity. In-silico studies examined drug-likeness, pharmacokinetics, and TNF-α dimer interactions. These results suggest that the four lead compounds possess promising profiles compared to standard therapies.

Theoretical Study on Intramolecular Hydrogen Bonds of Flavonoid Cocrystals.

This study investigates the role of intramolecular hydrogen bonds in the formation of cocrystals involving flavonoid molecules, focusing on three active pharmaceutical ingredients (APIs): chrysin (CHR), isoliquiritigenin (ISO), and kaempferol (KAE). These APIs form cocrystals with different cocrystal formers (CCFs) through intramolecular hydrogen bonding. We found that disruption of these intramolecular hydrogen bonds leads to decreased stability compared to molecules with intact bonds. The extrema of molecular electrostatic potential surfaces (MEPS) show that flavonoid molecules with disrupted intramolecular hydrogen bonds have stronger hydrogen bond donors and acceptors than those with intact bonds. Using the artificial bee colony algorithm, dimeric structures of these flavonoid molecules were explored, representing early-stage structures in cocrystal formation, including API-API, API-CCF, and CCF-CCF dimers. It was observed that the number and strength of dimeric interactions significantly increased, and the types of interactions changed when intramolecular hydrogen bonds were disrupted. These findings suggest that disrupting intramolecular hydrogen bonds generally hinders the formation of cocrystals. This theoretical study provides deeper insight into the role of intramolecular hydrogen bonds in the cocrystal formation of flavonoids.

Reproduction of experimental data for stacked caffeine dimers using various computational methods

Reliable description of stacking interaction of aromatic molecules is important for the understanding structure, stability, and functions of biopolymers. The caffeine molecule is an ideal object for this study as the stacking interactions are the preferential ones for self-associations of this hydrophobic molecule without H-bond donor groups. The analysis of anhydrous caffeine crystal structures revealed five types of caffeine stacking dimers. Geometry optimization of these dimers was performed using two molecular mechanics force fields, ab-initio method Møller Plesset of the second order (MP2), and density functional theory (DFT) with different functionals. The comparison of geometric parameters of the caffeine dimers obtained using different theoretical methods with those in crystals enables us to suggest the methods providing the most reliable stacking characteristics. These methods are: the MP2 with Basis Set Superposition Error correction (MP2/CP), Poltev force field, along with PBE0-DH, SCAN and PBE-D3 functionals of DFT. For the methods, which give the dimer interaction energy close to that obtained by MP2/CP method, the evaluated sublimation enthalpy values are shown to be close to the experimental data. Additionally, MP2/CP, Poltev FF and PBE0-DH functional showed to be the methods that describe well both the energy and geometry of the caffeine stacking dimer.

Hierarchical assembly and environmental enhancement of bacterial ice nucleators

Bacterial ice nucleating proteins (INPs) are exceptionally effective in promoting the kinetically hindered transition of water to ice. Their efficiency relies on the assembly of INPs into large functional aggregates, with the size of ice nucleation sites determining activity. Experimental freezing spectra have revealed two distinct, defined aggregate sizes, typically classified as class A and C ice nucleators (INs). Despite the importance of INPs and years of extensive research, the precise number of INPs forming the two aggregate classes, and their assembly mechanism have remained enigmatic. Here, we report that bacterial ice nucleation activity emerges from more than two prevailing aggregate species and identify the specific number of INPs responsible for distinct crystallization temperatures. We find that INP dimers constitute class C INs, tetramers class B INs, and hexamers and larger multimers are responsible for the most efficient class A activity. We propose a hierarchical assembly mechanism based on tyrosine interactions for dimers, and electrostatic interactions between INP dimers to produce larger aggregates. This assembly is membrane-assisted: Increasing the bacterial outer membrane fluidity decreases the population of the larger aggregates, while preserving the dimers. Inversely, Dulbecco's Phosphate-Buffered Saline buffer increases the population of multimeric class A and B aggregates 200-fold and endows the bacteria with enhanced stability toward repeated freeze-thaw cycles. Our analysis suggests that the enhancement results from the better alignment of dimers in the negatively charged outer membrane, due to screening of their electrostatic repulsion. This demonstrates significant enhancement of the most potent bacterial INs.

