GPCR targeting of E3 ubiquitin ligase MDM2 by inactive ß-arrestin.

E3 ubiquitin ligase Mdm2 facilitates ß-arrestin ubiquitination, leading to the internalization of G protein-coupled receptors (GPCRs). In this process, ß-arrestins bind to Mdm2 and recruit it to the receptor; however, the molecular architecture of the ß-arrestin-Mdm2 complex has not been elucidated yet. Here, we identified the ß-arrestin-binding region (ABR) on Mdm2 and solved the crystal structure of ß-arrestin1 in complex with Mdm2ABR peptide. The acidic residues of Mdm2ABR bind to the positively charged concave side of the ß-arrestin1 N-domain. The C-tail of ß-arrestin1 is still bound to the N-domain, indicating that Mdm2 binds to the inactive state of ß-arrestin1, whereas the phosphorylated C-terminal tail of GPCRs binds to activate ß-arrestins. The overlapped binding site of Mdm2 and GPCR C-tails on ß-arrestin1 suggests that the binding of GPCR C-tails might trigger the release of Mdm2. Moreover, hydrogen/deuterium exchange experiments further show that Mdm2ABR binding to ß-arrestin1 induces the interdomain interface to be more dynamic and uncouples the IP6-induced oligomer of ß-arrestin1. These results show how the E3 ligase, Mdm2, interacts with ß-arrestins to promote the internalization of GPCRs.

Polyaromatic hydrocarbon thin film layers on glass, dust, and polyurethane foam surfaces.

An investigation was conducted into the dynamic behavior of two polyaromatic hydrocarbon (PAH) semi-volatile organic compound (SVOC) naphthalene (NAP) and benzo [ghi]perylene (BghiP) in air and on various surfaces including glass, dust, and polyurethane foam (PUF) to understand their interaction with different media. A confocal fluorescence microscope and an infrared microscope were employed to detect and monitor the concentration-, time-, and temperature-dependent changes of the aromatic NAP and BghiP species on the surfaces. Infrared two-dimensional mapping of the vibrational characteristic peaks was used to track the two PAHs on the surfaces. Gas chromatography-mass spectrometry (GC-MS) was employed to measure the gaseous concentrations. The sorption of NAP and BghiP on the surfaces was estimated using Arizona desert sand fine (ISO 12103-1 A2) dust and organic contaminant household (SRM 2585) dust. The surface-to-air partition coefficients of NAP and BghiP were estimated on the different surfaces of glass, dust, and PUF. Molecular dynamic simulations were performed on dust surfaces based on the Hatcher model to understand the behavior of NAP and BghiP on dust surfaces. The Weschler-Nazaroff model was introduced to predictPAH film accumulation on the surfaces, providing a better understanding of PAH interaction with different environmental media. These findings could contribute to developing effective strategies to mitigate the adverse impact of PAHs on the environment and human health.

Equilibria of semi-volatile isothiazolinones between air and glass surfaces measured by gas chromatography and Raman spectroscopy.

Trace amounts of semi-volatile organic compounds (SVOCs) of the two isothiazolinones of 2-methylisothiazol-3(2H)-one (MIT) and 2-octyl-4-isothiazolin-3-one (OIT) were detected both in the air and on glass surfaces. Equilibria of SVOCs between air and glass were examined by solid phase microextraction-gas chromatography/mass spectrometry (SPME-GC/MS). Surface to air distribution ratios of Ksa for MIT and OIT were determined to be 5.10 m and 281.74 m, respectively, suggesting more abundant MIT in the gas phase by a factor of ∼55. In addition, a facile method of silver nanocube (AgNC)-assisted surface-enhanced Raman scattering (SERS) has been developed for the rapid and sensitive detection of MIT and OIT on glass surfaces. According to MIT and OIT concentration-correlated SERS intensities of Raman peaks at ∼1585 cm-1 and ∼1125 cm-1, respectively. Their calibration curves have been obtained in the concentration ranges between 10-3 to 10-10 M and 10-3 to 10-11 M with their linearity of 0.9986 and 0.9989 for MIT and OIT, respectively. The limits of detection (LODs) of the two isothiazolinones were estimated at 10-10 M, and 10-11 M for MIT and OIT, respectively. Our results indicate that AgNC-assisted SERS spectra are a rapid and high-ultrasensitive method for the quantification of MIT and OIT in practical applications. The development of analytical methods and determination of the Ksa value obtained in this study can be applied to the prediction of the exposure to MIT and OIT from various chemical products and dynamic behaviors to assess human health risks in indoor environments.

