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https://www.readbyqxmd.com/read/28212487/interactions-between-membranes-and-metaphilic-polypeptide-architectures-with-diverse-sidechain-populations
#1
Michelle W Lee, Ming Han, Guilherme Volpe Bossa, Carly Snell, Ziyuan Song, Haoyu Tang, Lichen Yin, Jianjun Cheng, Sylvio May, Erik Luijten, Gerard C L Wong
At physiological conditions, most proteins or peptides can fold into relatively stable structures that present on their molecular surfaces specific chemical patterns partially smeared out by thermal fluctuations. These nanoscopically defined patterns of charge, hydrogen bonding, and/or hydrophobicity, along with their elasticity and shape stability (folded proteins have Young's moduli of ~1 × 10(8) Pa), largely determine and limit the interactions of these molecules, such as molecular recognition and allosteric regulation...
February 17, 2017: ACS Nano
https://www.readbyqxmd.com/read/28211915/structure-of-the-shr-scr-heterodimer-bound-to-the-bird-idd-transcriptional-factor-jkd
#2
Yoshinori Hirano, Masahiro Nakagawa, Tomoe Suyama, Kohji Murase, Maya Shirakawa, Seiji Takayama, Tai-Ping Sun, Toshio Hakoshima
The plant-specific GAI, RGA and SCR (GRAS) family proteins play critical roles in plant development and signalling. Two GRAS proteins, SHORT-ROOT (SHR) and SCARECROW (SCR), cooperatively direct asymmetric cell division and the patterning of root cell types by transcriptional control in conjunction with BIRD/INDETERMINATE DOMAIN (IDD) transcription factors, although precise details of these specific interactions and actions remain unknown. Here, we present the crystal structures of the SHR-SCR binary and JACKDAW (JKD)/IDD10-SHR-SCR ternary complexes...
February 17, 2017: Nature Plants
https://www.readbyqxmd.com/read/28211542/identification-of-the-core-regulators-of-the-hla-i-peptide-binding-process
#3
Yu-Hang Zhang, Zhihao Xing, Chenglin Liu, ShaoPeng Wang, Tao Huang, Yu-Dong Cai, Xiangyin Kong
During the display of peptide/human leukocyte antigen (HLA) -I complex for further immune recognition, the cleaved and transported antigenic peptides have to bind to HLA-I protein and the binding affinity between peptide epitopes and HLA proteins directly influences the immune recognition ability in human beings. Key factors affecting the binding affinity during the generation, selection and presentation processes of HLA-I complex have not yet been fully discovered. In this study, a new method describing the HLA class I-peptide interactions was proposed...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211111/regulation-of-nrf-operon-expression-in-pathogenic-enteric-bacteria-sequence-divergence-reveals-new-regulatory-complexity
#4
Rita E Godfrey, David J Lee, Stephen J W Busby, Douglas F Browning
The Escherichia coli K-12 nrf operon encodes a periplasmic nitrite reductase, the expression of which is driven from a single promoter, pnrf. Expression from pnrf is activated by the FNR transcription factor in response to anaerobiosis and further increased in response to nitrite by the response regulator proteins, NarL and NarP. FNR-dependent transcription is suppressed by the binding of two nucleoid associated proteins, IHF and Fis. As Fis levels increase in cells grown in rich medium, the positioning of its binding site, overlapping the promoter -10 element, ensures that pnrf is sharply repressed...
February 17, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28210877/quantum-mechanical-treatment-of-as-3-thiol-model-compounds-implication-for-the-core-structure-of-as-iii-metallothionein
#5
Roobee Garla, Narinder Kaur, Mohinder Pal Bansal, Mohan Lal Garg, Biraja Prasad Mohanty
Exposure to inorganic arsenic (As) is one of the major health concerns in several regions around the world. Binding of As(III) with thiols is central to the mechanisms related to its toxicity, detoxification, and therapeutic effects. Due to its high thiol content, metallothionein (MT) is presumed to play an important role in case of arsenic toxicity. Consequences of these As-thiol interactions are not yet clear due to various difficulties in the characterization of arsenic bound proteins by spectroscopic techniques...