Structural and functional insights into the T-even type bacteriophage topoisomerase II.

T-even type bacteriophages are virulent phages commonly used as model organisms, playing a crucial role in understanding various biological processes. One such process involves the regulation of DNA topology during phage replication upon host infection, governed by type IIA DNA topoisomerases. In spite of various studies on prokaryotic and eukaryotic counterparts, viral topoisomerase II remains insufficiently understood, especially the unique domain composition of T4 phage. In this study, we determine the cryo-EM structures of topoisomerase II from T4 and T6 phages, including full-length structures of both apo and DNA-binding states which have never been determined before. Together with other conformational states, these structures provide an explicit blueprint of mechanisms of phage topoisomerase II. Particularly, the asymmetric dimeric interactions observed in cryo-EM structures of T6 phage topoisomerase II ATPase domain and central domain bound with DNA shed light on the asynchronous ATP usage and asynchronous cleavage of the G-segment DNA, respectively. The elucidation of phage topoisomerase II's structures and functions not only enhances our understanding of mechanisms and evolutionary parallels with prokaryotic and eukaryotic homologs but also highlights its potential as a model for developing type IIA topoisomerase inhibitors.

Hydride and halide abstraction reactions behind the enhanced basicity of Be and Mg clusters with nitrogen bases.

In this study, we investigate the protonation effects on the structure, relative stability and basicity of complexes formed by the interaction of monomers and dimers of BeX2 and MgX2 (X = H, F) with NH3, CH2NH, HCN, and NC5H5 bases. Calculations were performed using the M06-2X/aug-cc-pVTZ formalism, along with QTAIM, ELF and NCI methods for electron density analysis and MBIE and LMO-EDA energy decomposition analyses for interaction enthalpies. The protonation of the MH2- and M2H4-Base complexes occurs at the negatively charged hydrogen atoms of the MH2 and M2H4 moieties through typical hydride abstraction reactions, while protonation at the N atom of the base is systematically less exothermic. The preference for the hydride transfer mechanism is directly associated with the significant exothermicity of H2 formation through the interaction between H- and H+, and the high hydride donor ability of these complexes. The basicity of both, MH2 and M2H4 compounds increases enormously upon association with the corresponding bases, with the increase exceeding 40 orders of magnitude in terms of ionization constants. Due to the smaller exothermicity of HF formation, the basicity of fluorides is lower than that of hydrides. In Be complexes, the protonation at the N atom of the base dominates over the fluoride abstraction mechanism. However, for the Mg complexes the fluoride abstraction mechanism is energetically the most favorable process, reflecting the greater facility of Mg complexes to lose F-.

Structural Insights into the Role of the Proline Rich Region in Tau Function.

Tau is a microtubule–associated protein that plays an important role in modulating axonal microtubules in neurons. Intracellular tau aggregates are found in a broad class of disorders, including Alzheimer&#8242s disease, termed tauopathies. Tau is an intrinsically disordered protein, and its structural disorder appears to be critical to its microtubule-related functions. Tubulin binding sites are found in tau&#8242s proline-rich region (PRR), microtubule binding repeats (MTBR: R1–R4), and pseudo–repeat, R′. While many post-translational modifications have been identified on tau, phosphorylation sites, which both regulate tubulin dimer and microtubule interactions and are correlated with disease, cluster with high frequency within the PRR. Here, we use fluorescence correlation spectroscopy and structural mass spectrometry techniques to characterize the impact of phosphomimic mutations in the PRR on tubulin dimer binding and probe the structure of the PRR–tubulin dimer complex. We find that phosphomimics cumulatively diminish tubulin dimer binding and slow microtubule polymerization. Additionally, we map two ~15 residue regions of the PRR as primary tubulin dimer binding sites and propose a model in which PRR enhances lateral interactions between tubulin dimers, complementing the longitudinal interactions observed for MTBR. Together these measurements provide insight into the previously overlooked relevance of tau&#8242s PRR in functional interactions with tubulin.