Carbon capture and biocatalytic oxygen production of photosystem II from thylakoids and microalgae on nanobiomaterials.

Enhanced carbon capture and oxygen production via water splitting was observed by controlling the plasmon-induced resonance energy transfer (PIRET) for photosystem II (PSII) in thylakoid extracts and spirulina assembled on gold nanoparticle (AuNP) dimer arrays. The two types of vertical (V) and horizontal (H) AuNP dimer arrays were uniformly inserted inside pore diameter-controlled templates. Based on the theoretical calculations, the longitudinal mode of the H AuNP dimer array was found to be sensitive to the nanogap distances between the two AuNPs in resonance with the absorption at P680 of the PSII. The longitudinal modes that interacted with P680 of PSII increased from the V to the H conformer. The optical properties from the H AuNP dimer array caused overlapping absorbance and photoluminescence with PSII, and the H AuNP dimer arrays exhibited a significant increase in carbon capture and oxygen generation rates in comparison with those of the bare PSII protein complex under light irradiation via the controlled PIRET process.

Analysis of semi-volatile organic compounds in indoor dust and organic thin films by house type in South Korea.

In this study, semi-volatile organic compounds (SVOCs) in samples of indoor dust and organic thin films obtained from 100 residential houses in South Korea, were examined, based on both target analysis using gas chromatography-mass spectrometry (GC-MS) and non-target analysis by gas chromatography-quadrupole time-of flight mass spectrometry (GC-QTOF-MS) screening. In the targeted approach, phthalates and polycyclic aromatic hydrocarbons (PAHs) were analyzed in dust and organic film samples, to find that both these classes of SVOCs were detected in dust and organic film samples, with the median concentrations of eight phthalates (Σ8 phthalate) and 16 PAHs (Σ16 PAH) being 1015.93 µg/g and 1824.97 ng/g in the dust samples, and 75.79 µg/m2 and 2252.78 ng/m2 in the organic film samples, respectively. Among the phthalates, in all house types. bis(2-ethylhexyl) phthalate (DEHP) was detected at the highest concentration, followed by dibutyl phthalate (DBP) and diisobuthyl phthalate (DiBP), with DEHP levels found to be highest in dwelling houses. DEHP levels were found to be significantly associated with building age and renovation status. Lower levels of DEHP were detected in houses less than 10 years old or that had undergone renovation in the previous 10 years. Among the assessed PAHs, a significant correlation was detected between benzo(a)pyrene in dust and building age (p < 0.05). These findings imply that the inhabitants of older houses are at a greater risk of exposure to SVOCs originating from indoor dust and organic films. Non-target screening of selected dust and organic film samples using GC-QTOF-MS data revealed the presence of numerous SVOC compounds, including triphenylphosphine oxide, (Z)-9-octadecenamide, and cyclosiloxanes, along with certain organophosphate flame retardants including tris(1-chloro-2-propyl) phosphate (TCPP) and tris(1,3-dichloroisopropyl) phosphate (TDCPP), and plasticizers. These compounds identified in the non-target screening are of emerging concern, and their presence in dust and organic films needs to be estimated.

The point mutation of the cholesterol trafficking membrane protein NPC1 may affect its proper function in more than a single step: Molecular dynamics simulation study.

