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Interaction specific binding hotspots in Endonuclease colicin-immunity protein complex from MD simulations

Science China Chemistry 2013年第8期56卷 1143-1151页

作者： YAO XueXia JI ChangGe XIE DaiQian ZhANG john Z.h. School of Chemistry and Chemical Engineering Nanjing University College of Engineering Nanjing Agricultural University State Key Laboratory of Precision Spectroscopy Department of PhysicsEast China Normal University Department of Chemistry New York University

The binding of Endonuclease colicin 9 (E9) by Immunity protein 9 (Im9) was found to involve some hotspots from helix III of Im9 on protein-protein interface that contribute the dominant binding energy to the *** the current work,MD simulations of the WT and three hotspot mutants (D51A,Y54A and Y55A of Im9) of the E9-Im9 complexes were carried out to investigate specific interaction mechanisms of these three hotspot *** changes of binding energy between the WT and mutants of the complex were computed by the MM/PBSA method using a polarized force field and were in excellent agreement with experiment values,verifying that these three residues were indeed hotspots of the binding *** decomposition analysis revealed that binding by D51 to E9 was dominated by electrostatic interaction due to the presence of the carboxyl group of Asp51 which hydrogen bonds to *** binding by hotspots Y54 and Y55,van der Waals interaction from the aromatic side chain of tyrosine provided the dominant *** comparison,calculation by using the standard (nonpolarizable) AMBER99SB force field produced binding energy changes from these mutations in opposite direction to the experimental *** hydrogen bond analysis showed that conformations sampled from MD simulation in the standard AMBER force field were distorted from the native state and they disrupted the inter-protein hydrogen bond network of the protein-protein *** current work further demonstrated that electrostatic polarization plays a critical role in modulating protein-protein binding.

关键词： protein-protein interaction binding hotspot mutation Endonuclease Colicin immunity protein MD simulation

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Inhibition of hepatitis C virus replication by single-stranded RNA structural mimics

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World Journal of Gastroenterology 2010年第17期16卷 2100-2108页

作者： Robert Smolic Martina Smolic john h Andorfer Catherine h Wu Robert M Smith George Y Wu Department of Medicine Division of Gastroenterology-HepatologyUniversity of Connecticut Health Center263 Farmington Ave.FarmingtonCT 06030-1845United States

AIM: To examine the effect of hepatitis C virus (hCV) structural mimics of regulatory regions of the genome on hCV ***: hCV RNA structural mimics were constructed and tested in a hCV genotype 1b aBB7 replicon,and a Japanese fulminant hepatitis-1 (JFh-1) hCV genotype 2a infection *** sequences were computer-predicted to adopt stem-loop structures identical to the corresponding elements in full-length viral ***7.5 cells bearing the BB7 replicon or infected with JFh-1 virus were transfected with expression vectors generating hCV mimics and *** hCV RNA and protein levels were quantified by real-time polymerase chain reaction and Western blotting,*** evaluate possible antisense effects,complementary RNAs spanning a mimic were ***: In the BB7 genotype 1b replicon system,mimics of the polymerase (NS-5B),X and BA regions inhibited replication by more than 90%,50%,and 60%,*** the JFh-1 genotype 2 infection system,mimics that were only 74% and 46% identical in sequence relative to the corresponding region in JFh-1 inhibited hCV replication by 91.5% and 91.2%,respectively,as effectively as a mimic with complete identity to hCV genotype *** inhibitory effects were confirmed by NS3 protein *** RNA molecules spanning the 74% identical mimic had no significant ***: hCV RNA structural mimics can inhibit hCV RNA replication in replicon and infectious hCV systems and do so independent of close sequence identity with the target.

关键词： hepatitis C virus Japanese fulminant hepatitis virus Complementarity RNA sequence hybridization

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Flow turbulence presented by different vegetation spacing sizes within a submerged vegetation patch

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Journal of hydrodynamics 2023年第6期35卷 1131-1145页

作者： Chukwuemeka Kingsley john Jaan h.Pu Yakun Guo Prashanth R.hanmaiahgari Manish Pandey Faculty of Engineering and Informatics University of BradfordBradfordUK Department of Civil Engineering Indian Institute of TechnologyKharagpurIndia National Institute of Technology(NIT) WarangalIndia

This study presents results from a vegetation-induced flow experimental study which investigates 3-D turbulence structure profiles,including Reynolds stress,turbulence intensity and bursting analysis of open channel *** vegetation densities have been built between the adjacent vegetations,and the flow measurements are taken using acoustic Doppler velocimeter(ADV)at the locations within and downstream of the vegetation *** different tests are conducted,where the first test has compact vegetations,while the second and the third tests have open spaces created by one and two empty vegetation slots within the vegetated *** reveals that over 10%of eddies size is generated within the vegetated zone of compact vegetations as compared with the fewer *** turbulence structures variation is also observed at the points in the non-vegetated *** findings from burst-cycle analysis show that the sweep and outward interaction events are dominant,where they further increase away from the *** effect of vegetation on the turbulent burst cycle is mostly obvious up to approximately two-third of vegetation height where this phenomenon is also observed for most other turbulent structure.

