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  • Article
    Lan J, Liu L, Li Z, Zeng R, Chen L, He Y, Wei H, Ding Y, Zhang T.
    Talanta. 2024 Jan 15;267:125104.
    Biothiols and its metabolite SO2 derivatives play vital roles in various physiological processes. Although a few probes have been designed for monitoring the metabolism of biothiols, developing multi-signal fluorescent probes with practicability for simultaneously distinguishing biothiols (GSH, Cys and Hcy) and real-time visualizing SO2 derivatives is an enormous challenge. To better visualize biothiols metabolism in vitro and vivo, we developed a novel multi-signal NIR fluorescent probe (probe 2) with mitochondria-targeted for distinguishing biothiols and its metabolism, based on an ICT-PET synergetic mechanism. Probe 2 with dual recognition sites distinguishing detected Cys/Hcy (Red-Green), GSH (Green) and SO32- (Blue) via three channels. First probe 2 distinguished Cys and GSH to estimate main biothiols in living cells through the ratio changes of two well-defined emission bands (Red-Green), and then imaged its metabolite SO2 with ratiometric fluorescence (Red-Blue), eliminating the interference by different biothiols. Notably, probe 2 exhibits satisfactory sensitivity (detection limit: 0.21, 0.13, 0.14 and 3.06 μM for Cys, Hcy, GSH and SO32-, respectively), high selectivity, reliability at physiological pH, and rapid fluorescence response (within 10 min). Given these advantages, probe 2 has been successfully applied to the real-time monitor GSH metabolic process in MCF-7 cells and biothiols metabolism in breast cancer, suggesting biothiols metabolic changes might be a diagnostic indicator during cancer treatment. So probe 2 is a convenient and efficient tool for understanding the physiological functions of biothiols and its metabolism.
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  • Article
    Shang Y, Wu F, Wei S, Guo W, Chen J, Huang W, Hu M, Wang Y.
    Chemosphere. 2020 Feb;241:125104.
    Both nanoparticles (NPs) and ocean acidification (OA) pose threats to marine animals as well as marine ecosystems. The present study aims to evaluate the combined effects of NPs and OA on specific dynamic action (SDA) of mussels. The thick shell mussels Mytilus coruscus were exposed to two levels of pH (7.3 and 8.1) and three concentrations of TiO2 NPs (0, 2.5, and 10 mg L-1) for 14 days followed by a 7-day recovery period. The SDA parameters, including standard metabolic rate, peak metabolic rate, aerobic metabolic scope, SDA slope, time to peak, SDA duration and SDA, were measured. The results showed that TiO2 NPs and low pH significantly affected all parameters throughout the experiment. When the mussels were exposed to seawater acidification or TiO2 NPs conditions, standard metabolic rate, aerobic metabolic scope, SDA slope and SDA significantly decreased, whereas peak metabolic rate, time to peak and SDA duration significantly increased. In addition, interactive effects between TiO2 NPs and pH were observed in SDA parameters except time to peak and SDA. Therefore, the synergistic effect of TiO2 NPs and low pH can adversely affect the feeding metabolism of mussels.
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  • Article
    Isanapong J, Pornwongthong P.
    J Hazard Mater. 2021 06 05;411:125104.
    Laccase is an effective biocatalyst in bioremediation process; however, the application of the enzyme is limited due to its cost, recovery, and stability. In this study, we developed, characterized and evaluated the efficiency of immobilized laccase on zinc oxide nanostructure to catalyze biodegradation of TBA in comparison to the suspended enzyme. The results showed that both immobilized and suspended laccase were capable of catalyzing TBA biodegradation; however, the efficiency of the immobilized laccase on TBA removal was higher than that of the suspended enzyme. The repeatability testing revealed the potential of the immobilized laccase for repeatedly catalyzing TBA biodegradation with storage capacity. While the Vmax of immobilized enzyme was higher than suspended laccase (2.25 ± 0.542 mg TBA/h∙U vs. 1.47 ± 0.185 mg TBA/h∙U), the km of the immobilized enzyme was higher than the suspended laccase (67.9 ± 20.5 mg TBA/L vs. 33.5 ± 7.10 mg TBA/L). This suggests that the immobilized laccase is better in TBA removal, but has lower affinity with TBA than the suspended enzyme. Thus, immobilization of the enzyme can be applied to increase the efficiency and minimize the use of laccase for TBA remediation.
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  • Article
    Zhang Y, Ertbjerg P.
    Food Chem. 2019 Nov 30;299:125104.