The Niemann-Pick type C1 (NPC1) protein is one of the key players of cholesterol trafficking from the lysosome and its function is closely coupled with the Niemann-Pick type C2 (NPC2) protein. The dysfunction of one of these proteins can cause problems in the overall cholesterol homeostasis and leads to a disease, which is called the Niemann-Pick type C (NPC) disease. The parts of the cholesterol transport mechanism by NPC1 have begun to recently emerge, especially after the full-length NPC1 structure was determined from a cryo-EM study. However, many details about the overall cholesterol trafficking process by NPC1 still remain to be elucidated. Notably, the NPC1 could act as one of the target proteins for the control of infectious diseases due to its role as the virus entry point into the cells as well as for cancer treatment due to the inhibitory effect of tumor growth. A mutation of NPC1 can leads to dysfunctions and understanding this process can provide valuable insights into the mechanisms of the corresponding protein and the therapeutic strategies against the disease that are caused by the mutation. It has been found that patients with the point mutation R518W (or R518Q) on the NPC1 show the accumulation of lipids within the lysosomal lumen. In this paper, we report how the corresponding mutation can affect the cholesterol transport process by NPC1 in the different stages by the molecular dynamics simulations. The simulation results show that the point mutation intervenes at least at two different steps during the cholesterol transport by NPC1 and NPC2 in combination, which includes the association step of NPC2 with the NPC1, the cholesterol transfer step from NPC2 to NPC1-NTD while the cholesterol passage within the NPC1 via a channel is relatively unaffected by R518W mutation. The detailed analysis of the resulting simulation trajectories reveals the important structural features that are essential for the proper functioning of the NPC1 for the cholesterol transport, and it shows how the overall structure, which thereby includes the function, can be affected by a single mutation.

Surface-dependent gas equilibrium of semi-volatile organic compounds on glass, wood, and polyurethane foam using SPME-GC/MS.

The surface-dependent evaporation behavior of phthalates as semi-volatile organic compounds (SVOCs) on glass, wood, and polyurethane foam (PUF) was investigated. Three phthalates of di-2-ethylhexyl phthalate (DEHP), butyl benzyl phthalate (BBP), and dibutyl phthalate (DBP) were studied to compare the amount of gases vaporized from their surfaces. A 10 mL silicate glass vial was used to compare the gas equilibrium of the phthalates after 2 h. The gases accumulated in the air were transferred to a solid-phase microextraction (SPME) column and analyzed by gas chromatography-mass spectrometry (GC-MS). As correlated with the physicochemical properties of the phthalates, including molecular weights and vapor pressure, the surface-air partition coefficients (Ksa) were found to be in the range of 101-105 m, 106-107 m, and 107-109 m on glass, wood, and PUF, respectively, implying that a significant amount of phthalates are retained on wood and PUF surfaces as compared to glass, and only a trace amount of phthalates can be volatilized into the air, especially the less volatile DEHP. The three-dimensional (3D) morphologies of glass and wood were also examined using a white-light interferometric surface profile microscope and an atomic force microscope (AFM). In contrast to smooth glass surfaces within the sub-micrometer vertical range, the wood surfaces exhibited uneven irregular structures at a height of 5-30 µm. The rough wood surfaces were found to adsorb substantial amounts of gases to prevent the effective volatilization of phthalates into the air, especially the low molecular DBP. Our results imply that wood and PUF surfaces may be superior to glass surfaces in storage and reduction of phthalates in the air, especially DBP.

Surface-Enhanced Raman Sensing of Semi-Volatile Organic Compounds by Plasmonic Nanostructures.