关键词： Velocity profiles acoustic Doppler velocimeter(ADV) turbulent intensities Reynolds stress turbulent bursting vegetated flow vegetation spacing sizes

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The immunology of human cytomegalovirus latency： could latent infection be cleared by novel immunotherapeutic strategies？

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Cellular & Molecular Immunology 2015年第2期12卷 128-138页

作者： Mark R Wills Emma Poole Betty Lau Ben Krishna john h Sinclair Department of Medicine University of Cambridge Cambridge UK

While the host immune response following primary human cytomegalovirus （hCMV） infection is generally effective at stopping virus replication and dissemination, virus is never cleared by the host and like all herpesviruses, persists for life. At least in part, this persistence is known to be facilitated by the ability of hCMV to establish latency in myeloid cells in which infection is essentially silent with, importantly, a total lack of new virus production. however, although the viral transcription programme during latency is much suppressed, a number of viral genes are expressed during latent infection at the protein level and many of these have been shown to have profound effects on the latent cell and its environment. Intriguingly, many of these latency-associated genes are also expressed during lyric infection. Therefore, why the same potent host immune responses generated during lytic infection to these viral gene products are not recognized during latency, thereby allowing clearance of latently infected cells, is far from clear. Reactivation from latency is also a major cause of hCMV-mediated disease, particularly in the immune compromised and immune naive, and is also likely to be a major source of virus in chronic subclinical hCMV infection which has been suggested to be associated with long-term diseases such as atherosclerosis and some neoplasias. Consequently, understanding latency and why latenUy infected cells appear to be immunoprivileged is crucial for an understanding of the pathogenesis of hCMV and may help to design strategies to eliminate latent virus reservoirs, at least in certain clinical settings.

关键词： Cytomegalovirus latency immune evasion immunotherapeutic

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XFEL data analysis for structural biology

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Frontiers of Electrical and Electronic Engineering in China 2016年第3期4卷 159-176页

作者： haiguang Liu john C. h. Spence Complex Systems Division Beiiin.q Computational Science Research Center Beijing 100193 China Physics Department Arizona State University Tempe AZ 85287 USA

X-ray Free Electron Lasers （XFELs） have advanced research in structure biology, by exploiting their ultra-short and bright X-ray pulses. The resulting ＂diffraction before destruction＂ experimental approach allows data collection to outrun radiation damage, a crucial factor that has often limited resolution in the structure determination of biological molecules. Since the first hard X-ray laser （the Linac Coherent Light Source （LCLS） at SLAC） commenced operation in 2009, serial femtosecond crystallography （SFX） has rapidly matured into a method for the structural analysis of nano- and micro-crystals. At the same time, single particle structure determination by coherent diffractive imaging, with one particle （such as a virus） per shot, has been under intense development. In this review we describe these applications of X-ray lasers in structural biology, with a focus particularly on aspects of data analysis for the computational research community. We summarize the key problems in data analysis and model reconstruction, and provide perspectives on future research using computational methods.

关键词： X-my Free Electron Laser single particle scattering serial crystallography phase retrieval orientationrecovery

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Brain of the blind:transcriptomics of the golden-line cavefish brain

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Current Zoology 2018年第6期64卷 765-773页

作者： Fanwei MENG Yahui ZhAO Tom TITUS Chunguang ZhANG john h.POSTLEThWAIT State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of SciencesBeijing 100101China Institute of Neuroscience University of OregonEugeneOR 97403USA

The genus Sinocyclocheilus (golden-line barbel) includes 25species of cave-dwelling blind fish (cavefish)and more than 30 surface-dwelling species with normal *** environments are dark and generally nutrient-poor with few *** of several genera evolved convergent morphological adaptations in visual,pigmentation,brain,olfactory,and digestive systems. We compared brain morphology and gene expression patterns in a cavefish Sinocyclocheilus anophthalmus with those of a closely related surface-dwelling species *** showed that cavefish have a longer olfactory tract and a much smaller optic tectum than surface *** by RNA-seq revealed that many genes upregulated in cavefish are related to lysosomes and the degradation and metabolism of proteins,amino acids,and *** down- regulated in cavefish tended to involve "activation of gene expression in cholesterol biosynthesis" and cholesterol degradation in the *** encoding Srebfs (sterol regulatory element- binding transcription factors)and Srebf targets,including enzymes in cholesterol synthesis,were downregulated in cavefish brains compared with surface fish *** gene encoding Cyp46a1, which eliminates cholesterol from the brain,was also downregulated in cavefish brains,while the total level of cholesterol in the brain remained *** brains misexpressed several genes encoding proteins in the hypothalamus-pituitary axis,including Trh,Sst,Crh,Pomc,and *** results suggest that the rate of lipid biosynthesis and breakdown may both be depressed in golden-line cavefish brains but that the lysosome recycling rate may be increased in cavefish;properties that might be related to differences in nutrient availability in caves.

