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Spatial resolution and location impact group structure in a marine food web 期刊论文
ECOLOGY LETTERS, 2020
作者:  Ohlsson, Mikael;  Eklof, Anna
收藏  |  浏览/下载:7/0  |  提交时间:2020/07/14
Communities  ecological networks  food webs  group model  group structure  spatial location  spatial resolution  
Synthesis and properties of free-standing monolayer amorphous carbon 期刊论文
NATURE, 2020, 577 (7789) : 199-+
作者:  Toh, Chee-Tat;  Zhang, Hongji;  Lin, Junhao;  Mayorov, Alexander S.;  Wang, Yun-Peng;  Orofeo, Carlo M.;  Ferry, Darim Badur;  Andersen, Henrik;  Kakenov, Nurbek;  Guo, Zenglong;  Abidi, Irfan Haider;  Sims, Hunter;  Suenaga, Kazu;  Pantelides, Sokrates T.;  Ozyilmaz, Barbaros
收藏  |  浏览/下载:7/0  |  提交时间:2020/07/03

Bulk amorphous materials have been studied extensively and are widely used, yet their atomic arrangement remains an open issue. Although they are generally believed to be Zachariasen continuous random networks(1), recent experimental evidence favours the competing crystallite model in the case of amorphous silicon(2-4). In two-dimensional materials, however, the corresponding questions remain unanswered. Here we report the synthesis, by laser-assisted chemical vapour deposition(5), of centimetre-scale, free-standing, continuous and stable monolayer amorphous carbon, topologically distinct from disordered graphene. Unlike in bulk materials, the structure of monolayer amorphous carbon can be determined by atomic-resolution imaging. Extensive characterization by Raman and X-ray spectroscopy and transmission electron microscopy reveals the complete absence of long-range periodicity and a threefold-coordinated structure with a wide distribution of bond lengths, bond angles, and five-, six-, seven- and eight-member rings. The ring distribution is not a Zachariasen continuous random network, but resembles the competing (nano)crystallite model(6). We construct a corresponding model that enables density-functional-theory calculations of the properties of monolayer amorphous carbon, in accordance with observations. Direct measurements confirm that it is insulating, with resistivity values similar to those of boron nitride grown by chemical vapour deposition. Free-standing monolayer amorphous carbon is surprisingly stable and deforms to a high breaking strength, without crack propagation from the point of fracture. The excellent physical properties of this stable, free-standing monolayer amorphous carbon could prove useful for permeation and diffusion barriers in applications such as magnetic recording devices and flexible electronics.


  
Structure and catalytic mechanism of a human triacylglycerol-synthesis enzyme 期刊论文
NATURE, 2020, 581 (7808) : 323-+
作者:  Nikoo, Mohammad Samizadeh;  Jafari, Armin;  Perera, Nirmana;  Zhu, Minghua;  Santoruvo, Giovanni;  Matioli, Elison
收藏  |  浏览/下载:20/0  |  提交时间:2020/07/03

Triacylglycerols store metabolic energy in organisms and have industrial uses as foods and fuels. Excessive accumulation of triacylglycerols in humans causes obesity and is associated with metabolic diseases(1). Triacylglycerol synthesis is catalysed by acyl-CoA diacylglycerol acyltransferase (DGAT) enzymes(2-4), the structures and catalytic mechanisms of which remain unknown. Here we determined the structure of dimeric human DGAT1, a member of the membrane-bound O-acyltransferase (MBOAT) family, by cryo-electron microscopy at approximately 3.0 angstrom resolution. DGAT1 forms a homodimer through N-terminal segments and a hydrophobic interface, with putative active sites within the membrane region. A structure obtained with oleoyl-CoA substrate resolved at approximately 3.2 angstrom shows that the CoA moiety binds DGAT1 on the cytosolic side and the acyl group lies deep within a hydrophobic channel, positioning the acyl-CoA thioester bond near an invariant catalytic histidine residue. The reaction centre is located inside a large cavity, which opens laterally to the membrane bilayer, providing lipid access to the active site. A lipid-like density-possibly representing an acyl-acceptor molecule-is located within the reaction centre, orthogonal to acyl-CoA. Insights provided by the DGAT1 structures, together with mutagenesis and functional studies, provide the basis for a model of the catalysis of triacylglycerol synthesis by DGAT.