Facile detection of indoor semi-volatile organic compounds (SVOCs) is a critical issue to raise an increasing concern to current researchers, since their emissions have impacted the health of humans, who spend much of their time indoors after the recent incessant COVID-19 pandemic outbreaks. Plasmonic nanomaterial platforms can utilize an electromagnetic field to induce significant Raman signal enhancements of vibrational spectra of pollutant molecules from localized hotspots. Surface-enhanced Raman scattering (SERS) sensing based on functional plasmonic nanostructures has currently emerged as a powerful analytical technique, which is widely adopted for the ultra-sensitive detection of SVOC molecules, including phthalates and polycyclic aromatic hydrocarbons (PAHs) from household chemicals in indoor environments. This concise topical review gives updated recent developments and trends in optical sensors of surface plasmon resonance (SPR) and SERS for effective sensing of SVOCs by functionalization of noble metal nanostructures. Specific features of plasmonic nanomaterials utilized in sensors are evaluated comparatively, including their various sizes and shapes. Novel aptasensors-assisted SERS technology and its potential application are also introduced for selective sensing. The current challenges and perspectives on SERS-based optical sensors using plasmonic nanomaterial platforms and aptasensors are discussed for applying indoor SVOC detection.

Molecular dynamics study with mutation shows that N-terminal domain structural re-orientation in Niemann-Pick type C1 is required for proper alignment of cholesterol transport.

The lysosomal membrane protein Niemann-Pick type C1 (NPC1) and Niemann-Pick type C2 (NPC2) are main players of cholesterol control in the lysosome and it is known that the mutation on these proteins leads to the cholesterol trafficking-related neurodegenerative disease, which is called the NPC disease. The mutation R518W or R518Q on the NPC1 is one of the type of disease-related mutation that causes cholesterol transports to be cut in half, which results in the accumulation of cholesterol and lipids in the late endosomal/lysosomal compartment of the cell. Even though there has been significant progress with understanding the cholesterol transport by NPC1 in combination with NPC2, especially after the structural determination of the full-length NPC1 in 2016, many details such as the interaction of the full-length NPC1 with the NPC2, the molecular motions responsible for the cholesterol transport during and after this interaction, and the structure and the function relations of many mutations are still not well understood. In this study, we report the extensive molecular dynamics simulations in order to gain insight into the structure and the dynamics of NPC1 lumenal domain for the cholesterol transport and the disease behind the mutation (R518W). It was found that the mutation induces a structural shift of the N-terminal domain, toward the loop region in the middle lumenal domain, which is believed to play a central role in the interaction with NPC2 protein, so the interaction with the NPC2 protein might be less favorable compared to the wild NPC1. Also, the simulation indicates the possible re-orientation of the N-terminal domain with both the wild and the R518W-mutated NPC1 after receiving the cholesterol from the NPC2 that align to form an internal tunnel, which is a possible pose for further action in cholesterol trafficking. We believe the current study can provide a better understanding of the cholesterol transport by NPC1 especially the role of NTD of NPC1 in combination with NPC2 interactions.

Computational Probing of Temperature-Dependent Unfolding of a Small Globular Protein: From Cold to Heat Denaturation.

Fully atomistic replica exchange molecular dynamics simulations are performed to compute the stability curve of a small globular protein as accurately as possible. To investigate the individual roles of the protein and water parts, we compute the conformational entropy change of this protein directly from the simulation ensembles. This entropy calculation enables complete separations of the unfolding changes of enthalpy and the entropy into their own protein and hydration components. From this decomposition, we are able to determine the main thermodynamic factors governing the cold and heat unfolding events: the cold and heat unfolding events are largely driven by the hydration enthalpy gain and the protein conformational entropy gain, respectively. This computational study discloses several temperature-dependent unfolding thermodynamic behaviors of the protein and water compartments and establishes their unique relationship. Upon unfolding, the changes of enthalpy and entropy in the protein part are all positive convex functions of temperature, whereas the equivalent changes in the water part are all negative concave functions of temperature. Hence, these two mutually opposing effects from the protein and water parts dictate the thermodynamics of unfolding. Furthermore, consistent with the temperature-dependent behaviors of the protein part, the changes of the solvent-accessible surface area and the radius of gyration of the protein upon unfolding are also convex functions of temperature. Hence, all these new temperature dependences, combined together, pave the way to unveiling the thermodynamic and structural features of protein denaturation events at various temperature conditions.

Characterization of the fragmentation behaviors of protonated α-cyclodextrin generated by electrospray ionization.

