Molecular dynamics simulation strategies for protein-micelle complexes

Cheng, X.,Kim, J.K.,Kim, Y.,Bowie, J.U.,Im, W. Elsevier Pub. Co 2016 Biochimica et biophysica acta, Biomembranes Vol.1858 No.7

The structure and stability of membrane proteins can vary widely in different detergents and this variability has great practical consequences for working with membrane proteins. Nevertheless, the mechanisms that operate to alter the behavior of proteins in micelles are poorly understood and not predictable. Atomic simulations could provide considerable insight into these mechanisms. Building protein-micelle complexes for simulation is fraught with uncertainty, however, in part because it is often unknown how many detergent molecules are present in the complex. Here, we describe several convenient ways to employ Micelle Builder in CHARMM-GUI to rapidly construct protein-micelle complexes and performed simulations of the isolated voltage-sensor domain of voltage-dependent potassium-selective channel and an antimicrobial peptide papiliocin with varying numbers of detergents. We found that once the detergent number exceeds a threshold, protein-detergent interactions change very little and remain very consistent with experimental observations. Our results provide a platform for future studies of the interplays between protein structure and detergent properties at the atomic level. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

The X-Ray Modulation of PSR J2032+4127/MT91 213 during the Periastron Passage in 2017

Li, K. L.,Takata, J.,Ng, C. W.,Kong, A. K. H.,Tam, P. H. T.,Hui, C. Y.,Cheng, K. S. American Astronomical Society 2018 The Astrophysical journal Vol.857 No.2

High-energy Emissions from the Pulsar/Be Binary System PSR J2032+4127/MT91 213

Takata, J.,Tam, P. H. T.,Ng, C. W.,Li, K. L.,Kong, A. K. H.,Hui, C. Y.,Cheng, K. S. American Astronomical Society 2017 The Astrophysical journal Vol.836 No.2

<P>PSR. J2032+4127 is a radio-loud gamma-ray-emitting pulsar; it is orbiting around a high-mass Be type star with a very long orbital period of 25-50 years, and is approaching periastron, which will occur in late 2017/early 2018. This system comprises a young pulsar and a Be type star, which is similar to the so-called gamma-ray binary PSR. B1259-63/LS2883. It is expected therefore that PSR. J2032+4127 shows an enhancement of high-energy emission caused by the interaction between the pulsar wind and Be wind/disk around periastron. Ho et al. recently reported a rapid increase in the X-ray flux from this system. In this paper, we also confirm a rapid increase in the X-ray flux along the orbit, while the GeV flux shows no significant change. We discuss the high-energy emissions from the shock caused by the pulsar wind and stellar wind interaction and examine the properties of the pulsar wind in this binary system. We argue that the rate of increase of the X-ray flux observed by Swift indicates (1) a variation of the momentum ratio of the two-wind interaction region along the orbit, or (2) an evolution of the magnetization parameter of the pulsar wind with the radial distance from the pulsar. We also discuss the pulsar wind/Be disk interaction at the periastron passage, and propose the possibility of formation of an accretion disk around the pulsar. We model high-energy emissions through the inverse-Compton scattering process of the cold-relativistic pulsar wind off soft photons from the accretion disk.</P>

반추위액으로부터 혐기성 미생물(박테리아 , 프로토조아 및 곰팡이)의 분리 방법

신기준,이성실,하종규,박정근,케이제이쳉 한국동물자원과학회 2000 한국축산학회지 Vol.42 No.5

Separation methods for rumen microbial fractions contained the bacterial, protozoal and fungal fraction which are the most useful to assess the relative contribution of microbial groups for digestion of feedstuffs and the useful tools to study the rumen microbiology. The fractionation methods have been classified into three main categories; physical method based on cell size and weight, chemical method based on the microbial sensitivity to some chemicals, and physicochemical methods. After microbial groups were selected by physical treatment(centrifuge, filtering and autoclaves), chemical treatment(by the addition of antibiotics and/or some chemicals) and physicochemical treatments of rumen fluid, enumerated each microbial fraction using microscopy and roll-tube methods, and then estimated each separation method. This study emphasized the relative advantageous of the different methods and the factors to be kept in mind when choosing the most appropriate method for a definite goal. Physical treatment(filteration with nylon cloth had larger pore size about 500㎛ or centrifugation) was estimated potentially sufficient to separate protozoal fraction alone from the rumen fluids, due to the phenomenal differences their cell size and weight compared to other microbes, but must be considered of the some kinds of bacteria and/or fungal spores can be survive in protozoa) cell. When separating the microbial groups from the rumen fluids, a physicochemical method is probably the best method, especially when needed separation of bacterial fraction and fungal fraction. And the physicochemical method gave more precise results are presented in Fig. 4 in the main segments of the paper.

