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https://www.readbyqxmd.com/read/28227171/structural-classification-of-protein-sequences-based-on-signal-processing-and-support-vector-machines
#1
Charalambos Chrysostomou, Huseyin Seker, Charalambos Chrysostomou, Huseyin Seker, Huseyin Seker, Charalambos Chrysostomou
The function of any protein depends directly on its secondary and tertiary structure. Proteins can fold into a three-dimensional shape, which is primarily depended on the arrangement of amino acids in the primary structure. In recent years, with the explosive sequencing of proteins, it is unfeasible to perform detailed experimental studies, as these methodologies are very expensive and time consuming. This leaves the structure of the majority of currently available protein sequences unknown. In this paper, a predictive model is therefore presented for the classification of protein sequence's secondary structures, namely alpha helix and beta sheet...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226941/large-deflection-statics-analysis-of-active-cardiac-catheters-through-co-rotational-modelling
#2
Peng Qi, Chen Qiu, Aadarsh Mehndiratta, I-Ming Chen, Haoyong Yu, Peng Qi, Chen Qiu, Aadarsh Mehndiratta, I-Ming Chen, Haoyong Yu, Peng Qi, Aadarsh Mehndiratta, I-Ming Chen, Haoyong Yu, Chen Qiu
This paper presents a co-rotational concept for large-deflection formulation of cardiac catheters. Using this approach, the catheter is first discretized with a number of equal length beam elements and nodes, and the rigid body motions of an individual beam element are separated from its deformations. Therefore, it is adequate for modelling arbitrarily large deflections of a catheter with linear elastic analysis at the local element level. A novel design of active cardiac catheter of 9 Fr in diameter at the beginning of the paper is proposed, which is based on the contra-rotating double helix patterns and is improved from the previous prototypes...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28223923/embryonic-and-postnatal-expression-of-aryl-hydrocarbon-receptor-mrna-in-mouse-brain
#3
Eiki Kimura, Chiharu Tohyama
Aryl hydrocarbon receptor (AhR), a member of the basic helix-loop-helix-Per-Arnt-Sim transcription factor family, plays a critical role in the developing nervous system of invertebrates and vertebrates. Dioxin, a ubiquitous environmental pollutant, avidly binds to this receptor, and maternal exposure to dioxin has been shown to impair higher brain functions and dendritic morphogenesis, possibly via an AhR-dependent mechanism. However, there is little information on AhR expression in the developing mammalian brain...
2017: Frontiers in Neuroanatomy
https://www.readbyqxmd.com/read/28223511/a-signal-sequence-suppressor-mutant-that-stabilizes-an-assembled-state-of-the-twin-arginine-translocase
#4
Qi Huang, Felicity Alcock, Holger Kneuper, Justin C Deme, Sarah E Rollauer, Susan M Lea, Ben C Berks, Tracy Palmer
The twin-arginine protein translocation (Tat) system mediates transport of folded proteins across the cytoplasmic membrane of bacteria and the thylakoid membrane of chloroplasts. The Tat system of Escherichia coli is made up of TatA, TatB, and TatC components. TatBC comprise the substrate receptor complex, and active Tat translocases are formed by the substrate-induced association of TatA oligomers with this receptor. Proteins are targeted to TatBC by signal peptides containing an essential pair of arginine residues...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28223110/h2a-and-ca-l-hipposin-gene-characteristic-analysis-and-expression-responses-to-aeromonas-hydrophila-infection-in-carassius-aurutus
#5
Xianghui Kong, Xiangmin Wu, Chao Pei, Jie Zhang, Xianliang Zhao, Li Li, Guoxing Nie, Xuejun Li
Antimicrobial peptide is an important component of the host innate immune system and thus serves a crucial function in host defense against microbial invasion. In this study, H2A and derived antimicrobial peptide Ca-L-hipposin were cloned and characterized in Carassius aurutus. The gene H2A full-length cDNA is 908 bp and includes a 5'-terminal untranslated region (UTR) of 55 bp and a 3'-terminal UTR of 466 bp with a canonical polyadenylation signal sequence AATAA, as well as an open reading frame (ORF) of 387 bp encoding a polypeptide of 128 amino acids, with a molecular weight of 13...