RATIONALE: Electrospray ionization (ESI) of an aqueous solution of α-cyclodextrin (α-CD) gave a protonated molecule, [α-CD + H]+ . The fragmentation behavior of the protonated molecule, including direct decomposition and ring cleavage, was investigated by varying the source fragmentor voltage. The possible chemical structures of the product ions were also examined using electronic structure calculations. METHODS: An aqueous α-CD solution was ionized by ESI and the source fragmentor voltage was varied to examine changes of the product ions depending on collision energy. The structures and energies of the precursor and product ions were obtained by electronic structure calculations using Spartan'10 and Gaussian09. RESULTS: The major product ions were [M + H - 162m]+ (where m = 1-5), with the most abundant being [M + H - 162 × 4]+ . The product ions had two chemical structures of the cationic site in the ether linkage ([DPDn - OH]+ ) and in the terminal oxonium ion ([DPn - OH]+ ) formed by direct decomposition of [α-CD + H]+ and fragmentation of the open structure ([DP6 - OH]+ ), respectively. The [DP6 - OH]+ ion is more stable than the [α-CD + H]+ ion. CONCLUSIONS: The fragmentation behavior of protonated α-CD was characterized by two pathways: direct decomposition of [α-CD + H]+ and decomposition of the [DP6 - OH]+ open structure. Differences in the relative abundances of product ions were explained by the different fragmentation pathways of [α-CD + H]+ and [DP6 - OH]+ .

Crystal structures of Uso1 membrane tether reveal an alternative conformation in the globular head domain.

Membrane tethers play a critical role in organizing the complex molecular architecture of eukaryotic cells. Uso1 (yeast homolog of human p115) is essential for tethering in vesicle transport from ER to Golgi and interacts with Ypt1 GTPase. The N-terminal globular head domain of Uso1 is responsible for Ypt1 binding; however, the mechanism of tethering between ER transport vesicles and Golgi is unknown. Here, we determined two crystal structures for the Uso1 N-terminal head domain in two alternative conformations. The head domain of Uso1 exists as a monomer, as confirmed using size-exclusion chromatography coupled to multi-angle light scattering and analytical gel filtration. Although Uso1 consists of a right-handed α-solenoid, like that in mammalian homologs, the overall conformations of both Uso1 structures were not similar to previously known p115 structures, suggesting that it adopts alternative conformations. We found that the N- and C-terminal regions of the Uso1 head domain are connected by a long flexible linker, which may mediate conformational changes. To analyse the role of the alternative conformations of Uso1, we performed molecular docking of Uso1 with Ypt1, followed by a structural comparison. Taken together, we hypothesize that the alternative conformations of Uso1 regulate the precise docking of vesicles to Golgi.

Equilibrium structures of water molecules confined within a multiply connected carbon nanotube: a molecular dynamics study.

Water confinement inside a carbon nanotube (CNT) has been one of the most exciting subjects of both experimental and theoretical interest. Most of the previous studies, however, considered CNT structures with simple cylindrical shapes. In this paper, we report a classical molecular dynamics study of the equilibrium structural arrangement of water molecules confined in a multiply connected carbon nanotube (MCCNT) containing two Y-junctions. We investigate the structural arrangement of the water molecules in the MCCNT in terms of the density of water molecules and the average number of hydrogen bonds per water molecule. Our results show that the structural rearrangement of the H2O molecules takes place several angstroms ahead of the Y-junction, rather than only at the CNT junction itself. This phenomenon arises because it is difficult to match the boundary condition for hydrogen bonding in the region where two different hydrogen-bonded structures are interconnected with each other.

Conformational sampling of metastable states: Tq-REM as a novel replica exchange method.

