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A recent study showed that just one point mutation F33 to Y in the complementarity-determining region 1 of heavy chain (H-CDR1) could lead to the auto-antibody losing its DNA binding ability. However, the potential molecular mechanisms have not been well elucidated. In this study, we investigated how the antibody lost the DNA binding ability caused by mutation F33 to Y in the H-CDR1. We found that the electrostatic force was not the primary driving force for the interaction between anti-DNA antibodies and the antigen single strand DNA (ssDNA), and that the H-CDR2 largely contributed to the binding of antigen ssDNA, even larger than H-CDR1. The H-F33Y mutation could increase the hydrogen-bond interaction but impair the pi-pi stacking interaction between the antibody and ssDNA. We further found that F33H, W98H and Y95L in the wiletype antibody could form the stable pi-pi stacking interaction with the nucleotide bases of ssDNA. However, the Y33 in mutant could not form the parallel sandwich pi-pi stacking interaction with the ssDNA. To further confirm the importance of pi-pi stacking, the wildtype antibody and the mutants (F33YH, F33AH, W98AH and Y95AL) were experimentally expressed in CHO cells and purified, and the results from ELISA clearly showed that all the mutants lost the ssDNA binding ability. Taken together, our findings may not only deepen the understanding of the underlying interaction mechanism between autoantibody and antigen, but also broad implications in the field of antibody engineer.

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This work conducts the comprehensive theoretical study on the non-covalent complexation between cyclocarbons and C60 fullerene for the first time. The binding energy between cyclocarbons and C60 fullerene is significantly stronger than that between two C18 or two C60 fullerenes, indicating a particularly strong affinity. The cyclocarbons and C60 fullerene can spontaneously assemble into complexes in the gas phase at room temperature, and the hydrophobic effect caused by the solvent environment can promote this binding. The binding strength with C60 fullerene increases almost linearly with the increase of cyclocarbon size, and the C34@C60 dimer exhibits a perfect nano-Saturn structure. As the ring size increases, the angle between the two cyclocarbons of the 2:1 trimers formed by cyclocarbons and C60 fullerene gradually decreases. In C60@2C34 trimer, the fullerene is symmetrically surrounded by two cyclocarbons. The results on the trimers formed by cyclocarbon and C60 fullerenes in a 1:2 ratio showed when the cyclocarbon sandwiched between two fullerenes is not quite large, the trimers exhibit an ideal dumbbell-like structure, and the presence of the first fullerene has a significant synergistic effect on the binding of the second one. The cyclocarbon greatly promotes the dimerization of fullerenes, which acted as a "molecular glue".

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Human liver microsomes containing various drug-metabolizing cytochrome P450 (P450) enzymes, along with their NADPH-reductase bound to phospholipid membranes, were absorbed onto 1-pyrene butylamine pi-pi stacked with amine-functionalized multiwalled carbon nanotube-modified graphite electrodes. The interfaced microsomal biofilm demonstrated direct electrochemical communication with the underlying electrode surface and enhanced oxygen reduction electrocatalytic activity typical of heme enzymes such as P450s over the unmodified electrodes and nonenzymatic currents. Similar enhancements in currents were observed when the bioelectrodes were constructed with recombinant P450 2C9 (single isoform) expressed bactosomes. The designed liver microsomal and 2C9 bactosomal bioelectrodes successfully facilitated the electrocatalytic conversion of diclofenac, a drug candidate, into 4'-hydroxydiclofenac. The enzymatic electrocatalytic metabolite yield was several-fold greater on the modified electrodes than on the unmodified bulk graphite electrodes adsorbed with a microsomal or bactosomal film. The nonenzymatic metabolite production was less than the enzymatically catalyzed metabolite yield in the designed microsomal and bactosomal biofilm electrodes. To test the throughput potential of the designed biofilms, eight-electrode array configurations were tested with the microsomal and bactosomal biofilms toward electrochemical 4'-hydroxydiclofenac metabolite production from diclofenac. The stability of the designed microsomal bioelectrode was assessed using nonfaradaic impedance spectroscopy over 40 h, which indicated good stability.