Mut-Map: Comprehensive Computational Pipeline for Structural Mapping and Analysis of Cancer-Associated Mutations.

Understanding the functional impact of genetic mutations on protein structures is essential for advancing cancer research and developing targeted therapies. The main challenge lies in accurately mapping these mutations to protein structures and analysing their effects on protein function. To address this, Mut-Map (https://genemutation.org/) is a comprehensive computational pipeline designed to integrate mutation data from the Catalogue Of Somatic Mutations In Cancer database with protein structural data from the Protein Data Bank and AlphaFold models. The pipeline begins by taking a UniProt ID and proceeds through mapping corresponding Protein Data Bank structures, renumbering residues, and assessing disorder percentages. It then overlays mutation data, categorizes mutations based on structural context, and visualizes them using advanced tools like MolStar. This approach allows for a detailed analysis of how mutations may disrupt protein function by affecting key regions such as DNA interfaces, ligand-binding sites, and dimer interactions. To validate the pipeline, a case study on the TP53 gene, a critical tumour suppressor often mutated in cancers, was conducted. The analysis highlighted the most frequent mutations occurring at the DNA-binding interface, providing insights into their potential role in cancer progression. Mut-Map offers a powerful resource for elucidating the structural implications of cancer-associated mutations, paving the way for more targeted therapeutic strategies and advancing our understanding of protein structure-function relationships.

Unconventional Radical and Radical-Hole Site-Based Interactions in Halogen-Bearing Dimers and Trimers: A Comparative Study.

Radical (R•) and R•-hole site-based interactions are comparatively studied, for the first time, using ab initio methods. In this regard, R•-bearing molecules •XO3 (where X = Cl, Br, and I) were subjected to direct interaction with NH3 within dimeric and trimeric forms in the form of NH3···•XO3/•XO3···NH3 and NH3···•XO3···NH3 complexes, respectively. As confirmed by electrostatic potential analysis, the studied R•-bearing molecules •XO3 had the outstanding potentiality to interact as Lewis acid centers via two positive sites dubbed as R• and R•-hole sites. Such an observation proposed the potentiality of the considered •XO3 molecules to engage in unconventional R• and well-established R•-hole site-based interactions with Lewis bases. This was confirmed by negative interaction (E int) energies, ranging from -4.93 to -19.89 kcal/mol, with higher favorability for R• site-based interactions over the R•-hole site-based ones. MP2 energetic features furnished higher preferability for the R• site-based interactions than the R•-hole site-based ones in the case of chlorine- and bromine-bearing complexes, and the reverse was true for the iodine-bearing complexes. Moreover, elevated E int values were recorded for the NH3···•XO3···NH3 trimers over the NH3···•XO3 and •XO3···NH3 dimers, outlining the higher preference of the •XO3 molecules to engage in R• and R•-hole site-based interactions in the trimeric form over the dimeric one. These results might be considered a requisite linchpin for numerous forthcoming supramolecular chemistry and crystal engineering studies.

Design of Point Charge Models for Divalent Metal Cations Targeting Quantum Mechanical Ion–Water Dimer Interactions

Divalent metal cations are of vital importance in biochemistry and materials science, and their structural and thermodynamic properties in aqueous solution have often been used as targets for the development of ion models. This study presented a strategy for designing nonbonded point charge models of divalent metal cations (Mg2+ and Ca2+) and Cl− by targeting quantum mechanics (QM)-based ion–water dimer interactions. The designed models offered an accurate representation of ion–water interactions in the gas phase and showed reasonable performance for non-targeted properties in aqueous solutions, such as the ion–water oxygen distance (IOD), coordination number (CN), and density and viscosity of MgCl2 and CaCl2 solutions at low concentrations. Our metal cation models yielded considerable overestimates of the hydration free energies (HFEs) of the ions, whereas the Cl− model displayed good performance. Together with the overestimated density and viscosity of the salt solutions, these results indicated the necessity of re-optimizing ion–ion interactions and/or including polarization effects in the design of ion models. The designed Mg2+ model was capable of maintaining the crystal metal-binding networks during MD simulation of a metalloprotein, indicating great potential for biomolecular simulations. This work highlighted the potential of QM-based ion models to advance the study of metal ion interactions in biological and material systems.