March 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28210265/rna-seq-of-guar-cyamopsis-tetragonoloba-l-taub-leaves-de-novo-transcriptome-assembly-functional-annotation-and-development-of-genomic-resources
#6
Umesh K Tanwar, Vikas Pruthi, Gursharn S Randhawa
Genetic improvement in industrially important guar (Cyamopsis tetragonoloba, L. Taub.) crop has been hindered due to the lack of sufficient genomic or transcriptomic resources. In this study, RNA-Seq technology was employed to characterize the transcriptome of leaf tissues from two guar varieties, namely, M-83 and RGC-1066. Approximately 30 million high-quality pair-end reads of each variety generated by Illumina HiSeq platform were used for de novo assembly by Trinity program. A total of 62,146 non-redundant unigenes with an average length of 679 bp were obtained...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28210240/distinctive-nuclear-localization-signals-in-the-oomycete-phytophthora-sojae
#7
Yufeng Fang, Hyo Sang Jang, Gregory W Watson, Dulani P Wellappili, Brett M Tyler
To date, nuclear localization signals (NLSs) that target proteins to nuclei in oomycetes have not been defined, but have been assumed to be the same as in higher eukaryotes. Here, we use the soybean pathogen Phytophthora sojae as a model to investigate these sequences in oomycetes. By establishing a reliable in vivo NLS assay based on confocal microscopy, we found that many canonical monopartite and bipartite classical NLSs (cNLSs) mediated nuclear import poorly in P. sojae. We found that efficient localization of P...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28209119/plastome-phylogeny-and-early-diversification-of-brassicaceae
#8
Xinyi Guo, Jianquan Liu, Guoqian Hao, Lei Zhang, Kangshan Mao, Xiaojuan Wang, Dan Zhang, Tao Ma, Quanjun Hu, Ihsan A Al-Shehbaz, Marcus A Koch
BACKGROUND: The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies. RESULTS: Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28208699/induction-of-syndecan-4-by-organic-inorganic-hybrid-molecules-with-a-1-10-phenanthroline-structure-in-cultured-vascular-endothelial-cells
#9
Takato Hara, Takayuki Kojima, Hiroka Matsuzaki, Takehiro Nakamura, Eiko Yoshida, Yasuyuki Fujiwara, Chika Yamamoto, Shinichi Saito, Toshiyuki Kaji
Organic-inorganic hybrid molecules constitute analytical tools used in biological systems. Vascular endothelial cells synthesize and secrete proteoglycans, which are macromolecules consisting of a core protein and glycosaminoglycan side chains. Although the expression of endothelial proteoglycans is regulated by several cytokines/growth factors, there may be alternative pathways for proteoglycan synthesis aside from downstream pathways activated by these cytokines/growth factors. Here, we investigated organic-inorganic hybrid molecules to determine a variant capable of analyzing the expression of syndecan-4, a transmembrane heparan-sulfate proteoglycan, and identified 1,10-phenanthroline (o-Phen) with or without zinc (Zn-Phen) or rhodium (Rh-Phen)...
February 8, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28207813/interacting-networks-of-resistance-virulence-and-core-machinery-genes-identified-by-genome-wide-epistasis-analysis
#10
Marcin J Skwark, Nicholas J Croucher, Santeri Puranen, Claire Chewapreecha, Maiju Pesonen, Ying Ying Xu, Paul Turner, Simon R Harris, Stephen B Beres, James M Musser, Julian Parkhill, Stephen D Bentley, Erik Aurell, Jukka Corander
Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. We apply genomeDCA to two large population data sets representing the major human pathogens Streptococcus pneumoniae (pneumococcus) and Streptococcus pyogenes (group A Streptococcus)...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28207270/intracellular-delivery-colloidally-stable-core-crosslinked-triblock-copolymer-micelles-with-glutathione-responsive-enhanced-drug-release-for-cancer-therapy
#11
Jung Kwon Oh, Depannita Biswas, So Young An, Yijing Li, Xiangtao Wang
Design and development of amphiphilic block copolymer-based nanocarriers exhibiting enhanced colloidal stability upon dilution in the blood and cellular glutathione-responsive rapid drug release is highly desired for tumor-targeting chemotherapy. Herein, we report a novel ABA-type triblock copolymer consisting of a hydrophilic central poly(ethylene glycol) block and two terminal hydrophobic blocks of a polymethacrylate having pendant disulfides (PHMssEt), thus PHMssEt-b-PEG-b-PHMssEt (ssTP). Aqueous self-assembly and following disulfide-exchange reaction of the resulting ssTP allows for formation of core-crosslinked micelles (CCMs) through the formation of new disulfide linkages, retaining enhanced colloidal stability in physiological condition and in the presence of proteins...