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Sodium-ion batteries (SIBs) are a possible candidate to create safe, sustainable, and cost-effective batteries. Solid sodium-ion conducting organically modified ionogel electrolytes are investigated. Silica-based ionogels typically consist of an ionic liquid electrolyte (ILE) confined within a silica matrix and possess high thermal stability, good ionic conductivity, safety, and good electrochemical stability. However, they readily deteriorate when stress is applied, decreasing the electrolyte's and battery's overall performance. The mechanical characteristics of silica can be improved using organic moieties, creating Ormosils®. Silica-based ionogels with phenyl-modified silanes improve the mechanical characteristics by a reduction of their Young's modulus (from 29 to 6 MPa). This is beneficial to the charge-transfer resistance, which decreases after implementing the electrolyte in half cells, demonstrating the improved interfacial contact. Most importantly, the phenyl groups change the interacting species at the silica interface. Cationic imidazolium species pi-stacked to the phenyl groups of the silica matrix, pushing the anions to the bulk of the ILE, which affects the ionic conductivity and electrochemical stability, and might affect the quality of the SEI in half cells. In essence, the work at hand can be used as a directory to improve mechanical characteristics and modify and control functional properties of ionogel electrolytes.

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Interactions between the popular sunscreen ingredients oxybenzone and homosalate and DNA bases have been studied using density functional theory and ab initio methods. Low-energy structures for each sunscreen ingredient interacting with each nucleotide base in either a pi-stacked or hydrogen-bonded fashion were found. The binding energies are comparable to those for the Watson-Crick-Franklin Ade-Thy and Cyt-Gua pairs. Pi-stacked and hydrogen-bonded structures are comparable in energy, with hydrogen-bonded structures having a more negative counterpoise-corrected binding energy, while the final pi-stacked structures are lower in energy. This is due to a geometrical rearrangement required to form the hydrogen bonds that raise the total energy of the complex. It was also found that when using the M06-2X density functional, the STO-3G basis set favors hydrogen bonding, but 6-31G(d) and 6-31 + G(s) basis sets predict similar binding geometries.

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OBJECTIVE: This study aims to investigate the use of single residue substitution to promote the formation of pi-stacking interactions between peptides and Human leukocyte antigen (HLA)-A*2402 molecules to improve the affinity of peptides and HLA molecules, as well as the level of cytotoxic T lymphocyte (CTL) cells activated by peptides-HLA (p-HLA) complex. METHODS: Molecular docking and molecular dynamics simulation were used to simulate and analyze the interactions and binding free energies between HLA-A*2402-restricted antigen peptides and HLA molecules, before and after the single residue substitution. HLA-A*2402 restricted antigen peptides before and after the single residue replacement were loaded into dendritic cells (DCs) in vitro, and further Enzyme-Linked ImmunoSpot (ELispot) test was carried out to evaluate the effect of modified antigen peptides on the immune activation of CTL cells. RESULT: After replacing the antigen peptides with a single residue, some of them could promote the formation of pi-stacking interaction. The binding free energy between the modified antigen peptides and HLA-A*2402, as well as the level of immune activation of CTL cells were mostly higher than before, especially after the replacement of the 9th residue of the polypeptide, such as C9F and C9W. There was a significant negative correlation between the level of activated CTL cells by modified antigen peptides and the total interaction amount of hydrogen bonds and salt bridges. CONCLUSION: Promoting the formation of pi-stacking interaction between antigen peptides and HLA-A*2402 molecules could increase the total binding free energy of p-HLA complex and the level of CTL cells activation. In addition, the amount of hydrogen bonds and salt bridges between peptides and HLA could reduce the level of immune activation. All the characteristics above can improve the immunogenicities of the weak antigens.