    The role of protein denaturation in formation of thaw loss is currently not well understood. This study investigated denaturation of myofibrillar and sarcoplasmic proteins of pork loins caused by freezing-thawing in relation to freezing rate. Compared to fast freezing, slow freezing caused 28% larger thaw loss, decreased water-holding capacity of myofibrils and increased surface hydrophobicity, indicating more pronounced denaturation of myofibrillar proteins. We here propose a model: In slow freezing protons are concentrated in the unfrozen water resulting in reduced pH in proximity of structural proteins causing protein denaturation. In parallel, large ice crystals are formed outside of muscle fibers resulting in transversal shrinkage. In fast freezing small ice crystals trap protons and cause less severe protein denaturation and reduced thaw loss. Differential scanning calorimetry and tryptophan fluorescence spectra indicated sarcoplasmic protein denaturation in drip due to freezing-thawing. However, sarcoplasmic protein denaturation was independent of freezing rate.
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  • Article
    Ohashi A, Ohshima K, Ohsaki S, Nakamura H, Watano S.
    Int J Pharm. 2024 Dec 19;670:125104.
    Combination therapy using multiple drugs has the potential for synergistic therapeutic effects and reduction in the administered dose. Furthermore, when combined with a drug delivery system, the therapeutic agents can effectively be targeted and delivered to the affected area. Therefore, a single carrier capable of encapsulating multiple drugs is of clinical significance. This study focused on cyclodextrin-based metal-organic frameworks (CD-MOFs) with high biocompatibility and hydrophobic and hydrophilic pores, because their amphiphilic pores should be suitable for encapsulating multiple drugs. First, the drug encapsulation ability of 5-fluorouracil (5FU) and ascorbic acid (ASC) into the γ-CD-MOF through experiments was compared with that of grand canonical Monte Carlo (GCMC) simulations. The drugs were suggested to encapsulate in the different pores of γ-CD-MOF depending on the hydrophilicity of the drug. In addition, the multi-drug encapsulation ability of the γ-CD-MOF was experimentally and numerically confirmed. In the simultaneous encapsulation experiments, the encapsulation amounts of 5FU and ASC were measured to be 0.0536 and 1.67 mol/mol, respectively. Also, the GCMC simulation demonstrated the simultaneous encapsulation of the two drugs, in which the loaded amounts of 5FU and ASC were calculated as 0.867 and 1.67 mol/mol, respectively. The encapsulation ability of multi-drug with hydrophilicity and hydrophobicity into the γ-CD-MOF was experimentally and numerically confirmed. The findings obtained in this study suggested that γ-CD-MOF will greatly contribute as a multi-drug carrier.
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  • Article
    Weinrich S, Mauky E, Schmidt T, Krebs C, Liebetrau J, Nelles M.
    Bioresour Technol. 2021 Aug;333:125104.
    Due to a limited number of available measurements on agricultural biogas plants, established process models, such as the Anaerobic Digestion Model No. 1 (ADM1), are rarely applied in practise. To provide a reliable basis for model-based monitoring and control, different model simplifications of the ADM1 were implemented for process simulation of semi-continuous anaerobic digestion experiments using agricultural substrates (maize silage, sugar beet silage, rye grain and cattle manure) and industrial residues (grain stillage). Individual model structures enable a close depiction of biogas production rates and characteristic intermediates (ammonium nitrogen, propionic and acetic acid) with equal accuracy as the original ADM1. The impact of different objective functions and standard parameter values on parameter estimates of first-order hydrolysis constants and microbial growth rates were evaluated. Due to the small number of required model parameters and suitable system characteristics, simplified model structures show clear advantages for practical application on agricultural biogas plants.
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  • Article
    Albano G, Moor M, Dolder S, Siegrist M, Wagner CA, Biber J, Hernando N, Hofstetter W, Bonny O, Fuster DG.
    PLoS One. 2015;10(4):e0125104.