Supramolecular assembly governed by tetrel, CN⋅⋅⋅π and other weak noncovalent interactions in two acrylonitrile derivatives with D-π-A topology: Crystallography, optical properties and theoretical studies

Two D-π-A acrylonitriles, (Z)-3-(4-methoxyphenyl)-2-(pyridin-4-yl)acrylonitrile (1) and (Z)-3-(4-piperidin-1-yl)-2-(pyridin-4-yl)acrylonitrile (2), were synthesized to investigate how the varying donor moieties affect their structural and optical properties. Compound 1 crystallized with two crystallographically independent molecules, each showing different orientations of the methoxy group, and exhibited herringbone molecular arrangement in the solid-state. This structure is stabilized by CH···N/π interactions, π-stacking, cyano···π stacking (CN···π) and a σ-hole tetrel bond involving the C and O atoms of the methoxy group. Compound 2 crystallized with a single molecule in the asymmetric unit and displayed columnar packing mode. This structure is stabilized intermolecular CH···N interactions, where all nitrogen atoms serve as acceptors, as well as by intermolecular CH···π interactions and π-stacking between adjacent pyridyl rings. Hirshfeld surfaces and 2D-fingerprint plots revealed the effect of donor moieties on the intermolecular interactions. The energetics of the molecular dimers observed in these structures were characterized by both CLP-PIXEL energy and DFT calculations. The nature of the tetrel bond was characterized using molecular electrostatic surface potential and deformation electron density maps. Theoretical charge density analysis was performed to characterize the noncovalent interactions in various molecular dimers of 1 and 2. The absorption spectra of compounds 1 and 2 exhibit a 40 nm red-shift in solution, attributed to the presence of the piperidyl moiety in compound 2.

Abstract Tu078: Mechanistic basis of protein phosphatase 2A inhibition by I2PP2A dimerization: A key step in βAR resensitization

Dysfunction of beta-adrenergic receptor (βAR) is a key hallmark of heart failure, wherein mechanisms of phosphorylation-mediated desensitization of βARs are well understood. However, less is known about dephosphorylation-mediated resensitization of βARs that is regulated by protein phosphatase 2A (PP2A) in heart failure. Our previous studies have shown that agonist stimulation of βAR activates phosphoinositide 3-kinase γ (PI3Kγ) which phosphorylates endogenous inhibitor of PP2A (I2PP2A) on serine residues 9 & 93. Phosphorylated I2PP2A (pI2PP2A) binds to PP2A inhibiting its activity thereby, impairing βAR resensitization. Although structural studies have shown I2PP2A to be a dimer, yet little is understood about the mechanistic basis of PP2A inhibition by I2PP2A. We therefore hypothesized that phosphorylation of I2PP2A promotes dimerization driving robust interaction with PP2A resulting in inhibition of PP2A and impairment in βAR resensitization. To test for dimerization, hemagglutinin (HA)-tagged I2PP2A and Myc-tagged I2PP2A were generated and co-expressed in HEK 293 cells. Immunoprecipitation of HA-I2PP2A led to significant co-immunoprecipitation of Myc-I2PP2A reflecting the ability of I2PP2A to dimerize. To determine whether phosphorylation is key for dimerization, phospho-mimetic mutants of I2PP2A (S9,93A (inactive) or S9,93D (active)) were generated. Immunoblotting of cellular lysates with expression of these phospho-mimetics showed that S9,93D exclusively formed dimers, while S9,93A I2PP2A only formed monomers suggesting that phosphorylation is key facilitator of dimerization. The role of I2PP2A phosphorylation in its dimerization and PP2A interaction with consequences on βAR resensitization will be presented. Determining the mechanistic basis of this understudied pathway is critical as human heart failure is associated with increased PI3Kγ activity, elevated expression of I2PP2A and reduced βAR function. Key words: Desensitization, Resensitization, I2PP2A, PP2A, Dimerization