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Poly(glycerol sebacate) (PGS), a soft, tough elastomer with excellent biocompatibility, has been exploited successfully in many tissue engineering applications. Although tunable to some extent, the rapid in vivo degradation kinetics of PGS is not compatible with the healing rate of some tissues. The incorporation of L-glutamic acid into a PGS network with an aim to retard the degradation rate of PGS through the formation of peptide bonds was conducted in this study. A series of poly(glycerol sebacate glutamate) (PGSE) containing various molar ratios of sebacic acid/L-glutamic acid were synthesized. Two kinds of amino-protected glutamic acids, Boc-L-glutamic acid and Z-L-glutamic acid were used to prepare controls that consist of no peptide bonds, denoted as PGSE-B and PGSE-Z, respectively. The prepolymers were characterized using 1H-NMR spectroscopy. Cured elastomers were characterized using FT-IR, DSC, TGA, mechanical testing, and contact angle measurement. In vitro enzymatic degradation of PGSE over a period of 28 days was investigated. FT-IR spectroscopy confirmed the formation of peptide bonds. The glass transition temperature for the elastomer was found to increase as the ratio of sebacic acid/glutamic acid was increased to four. The decomposition temperature of the elastomer decreased as the amount of glutamic acid was increased. PGSE exhibited less stiffness and larger elongation at break as the ratio of sebacic acid/glutamic acid was decreased. Notably, PGSE-Z was stiffer and had smaller elongation at break than PGSE and PGSE-B at the same molar ratio of monomers. The results of in vitro enzymatic degradation demonstrated that PGSE has a lower degradation rate than does PGS, whereas PGSE-B and PGSE-Z degrade at a greater rate than does PGS. SEM images suggest that the degradation of these crosslinked elastomers is due to surface erosion. The cytocompatibility of PGSE was considered acceptable although slightly lower than that of PGS. The altered mechanical properties and retarded degradation kinetics for PGSE reflect the influence of peptide bonds formed by the introduction of L-glutamic acid. PGSE displaying a lower degradation rate compared to that for PGS can be used as a scaffold material for the repair or regeneration of tissues that are featured by a low healing rate.

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This study expands and combines concepts from two of our earlier studies. One study reported the complementary halogen bonding and π-π charge transfer complexation observed between isomeric electron rich 4-N,N-dimethylaminophenylethynylpyridines and the electron poor halogen bond donor, 1-(3,5-dinitrophenylethynyl)-2,3,5,6-tetrafluoro-4-iodobenzene while the second study elaborated the ditopic halogen bonding of activated pyrimidines. Leveraging our understanding on the combination of these non-covalent interactions, we describe cocrystallization featuring ditopic halogen bonding and π-stacking. Specifically, red cocrystals are formed between the ditopic electron poor halogen bond donor 1-(3,5-dinitrophenylethynyl)-2,4,6-triflouro-3,5-diiodobenzene and each of electron rich pyrimidines 2- and 5-(4-N,N-dimethyl-aminophenylethynyl)pyrimidine. The X-ray single crystal structures of these cocrystals are described in terms of halogen bonding and electron donor-acceptor π-complexation. Computations confirm that the donor-acceptor π-stacking interactions are consistently stronger than the halogen bonding interactions and that there is cooperativity between π-stacking and halogen bonding in the crystals.

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The powerful independent gradient model (IGM) method has been increasingly popular in visual analysis of intramolecular and intermolecular interactions in recent years. However, we frequently observed that there is an evident shortcoming of IGM map in graphically studying weak interactions, that is its isosurfaces are usually too bulgy; in these cases, not only the graphical effect is poor, but also the color on some areas on the isosurfaces is inappropriate and may lead to erroneous analysis conclusions. In addition, the IGM method was originally proposed based on promolecular density, which is quite crude and does not take actual electronic structure into account. In this article, we propose an improvement version of IGM, namely IGM based on Hirshfeld partition of molecular density (IGMH), which replaces the free-state atomic densities involved in the IGM method with the atomic densities derived by Hirshfeld partition of actual molecular electron density. This change makes IGM have more rigorous physical background. A large number of application examples in this article, including molecular and periodic systems, weak and chemical bond interactions, fully demonstrate the important value of IGMH in intuitively understanding interactions in chemical systems. Comparisons also showed that the IGMH usually has markedly better graphical effect than IGM and overcomes known problems in IGM. Currently IGMH analysis has been supported in our wavefunction analysis code Multiwfn (http://sobereva.com/multiwfn). We hope that IGMH will become a new useful method among chemists for exploring interactions in wide variety of chemical systems.