    Osteoclasts are multinucleated bone degrading cells. Phosphate is an important constituent of mineralized bone and released in significant quantities during bone resorption. Molecular contributors to phosphate transport during the resorptive activity of osteoclasts have been controversially discussed. This study aimed at deciphering the role of sodium-dependent phosphate transporters during osteoclast differentiation and bone resorption. Our studies reveal RANKL-induced differential expression of sodium-dependent phosphate transport protein IIa (NaPi-IIa) transcript and protein during osteoclast development, but no expression of the closely related NaPi-IIb and NaPi-IIc SLC34 family isoforms. In vitro studies employing NaPi-IIa-deficient osteoclast precursors and mature osteoclasts reveal that NaPi-IIa is dispensable for bone resorption and osteoclast differentiation. These results are supported by the analysis of structural bone parameters by high-resolution microcomputed tomography that yielded no differences between adult NaPi-IIa WT and KO mice. By contrast, both type III sodium-dependent phosphate transporters Pit-1 and Pit-2 were abundantly expressed throughout osteoclast differentiation, indicating that they are the relevant sodium-dependent phosphate transporters in osteoclasts and osteoclast precursors. We conclude that phosphate transporters of the SLC34 family have no role in osteoclast differentiation and function and propose that Pit-dependent phosphate transport could be pivotal for bone resorption and should be addressed in further studies.
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  • Article
    Bencardino M, D'Amore F, Angot H, Angiuli L, Bertrand Y, Cairns W, Diéguez MC, Dommergue A, ... Show More Ebinghaus R, Esposito G, Komínková K, Labuschagne C, Mannarino V, Martin L, Martino M, Neves LM, Mashyanov N, Magand O, Nelson P, Norstrom C, Read K, Sholupov S, Skov H, Tassone A, Vítková G, Cinnirella S, Sprovieri F, Pirrone N.
    Environ Pollut. 2024 Dec 15;363(Pt 2):125104.
    The Global Mercury Observation System (GMOS) network, initially a five-year project (2010-2015) funded by the European Commission, continued as a GEO Flagship program to support the Global Observation System for Mercury (GOS4M). GMOS was envisioned as a coordinated global observing system to monitor atmospheric mercury (Hg) on a global scale, to support and evaluate the effective implementation of the Minamata Convention on Mercury (MCM). Twenty-eight ground-based stations have participated in monitoring activities, following GMOS sampling protocols and related data quality control management. The GMOS network provides representative coverage of all latitudes, from the Northern Hemisphere to the Southern Hemisphere including the Arctic Circle, Antarctica, and the Tropical Zone. This work presents atmospheric Hg data, available as Total Gaseous Mercury (TGM) or Gaseous Elemental Mercury (GEM) concentrations, recorded within the GMOS network from 2011 to 2020. TGM/GEM concentrations were analysed in terms of their variability along latitudinal areas, considering their comparability, temporal trends and patterns. The main results confirmed a clear gradient of TGM/GEM concentrations between the northern (1.58 ± 0.31 ng/m3) and southern (0.97 ± 0.14 ng/m3) hemispheres. Decreasing trends in TGM/GEM levels were found to be strongly significant only for selected remote stations with at least 5 years of data coverage. Seasonality in atmospheric TGM/GEM concentrations was observed to increase with latitude and is greater at inland sites than at coastal sites.
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  • Article
    He M, Zhang M, Gao T, Liu Z, Chen L, Liu Y, Huang Y, Teng F, Li Y.
    Int J Biol Macromol. 2023 Jul 31;244:125104.
    In this study, we used succinic anhydride (SA) acylation and dextran (DX) glycosylation modified soybean isolate protein (SPI) to develop self-assembled SPI-SA-DX adduct-based nanogels. Degree of modification, SDS-PAGE, and FT-IR studies showed that the amino group of the SPI was replaced by hydrophilic dextran and succinic acid carboxyl groups. Dextran chain and anhydride group attachment to the soybean protein surface enhanced hydrophilicity and spatial site blocking. Modification-induced protein structure unfolding, free sulfhydryl groups to be converted to disulfide bonds, and reduced surface hydrophobicity (H0). H0 was lowest at 33,750 ± 1008.29 when SA content = 10 % protein content (SPI-SA3-DX). The nanometer gel based on SPI-SA3-DX had the maximum turbidity and clear transparent solution without precipitation. Its particle size and polymer dispersibility index (PDI) were also the smallest, with values of (106.87 ± 4.51) nm and 0.21 ± 0.009, respectively. Transmission electron microscopy showed that nanogels had subspherical shell-core structures. Nanogels were stable under different pH, ionic strength, high temperature, and storage conditions.
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  • Article
    Jȩdrzejewski-Szmek Z, Blackwell KT.
    J Chem Phys. 2016 Mar 28;144(12):125104.