Although the replica exchange methods (REMs) were developed as efficient conformational sampling methods for bio-molecular simulations, their application to very large bio-systems is somewhat limited. We propose a new replica exchange scheme (Tq-REM) created by combining the conventional temperature-REM (T-REM) and one of the Hamiltonian-REMs, q-REM, using the effective potential with reduced barriers. In the proposed Tq-REM scheme, high temperature replicas in T-REM are substituted with q-replicas. This combined scheme is expected to exploit advantages of the T-REM and q-REM resulting in improved sampling efficiency while minimizing the drawbacks of both approaches. We investigated the performance of Tq-REM compared with T-REM by performing all-atom MD simulations on Met-enkephalin, (AAQAA)3, and Trpzip2. It was found that convergence of the free energy surfaces was improved by Tq-REM over the conventional T-REM. In particular, the trajectories of Tq-REM were able to sample the relevant conformations for all of the metastable folding intermediates, while some of the local minimum structures are poorly represented by T-REM. The results of the present study suggest that Tq-REM can provide useful tools to investigate systems where metastable states play important roles.

Investigation on critical structural motifs of ligands for triggering glucocorticoid receptor nuclear migration through molecular docking simulations.

The glucocorticoid receptor (GR), a transcription factor regulating gene expression in a ligand-dependent fashion, is known for flexibility in adapting various ligands with their structures ranging from steroid to non-steroid. However, in our previous study, GR shows a stringent discrimination against a set of steroid ligands with highly similar structures for triggering its nuclear migration. In order to resolve this puzzle, we employed molecular docking simulations to investigate the origin of this structural discrimination. By analyzing the docking orientations and the related ligand-GR interaction patterns, we found that the hydrophilicity mismatch between the docking ligand and the GR ligand-binding site is the main cause combined with the steric hindrance and structural rigidness of these steroid ligands. Furthermore, we utilized this knowledge to rationalize how the structure-binding interaction of non-steroid ligands triggers GR nuclear migration with their structures available in Protein Data Bank.

The role of the acidic domain of α-synuclein in amyloid fibril formation: a molecular dynamics study.

The detailed mechanism of the pathology of α-synuclein in the Parkinson's disease has not been clearly elucidated. Recent studies suggested a possible chaperone-like role of the acidic C-terminal region of α-synuclein in the formation of amyloid fibrils. It was also previously demonstrated that the α-synuclein amyloid fibril formation is accelerated by mutations of proline residues to alanine in the acidic region. We performed replica exchange molecular dynamics simulations of the acidic and nonamyloid component (NAC) domains of the wild type and proline-to-alanine mutants of α-synuclein under various conditions. Our results showed that structural changes induced by a change in pH or an introduction of mutations lead to a reduction in mutual contacts between the NAC and acidic regions. Our data suggest that the highly charged acidic region of α-synuclein may act as an intramolecular chaperone by protecting the hydrophobic domain from aggregation. Understanding the function of such chaperone-like parts of fibril-forming proteins may provide novel insights into the mechanism of amyloid formation.

A fully atomistic computer simulation study of cold denaturation of a ß-hairpin.

Cold denaturation is a fundamental phenomenon in aqueous solutions where the native structure of proteins disrupts on cooling. Understanding this process in molecular details can provide a new insight into the detailed natures of hydrophobic forces governing the stability of proteins in water. We show that the cold-denaturation-like phenomenon can be directly observed at low temperatures using a fully atomistic molecular dynamics simulation method. Using a highly optimized protein force field in conjunction with three different explicit water models, a replica exchange molecular dynamics simulation scheme at constant pressures allows for the computation of the melting profile of an experimentally well-characterized ß-hairpin peptide. For all three water models tested, the simulated melting profiles are indicative of possible cold denaturation. From the analysis of simulation ensembles, we find that the most probable cold-denatured structure is structurally compact, with its hydrogen bonds and native hydrophobic packing substantially disrupted.

Strategies for the modification of adhesion at graphene/Al Interfaces: a first principles study.