February 18, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28223044/7x7-rmsd-matrix-a-new-method-for-quantitative-comparison-of-the-transmembrane-domain-structures-in-the-g-protein-coupled-receptors
#6
Ting Wang, Yang Wang, Leihan Tang, Yong Duan, Haiguang Liu
The G-protein coupled receptors (GPCRs) share a conserved heptahelical fold in the transmembrane (TM) region, but the exact arrangements of the seven TM helices vary with receptors and their activation states. The differences or the changes have been observed in the experimentally solved structures, but have not been systematically and quantitatively investigated due to lack of suitable methods. In this work, we describe a novel method, called 7x7 RMSD matrix that is proposed specifically for comparing the characteristic 7TM bundle structures of GPCRs...
February 18, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28221775/electrostatic-interactions-as-mediators-in-the-allosteric-activation-of-pka-ri%C3%AE
#7
Emilia Pecora de Barros, Robert D Malmstrom, Kimya Nourbakhsh, Jason Cruz Del Rio, Alexandr P Kornev, Susan S Taylor, Rommie E Amaro
Close-range electrostatic interactions that form salt bridges are key components of protein stability. Here we investigate the role of these charged interactions in modulating the allosteric activation of Protein Kinase A (PKA) via computational and experimental mutational studies on a conserved basic patch located in the regulatory subunit's B/C helix. Molecular dynamics simulations evidenced the presence of an extended network of fluctuating salt bridges spanning the helix and connecting the two cAMP binding domains in its extremities...
February 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28221748/fe3-ph-thermo-responsive-supramolecular-hydrogel-with-multi-shape-memory-effect
#8
Xiaoxia Le, Wei Lu, He Xiao, Li Wang, Chunxin Ma, Jiawei Zhang, Youju Huang, Tao Chen
Poor, non-tunable mechanical properties as well as finite shape memory performance pose a barrier to shape memory hydrogels to realize practical applications. Here, a new shape memory hydrogel with tunable mechanical properties and multi-shape memory effect was presented. Three programmable reversible systems including PBA-diol ester bonds, AAc-Fe3+ and coil-helix transition of agar were applied to memorize temporary shapes and endow the hydrogel with outstanding multi-shape memory functionalities. Moreover, through changing the crosslinking densities, the mechanical properties of the as-prepared hydrogel can be adjusted...
February 21, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28220789/stim1-activates-crac-channels-through-rotation-of-the-pore-helix-to-open-a-hydrophobic-gate
#9
Megumi Yamashita, Priscilla S-W Yeung, Christopher E Ing, Beth A McNally, Régis Pomès, Murali Prakriya
Store-operated Ca(2+) release-activated Ca(2+) (CRAC) channels constitute a major pathway for Ca(2+) influx and mediate many essential signalling functions in animal cells, yet how they open remains elusive. Here, we investigate the gating mechanism of the human CRAC channel Orai1 by its activator, stromal interacting molecule 1 (STIM1). We find that two rings of pore-lining residues, V102 and F99, work together to form a hydrophobic gate. Mutations of these residues to polar amino acids produce channels with leaky gates that conduct ions in the resting state...
February 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28220706/human-cannabinoid-receptor-2-ligand-interaction-motif-transmembrane-helix-2-cysteine-c2-59-89-as-determinant-of-classical-cannabinoid-agonist-activity-and-binding-pose
#10
Han Zhou, Yan Peng, Aneetha Halikhedkar, Pusheng Fan, David R Janero, Ganesh A Thakur, Richard Warren Mercier, Xin Sun, Xiaoyu Ma, Alexandros Makriyannis
Cannabinoid receptor 2 (CB2R)-dependent signaling is implicated in neuronal physiology and immune surveillance by brain microglia. Selective CB2R agonists hold therapeutic promise for inflammatory and other neurological disorders. Information on human CB2R (hCB2R) ligand-binding and functional domains is needed to inform the rational design and optimization of candidate drug-like hCB2R agonists. Prior demonstration that hCB2R transmembrane helix 2 (TMH2) cysteine C2.59(89) reacts with small-molecule methanethiosulfonates showed that this cysteine residue is accessible to sulfhydryl derivatization reagents...