    Stochastic simulation of cell signaling pathways and genetic regulatory networks has contributed to the understanding of cell function; however, investigation of larger, more complicated systems requires computationally efficient algorithms. τ-leaping methods, which improve efficiency when some molecules have high copy numbers, either use a fixed leap size, which does not adapt to changing state, or recalculate leap size at a heavy computational cost. We present a hybrid simulation method for reaction-diffusion systems which combines exact stochastic simulation and τ-leaping in a dynamic way. Putative times of events are stored in a priority queue, which reduces the cost of each step of the simulation. For every reaction and diffusion channel at each step of the simulation the more efficient of an exact stochastic event or a τ-leap is chosen. This new approach removes the inherent trade-off between speed and accuracy in stiff systems which was present in all τ-leaping methods by allowing each reaction channel to proceed at its own pace. Both directions of reversible reactions and diffusion are combined in a single event, allowing bigger leaps to be taken. This improves efficiency for systems near equilibrium where forward and backward events are approximately equally frequent. Comparison with existing algorithms and behaviour for five test cases of varying complexity shows that the new method is almost as accurate as exact stochastic simulation, scales well for large systems, and for various problems can be significantly faster than τ-leaping.
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  • Article
    Reppert M, Roy AR, Tokmakoff A.
    J Chem Phys. 2015 Mar 28;142(12):125104.
    We present a systematic isotope labeling study of the protein G mutant NuG2b as a step toward the production of reliable, structurally stable, experimental standards for amide I infrared spectroscopic simulations. By introducing isotope enriched amino acids into a minimal growth medium during bacterial expression, we induce uniform labeling of the amide bonds following specific amino acids, avoiding the need for chemical peptide synthesis. We use experimental data to test several common amide I frequency maps and explore the influence of various factors on map performance. Comparison of the predicted absorption frequencies for the four maps tested with empirical assignments to our experimental spectra yields a root-mean-square error of 6-12 cm(-1), with outliers of at least 12 cm(-1) in all models. This means that the predictions may be useful for predicting general trends such as changes in hydrogen bonding configuration; however, for finer structural constraints or absolute frequency assignments, the models are unreliable. The results indicate the need for careful testing of existing literature maps and shed light on possible next steps for the development of quantitative spectral maps.
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  • Article
    de Vries R.
    J Chem Phys. 2011 Sep 28;135(12):125104.
    A large literature exists on modeling the influence of sequence-specific DNA-binding proteins on the shape of the DNA double helix in terms of one or a few fixed constraints. This approach is inadequate for the many proteins that bind DNA sequence independently, and that are present in very large quantities rather than as a few copies, such as the nucleoid proteins in bacterial cells. The influence of such proteins on DNA configurations is better modeled in terms of a great number of mobile constraints on the DNA. Types of constraints that mimic the influence of various known non-specifically DNA binding proteins include DNA bending, wrapping, and bridging. Using Monte-Carlo simulations, we here investigate the influence of (non-interacting) mobile DNA-protein-DNA bridges on the configurations of a 1000 bp piece of linear DNA, for both homogeneous DNA and DNA with an intrinsic planar bend. Results are compared to experimental data on the bacterial nucleoid protein H-NS that forms DNA-protein-DNA bridges. In agreement with data on H-NS, we find very strong positioning of DNA-protein-DNA bridges in the vicinity of planar bends. H-NS binds to DNA very cooperatively, but for non-interacting bridges we only find a moderate DNA-induced clustering. Finally, it has been suggested that H-NS is an important contributor to the extreme condensation of bacterial DNA into a nucleoid structure, but we find only a moderate compaction of DNA coils with increasing numbers of non-interacting bridges. Our results illustrate the importance of quantifying the various effects on DNA configurations that have been proposed for proteins that bind DNA sequence independently.
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  • Article
    Lee S, Tran CV, Nguyen TT.
    J Chem Phys. 2011 Mar 28;134(12):125104.
    The problem of inhibiting viral DNA ejection from bacteriophages by multivalent counterions, specifically Mg(+2) counterions, is studied. Experimentally, it is known that MgSO(4) salt has a strong and nonmonotonic effect on the amount of DNA ejected. There exists an optimal concentration at which the minimum amount of DNA is ejected from the virus. At lower or higher concentrations, more DNA is ejected from the capsid. We propose that this phenomenon is the result of DNA overcharging by Mg(+2) multivalent counterions. As Mg(+2) concentration increases from zero, the net charge of DNA changes from negative to positive. The optimal inhibition corresponds to the Mg(+2) concentration where DNA is neutral. At lower/higher concentrations, DNA genome is charged. It prefers to be in solution to lower its electrostatic self-energy, which consequently leads to an increase in DNA ejection. By fitting our theory to available experimental data, the strength of DNA-DNA short range attraction energies, mediated by Mg(+2), is found to be -0.004 k(B)T per nucleotide base. This and other fitted parameters agree well with known values from other experiments and computer simulations. The parameters are also in agreement qualitatively with values for tri- and tetravalent counterions.