Cryo-electron microscopy structures and functional and mutagenesis studies provide insights into the catalysis of triacylglycerol synthesis by human acyl-CoA diacylglycerol acyltransferase at its intramembrane active site.


  
Action of a minimal contractile bactericidal nanomachine 期刊论文
NATURE, 2020, 580 (7805) : 658-+
作者:  Peng, Ruchao;  Xu, Xin;  Jing, Jiamei;  Wang, Min;  Peng, Qi;  Liu, Sheng;  Wu, Ying;  Bao, Xichen;  Wang, Peiyi;  Qi, Jianxun;  Gao, George F.;  Shi, Yi
收藏  |  浏览/下载:13/0  |  提交时间:2020/07/03

The authors report near-atomic resolution structures of the R-type bacteriocin from Pseudomonas aeruginosa in the pre-contraction and post-contraction states, and these structures provide insight into the mechanism of action of molecular syringes.


R-type bacteriocins are minimal contractile nanomachines that hold promise as precision antibiotics(1-4). Each bactericidal complex uses a collar to bridge a hollow tube with a contractile sheath loaded in a metastable state by a baseplate scaffold(1,2). Fine-tuning of such nucleic acid-free protein machines for precision medicine calls for an atomic description of the entire complex and contraction mechanism, which is not available from baseplate structures of the (DNA-containing) T4 bacteriophage(5). Here we report the atomic model of the complete R2 pyocin in its pre-contraction and post-contraction states, each containing 384 subunits of 11 unique atomic models of 10 gene products. Comparison of these structures suggests the following sequence of events during pyocin contraction: tail fibres trigger lateral dissociation of baseplate triplexes  the dissociation then initiates a cascade of events leading to sheath contraction  and this contraction converts chemical energy into mechanical force to drive the iron-tipped tube across the bacterial cell surface, killing the bacterium.


  
Subhourly rainfall in a convection-permitting model 期刊论文
ENVIRONMENTAL RESEARCH LETTERS, 2020, 15 (3)
作者:  Meredith, Edmund P.;  Ulbrich, Uwe;  Rust, Henning W.
收藏  |  浏览/下载:9/0  |  提交时间:2020/07/02
subhourly precipitation  convection-permitting model  climate  precipitation  high resolution  
Cryo-EM structure of SWI/SNF complex bound to a nucleosome 期刊论文
NATURE, 2020
作者:  Hang, Saiyu;  Paik, Donggi;  Yao, Lina;  Kim, Eunha;  Trinath, Jamma;  Lu, Jingping;  Ha, Soyoung;  Nelson, Brandon N.;  Kelly, Samantha P.;  Wu, Lin;  Zheng, Ye;  Longman, Randy S.;  Rastinejad, Fraydoon;  Devlin, A. Sloan;  Krout, Michael R.;  Fischbach, Michael A.;  Littman, Dan R.;  Huh, Jun R.
收藏  |  浏览/下载:7/0  |  提交时间:2020/07/03

The chromatin-remodelling complex SWI/SNF is highly conserved and has critical roles in various cellular processes, including transcription and DNA-damage repair(1,2). It hydrolyses ATP to remodel chromatin structure by sliding and evicting histone octamers(3-8), creating DNA regions that become accessible to other essential factors. However, our mechanistic understanding of the remodelling activity is hindered by the lack of a high-resolution structure of complexes from this family. Here we report the cryo-electron microscopy structure of Saccharomyces cerevisiae SWI/SNF bound to a nucleosome, at near-atomic resolution. In the structure, the actin-related protein (Arp) module is sandwiched between the ATPase and the rest of the complex, with the Snf2 helicase-SANT associated (HSA) domain connecting all modules. The body contains an assembly scaffold composed of conserved subunits Snf12 (also known as SMARCD or BAF60), Snf5 (also known as SMARCB1, BAF47 or INI1) and an asymmetric dimer of Swi3 (also known as SMARCC, BAF155 or BAF170). Another conserved subunit, Swi1 (also known as ARID1 or BAF250), resides in the core of SWI/SNF, acting as a molecular hub. We also observed interactions between Snf5 and the histones at the acidic patch, which could serve as an anchor during active DNA translocation. Our structure enables us to map and rationalize a subset of cancer-related mutations in the human SWI/SNF complex and to propose a model for how SWI/SNF recognizes and remodels the +1 nucleosome to generate nucleosome-depleted regions during gene activation(9).