Possibility of improving the adhesion at graphene/Al interfaces has been investigated by predicting interactions between monolayer graphene and Al (111) plane using first principles simulations. For the property modifications, either Ni atoms were adsorbed on one side of the graphene or the graphene is substitutionally doped with B. It was predicted that the adatoms or dopants modify local electronic or orbital structure, which subsequently promotes the bonding between the graphene and Al at local level thereby improving the bond strength at the interface. While improvement of interfacial properties was expected with the surface modification by a foreign element adsorption or substitutional doping of the graphene, low-concentration substitutional doping was predicted to be more effective in achieving improved adhesive properties of the graphene/Al nanointerface.

A docking study of enhanced intracellular survival protein from Mycobacterium tuberculosis with human DUSP16/MKP-7.

The intracellular pathogen Mycobacterium tuberculosis (Mtb) causes tuberculosis, and one of its secreted effector proteins, called enhanced intracellular survival (Eis) protein, enhances its survival in macrophages. Mtb Eis activates JNK-specific dual-specificity protein phosphatase 16 (DUSP16)/mitogen-activated protein kinase phosphatase-7 (MKP-7) through the acetylation on Lys55, thus inactivating JNK by dephosphorylation. Based on the recently reported crystal structure of Mtb Eis, a docking model for the binding of Mtb Eis to DUSP16/MKP-7 was generated. In the docking model, the substrate helix containing Lys55 of DUSP16/MKP-7 fits nicely into the active-site cleft of Mtb Eis; the twisted ß-sheet of Eis domain II embraces the substrate helix from one side. Most importantly, the side-chain of Lys55 is inserted toward acetyl-CoA and the resulting distance is 4.6 Å between the NZ atom of Lys55 and the carbonyl carbon of the acetyl group in acetyl-CoA. The binding of Mtb Eis and DUSP16/MKP-7 is maintained by strong electrostatic interactions. The active-site cleft of Mtb Eis has a negatively charged surface formed by Asp25, Glu138, Asp286, Glu395 and the terminal carboxylic group of Phe396. In contrast, DUSP16/MKP-7 contains five basic residues, Lys52, Lys55, Arg56, Arg57 and Lys62, which point toward the negatively charged surface of the active-site pocket of Mtb Eis. Thus, the current docking model suggests that the binding of DUSP16/MKP-7 to Mtb Eis should be established by charge complementarity in addition to a very favorable geometric arrangement. The suggested mode of binding requires the dissociation of the hexameric Mtb Eis into dimers or monomers. This study may be useful for future studies aiming to develop inhibitors of Mtb Eis as a new anti-tuberculosis drug candidate.

Site specificity on OH α-H abstraction reaction for a zwitterionic ß-hairpin peptide in aqueous solution: a theoretical investigation.

Protein backbone oxidation was investigated by studying the α-H abstraction reaction in a ß-hairpin peptide, called Chignolin (PDB ID 1UAO), with density functional theory calculation at B3LYP/6-31G(d,p) without any constraint. In order to stabilize the zwitterionic form of Chignolin with the salt bridges, the effects of aqueous solution were implemented by using microsolvation combined with a conductor-like polarizable continuum model (CPCM). Comparison between three glycine residues located at three different sites in Chignolin was used to examine the possible site specificity of this backbone oxidation. To construct the reaction profile of these α-H abstraction reactions, the pre- and postreactive complexes along with their associated transition states were located and verified with the intrinsic reaction coordinate (IRC) method. The bond dissociation energy and reaction rates of these OH α-H abstraction reactions were calculated with transition state theory. The differences in this abstraction reaction between the neutral and zwitterionic forms of Chignolin were also compared. A molecular dynamics simulation was implemented to study the explicit solvation effect on the abstracted Chignolin structure. The range of the simulation time scale covers from femtoseconds to microseconds, i.e., from onset of the abstraction to the abstracted products reaching thermal equilibrium. Our results show that there are three kinds of site-specificity in this abstraction reaction. The reactivity and stability of the abstraction products and their abstraction modes are all dependent on the location where OH attacks. Furthermore, the free energy landscapes of these abstraction products are distinctively different. This may imply that the pathological disorders or diseases caused by this type of radicals are also dependent on the abstraction location.