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  • Article
    Moradi M, Babin V, Roland C, Sagui C.
    J Chem Phys. 2010 Sep 28;133(12):125104.
    Folded polyproline peptides can exist as either left-(PPII) or right-handed (PPI) helices, depending on their environment. In this work, we have characterized the conformations and the free energy landscapes of Ace-(Pro)(n)-Nme, n=2,3, ... ,9, and 13 peptides both in vacuo and in an implicit solvent environment. In order to enhance the sampling provided by regular molecular dynamics simulations, we have used the recently developed adaptively biased molecular dynamics method--which provides an accurate description of the free energy landscapes in terms of a set of relevant collective variables--combined with Hamiltonian and temperature replica exchange molecular dynamics methods. The collective variables, which are chosen so as to reflect the stable structures and the "slow modes" of the polyproline system, were based primarily on properties of length and of the cis/trans isomerization associated with the prolyl bonds. Results indicate that the space of peptide structures is characterized not just by pure PPII and PPI structures, but rather by a broad distribution of stable minima with similar free energies. These results are in agreement with recent experimental work. In addition, we have used steered molecular dynamics methods in order to quantitatively estimate the free energy difference of PPI and PPII for peptides of the length n=2, ... ,5 in vacuo and implicit water and qualitatively investigate transition pathways and mechanisms for the PPII to PPI transitions. A zipper-like mechanism, starting from either the center of the peptide or the amidated end, appear to be the most likely mechanisms for the PPII→PPI transition for the longer peptides.
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  • Article
    Chung SH, Son SJ, Min J.
    Nanotechnology. 2010 Mar 26;21(12):125104.
    We systematically analyzed the adhesion and the proliferation of cells on various nanoporous alumina surfaces to understand the effects of nanostructured surfaces on cell behavior. Various nanoporous surfaces were fabricated using the anodizing method and characterized by atomic force microscopy and scanning electron microscopy. The adhesion rate and proliferation rate of cells as functions of pore size and depth were statistically investigated using a colorimetric method. The adhesion rate of cells was not affected by the depth of the nanoporous surface whereas the proliferation of cells dramatically increased when the aspect ratio of the nanopore was near unity. This phenomenon was further verified by comparing the change in roughness of the cytoplasmic layer of cells adhered on a nanoporous surface with that of a bare nanoporous surface. The proliferation of cells was also influenced by the pore size of the nanoporous surface because the nanostructure could control the interaction between extracellular matrix (ECM) molecules and the surface. In conclusion, the nanostructured surfaces affected cell adhesion and proliferation by increasing the surface area to which the cells could adhere, and the interactions between small ECM molecules were influenced by the sufficiently small structures of the nanosurface.
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  • Article
    Krishnakumar P, Sundaramurthy S, Baredar P, Suresh A, Khan MA, Sharma G, Zahmatkesh S, Amesho KTT, Sillanpää M.
    Environ Sci Pollut Res Int. 2023 Dec;30(60):125104-125116.
    There are several environmental and human health impacts if human hair waste is not adequately disposed of. In this study, pyrolysis of discarded human hair was carried out. This research focused on the pyrolysis of discarded human hair under controlled environmental conditions. The effects of the mass of discarded human hair and temperature on bio-oil yield were studied. The proximate and ultimate analyses and calorific values of disposed of human hair, bio-oil, and biochar were determined. Further, chemical compounds of bio-oil were analyzed using a gas chromatograph and a mass spectrometer. Finally, the kinetic modeling and behavior of the pyrolysis process were characterized through FT-IR spectroscopy and thermal analysis. Based on the optimized mass of disposed of human hair, 250 g had a better bio-oil yield of 97% in the temperature range of 210-300 °C. The different parameters of bio-oil were: pH (2.87), specific gravity (1.17), moisture content (19%), heating value (19.34 MJ/kg), and viscosity (50 CP). C (56.4%), H (6.1%), N (0.16%), S (0.01%), O (38.4%), and Ash (0.1%) were discovered to be the elemental chemical composition of bio-oil (on a dry basis). During breakdown, the release of different compounds like hydrocarbons, aldehydes, ketones, acids, and alcohols takes place. According to the GC-MS results, several amino acids were discovered in the bio-oil, 12 abundant in the discarded human hair. The FTIR and thermal analysis found different concluding temperatures and wave numbers for functional groups. Two main stages are partially separated at about 305 °C, with maximum degradation rates at about 293 oC and 400-4140 °C, respectively. The mass loss was 30% at 293 0C and 82% at temperatures above 293 0C. When the temperature reached 4100C, the entire bio-oil from discarded human hair was distilled or thermally decomposed.
