The Experts below are selected from a list of 315 Experts worldwide ranked by ideXlab platform
Soohyung Park - One of the best experts on this subject based on the ideXlab platform.
-
Quantitative Characterization of Protein-Lipid Interactions by Free Energy Simulation between Binary Bilayers.
Journal of chemical theory and computation, 2019Co-Authors: Soohyung Park, Min Sun Yeom, Olaf S. Andersen, Richard W. PastorAbstract:Using a recently developed binary bilayer system (BBS) consisting of two patches of laterally contacting bilayers, umbrella sampling molecular dynamics (MD) simulations were performed for Quantitative Characterization of protein-lipid interactions. The BBS is composed of 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) with an embedded model membrane protein, a gramicidin A (gA) channel. The calculated free energy difference for the transfer of a gA channel from DLPC (hydrophobic thickness ≈ 21.5 A) to DMPC (hydrophobic thickness ≈ 25.5 A) bilayers, ΔG(DLPC → DMPC), is -2.2 ± 0.7 kcal/mol. This value appears at odds with the traditional view that the hydrophobic length of the gA channel is ∼22 A. To understand this discrepancy, we first note that recent MD simulations by different groups have shown that lipid bilayer thickness profiles in the vicinity of a gA channel differ qualitatively from the deformation profile predicted from continuum elastic bilayer models. Our MD simulations at low and high gA:lipid molar ratios and different membrane compositions indicate that the gA channel's effective hydrophobic length is ∼26 A. Using this effective hydrophobic length, ΔG(DLPC → DMPC) determined here is in excellent agreement with predictions based on continuum elastic models (-3.0 to -2.2 kcal/mol) where the bilayer deformation energy is approximated as a harmonic function of the mismatch between the channel's effective hydrophobic length and the hydrophobic thickness of the bilayer. The free energy profile for gA in the BBS includes a barrier at the interface between the two bilayers which can be attributed to the line tension at the interface between two bilayers with different hydrophobic thicknesses. This observation implies that translation of a peptide between two different regions of a cell membrane (such as between the liquid ordered and disordered phases) may include effects of a barrier at the interface in addition to the relative free energies of the species far from the interface. The BBS allows for direct transfer free energy calculations between bilayers without a need of a reference medium, such as bulk water, and thus provides an efficient simulation protocol for the Quantitative Characterization of protein-lipid interactions at all-atom resolution.
-
Quantitative Characterization of Cholesterol Partitioning between Binary Bilayers.
Journal of chemical theory and computation, 2018Co-Authors: Soohyung ParkAbstract:We have devised a practical simulation protocol for Quantitative Characterization of cholesterol (Chol) partitioning between bilayers with different lipid types. The simulation model contains two patches of laterally contacting lipid bilayers, where the host lipids of each bilayer are allowed to self-adjust their packing. For two combinations of bilayers with different lipid types, 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), the simulation model has been verified by self-adjusted lipid packing in each bilayer, convergence of Chol partitioning between different Chol initial distributions, and relative diffusion coefficients consistent to those from experiments. The calculated Chol partition coefficient between POPC and DOPC bilayers from the Chol partitioning simulations in the POPC-DPPC and DOPC-DPPC binary bilayer systems shows an excellent agreement with that from available Chol exchange e...
-
Quantitative Characterization of Membrane Protein-Lipid Interactions
Biophysical Journal, 2014Co-Authors: Soohyung ParkAbstract:Protein-lipid interactions are important for membrane protein (MP) structure, function, and organization. Qualitatively, bilayer regulation of MP function or sorting has been under stood in terms of the "hydrophobic match" between MP and the lipid bilayer. However, due to difficulties in Quantitative Characterization of protein-lipid interactions (even in computational studies), it is difficult to understand, even on a case-by-case basis, how much and why protein stability differs from bilayer to bilayer, and how much protein-lipid interactions and a bilayer deformation penalty (caused by inclusion of the protein) contribute to such stability difference. As a first step of Quantitative Characterization, we calculated the transfer free energy of gramicidin A (gA) in binary lipid systems. To obtain insight into the impact of bilayer thickness and curvature on gA-lipid interactions, we have chosen two types of binary lipid systems: (1) DLPC DMPC and (2) DLPC DLPE. In order to improve sampling and accuracy of the potential of mean force (PMF), we employed window exchange umbrella sampling molecular dynamics (WEUSMD) technique with an optimal parameter set. We will discuss the preference of gA (channel) dimer to be in DLPC compared to DMPC and DLPE bilayers. For consistency check, transfer free energy calculation is required for the binary lipid system: DMPC → DLPE. Agreement will validate that the separately calculated transfer free energy profiles can be combined to characterize the changes of the gA-lipid interactions in any two chosen bilayer types. This will allow us to Quantitatively map the equilibrium states of gA in bilayers with different properties and to Quantitatively elucidate the consequences by the free energy decomposition method.