Highly efficient uranium uptake by the eco-designed cocamidopropyl betaine-decorated Na-P1 coal fly-ash zeolite

In some locations around the globe, the U concentrations may exceed WHO standards by 2-folds therefore, effective yet environmentally wise solutions to purify radioactive waters are of significant importance. Here, the optimized and fully controlled coal-fly-ash based Na-P1 zeolite functionalization by employing novel, biodegradable biosurfactant molecule - cocamidopropyl betaine (CAPB) is showcased. The zeolite’s surface decoration renders three composites with varying amounts of introduced CAPB molecule (Na-P1 @ CAPB), with 0.44, 0.88, and 1.59-times External Cation Exchange Capacity (ECEC). Wet-chemistry experiments revealed extremely high U adsorption capacity (qmax = 137.1 mg U/g) unveiling preferential interactions of uranyl dimers with CAPB molecules coupled with ion-exchange between Na+ ions. Multimodal spectroscopic analyses, including Fourier-Transformed Infra-Red (FT-IR), X-ray Photoelectron (XPS), and X-ray Absorption Fine Structure (XAFS), showed the hexavalent oxidation state of U, and no secondary release of the CAPB molecule from the composite. The EXAFS signals fingerprint changes in the interatomic distances of adsorbed U, showing the impact of the O and N, heteroatoms present in the CAPB molecule on U binding mechanism. The presented research outcomes showcase the easy, scalable, optimized, and environmentally friendly synthesis of biofunctional zeolite effectively purifying the real-life U-bearing wastewaters from the vicinity of the Pribram deposit (Czech Republic).

A polarizable valence electron density based force field for high-energy interactions between atoms and molecules.

High-accuracy molecular force field models suited for hot gases and plasmas are not as abundant as those geared toward ambient pressure and temperature conditions. Here, we present an improved version of our previous electron-density based force field model that can now account for polarization effects by adjusting the atomic valence electron contributions to match abinitio calculated Mulliken partial charges. Using a slightly modified version of the Hohenberg-Kohn theorem, we also include an improved theoretical formulation of our model when applied to systems with degenerate ground states. We present two variants of our polarizable model, fitted from abinitio reference data calculated at CCSD(T)/cc-pVTZ and CCSD(T)/CEP-31G levels of theory, that both accurately model water dimer interaction energies. Further improvements include the additional interaction components with fictitious non-spherically symmetric, yet atom-centered, electron densities and fitting the exchange and correlation coefficients against analytical expressions. The latter removes all unphysical oscillations that are observed in the previous non-polarizable variant of our force field.

Competition between O-H and S-H Intermolecular Interactions in Conformationally Complex Systems: The 2-Phenylethanethiol and 2-Phenylethanol Dimers.

Noncovalent interactions involving sulfur centers play a relevant role in biological and chemical environments. Yet, detailed molecular descriptions are scarce and limited to very simple model systems. Here we explore the formation of the elusive S-H···S hydrogen bond and the competition between S-H···O and O-H···S interactions in pure and mixed dimers of the conformationally flexible molecules 2-phenylethanethiol (PET) and 2-phenylethanol (PEAL), using the isolated and size-controlled environment of a jet expansion. The structure of both PET-PET and PET-PEAL dimers was unraveled through a comprehensive methodology that combined rotationally resolved microwave spectroscopy, mass-resolved isomer-specific infrared laser spectroscopy, and quantum chemical calculations. This synergic experimental-computational approach offered unique insights into the potential energy surface, conformational equilibria, molecular structure, and intermolecular interactions of the dimers. The results show a preferential order for establishing hydrogen bonds following the sequence S-H···S < S-H···O ≲ O-H···S < O-H···O, despite the hydrogen bond only accounting for a fraction of the total interaction energy.