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The fine structure in the spectral lines of the visible fluorescence of Tb3+ complexes are replaced by a single peak in the case of a singular molecular complex Tb(H3 PTC)3 , where H4 PTC represents perylene-3,4,9,10-tetracarboxylic acid, and its emission wavelength depends on the film thickness. This single peak challenges the old creed that the f-orbital electrons of Tb3+ are always protected from the influence of the surrounding atoms. We perform density functional theory calculations to show that the wavefunction of the ground state is localized and in addition, spin-polarized, and this facilitates fluorescent transitions under UV to the first excited state instead of the fundamental state. We discuss the possibility of making a spintronic device with the molecule, Tb(H3 PTC)3 .

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Self-assembling filomicelles (FM) are of great interest to nanomedicine due to their structural flexibility, extensive systemic circulation time, and amenability to unique "cylinder-to-sphere" morphological transitions. However, current fabrication techniques for FM self-assembly are highly variable and difficult to scale. Here, we demonstrate that tetrablock copolymers composed of poly(ethylene glycol)-b-poly(propylene sulfide) (PEG-b-PPS) diblocks linked by a pi-stacking perylene bisimide (PBI) moiety permit rapid, scalable, and facile assembly of FM via the flash nanoprecipitation (FNP) method. Co-assembling the tetrablocks and PEG-b-PPS diblocks at different molar ratios resulted in mixed PBI-containing FM (mPBI-FM) with tunable length and flexibility. The flexibility of mPBI-FM can be optimized to decrease uptake by macrophages in vivo, leading to increased circulation time versus (-)PBI-FM without PBI tetrablocks after intravenous administration in mice. While PEG-b-PPS diblocks form FM within a narrow range of hydrophilic weight fractions, incorporation of pi-stacking PBI groups expanded this range to increase favorability of FM assembly. Furthermore, the aggregation-dependent fluorescence of PBI shifted during oxidation-induced "cylinder-to-sphere" transitions of mPBI-FM into micelles, resulting in a distinct emission wavelength for filamentous versus spherical nanostructures. Thus, incorporation of pi-stacking allows for rapid, scalable assembly of FM with tunable flexibility and stability for theranostic and nanomedicine applications.

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Aromatic molecules such as pyrenes are a unique class of building units for graphene functionalization, forming highly ordered π-π stacks while peptides provide more complex, biocompatible linkers. Understanding the adsorption and stacking behavior of these molecules and their influence on material properties is an essential step in enabling highly repeatable 2D material-based applications, such as biosensors, gas sensors, and solar cells. In this work, we characterize pyrene and peptide self-assembly on graphene substrates using fluorescence microscopy, atomic force microscopy and electrolyte-gated field-effect measurements supported by quantum mechanical calculations. We find distinct binding and assembly modes for pyrenes versus peptides with corresponding distinct electronic signatures in their characteristic charge neutrality point and field-effect slope responses. Our data demonstrates that pyrene- and peptide-based self-assembly platforms can be highly beneficial for precisely customizing graphene electronic properties for desired device technologies such as transport-based biosensing graphene field-effect transistors.

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The research in storage and conversion of energy is an everlasting process. The use of fuel cells is very tempting but up to now there are still several conceptual challenges to overcome. Especially, the requirement of liquid water causes difficulties due to the temperature limit. Therefore, imidazoles and triazoles are increasingly investigated in a manifold of experimental and theoretical publications as they are both very promising in overcoming this problem. Recently, triazoles were found to be superior to imidazoles in proton conduction. An ab-initio molecular dynamics simulation of pure triazole phases for investigating the behavior of both tautomer species of the triazole molecule has never been done. In this work, we investigate the structural and dynamical properties of two different solid phases and the liquid phase at two different temperatures. We are able to show how the distinct tautomers contribute to the mechanism of proton conduction, to compute dynamical properties of the four systems and to suggest a mechanism of reorientation in solid phase.