Meral Dogan - One of the best experts on this subject based on the ideXlab platform.
-
Quantitative Characterization of the mesothelioma-inducing erionite series minerals by transmission electron microscopy and energy dispersive spectroscopy.
Scanning, 2011Co-Authors: Meral DoganAbstract:Air-collected erionite series minerals from Cappadocia region of Turkey were characterized Quantitatively by using transmission electron microscopy (TEM) equipped with energy dispersive spectroscopy (EDS). Field emission scanning electron microscopy aided identification of fibrous minerals. Quantitative Characterization guidelines for positive identification of erionites proposed by Dogan and Dogan (2008) was applied and the modified balance error formula (E%
Ching-ya Chen - One of the best experts on this subject based on the ideXlab platform.
-
Quantitative Characterization of nanoparticles in blood by transmission electron microscopy with a window-type microchip nanopipet.
Analytical chemistry, 2012Co-Authors: Lin-ai Tai, Yu-ting Kang, Yu-ching Chen, Yu-chao Wang, Yu-jing Wang, Kuo-liang Liu, Chiu-yen Wang, Ching-ya ChenAbstract:Transmission electron microscopy (TEM) is a unique and powerful tool for observation of nanoparticles. However, due to the uneven spatial distribution of particles conventionally dried on copper grids, TEM is rarely employed to evaluate the spatial distribution of nanoparticles in aqueous solutions. Here, we present a microchip nanopipet with a narrow chamber width for sorting nanoparticles from blood and preventing the aggregation of the particles during the drying process, enabling Quantitative analysis of their aggregation/agglomeration states and the particle concentration in aqueous solutions. This microchip is adaptable to all commercial TEM holders. Such a nanopipet proves to be a simple and convenient sampling device for TEM image-based Quantitative Characterization.
Peter Ercius - One of the best experts on this subject based on the ideXlab platform.
-
Quantitative Characterization of high temperature oxidation using electron tomography and energy dispersive x ray spectroscopy
Scientific Reports, 2018Co-Authors: Jihan Zhou, Matthew Taylor, Georgian Melinte, Ashwin J Shahani, C C Dharmawardhana, Hendrik Heinz, Peter W Voorhees, J H Perepezko, Karen C Bustillo, Peter ErciusAbstract:We report Quantitative Characterization of the high temperature oxidation process by using electron tomography and energy-dispersive X-ray spectroscopy. As a proof of principle, we performed 3D imaging of the oxidation layer of a model system (Mo3Si) at nanoscale resolution with elemental specificity and probed the oxidation kinetics as a function of the oxidation time and the elevated temperature. Our tomographic reconstructions provide detailed 3D structural information of the surface oxidation layer of the Mo3Si system, revealing the evolution of oxidation behavior of Mo3Si from early stage to mature stage. Based on the relative rate of oxidation of Mo3Si, the volatilization rate of MoO3 and reactive molecular dynamics simulations, we propose a model to explain the mechanism of the formation of the porous silica structure during the oxidation process of Mo3Si. We expect that this 3D Quantitative Characterization method can be applied to other material systems to probe their structure-property relationships in different environments.
Ashok Prasad - One of the best experts on this subject based on the ideXlab platform.
-
Quantitative Characterization of genetic parts and circuits for plant synthetic biology
Nature methods, 2015Co-Authors: Katherine A Schaumberg, Mauricio S. Antunes, Tessema K. Kassaw, Christopher S Zalewski, June I. Medford, Ashok PrasadAbstract:Plant synthetic biology promises immense technological benefits, including the potential development of a sustainable bio-based economy through the predictive design of synthetic gene circuits. Such circuits are built from Quantitatively characterized genetic parts; however, this Characterization is a significant obstacle in work with plants because of the time required for stable transformation. We describe a method for rapid Quantitative Characterization of genetic plant parts using transient expression in protoplasts and dual luciferase outputs. We observed experimental variability in transient-expression assays and developed a mathematical model to describe, as well as statistical normalization methods to account for, this variability, which allowed us to extract Quantitative parameters. We characterized >120 synthetic parts in Arabidopsis and validated our method by comparing transient expression with expression in stably transformed plants. We also tested >100 synthetic parts in sorghum (Sorghum bicolor) protoplasts, and the results showed that our method works in diverse plant groups. Our approach enables the construction of tunable gene circuits in complex eukaryotic organisms.