Subunit Communication within Dimeric SF1 DNA Helicases

Monomers of the Superfamily (SF) 1 helicases, E. coli Rep and UvrD, can translocate directionally along single stranded (ss) DNA, but must be activated to function as helicases. In the absence of accessory factors, helicase activity requires Rep and UvrD homo-dimerization. The ssDNA binding sites of SF1 helicases contain a conserved aromatic amino acid (Trp250 in Rep and Trp256 in UvrD) that stacks with the DNA bases. Here we show that mutation of this Trp to Ala eliminates helicase activity in both Rep and UvrD. Rep(W250A) and UvrD(W256A) can still dimerize, bind DNA, and monomers still retain ATP-dependent ssDNA translocase activity, although with ∼10-fold lower rates and lower processivities than wild type monomers. Although neither wtRep monomers nor Rep(W250A) monomers possess helicase activity by themselves, using both ensemble and single molecule methods, we show that helicase activity is achieved upon formation of a Rep(W250A)/wtRep hetero-dimer. An ATPase deficient Rep monomer is unable to activate a wtRep monomer indicating that ATPase activity is needed in both subunits of the Rep hetero-dimer. We find the same results with E. coli UvrD and its equivalent mutant (UvrD(W256A)). Importantly, Rep(W250A) is unable to activate a wtUvrD monomer and UvrD(W256A) is unable to activate a wtRep monomer indicating that specific dimer interactions are required for helicase activity. We also demonstrate subunit communication within the dimer by virtue of Trp fluorescence signals that only are present within the Rep dimer, but not the monomers. These results bear on proposed subunit switching mechanisms for dimeric helicase activity.

Investigation of the structure and multi-stimuli-responsive behavior of ion-associated salt solvates of binary crystals

Investigation of the intermolecular interactions and crystal packing to understand crystal growth is a prime objective of crystal engineering. Solvent molecules within crystal assist the supramolecular aggregation, however, control over their lattice incorporation remains uncertain. In this work, we report three solvates of an ionic organic salt of a diazo-naphthol sulfonate (1) and 1,10-phenanthroline with one (2), three (3) and four (4) lattice water molecules. Attempts to isolate the dihydrate form were unsuccessful, while the monohydrate of 1 has been crystallised for comparative structural investigations. Structural studies reveal the existence of intriguing sulfonate-diazo intermolecular interactions responsible for centrosymmetric dimerization of the organosulfonate 1, which also persist in 2–4, validating higher preference and robustness of the synthon. Repetitive aggregation of the sulfonate-diazo interaction in 1 leads to the formation of linear π-stacked aggregate, which further aggregates through the lattice water molecules. The structural comparison indicates the preferential formation of the organo-sulfonate dimers in hydrated salts 2–4. Further, sandwich tetramers in 2 and 4 are formed by charge transfer interaction of the organo-sulfonate dimers with pyridinium coformer on either side, which are further associated by the lattice water molecules into disparately packed 3-dimensional supramolecules. The organo-sulfonates in 3 form a similar type of extended π-stacked chains as in 1, which are flanked by pyridinium ions to form hydrogen-bonded tapes, which are helped by the lattice water molecules to grow as segregated stacked layer solid. The characteristic absorption frequency of the diazo functionality is blue-shifted in infrared spectra of the cocrystal forms, indicating the presence of charge transfer interactions. The presence of dynamic solvent and protons in the lattice makes the solid forms multi-stimuli-responsive to exhibit mechano and vapochromic response. These phenomena have been studied in detail with the help of thermal, spectroscopic, and powder-diffraction studies.

A Conserved Intramolecular Ion-Pair Plays a Critical but Divergent Role in Regulation of Dimerization and Transport Function among the Monoamine Transporters.

