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NMR and X-ray structures of the putative sterol carrier protein 2 from Thermus thermophilus HB8 show conformational changes

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Journal of Structural and Functional Genomics 2010年第4期11卷 247-256页

作者： Goroncy, Alexander K. Murayama, Kazutaka Shirouzu, Mikako Kuramitsu, Seiki Kigawa, Takanori Yokoyama, Shigeyuki RIKEN Systems and Structural Biology Center Tsurumi-ku Yokohama Kanagawa 1-7-22 Suehiro-cho Japan Tohoku University Biomedical Engineering Research Organization Sendai 980-8575 Japan RIKEN SPring-8 Center Harima Institute Sayo Hyogo 679-5148 1-1-1 Kouto Japan Graduate School of Science Osaka University Toyonaka Osaka 560-0043 Japan Department of Computational Intelligence and Systems Science Interdisciplinary Graduate School of Science and Engineering Tokyo Institute of Technology Yokohama Japan Department of Biophysics and Biochemistry Graduate School of Science University of Tokyo Tokyo Japan

Sterol carrier protein 2 (SCP-2), also known as nonspecific lipid transfer protein, is a ubiquitous intracellular ~13 kDa protein found in mammals, insects, plants, archaea, and bacteria. Vertebrate SCP-2 has been implicated in a wide range of lipid-related functions in vitro, although its actual physiological role is still unknown. Tunnels in the protein serve as fatty acid binding vehicles. Here we report the first putative SCP-2 structure from a bacterium: specifically, the NMR and X-ray structures of the TTHA0401 protein (also designated as TT1886) from the extremely thermophilic bacterium Thermus thermophilus. The NMR structure and the two chain structures (chain A and chain B) of the asymmetric crystallographic unit (space group (P2₁2 ₁2₁)) revealed an internal cavity. However, this cavity is open to the outside, forming a tunnel, in only one of those structures (chain A, X-ray). The location of this tunnel is different from the one found in other SCP-2 proteins, and inaccessible cavities have not been seen before in SCP structures. We present evidence that at physiological concentrations, TTHA0401 likely exists as a monomer in equilibrium between open and closed conformations. This equilibrium is influenced by temperature-dependent dynamics, and is likely to be very different at the high temperatures preferred by this hyperthermophilic bacterium. Alternatively, another protein binding to TTHA0401 may induce a conformational change, which would constitute an intriguing metabolic regulation method in bacteria. © 2010 Springer science+Business Media B.V.

关键词： Closed cavity Conformational change Crystal packing Hydrophobic tunnel Lipid binding Protein dynamics

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On the analysis of self-adaptive evolution strategies on elliptic model: First results 10

On the analysis of self-adaptive evolution strategies on ell...

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12th Annual Genetic and Evolutionary Computation Conference, GECCO-2010

作者： Melkozerov, Alexander Beyer, Hans-Georg Department of Television and Control Tomsk State University of Control Systems and Radioelectronics Lenin ave. 40 634050 Tomsk Russia Research Center Process and Product Engineering Department of Computer Science Vorarlberg University of Applied Sciences Hochschulstr. 1 A-6850 Dornbirn Austria

ISBN: (纸本)9781450300728

In this paper, first results on the analysis of self-adaptive evolution strategies (ES) with intermediate multirecombination on the elliptic model are presented. Equations describing the ES behavior on the ellipsoid will be derived using a deterministic approach and experimentally verified. A relationship between newly obtained formulae for the elliptic model and previous theoretical results will be discussed. Copyright 2010 ACM.

关键词： Evolutionary algorithms

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SLAMM - Automating memory analysis for numerical algorithms

SLAMM - Automating memory analysis for numerical algorithms

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作者： Dennis, John M. Jessup, Elizabeth R. Waite, William M. Computational and Information Systems Laboratory National Center for Atmospheric Research Boulder CO 80305 United States Department of Computer Science University of Colorado Boulder CO 80309 United States Department of Electrical and Computer Engineering University of Colorado Boulder CO 80309 United States

Memory efficiency is overtaking the number of floating-point operations as a performance determinant for numerical algorithms. Integrating memory efficiency into an algorithm from the start is made easier by computational tools that can quantify its memory traffic. The Sparse Linear Algebra Memory Model (SLAMM) is implemented by a source-to-source translator that accepts a MATLAB specification of an algorithm and adds code to predict memory traffic. Our tests on numerous small kernels and complete implementations of algorithms for solving sparse linear systems show that SLAMM accurately predicts the amount of data loaded from the memory hierarchy to the L1 cache to within 20% error on three different compute platforms. SLAMM allows us to evaluate the memory efficiency of particular choices rapidly during the design phase of an iterative algorithm, and it provides an automated mechanism for tuning exisiting implementations. It reduces the time to perform a priori memory analysis from as long as several days to 20 minutes. © 2010 Elsevier B.V. All rights reserved.