반추위 혐기성 미생물(박테리아 , 프로토조아 및 곰팡이)이 세포벽 구성물질의 분해에 미치는 상대적 역할

신기준,이성실,하종규,박정근,케이제이쳉 한국동물자원과학회 2000 한국축산학회지 Vol.42 No.5

To study the relative contributions of microbial groups (bacteria, protozoa and fungi) in rumen fluids to the overall process of cell wall digestion in the rumen, representatives of these groups were selected by physical treatment, chemical treatment and physicochemical treatments of whole rumen fluids. Physical treatments were performed by centrifuge, filteration and autoclave based on their size and weight. Chemical treatments were also performed by the addition of antibiotics and chemicals to rumen fluids as follows; antibacterial agent[streptomycin sulfate, penicillin G potassium and chloramphenicol(0.010㎎/㎖l each)], antiprotozoan agent[copper sulfate(0.15㎎/㎖), sodium lauryl sulfate (0.010mglml) and dioctyl sulfossucinate sodium salts(0.200㎎/㎖}], and antifungal agent[cychloheximide (0.05㎎/㎖) and nystatin(200U/㎖)]. To evaluate the potential activity and relative contribution to degradation of cell walls by specific microbial groups, the following fractions were prepared: a positive system (whole ruminal fluid), a bacterial (B) system, a protozoan (P) system, a fungal (F) system and a negative system (cell free rumen fluid). To assess the interactions between specific microbial fractions mixed cultures (B+P, B+F, and P+F) were also assigned. Patterns of degradation due to the various treatments resulted in three distinct groups of data based on the degradation rate of cell wall material and on cell wall degrading enzyme activities. The order of degradation was Positive and F systems $gt; B system $gt; Negative and P systems. Therefore, fungal activity was responsible for most of the cell wall degradation. Cell wall degradation by the anaerobic bacterial fraction was significantly less than by the fungal fraction and the protozoan fraction failed to grow under the conditions used. In general, in the mixed culture systems the co-culture systems demonstrated a decrease in cellulolysis compared with the monoculture systems. When one microbial fraction was associated with another microbial fraction, two types of results were obtained. The protozoan fraction inhibited cellulolysis of cell wall material by both the bacterial and fungal fraction, while in the coculture between the bacterial fraction and fungal fraction, a synergistic interaction was detected.

Temporal-spatial structures of plasmas flows and turbulence around tearing mode islands in the edge tokamak plasmas

Zhao, K.J.,Nagashima, Y.,Li, F.M.,Shi, Yuejiang,Diamond, P.H.,Dong, J.Q.,Itoh, K.,Itoh, S.-I.,Zhuang, G.,Liu, H.,Chen, Z.P.,Cheng, J.,Nie, L.,Ding, Y.H.,Hu, Q.M.,Chen, Z.Y.,Rao, B.,Cheng, Z.F.,Gao, L. IOP 2017 Nuclear fusion Vol.57 No.12

<P>The temporal-spatial structures of plasma flows and turbulence around tearing mode islands are presented. The experiments were performed using Langmuir probe arrays in the edge plasmas of J-TEXT tokamak. The correlation analyses clearly show that the flows have similar structures of <I>m</I>/<I>n</I>  =  3/1 as the magnetic island does (<I>m</I> and <I>n</I> are the poloidal and toroidal mode numbers, respectively). The sign of the potential fluctuations for the flows inverses and the powers significantly reduce at <I>q</I>  =  3 surface. Approaching to the last closed flux surface for the magnetic islands, the radially elongated flow structure forms. The flows are concentrated near separatrix and show quadrupole structures. The turbulence is concentrated near X-point and partly trapped inside the magnetic islands.</P>

Mode Change of a Gamma-Ray Pulsar, PSR J2021+4026

Zhao, J.,Ng, C. W.,Lin, L. C. C.,Takata, J.,Cai, Y.,Hu, C.-P.,Yen, D. C. C.,Tam, P. H. T.,Hui, C. Y.,Kong, A. K. H.,Cheng, K. S. American Astronomical Society 2017 The Astrophysical journal Vol.842 No.1

<P>A glitch of a pulsar is known as a sudden increase in the spin frequency and spin-down rate (frequency time derivative), and it can be caused by a sudden release of the stress built up in the solid crust of the star or pinned vortices in the superfluid interior. PSR J2021+4026 is the first pulsar that shows a significant change in the gamma-ray flux and pulse profile at the glitch that occurred around 2011 October 16. We report the results of timing and spectral analysis of PSR J2021+4026 using similar to 8 yr Fermi. Large Area Telescope data. We find that the pulsar stayed at a high spin-down rate (similar to 4% higher than the pre-glitch value) and a low gamma-ray state (similar to 18% lower) for about 3 yr. after the glitch. Around 2014 December, the spin-down rate and gamma-ray flux gradually returned to pre-glitch values within a timescale of a. few months. The phase-resolved spectra and pulse profiles after the relaxation are also consistent with those before the glitch. The observed long-term evolution of the spin-down rate and the gamma-ray flux indicates that the glitch triggered a mode change in the global magnetosphere. We speculate that the glitch changed. the local magnetic field structure around the polar cap and/or the inclination angle of the. dipole axis, leading to. a change in the electric current circulating in the. magnetosphere.</P>

