Direct visualization of the dynamics of membrane-anchor proteins in living cells

Dynamic properties of proteins have crucial roles in understanding protein function and molecular mechanism within cells. In this paper, we combined total internal reflection fluorescence microscopy with oblique illumination fluorescence microscopy to observe directly the movement and localization of membrane-anchored green fluorescence proteins in living cells. Total internal reflect illumination allowed the observation of proteins in the cell membrane of living cells since the penetrate depth could be adjusted to about 80 nm, and oblique illumination allowed the observation of proteins both in the cytoplasm and apical membrane, which made this combination a promising tool to investigate the dynamics of proteins through the whole cell. Not only individual protein molecule tracks have been analyzed quantitatively but also cumulative probability distribution function analysis of ensemble trajectories has been done to reveal the mobility of proteins. Finally, single particle tracking has acted as a compensation for single molecule tracking. All the results exhibited green fluorescence protein dynamics within cytoplasm, on the membrane and from cytoplasm to plasma membrane.

Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

Formation of an fcc phase through a bcc metastable state in crystallization of charged colloidal particles

By in situ monitoring structural changes with the reflection spectrometer during the colloidal crystallization, we present direct experimental evidence of liquid-bcc-fcc phase transition in crystallization of charged colloidal particles, as a manifestation of the Ostwald's step rule. In addition, the lifetime of the bcc metastable structure in this system decreases significantly with increasing particle volume fraction, offering a possible explanation for "exceptions" to the step rule.

Potential sputtering by Highly Charged Ion bombardment on Au surface

The sputtered particle yields produced by Pbq+ (q=4-36) with constant kinetic energy bombardment on An surface were measured. The sputtering Could be separated to two parts: no potential sputtering is observed when q<24 (E-pot = 9.6 keV) and the sputtering yield increases with E-pot(1.2) for the higher charge states of q >= 24. The potential sputtering is mainly contributed by the relaxation of electronic excitations on target surface produced by the potential energy transfer from projectile to target atoms.

A Particle-in-cell scheme of the RFQ in the SSC-Linac

A 52 MHz Radio Frequency Quadrupole (RFQ) linear accelerator (linac) is designed to serve as an initial structure for the SSC-Linac system (injector into Separated Sector Cyclotron). The designed injection and output energy are 3.5 keV/u and 143 keV/u, respectively. The beam dynamics in this RFQ have been studied using a three-dimensional Particle-In-Cell (PIC) code BEAMPATH. Simulation results show that this R,FQ structure is characterized by stable values of beam transmission efficiency (at least 95%) for both zero-current mode and the space charge dominated regime. The beam accelerated in the RFQ has good quality in both transverse and longitudinal directions, and could easily be accepted by Drift Tube Linac (DTL). The effect of the vane error and that of the space charge on the beam parameters have been studied as well to define the engineering tolerance for RFQ vane machining and alignment.

Natural 13C abundance as a tracer for studies of soil organic matter dynamics

A method for measuring the long- and medium-term turnover of soil organic matter is described. Its principle is based on the variations of 13C natural isotope abundance induced by the repeated cultivations of a plant with a high 13C/12C ratio (C4 photosynthetic pathway) on a soil which has never carried any such plant. The 13C/12C ratio in soil organic matter being about equal to the 13C/12C ratio of plant materials from which it is derived, changing the 13C content of the organic inputs to the soil (by altering vegetation from C3 type into C4 type) is equivalent to a true labelling in situ of the organic matter. Two cases of continuous corn cultivation (Zea mays: δ13C = −12%.) on soils whose initial organic matter average δ13C is −26%. were studied. The quantity of organic carbon originating from corn (that is the quantity which had turned-over since the beginning of continuous cultivation) was estimated using the 13C natural abundance data. After 13 yr, 22% of total organic carbon had turned-over, in the system studied. Particle size fractions coarser than 50μm on the one hand, and finer than 2μm on the other. contained the youngest organic matters. The turnover rate of silt-sized fractions was slower

Molecular dynamics study on the phase diagrams of linear and branched chain molecules

The particle transfer molecular dynamics is used to study the phase equilibria of linear and branched chain molecules. The scaling of the critical temperature versus chain length is obtained and the critical densities are found to decrease with increasing chain length, which are in agreement with the results of experiment and theory. The phase diagrams of the linear and the branched chain molecules nearly overlap with each other. Moreover, the radial distribution functions of linear and branched chain molecules in gas phase are very similar, but in the liquid phase, they are different for different kinds of chains.

A preliminary study on fingerprinting approach in marine sediment dynamics with the rare earth elements

Locating the quantitized natural sediment fingerprints is an important work for marine sediment dynamics study. The total of 146 sediment samples were collected from the Shelf of the East China Sea and five rivers, including Huanghe (Yellow), Changjiang (Yangtze), Qiantang, Ou and Min River. The sediment grain size and the contents of rare earth elements (REEs) were measured with laser particle size analyzer and ICP-MS technology. The results show that absolute REE content (Sigma REE) and the concentration ratio of light REEs to heavy REEs (L/HREE) are different in the sediments among those rivers. There are higher REE contents in being less than 2 m and 2-31 mu m fractions in the Changjiang Estuary surface sediments. The REE contents of bulk sediment are dominated by the corresponding values of those leading size-fractions. Sigma REE of sediment is higher close to the estuaries and declines seaward on the inner shelf of the East China Sea (ECS). The L/HREE ratio has a tendency of increase southward from 28 degrees N. Hydrodynamic conditions plays a predominate role on spacial distributions of the surficial sediment's REE parameters. In some situations, the currents tend to remove the coarser light grains from initial populations, as well as the deposit of the finer heavy mineral grains. In other situations, the currents will change the ratio of sediment constituents, such as ratio between silts and clays in the sediments. As a result, the various values of Sigma REE or L/HREE ratio in different bulk sediments are more affected by the change of size-fractions than source location. Under the long-term stable hydrodynamic environment, i.e., the East China Sea Shelf, new sediment transport model based on the size and density gradation concept may help to understand the spatial distribution patterns of REE parameters.