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  • Article
    Young TM, Roberts CJ.
    J Chem Phys. 2009 Sep 28;131(12):125104.
    Reversible formation of weakly associated protein oligomers or clusters is a key early step in processes such as protein aggregation and colloidal phase separation. A previously developed cell-based, quasichemical model for lattice fluids [T. M. Young and C. J. Roberts, J. Chem. Phys. 127, 165101 (2007)] is extended here to treat continuous-space systems. It is illustrated using two simplified limiting cases for globular proteins at the isoelectric point: spherical square-well (SW) particles with an isotropic short-ranged attraction and screened dipolar particles with SW attractions and square-shoulder repulsions. Cluster free energies (DeltaA(i)) and structures are analyzed as a function of the reduced second virial coefficient b(2)(*). DeltaA(i) values and the average structures of clusters up to pentamers have distinct differences due to the anisotropic nature of the dipolar interactions. However, DeltaA(i) values can be mapped semiquantitatively between the two cases if compared at common values of b(2)(*). Free energy landscapes of oligomerization are constructed, illustrating significant differences in landscape ruggedness for small clusters of dipolar versus SW fluids, and suggesting a possible molecular interpretation for empirical models of nucleation-dependent aggregation of proteins.
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  • Article
    Muff S, Caflisch A.
    J Chem Phys. 2009 Mar 28;130(12):125104.
    The rate of protein folding is governed by the transition state so that a detailed characterization of its structure is essential for understanding the folding process. In vitro experiments have provided a coarse-grained description of the folding transition state ensemble (TSE) of small proteins. Atomistic details could be obtained by molecular dynamics (MD) simulations but it is not straightforward to extract the TSE directly from the MD trajectories, even for small peptides. Here, the structures in the TSE are isolated by the cut-based free-energy profile (cFEP) using the network whose nodes and links are configurations sampled by MD and direct transitions among them, respectively. The cFEP is a barrier-preserving projection that does not require arbitrarily chosen progress variables. First, a simple two-dimensional free-energy surface is used to illustrate the successful determination of the TSE by the cFEP approach and to explain the difficulty in defining boundary conditions of the Markov state model for an entropically stabilized free-energy minimum. The cFEP is then used to extract the TSE of a beta-sheet peptide with a complex free-energy surface containing multiple basins and an entropic region. In contrast, Markov state models with boundary conditions defined by projected variables and conventional histogram-based free-energy profiles are not able to identify the TSE of the beta-sheet peptide.
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  • Article
    Ramachandran S, Kumar PB, Laradji M.
    J Chem Phys. 2008 Sep 28;129(12):125104.
    We study, using dissipative particle dynamics simulations, the effect of active lipid flip-flop on model fluid bilayer membranes. We consider both cases of symmetric as well as asymmetric flip-flops. Symmetric flip-flop leads to a steady state of the membrane with an effective temperature higher than that of the equilibrium membrane and an effective surface tension lower than that of the equilibrium membrane. Asymmetric flip-flop leads to transient conformational changes in the membrane in the form of bud or blister formation, depending on the flip rate.
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  • Article
    Mohan A, Kolomeisky AB, Pasquali M.
    J Chem Phys. 2008 Mar 28;128(12):125104.
    We investigate the voltage-driven translocation of an inhomogeneously charged polymer through a nanopore by utilizing discrete and continuous stochastic models. As a simplified illustration of the effect of charge distribution on translocation, we consider the translocation of a polymer with a single charged site in the presence and absence of interactions between the charge and the pore. We find that the position of the charge that minimizes the translocation time in the absence of pore-polymer interactions is determined by the entropic cost of translocation, with the optimum charge position being at the midpoint of the chain for a rodlike polymer and close to the leading chain end for an ideal chain. The presence of attractive and repulsive pore-charge interactions yields a shift in the optimum charge position toward the trailing end and the leading end of the chain, respectively. Moreover, our results show that strong attractive or repulsive interactions between the charge and the pore lengthen the translocation time relative to translocation through an inert pore. We generalize our results to accommodate the presence of multiple charged sites on the polymer. Our results provide insight into the effect of charge inhomogeneity on protein translocation through biological membranes.
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