关键词： MATLAB

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An accurate prediction method for protein structural class from signal patterns of NMR spectra in the absence of chemical shift assignments

An accurate prediction method for protein structural class f...

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10th IEEE International Conference on Bioinformatics and Bioengineering, BIBE-2010

作者： Arai, Hiromi Tochio, Naoya Kato, Tsuyoshi Kigawa, Takanori Yamamura, Masayuki Department of Computational Intelligence and Systems Science Interdisciplinary Graduate School of Science and Engineering Tokyo Institute of Technology 4259 Nagatsuta-cho Midori-ku Yokohama 226-8502 Japan RIKEN Systems and Structural Biology Center 1-7-22 Suehiro-cho Tsurumi Yokohama 230-0045 Japan Center for Informational Biology Ochanomizu University 2-1-1 Ohtsuka Bunkyo-ku Tokyo 112-8610 Japan

ISBN: (纸本)9780769540832

The structural class information about a protein is important to understand its biological properties. NMR is one of the most powerful tools to obtain structural information of proteins in atomic resolution. However, an analysis of protein three-dimensional structure from NMR spectra usually requires laborious chemical shift assignment. We developed a new method for predicting the protein structural class directly from the NMR spectra without any chemical shift assignment. The results show that our method outperforms the methods using current secondary structure prediction. © 2010 IEEE.

关键词： Proteins

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Physical Review E 2010年第1期82卷 011136-011136页

作者： Gao-Feng Gu (顾高峰) Wei-Xing Zhou (周炜星) School of Business East China University of Science and Technology Shanghai 200237 China Research Center for Econophysics East China University of Science and Technology Shanghai 200237 China School of Science East China University of Science and Technology Shanghai 200237 China Engineering Research Center of Process Systems Engineering (Ministry of Education) East China University of Science and Technology Shanghai 200237 China Research Center on Fictitious Economics & Data Science Chinese Academy of Sciences Beijing 100080 China

The detrending moving average (DMA) algorithm is a widely used technique to quantify the long-term correlations of nonstationary time series and the long-range correlations of fractal surfaces, which contains a parameter θ determining the position of the detrending window. We develop multifractal detrending moving average (MFDMA) algorithms for the analysis of one-dimensional multifractal measures and higher-dimensional multifractals, which is a generalization of the DMA method. The performance of the one-dimensional and two-dimensional MFDMA methods is investigated using synthetic multifractal measures with analytical solutions for backward (θ=0), centered (θ=0.5), and forward (θ=1) detrending windows. We find that the estimated multifractal scaling exponent τ(q) and the singularity spectrum f(α) are in good agreement with the theoretical values. In addition, the backward MFDMA method has the best performance, which provides the most accurate estimates of the scaling exponents with lowest error bars, while the centered MFDMA method has the worse performance. It is found that the backward MFDMA algorithm also outperforms the multifractal detrended fluctuation analysis. The one-dimensional backward MFDMA method is applied to analyzing the time series of Shanghai Stock Exchange Composite Index and its multifractal nature is confirmed.

关键词： Time series

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Tests of nonuniversality of the stock return distributions in an emerging market

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Physical Review E 2010年第6期82卷 066103-066103页

作者： Guo-Hua Mu (牟国华) Wei-Xing Zhou (周炜星) School of Business East China University of Science and Technology Shanghai 200237 China School of Science East China University of Science and Technology Shanghai 200237 China Research Center for Econophysics East China University of Science and Technology Shanghai 200237 China Engineering Research Center of Process Systems Engineering (Ministry of Education) East China University of Science and Technology Shanghai 200237 China Research Center on Fictitious Economics and Data Science Chinese Academy of Sciences Beijing 100080 China

There is convincing evidence showing that the probability distributions of stock returns in mature markets exhibit power-law tails and both the positive and negative tails conform to the inverse cubic law. It supports the possibility that the tail exponents are universal at least for mature markets in the sense that they do not depend on stock market, industry sector, and market capitalization. We investigate the distributions of intraday returns at different time scales (Δt=1, 5, 15, and 30 min) of all the A-share stocks traded in the Chinese stock market, which is the largest emerging market in the world. We find that the returns can be well fitted by the q-Gaussian distribution and the tails have power-law relaxations with the exponents increasing with Δt and being well outside the Lévy stable regime for individual stocks. We provide statistically significant evidence showing that, at small time scales Δt<15 min, the exponents logarithmically decrease with the turnover rate and increase with the market capitalization. When Δt>15 min, no conclusive evidence is found for a possible dependence of the tail exponent on the turnover rate or the market capitalization. Our findings indicate that the intraday return distributions at small time scales are not universal in emerging stock markets but might be universal at large time scales.