DISCOVERY OF AN ULTRACOMPACT GAMMA-RAY MILLISECOND PULSAR BINARY CANDIDATE

Kong, Albert K. H.,Jin, Ruolan,Yen, T.-C.,Hu, C.-P.,Hui, C. Y.,Tam, P. H. T.,Takata, J.,Lin, L. C. C.,Cheng, K. S.,Park, S. M.,Kim, C. L. IOP Publishing 2014 ASTROPHYSICAL JOURNAL LETTERS - Vol.794 No.2

<P>We report multi-wavelength observations of the unidentified Fermi object 2FGL J1653.6-0159. With the help of high-resolution X-ray observations, we have identified an X-ray and optical counterpart to 2FGL J1653.6-0159. The source exhibits a periodic modulation of 75 minutes in the optical and possibly also in the X-ray. We suggest that 2FGL J1653.6-0159 is a compact binary system with an orbital period of 75 minutes. Combining the gamma-ray and X-ray properties, 2FGL J1653.6-0159 is potentially a black-widow-/redback-type gamma-ray millisecond pulsar (MSP). The optical and X-ray light curve profiles show that the companion is mildly heated by the high-energy emission and that the X-rays are from intrabinary shock. Although no radio pulsation has yet been detected, we estimated that the spin period of the MSP is similar to 2 ms based on a theoretical model. If pulsation can be confirmed in the future, 2FGL J1653.6-0159 will become the first ultracompact rotation-powered MSP.</P>

Separation dynamics of hydrogen isotope gas in mesoporous and microporous adsorbent beds at 77 K: SBA-15 and zeolites 5A, Y, 10X

Chu, X.Z.,Cheng, Z.P.,Xiang, X.X.,Xu, J.M.,Zhao, Y.J.,Zhang, W.G.,Lv, J.S.,Zhou, Y.P.,Zhou, L.,Moon, D.K.,Lee, C.H. Pergamon Press ; Elsevier Science Ltd 2014 International journal of hydrogen energy Vol.39 No.9

The separation of a hydrogen isotope mixture on porous materials was studied using equilibrium and breakthrough experiments. The adsorption equilibria of H<SUB>2</SUB> and D<SUB>2</SUB> on SBA-15 with mesopores and molecular sieves 5A, Y, and 10X with micropores were measured at 77 K using the volumetric method. The breakthrough experiments of a H<SUB>2</SUB> and D<SUB>2</SUB> mixture in each adsorbent bed were carried out at various conditions of flow rate and pressure. The equilibrium ratio of D<SUB>2</SUB> to H<SUB>2</SUB> on mesoporous molecular sieves was larger than the ratio on microporous molecular sieves (SBA-15 > 10X > Y > 5A), but the difference among the adsorbents decreased with increases in pressure. On the other hand, the order of breakthrough separation factor showed the opposite result (SBA-15 < 10X < Y < 5A). The breakthrough separation factors for zeolite 10X was approximately equal to the equilibrium ratio of D<SUB>2</SUB> to H<SUB>2</SUB> at the corresponding partial pressures, whereas zeolites 5A and Y showed higher breakthrough separation factors than their equilibrium ratios. In SBA-15, the separation factors from breakthrough results were even smaller than the corresponding equilibrium ratio. In the microporous adsorbent with a limited pore size (zeolite 5A in the study), the diffusion mechanism contributed to the separation of hydrogen isotope gases as one of key factors.

EXPLORING THE X-RAY AND gamma-RAY PROPERTIES OF THE REDBACK MILLISECOND PULSAR PSR J1723-2837

Hui, C. Y.,Tam, P. H. T.,Takata, J.,Kong, A. K. H.,Cheng, K. S.,Wu, J. H. K.,Lin, L. C. C.,Wu, E. M. H. University of Chicago Press for the American Astro 2014 ASTROPHYSICAL JOURNAL LETTERS - Vol.781 No.1

We have investigated the X-ray and gamma-ray properties of the redback millisecond pulsar PSR J1723-2837 with XMM-Newton, Chandra, and Fermi. We have discovered the X-ray orbital modulation of this binary system with a minimum that coincides with the phases of radio eclipse. The X-ray emission is clearly non-thermal in nature, which can be described well by a simple power law with a photon index of similar to 1.2. The phase-averaged luminosity is similar to 9 x 10(31) erg s(-1) in 0.3-10 keV, which consumes similar to 0.2% of the spin-down power. We have detected the gamma-ray emission in 0.1-300 GeV from this system at a significance of similar to 6 sigma for the first time. The gamma-rays in this energy range consume similar to 2% of the spin-down power and can be modeled by a power law with a photon index of similar to 2.6. We discuss the high energy properties of the new redback in the context of an intrabinary shock model.