February 16, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/28207024/-ru-co-x-core-complexes-with-benzimidazole-ligands-synthesis-x-ray-structure-and-evaluation-of-anticancer-activity-in-vivo
#12
Gabriella Tamasi, Antonello Merlino, Federica Scaletti, Petra Heffeter, Anton A Legin, Michael A Jakupec, Walter Berger, Luigi Messori, Bernhard K Keppler, Renzo Cini
The reaction of [Ru(CO)6Cl2], 1, with N[combining low line](3)-methylbenzimidazole (MBI) and 5,6-dimethylbenzimidazole (DMBI) afforded two new complexes with the general formula fac-[Ru(II)(CO)3Cl2L], L = MBI (2) or DMBI (4). Crystals of cis,trans-[Ru(II)(CO)2Cl2(N[combining low line](3)-MBI)2], 3, were also obtained from the mother liquor that produced 2. In the presence of water, the dissociation of Ru-N, Ru-Cl and Ru-CO bonds occurred as a function of time, water content and pH. Density functional theory structure simulations/optimizations were carried out at the Becke3LYP level of theory for evaluating the relative stability of possible conformers...
February 16, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28205569/heteroaryldihydropyrimidine-hap-and-sulfamoylbenzamide-sba-inhibit-hepatitis-b-virus-replication-by-different-molecular-mechanisms
#13
Zheng Zhou, Taishan Hu, Xue Zhou, Steffen Wildum, Fernando Garcia-Alcalde, Zhiheng Xu, Daitze Wu, Yi Mao, Xiaojun Tian, Yuan Zhou, Fang Shen, Zhisen Zhang, Guozhi Tang, Isabel Najera, Guang Yang, Hong C Shen, John A T Young, Ning Qin
Heteroaryldihydropyrimidine (HAP) and sulfamoylbenzamide (SBA) are promising non-nucleos(t)ide HBV replication inhibitors. HAPs are known to promote core protein mis-assembly, but the molecular mechanism of abnormal assembly is still elusive. Likewise, the assembly status of core protein induced by SBA remains unknown. Here we show that SBA, unlike HAP, does not promote core protein mis-assembly. Interestingly, two reference compounds HAP_R01 and SBA_R01 bind to the same pocket at the dimer-dimer interface in the crystal structures of core protein Y132A hexamer...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28205532/system-wide-detection-of-protein-small-molecule-complexes-suggests-extensive-metabolite-regulation-in-plants
#14
Daniel Veyel, Sylwia Kierszniowska, Monika Kosmacz, Ewelina Maria Sokolowska, Aenne Michaelis, Marcin Luzarowski, Jagoda Szlachetko, Lothar Willmitzer, Aleksandra Skirycz
Protein small molecule interactions are at the core of cell regulation controlling metabolism and development. We reasoned that due to the lack of system wide approaches only a minority of those regulatory molecules are known. In order to see whether or not this assumption is true we developed an effective approach for the identification of small molecules having potential regulatory role that obviates the need of protein or small molecule baits. At the core of this approach is a simple biochemical co-fractionation taking advantage of size differences between proteins and small molecules...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28204951/possible-role-of-zinc-in-diminishing-lead-related-occupational-stress-a-zinc-nutrition-concern
#15
Ab Latif Wani, Ajaz Ahmad, G G H A Shadab, Jawed Ahmad Usmani
Lead and zinc are mostly present at the same occupational source and usually found as co-contaminants. Lead is known to associate with detrimental effects to humans. Zinc however is an essential nutrient and its deficiency causes debilitating effects on growth and development. Besides, it acts as core ion of important enzymes and proteins. The purpose of this study was to examine if zinc concentrations are associated with blood lead levels and if zinc may prevent lead-induced DNA damage. Blood samples were collected from 92 workers as participants occupationally exposed to lead or lead and zinc and 38 comparison participants having no history of such exposure...