关键词： Financial markets

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Preface

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Springer Series in Geomechanics and Geoengineering 2011年 v-vi页

作者： Borja, Ronaldo Darve, Félix Desrues, Jacques Muhlhaus, Hans Wan, Richard Department of Civil and Environmental Engineering Stanford University StanfordCA94305 United States CNRS UMR 5521 Grenoble-INP UJF-Grenoble 1 3SR-Lab GrenobleF-38041 France Earth Systems Science Computational Center The University of Queensland St. LuciaQLD4072 Australia Department of Civil Engineering University of Calgary CalgaryABT2N 1N4 Canada

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An Accurate Prediction Method for Protein Structural Class from Signal Patterns of NMR Spectra in the Absence of Chemical Shift Assignments

An Accurate Prediction Method for Protein Structural Class f...

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IEEE Symposium on Bioinformatics and Bioengineering (BIBE)

作者： Hiromi Arai Naoya Tochio Tsuyoshi Kato Takanori Kigawa Masayuki Yamamura Department of Computational Intelligence and Systems Science Interdisciplinary Graduate School of Science and Engineering Tokyo Institute of Technology Yokohama Japan RIKEN Systems and Structural Biology Center Yokohama Japan Center of Informational Biology Ochanomizu University Bunkyo Tokyo Japan

关键词： Prediction methods Nuclear magnetic resonance Protein engineering Chemical technology Chemical analysis Hydrogen Spine Chemical engineering Bioinformatics Biomedical engineering

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Two-dimensional graphene bridges enhanced photoinduced charge transport in dye-sensitized solar cells

Two-dimensional graphene bridges enhanced photoinduced charg...

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作者： Yang, Nailiang Zhai, Jin Wang, Dan Chen, Yongsheng Jiang, Lei Beijing University of Aeronautics and Astronautics Beijing 100191 China State Key Laboratory of Multi-phase Complex Systems Institute of Process Engineering Chinese Academy of Sciences Beijing 100190 China Center for Molecular Science Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China Institute of Polymer Chemistry College of Chemistry Nankai University Tianjin 300071 China

As a novel two-dimensional (2D) material, graphene shows great benefits in electric and material science. Compared to 1D nanomaterials, it may show more excellent properties. Here, we introduced graphene as 2D bridges into the nanocrystalline electrodes of dye-sensitized solar cells, which brought a faster electron transport and a lower recombination, together with a higher light scattering. On the basis of these advantages, the short-circuit current density was increased by 45% without sacrificing the open-circuit voltage, and the total conversion efficiency was 6.97%, which was increased by 39%, comparing with the nanocrystalline titanium dioxide photoanode, and it was also much better than the 1D nanomaterial composite electrode. © 2010 American Chemical Society.

关键词： Dye-sensitized solar cells

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Statistical properties of visibility graph of energy dissipation rates in three-dimensional fully developed turbulence

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Physica A: Statistical Mechanics and its Applications 2010年第13期389卷 2675-2681页

作者： Chuang Liu Wei-Xing Zhou Wei-Kang Yuan School of Business East China University of Science and Technology Shanghai 200237 China Engineering Research Center of Process Systems Engineering (Ministry of Education) East China University of Science and Technology Shanghai 200237 China Research Center for Econophysics East China University of Science and Technology Shanghai 200237 China School of Science East China University of Science and Technology Shanghai 200237 China Research Center on Fictitious Economics & Data Science Chinese Academy of Sciences Beijing 100080 China State Key Laboratory of Chemical Engineering East China University of Science and Technology Shanghai 200237 China

We study the statistical properties of complex networks constructed from time series of energy dissipation rates in three-dimensional fully developed turbulence using the visibility algorithm. The degree distribution is found to have a power-law tail with the tail exponent α = 3.0 . The exponential relation between the number of the boxes N B and the box size l B based on the edge-covering box-counting method illustrates that the network is not self-similar, which is also confirmed by the hub-hub attraction according to the visibility algorithm. In addition, it is found that the skeleton of the visibility network exhibits excellent allometric scaling with the scaling exponent η = 1.163 ± 0.005 .

关键词： Turbulence Energy dissipation rate Visibility graph Degree distribution Self-similarity Allometric scaling

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