February 21, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28220629/binding-of-hydroxylated-polybrominated-diphenyl-ethers-with-human-serum-albumin-spectroscopic-characterization-and-molecular-modeling
#11
Lulu Yang, Wu Yang, Zhiwei Wu, Zhongsheng Yi
Three hydroxylated polybrominated diphenyl ethers (OH-PBDEs), 3-OH-BDE-47, 5-OH-BDE-47, and 6-OH-BDE-47, were selected to investigate the interactions between OH-PBDEs with human serum albumin (HSA) under physiological conditions. The observed fluorescence quenching can be attributed to the formation of complexes between HSA and OH-PBDEs. The thermodynamic parameters at different temperatures indicate that the binding was caused by hydrophobic forces and hydrogen bonds. Molecular modeling and three-dimensional fluorescence spectrum showed conformational and microenvironmental changes in HSA...
February 21, 2017: Luminescence: the Journal of Biological and Chemical Luminescence
https://www.readbyqxmd.com/read/28220539/a-contiguous-gene-deletion-neighboring-twist1-identified-in-a-patient-with-saethre-chotzen-syndrome-associated-with-neurodevelopmental-delay-possible-contribution-of-hdac9
#12
Hiroko Shimbo, Tatsuki Oyoshi, Kenji Kurosawa
Saethre-Chotzen syndrome (SCS) is an autosomal dominant craniosynostotic disorder characterized by coronal synostosis, facial asymmetry, ptosis, and limb abnormalities. Haploinsufficiency of TWIST1, a basic helix-loop-helix transcription factor is responsible for SCS. Here, we report a 15-month-old male patient with typical clinical features of SCS in addition to developmental delay, which is a rare complication in SCS. He showed a de novo 0.9-Mb microdeletion in 7p21, in which TWIST1, NPMIP13, FERD3L, TWISTNB, and HDAC9 were included...
February 21, 2017: Congenital Anomalies
https://www.readbyqxmd.com/read/28220502/variations-on-a-nucleosome-theme-the-structural-basis-of-centromere-function
#13
Olga Moreno-Moreno, Mònica Torras-Llort, Fernando Azorín
The centromere is a specialized chromosomal structure that dictates kinetochore assembly and, thus, is essential for accurate chromosome segregation. Centromere identity is determined epigenetically by the presence of a centromere-specific histone H3 variant, CENP-A, that replaces canonical H3 in centromeric chromatin. Here, we discuss recent work by Roulland et al. that identifies structural elements of the nucleosome as essential determinants of centromere function. In particular, CENP-A nucleosomes have flexible DNA ends due to the short αN helix of CENP-A...
February 21, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28219928/mitochondria-control-store-operated-ca-2-entry-through-na-and-redox-signals
#14
Tsipi Ben-Kasus Nissim, Xuexin Zhang, Assaf Elazar, Soumitra Roy, Judith A Stolwijk, Yandong Zhou, Rajender K Motiani, Maxime Gueguinou, Nadine Hempel, Michal Hershfinkel, Donald L Gill, Mohamed Trebak, Israel Sekler
Mitochondria exert important control over plasma membrane (PM) Orai1 channels mediating store-operated Ca(2+) entry (SOCE). Although the sensing of endoplasmic reticulum (ER) Ca(2+) stores by STIM proteins and coupling to Orai1 channels is well understood, how mitochondria communicate with Orai1 channels to regulate SOCE activation remains elusive. Here, we reveal that SOCE is accompanied by a rise in cytosolic Na(+) that is critical in activating the mitochondrial Na(+)/Ca(2+) exchanger (NCLX) causing enhanced mitochondrial Na(+) uptake and Ca(2+) efflux...
February 20, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28219792/conjugative-type-iv-secretion-in-gram-positive-pathogens-trag-a-lytic-transglycosylase-and-endopeptidase-interacts-with-translocation-channel-protein-tram
#15
Verena Kohler, Ines Probst, Andreas Aufschnaiter, Sabrina Büttner, Lisa Schaden, Gerald Rechberger, Günther Koraimann, Elisabeth Grohmann, Walter Keller
Conjugative transfer plays a major role in the transmission of antibiotic resistance in bacteria. pIP501 is a Gram-positive conjugative model plasmid with the broadest transfer host-range known so far and is frequently found in Enterococcus faecalis and Enterococcus faecium clinical isolates. The pIP501 type IV secretion system is encoded by 15 transfer genes. In this work, we focus on the VirB1-like protein TraG, a modular peptidoglycan metabolizing enzyme, and the VirB8-homolog TraM, a potential member of the translocation channel...