The cryo-electron microscopy structure of the yeast SWI/SNF complex bound to a nucleosome substrate provides insights into the chromatin-remodelling function of this family of protein complexes and suggests mechanisms by which the mutated proteins may cause cancer.


  
Structural basis of energy transfer in Porphyridium purpureum phycobilisome 期刊论文
NATURE, 2020
作者:  Long, Haizhen;  Zhang, Liwei;  Lv, Mengjie;  Wen, Zengqi;  Zhang, Wenhao;  Chen, Xiulan;  Zhang, Peitao;  Li, Tongqing;  Chang, Luyuan;  Jin, Caiwei;  Wu, Guozhao;  Wang, Xi;  Yang, Fuquan;  Pei, Jianfeng;  Chen, Ping;  Margueron, Raphael;  Deng, Haiteng;  Zhu, Mingzhao;  Li, Guohong
收藏  |  浏览/下载:27/0  |  提交时间:2020/07/03

The cryo-electron microscopy structure of a phycobilisome from the red alga Porphyridium purpureum reveals how aromatic interactions between the linker proteins and the chromophores drive a unidirectional transfer of energy.


Photosynthetic organisms have developed various light-harvesting systems to adapt to their environments(1). Phycobilisomes are large light-harvesting protein complexes found in cyanobacteria and red algae(2-4), although how the energies of the chromophores within these complexes are modulated by their environment is unclear. Here we report the cryo-electron microscopy structure of a 14.7-megadalton phycobilisome with a hemiellipsoidal shape from the red alga Porphyridium purpureum. Within this complex we determine the structures of 706 protein subunits, including 528 phycoerythrin, 72 phycocyanin, 46 allophycocyanin and 60 linker proteins. In addition, 1,598 chromophores are resolved comprising 1,430 phycoerythrobilin, 48 phycourobilin and 120 phycocyanobilin molecules. The markedly improved resolution of our structure compared with that of the phycobilisome of Griffithsia pacifica(5) enabled us to build an accurate atomic model of the P. purpureum phycobilisome system. The model reveals how the linker proteins affect the microenvironment of the chromophores, and suggests that interactions of the aromatic amino acids of the linker proteins with the chromophores may be a key factor in fine-tuning the energy states of the chromophores to ensure the efficient unidirectional transfer of energy.


  
Sensitivity of Marine Heatwave Metrics to Ocean Model Resolution 期刊论文
GEOPHYSICAL RESEARCH LETTERS, 2019
作者:  Pilo, Gabriela S.;  Holbrook, Neil J.;  Kiss, Andrew E.;  Hogg, Andrew McC.
收藏  |  浏览/下载:9/0  |  提交时间:2020/02/17
marine heatwave  global ocean-sea ice model  model resolution  temperature extremes  
Meridional Heat Transport During Atmospheric Rivers in High-Resolution CESM Climate Projections 期刊论文
GEOPHYSICAL RESEARCH LETTERS, 2019
作者:  Shields, Christine A.;  Rosenbloom, Nan;  Bates, Susan C.;  Hannay, Cecile;  Hu, Aixue;  Payne, Ashley Elizabeth;  Rutz, Jonathan J.;  Truesdale, John
收藏  |  浏览/下载:10/0  |  提交时间:2020/02/17
atmospheric rivers  heat transport  CESM high-resolution model  ARTMIP  
Resolving seasonal rainfall changes in the Middle East during the last interglacial period 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2019, 116 (50) : 24985-24990
作者:  Ian J. Orland;  Feng He;  Miryam Bar-Matthews;  Guangshan Chen;  Avner Ayalon;  John E. Kutzbach
收藏  |  浏览/下载:5/0  |  提交时间:2020/02/18
paleoclimate  seasonal-resolution  oxygen isotopes  data-model comparison