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A novel catechol based dipodal fluorescent chelator N,N'-bis[3-[(E)-(2,3-dihydroxyphenyl)methyleneamino]propyl]propanediamide(MPC), has been developed and its photophysical behaviour was studied by experimental (UV-VIS and fluorescence) and DFT method. The design of the molecule has been inspired from the naturally occurring siderophore enterobactin, a catechol based chelator with amide linkage, that shows an excellent binding efficiency towards Fe(III). The dipodal molecule (MPC) presented here, carries two catechol pendant binding moieties linked to the malonate central unit through propylene spacers by amide linkage. MPC showed good selectivity for Fe(III) at 10-4 M concentration in aqueous medium amongst the biologically and environmentally important metal ions chosen viz., Na(I), K(I), Al(III), Cr(III), Fe(III), Fe(II), Co(II), Ni(II), Cu(II), and Zn(II), by demonstrating a remarkable quenching in the fluorescent emission from 262 a.u. to 55 a.u. at λmax = 477 nm. Also, the pre-organized assembled ligand favored an efficient Fe (III) encapsulation through coordination by imine nitrogen and catecholate oxygen donors. High formation constant (log ß = 31.3) for 1:1 metal-ligand complex evaluated by both potentiometric and spectrophotometric methods, established the strong binding efficiency of the ligand for Fe(III) metal ion. The binding stoichiometry in the complex was also confirmed from Stern -Volmer and Hill Plot analysis. Further investigation on the emission behavior of MPC in a completely DMSO system explored its suitability for extensive applications in the areas such as, metallurgy, material science, iron contamination remedial in the materials etc.. DFT studies suggest that the ligand displays a U-shaped geometry with a parallel π-stacking and the hydrogen bond between two arms. The experimental infrared, electronic, fluorescence, 1H nmr, 13C nmr spectra were correlated with the theoretical results. The nature of electronic transitions were identified from the TDDFT calculation. The ligand forms a hexa-coordinated complex with six Fe-O bonds extending an orthorhombic geometry due distortion from a regular octahedron.

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A category of parallel π-stacking interaction, termed pancake bonding, is surveyed. The main characteristics are: the interaction occurs among radicals with highly delocalized π-electrons in their singly occupied molecular orbitals (SOMOs), the contact distances in the π-stacking direction are shorter than the typical van der Waals distances, and the stabilization obtained by the bonding combination of the SOMO orbitals leads to direct atom-to-atom overlap with strong orientational preferences. These atypical intermolecular interactions contain a component of electron sharing between the radicals that can be viewed as covalent-like. Pancake bonded dimers characteristically have low-lying singlet and triplet states and show characteristic interlayer vibrational modes. Pancake bonded aggregates serve as molecular components in many conducting and other functional organic materials. The role of van der Waals (vdW) interactions in pancake bonded dimers, chains, and other aggregates is different from closed shell vdW aggregates: here the Pauli repulsions reduce the attractive dispersion interaction significantly. Fluxionality between π- and σ-bonded aggregates often occur in the context of pancake bonding. Both experimental and computational aspects are reviewed.

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The introduction of the trialkylsilylethynyl group to the acene core is known to predominantly transform the herringbone structure of pentacene to a slip-stacked packing. However, herein, the occurrence of an unforeseen polymorph of 6,13-bis(trimethylsilylethynyl)pentacene (TMS-pentacene), with an atypical γ-herringbone packing arrangement, is reported. Intermolecular noncovalent interactions in the γ-herringbone polymorph are determined from Hirshfeld surface and quantum theory of atoms-in-molecules (QTAIM) analyses. Furthermore, a comparative truncated symmetry-adapted perturbation theory (SAPT(0)) energy decomposition analysis discloses the role of exchange repulsions that govern molecular packing in the γ-herringbone polymorph. Moreover, the computationally predicted electronic coupling and anisotropic mobility reveal the possibility of enhanced hole transport (µh =3.7 cm2 V-1 s-1 ) in the γ-herringbone polymorph, in contrast to the reported polymorph with a hole mobility of µh =0.1 cm2 V-1 s-1 .

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Supramolecular hydrogels obtained by combining 5'-adenosine monophosphate (AMP) with Ag+ were fabricated in this work. Their gelation capability was enhanced by increasing the concentration of Ag+ or decreasing the pH. The gels are very sensitive to light, which endows them with potential applications as visible-light photosensitive materials. Coordination between the nucleobase of AMP and Ag+ , as well as π-π stacking of nucleobases, are considered to be the main driving forces for self-assembly. The hydrogels successfully achieved the encapsulation and enrichment of biomolecules. Hydrogen bonding between the amino group of guest molecules and silver nanoparticles along the nanofibers drives the enrichment and is considered to be a crucial interaction.