February 17, 2017: Plasmid
https://www.readbyqxmd.com/read/28218648/expression-purification-and-monitoring-of-conformational-changes-of-hcb2-tmh67h8-in-different-membrane-mimetic-lipid-mixtures-using-circular-dichroism-and-nmr-techniques
#16
Elvis K Tiburu, Jianqin Zhuang, Heidimarie N A Fleischer, Patrick K Arthur, Gordon A Awandare
This work was intended to develop self-assembly lipids for incorporating G-protein coupled receptors (GPCRs) in order to improve the success rate for nuclear magnetic resonance spectroscopy (NMR) structural elucidation. We hereby report the expression and purification of uniformly (15)N-labeled human cannabinoid receptor-2 domain in insect cell media. The domain was refolded by screening several membrane mimetic environments. Different q ratios of isotropic bicelles were screened for solubilizing transmembrane helix 6, 7 and 8 (TMH67H8)...
February 17, 2017: Membranes
https://www.readbyqxmd.com/read/28218530/ultrafast-excited-state-dynamics-in-a-molecular-motors-coupling-of-motor-length-to-medium-viscosity
#17
Jamie Conyard, Peter Stacko, Jiawen Chen, Sophie McDonagh, Christopher R Hall, Sergey P Laptenok, Wesley R Browne, Ben L Feringa, Stephen R Meech
Photochemically driven molecular motors convert the energy of incident radiation to intramolecular rotational motion. The motor molecules considered here execute four step unidirectional rotational motion. This comprises a pair of successive light induced isomerizations to a metastable state followed by thermal helix inversions. The internal rotation of a large molecular unit required in these steps is expected to be sensitive to both the viscosity of the medium and the volume of the rotating unit. In this work we describe a study of motor motion in both ground and excited states as a function of the size of the rotating units...
February 20, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28218252/dissecting-the-molecular-organization-of-the-translocon-associated-protein-complex
#18
Stefan Pfeffer, Johanna Dudek, Miroslava Schaffer, Bobby G Ng, Sahradha Albert, Jürgen M Plitzko, Wolfgang Baumeister, Richard Zimmermann, Hudson H Freeze, Benjamin D Engel, Friedrich Förster
In eukaryotic cells, one-third of all proteins must be transported across or inserted into the endoplasmic reticulum (ER) membrane by the ER protein translocon. The translocon-associated protein (TRAP) complex is an integral component of the translocon, assisting the Sec61 protein-conducting channel by regulating signal sequence and transmembrane helix insertion in a substrate-dependent manner. Here we use cryo-electron tomography (CET) to study the structure of the native translocon in evolutionarily divergent organisms and disease-linked TRAP mutant fibroblasts from human patients...
February 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28217789/interfacing-native-and-non-native-peptides-using-affimers-to-recognise-%C3%AE-helix-mimicking-foldamers
#19
Irene Arrata, Anna Barnard, Darren C Tomlinson, Andrew J Wilson
Selection methods are used to identify Affimers that recognise α-helix mimicking N-alkylated aromatic oligoamides thus demonstrating foldamer and natural α-amino acid codes are compatible.
February 20, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28216965/mutational-analysis-of-hepatitis-e-virus-orf1-y-domain-effects-on-rna-replication-and-virion-infectivity
#20
Mohammad Khalid Parvez
AIM: To investigate the role of non-structural open reading frame 1 "Y-domain" sequences in the hepatitis E virus (HEV) life cycle. METHODS: Sequences of human HEV Y-domain (amino acid sequences 216-442) and closely-related viruses were analyzed in silico. Site-directed mutagenesis of the Y-domain (HEV SAR55) was carried out and studied in the replicon-baculovirus-hepatoma cell model. In vitro transcribed mRNA (pSK-GFP) constructs were transfected into S10-3 cells and viral RNA replicating GFP-positive cells were scored by flow cytometry...
January 28, 2017: World Journal of Gastroenterology: WJG
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