The monoamine transporters, including the serotonin transporter (SERT), dopamine transporter (DAT), and norepinephrine transporter (NET), are the therapeutic targets for the treatment of many neuropsychiatric disorders. Despite significant progress in characterizing the structures and transport mechanisms of these transporters, the regulation of their transport functions through dimerization or oligomerization remains to be understood. In the present study, we identified a conserved intramolecular ion-pair at the third extracellular loop (EL3) connecting TM5 and TM6 that plays a critical but divergent role in the modulation of dimerization and transport functions among the monoamine transporters. The disruption of the ion-pair interactions by mutations induced a significant spontaneous cross-linking of a cysteine mutant of SERT and an increase in cell surface expression but with an impaired specific transport activity. On the other hand, similar mutations of the corresponding ion-pair residues in both DAT and NET resulted in an opposite effect on their oxidation-induced dimerization, cell surface expression, and transport function. Reversible biotinylation experiments indicated that the ion-pair mutations slowed down the internalization of SERT but stimulated the internalization of DAT. In addition, cysteine accessibility measurements for monitoring SERT conformational changes indicated that substitution of the ion-pair residues resulted in profound effects on the rate constants for cysteine modification in both the extracellular and cytoplasmatic substrate permeation pathways. Furthermore, molecular dynamics simulations showed that the ion-pair mutations increased the interfacial interactions in a SERT dimer but decreased it in a DAT dimer. Taken together, we propose that the transport function is modulated by the equilibrium between monomers and dimers on the cell surface, which is regulated by a potential compensatory mechanism but with different molecular solutions among the monoamine transporters. The present study provided new insights into the structural elements regulating the transport function of the monoamine transporters through their dimerization.

Defining Requirements for Heme Binding in PGRMC1 and Identifying Key Elements that Influence Protein Dimerization.

Progesterone receptor membrane component 1 (PGRMC1) binds heme via a surface-exposed site and displays some structural resemblance to cytochrome b5 despite their different functions. In the case of PGRMC1, it is the protein interaction with drug-metabolizing cytochrome P450s and the epidermal growth factor receptor that has garnered the most attention. These interactions are thought to result in a compromised ability to metabolize common chemotherapy agents and to enhance cancer cell proliferation. X-ray crystallography and immunoprecipitation data have suggested that heme-mediated PGRMC1 dimers are important for facilitating these interactions. However, more recent studies have called into question the requirement of heme binding for PGRMC1 dimerization. Our study employs spectroscopic and computational methods to probe and define heme binding and its impact on PGRMC1 dimerization. Fluorescence, electron paramagnetic resonance and circular dichroism spectroscopies confirm heme binding to apo-PGRMC1 and were used to demonstrate the stabilizing effect of heme on the wild-type protein. We also utilized variants (C129S and Y113F) to precisely define the contributions of disulfide bonds and direct heme coordination to PGRMC1 dimerization. Understanding the key factors involved in these processes has important implications for downstream protein-protein interactions that may influence the metabolism of chemotherapeutic agents. This work opens avenues for deeper exploration into the physiological significance of the truncated-PGRMC1 model and developing design principles for potential therapeutics to target PGRMC1 dimerization and downstream interactions.

Quantum Drude oscillators coupled with Coulomb potential as an efficient model for bonded and non-covalent interactions in atomic dimers.

The quantum Drude oscillator (QDO) model has been widely used as an efficient surrogate to describe the electric response properties of matter as well as long-range interactions in molecules and materials. Most commonly, QDOs are coupled within the dipole approximation so that the Hamiltonian can be exactly diagonalized, which forms the basis for the many-body dispersion method [Phys. Rev. Lett. 108, 236402 (2012)]. The dipole coupling is efficient and allows us to study non-covalent many-body effects in systems with thousands of atoms. However, there are two limitations: (i) the need to regularize the interaction at short distances with empirical damping functions and (ii) the lack of multipolar effects in the coupling potential. In this work, we convincingly address both limitations of the dipole-coupled QDO model by presenting a numerically exact solution of the Coulomb-coupled QDO model by means of quantum Monte Carlo methods. We calculate the potential-energy surfaces of homogeneous QDO dimers, analyzing their properties as a function of the three tunable parameters: frequency, reduced mass, and charge. We study the coupled-QDO model behavior at short distances and show how to parameterize this model to enable an effective description of chemical bonds, such as the covalent bond in the H2 molecule.