February 15, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28204885/de-bugging-and-maximizing-plant-cytochrome-p450-production-in-escherichia-coli-with-c-terminal-gfp-fusions
#16
Ulla Christensen, Dario Vazquez-Albacete, Karina M Søgaard, Tonja Hobel, Morten T Nielsen, Scott James Harrison, Anders Holmgaard Hansen, Birger Lindberg Møller, Susanna Seppälä, Morten H H Nørholm
Cytochromes P450 (CYP) are attractive enzyme targets in biotechnology as they catalyze stereospecific C-hydroxylations of complex core skeletons at positions that typically are difficult to access by chemical synthesis. Membrane bound CYPs are involved in nearly all plant pathways leading to the formation of high-value compounds. In the present study, we systematically maximize the heterologous expression of six different plant-derived CYP genes in Escherichia coli, using a workflow based on C-terminal fusions to the green fluorescent protein...
February 15, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28203483/galanin-protects-from-caspase-8-12-initiated-neuronal-apoptosis-in-the-ischemic-mouse-brain-via-galr1
#17
Yun Li, Zhu Mei, Shuiqiao Liu, Tong Wang, Hui Li, Xiao-Xiao Li, Song Han, Yutao Yang, Junfa Li, Zhi-Qing David Xu
Galanin (GAL) plays key role in many pathophysiological processes, but its role in ischemic stroke remains unclear. Here, the models of 1 h middle cerebral artery occlusion (MCAO)/1-7 d reperfusion (R)-induced ischemic stroke and in vitro cell ischemia of 1 h oxygen-glucose deprivation (OGD)/24 h reoxygenation in primary cultured cortical neurons were used to explore GAL's effects and its underlying mechanisms. The results showed significant increases of GAL protein levels in the peri-infarct region (P) and infarct core (I) within 48 h R of MCAO mice (p<0...
February 2017: Aging and Disease
https://www.readbyqxmd.com/read/28202673/molecular-architecture-of-polycomb-repressive-complexes
#18
REVIEW
Emily C Chittock, Sebastian Latwiel, Thomas C R Miller, Christoph W Müller
The polycomb group (PcG) proteins are a large and diverse family that epigenetically repress the transcription of key developmental genes. They form three broad groups of polycomb repressive complexes (PRCs) known as PRC1, PRC2 and Polycomb Repressive DeUBiquitinase, each of which modifies and/or remodels chromatin by distinct mechanisms that are tuned by having variable compositions of core and accessory subunits. Until recently, relatively little was known about how the various PcG proteins assemble to form the PRCs; however, studies by several groups have now allowed us to start piecing together the PcG puzzle...
February 8, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28201818/collective-repacking-reveals-that-the-structures-of-protein-cores-are-uniquely-specified-by-steric-repulsive-interactions
#19
J C Gaines, A Virrueta, D A Buch, S J Fleishman, C S O'Hern, L Regan
No abstract text is available yet for this article.
February 15, 2017: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/28199887/killing-colon-cancer-cells-through-pcd-pathways-by-a-novel-hyaluronic-acid-modified-shell-core-nanoparticle-loaded-with-rip3-in-combination-with-chloroquine
#20
Xueyan Hou, Chengli Yang, Lijing Zhang, Tingting Hu, Dan Sun, Hua Cao, Fan Yang, Gang Guo, Changyang Gong, Xiaoning Zhang, Aiping Tong, Rui Li, Yu Zheng
Due to extensive apoptosis defects and multidrug resistance, there is great interest regarding non-apoptotic programmed cell death (PCD) pathways, such as lysosomal-mediated programmed cell death (LM-PCD), necroptosis and autophagy. Because there is an intricate effector network among these PCD pathways, it is expected that they may act synergistically in cancer therapy. In this study, chloroquine (CQ) was found to significantly upregulate receptor-interacting protein kinase 3 (RIP3) expression, and RIP3 were involved in CQ-related autophagy...
January 2, 2017: Biomaterials
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