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Delivery of taxane-based chemotherapeutics including Docetaxel (DTX) by conventional polymeric micelles still suffers from insufficient stability and rapid premature release during the circulation, which limits their targeting and anticancer efficiency. To conquer these challenges, we developed a novel DTX-loaded Pi-Pi stacking-stabilized dendritic polymeric micelle for targeted therapy of liver cancer. This dendritic polymeric micelle, referred to DPM-DTX-cRGD, was self-assembled from DTX and biodegradable dendritic block copolymers Poly(amidoamine)-poly(γ-benzyl-l-Glutamate)-b-polyethylene glycol-cRGD (PAM-PBLG-b-PEG-cRGD). DPM-DTX-cRGD held robust stability due to its covalent dendritic structure and would load abundant DTX with excellent retention via Pi-Pi stacking between DTX and the aromatic groups of the PBLG segments. The cellular uptake studies demonstrated that the cRGD-conjugated dendritic polymeric micelle (DPM) exhibited much higher cellular uptake in human liver cancer HepG2 cells than non-targeted DPM. The MTT assay also confirmed that DPM-DTX-cRGD caused much greater cytotoxicity than non-targeted DPM-DTX and a clinically available DTX formulation (Taxotere®). Therefore, this DPM-DTX-cRGD provides a novel attractive approach for targeted therapy of liver cancer.

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A key parameter in the operation of an electrochemical double-layer capacitor is the voltage window, which dictates the device energy density and power density. Here we demonstrate experimental evidence that π-π stacking at a carbon-ionic liquid interface can modify the operation voltage of a supercapacitor device by up to 30%, and this can be recovered by steric hindrance at the electrode-electrolyte interface introduced by poly(ethylene oxide) polymer electrolyte additives. This observation is supported by Raman spectroscopy, electrochemical impedance spectroscopy, and differential scanning calorimetry that each independently elucidates the signature of π-π stacking between imidazole groups in the ionic liquid and the carbon surface and the role this plays to lower the energy barrier for charge transfer at the electrode-electrolyte interface. This effect is further observed universally across two separate ionic liquid electrolyte systems and is validated by control experiments showing an invariant electrochemical window in the absence of a carbon-ionic liquid electrode-electrolyte interface. As interfacial or noncovalent interactions are usually neglected in the mechanistic picture of double-layer capacitors, this work highlights the importance of understanding chemical properties at supercapacitor interfaces to engineer voltage and energy capability.

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Neurotoxic plaques composed of 39 to 42 residue-long amyloid beta peptides (Aßs) are copiously present in the brains of patients with Alzheimer's disease (AD). Erythrosine B (ER), a xanthene food dye, inhibits the formation of Aß fibrils and Aß-associated cytotoxicity in vitro. Here, in an attempt to elucidate the inhibition mechanism, we performed molecular dynamics (MD) simulations to demonstrate the conformational change of Aß40 induced by ER molecules in atomistic detail. During the simulation, the ER bound to the surfaces of both N-terminus and C-terminus regions of Aß40. Our result shows that ER interacts with the aromatic side chains at the N-terminus region resulting in destabilization of the inter-chain stacking of Aß40. Moreover, the stablility of the helical structures at the residues from 13 to 16 suggests that ER disturbs conformational transition of Aß40. At the C-terminus region, the bound ER blocks water molecules and stabilizes the α-helical structure. Regardless of the number of ER molecules used, the interruption of the formation of the salt-bridge between aspartic acid 23 and lysine 28 occurred. To further validate our analysis, binding free energies of ER at each binding site were evaluated. The finding of stronger binding energy at the N-terminus region supports an inhibition mechanism induced by stacking interaction between ER and phenylalanine. These findings could aid present and future treatment studies for AD by clarifying the inhibition mechanism of ER on the conformational transition of Aß40 at the molecular level.

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