关键词： cavefish cholesterol cyp46a optic tectum Sinocyclocheilus transcriptomics

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Probing calcium and sulfur distribution and pattern in hairs using micro-proton induced X-ray emission (MPIXE)

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Chinese Science Bulletin 2007年第21期52卷 2909-2912页

作者： TONG YongPeng LI ChangMing john h.T. LUONG Nuclear Technical Institute Shenzhen University Shenzhen 518060 China School of Chemical and Biomedical Engineering Nanyang Technological University Singapore Biotechnology Research Institute National Research (3ouncil of Canada Montreal: Quebec Canada H4P 2R2

More than 20 hair strands obtained from several people are analyzed by non-invasive micro-proton induced X-ray emission (PIXE) for probing calcium and sulfur distribution and pattern. The sulfur con- tent in woman’s hair along the longitudinal axis shows a monthly rhythm whereas the level of Ca is much higher in the medulla core and exhibits a daily rhythm both in male and female hair. The Ca content gradually decreases from the tip to the root position in the shedding process and more Ca can be found in black hair compared to white hair.

关键词：质子诱导X射线发射钙硫磺毛发

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Data and subject heterogeneity and data sharing:keys to translational success in spinal cord injury research?

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Neural Regeneration Research 2023年第8期18卷 1730-1731页

作者： Karim Fouad Olivia h.Wireman john C.Gensel Faculty of Rehabilitation Medicine Department of Physical TherapyNeuroscience and Mental Health InstituteUniversity of AlbertaAlbertaCanada Spinal Cord and Brain Injury Research Center(SCoBIRC) Department of PhysiologyUniversity of Kentucky College of MedicineLexingtonKYUSA

Spinal cord injury(SCI)is a highly devastating and com plex inj u ry with many seconda ry *** a treatment for SCI has been a rollercoaster ride through exciting peaks and sobering *** a matter of fact,there are still ... 详细信息

关键词： damage treatment SCI

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Crop phenotyping studies with application to crop monitoring

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The Crop Journal 2022年第5期10卷 1221-1223页

作者： Xiuliang Jin Wanneng Yang john h.Doonan Clement Atzberger Institute of Crop Sciences Chinese Academy of Agricultural Sciences/Key Laboratory of Crop Physiology and EcologyMinistry of AgricultureBeijing 100081China National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhan 430070HubeiChina The National Plant Phenomics Centre Institute of BiologicalRural and Environmental Sciences(IBERS)Aberystwyth UniversityAberystwythCeredigion SY233FLUK Institute of Geomatics University of Natural Resources and Life Sciences(BOKU)Peter Jordan Straße 821190 ViennaAustria

*** Crop yield must urgently be sustainably increased to accommodate a rising global population and anticipated climate change in the coming decades,in the face of plant stresses and limited resources[1].Conventional ... 详细信息

关键词： breeding Crop efficiency.

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Calculation of Collective Variable-based PMF by Combining WhAM with Umbrella Sampling

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Chinese Physics Letters 2012年第6期29卷 291-294页

作者： XU Wei-Xin LI Yang ZhANG john Z.h. State Key Laboratory of Precision Spectroscopy Department of PhysicsEast China Normal UniversityShanghai 200062 Institute of Theoretical and Computational Science Institutes for Advanced Interdisciplinary ResearchEast China Normal UniversityShanghai 200062 Department of Chemistry New York UniversityNew YorkNew York 10003USA

Potential of mean force (PMF) with respect to localized reaction coordinates (RCs) such as distance is often applied to evaluate the free energy profile along the reaction pathway for complex molecular ***,calculation of PMF as a function of global RCs is still a challenging and important problem in computational *** examine the combined use of the weighted histogram analysis method and the umbrella sampling method for the calculation of PMF as a function of a global RC from the coarse-grained Langevin dynamics simulations for a model *** method yields the folding free energy profile projected onto a global RC,which is in accord with benchmark *** this method rare global events would be sufficiently sampled because the biased potential can be used for restricting the global conformation to specific regions during free energy *** strategy presented can also be utilized in calculating the global intra- and intermolecular PMF at more detailed levels.

关键词： coordinates utilized calculating

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