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https://www.readbyqxmd.com/read/28742273/protein-secondary-structure-analysis-of-dried-blood-serum-using-infrared-spectroscopy-to-identify-markers-for-colitis-screening
#1
Jitto Titus, Hemendra Ghimire, Emilie Viennois, Didier Merlin, A G Unil Perera
There remains a great need for diagnosis of inflammatory bowel disease (IBD), for which the current technique, colonoscopy, is costly and also has risks for complications. Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) spectroscopy is a new screening technique to evaluate colitis. Using second derivative spectral deconvolution of the absorbance spectra, a full set of spectral markers were identified based on statistical analysis. Using this method, Amide I group frequencies, (specifically, alpha helix to beta sheet ratio of the protein secondary structure) were identified in addition to the previously reported glucose and mannose signatures in sera of chronic and acute mice models of colitis...
July 25, 2017: Journal of Biophotonics
https://www.readbyqxmd.com/read/28742210/clinical-research-on-correction-of-ankle-arthritis-related-factor-levels-via-urea
#2
C Sun, S Zhang, L Wei, J-Z Zhang
OBJECTIVE: To investigate the reliability of urea as the internal reference of ankle irrigating fluid in correction of synovial fluid and related factor concentration dilution times, and to further determine the factor expression level in synovial fluid. PATIENTS AND METHODS: A total of 91 patients, including 20 cases of non-posterior median foot lesions and 71 cases of unilateral ankle osteoarthritis, were enrolled in this study. AOFAS score, Takakura staging and visual analogue pain scale were given; the venous blood was collected and the ankle fluid and irrigating fluid were obtained from the affected side via puncture...
July 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28742165/system-analysis-identifies-distinct-and-common-functional-networks-governed-by-transcription-factor-ascl1-in-glioma-and-small-cell-lung-cancer
#3
Sainitin Donakonda, Swati Sinha, Shrinivas Nivrutti Dighe, Manchanahalli R Satyanarayana Rao
ASCL1 is a basic Helix-Loop-Helix transcription factor (TF), which is involved in various cellular processes like neuronal development and signaling pathways. Transcriptome profiling has shown that ASCL1 overexpression plays an important role in the development of glioma and Small Cell Lung Carcinoma (SCLC), but distinct and common molecular mechanisms regulated by ASCL1 in these cancers are unknown. In order to understand how it drives the cellular functional network in these two tumors, we generated a gene expression profile in a glioma cell line (U87MG) to identify ASCL1 gene targets by an si RNA silencing approach and then compared this with a publicly available dataset of similarly silenced SCLC (NCI-H1618 cells)...
July 25, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28741867/targeting-of-a-helix-loop-helix-transcriptional-regulator-by-a-short-helical-peptide
#4
Cornelia Roschger, Saskia Neukirchen, Brigitta Elsässer, Mario Schubert, Nicole Maeding, Thomas Verwanger, Barbara Krammer, Chiara Cabrele
The Id proteins (Id1-4) are cell cycle regulators that play a key role during development, in cancer and vascular disorders. They contain a conserved helix-loop-helix (HLH) domain that folds into a parallel four-helix bundle upon self- or heteroassociation with basic-HLH transcription factors. By using such protein-protein interactions, the Id proteins inhibit cell differentiation and promote cell cycle progression. Accordingly, their supporting role in cancer has been convincingly demonstrated, which makes these proteins interesting therapeutic targets...
July 25, 2017: ChemMedChem
https://www.readbyqxmd.com/read/28741346/occurrence-state-and-molecular-structure-analysis-of-extracellular-proteins-with-implications-to-the-dewaterability-of-waste-activated-sludge
#5
Boran Wu, Bing-Jie Ni, Kristine Horvat, Liyan Song, Xiaoli Chai, Xiaohu Dai, Devinder Mahajan
The occurrence state and molecular structure of extracellular proteins were analyzed to reveal the influencing factors on the water-holding capacities of protein-like substances in waste activated sludge (WAS). The gelation process of extracellular proteins verified that advanced oxidation processes (AOPs) for WAS dewaterability improvement eliminated the water affinity of extracellular proteins and prevented these macromolecules to form stable colloidal aggregation. Isobaric tags for relative and absolute quantitation proteomics identified that most of extracellular proteins were originally derived from intracellular part and the proteins originally located at extracellular part were mainly membrane-associated...
July 25, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28741070/late-onset-x-linked-adrenal-hypoplasia-dax-1-nr0b1-two-new-adult-onset-cases-from-a-single-center
#6
Nikolaos Kyriakakis, Tolulope Shonibare, Julie Kyaw-Tun, Julie Lynch, Carlos F Lagos, John C Achermann, Robert D Murray
PURPOSE: DAX-1 (NR0B1) is an orphan nuclear receptor, which plays a critical role in development and regulation of the adrenal gland and hypothalamo-pituitary-gonadal axis. Mutations in NR0B1 lead to adrenal hypoplasia congenita (AHC), hypogonadotropic hypogonadism (HH) and azoospermia in men. Presentation is typically with adrenal insufficiency (AI) during infancy or childhood. To date only eight cases/kindreds are reported to have presented in adulthood. METHODS: We describe two new cases of men with DAX-1 mutations who presented in adulthood and who were diagnosed at a large University Hospital...
July 24, 2017: Pituitary
https://www.readbyqxmd.com/read/28740863/a-nanosecond-time-resolved-xfel-analysis-of-structural-changes-associated-with-co-release-from-cytochrome-c-oxidase
#7
Atsuhiro Shimada, Minoru Kubo, Seiki Baba, Keitaro Yamashita, Kunio Hirata, Go Ueno, Takashi Nomura, Tetsunari Kimura, Kyoko Shinzawa-Itoh, Junpei Baba, Keita Hatano, Yuki Eto, Akari Miyamoto, Hironori Murakami, Takashi Kumasaka, Shigeki Owada, Kensuke Tono, Makina Yabashi, Yoshihiro Yamaguchi, Sachiko Yanagisawa, Miyuki Sakaguchi, Takashi Ogura, Ryo Komiya, Jiwang Yan, Eiki Yamashita, Masaki Yamamoto, Hideo Ago, Shinya Yoshikawa, Tomitake Tsukihara
Bovine cytochrome c oxidase (CcO), a 420-kDa membrane protein, pumps protons using electrostatic repulsion between protons transferred through a water channel and net positive charges created by oxidation of heme a (Fe a ) for reduction of O2 at heme a3 (Fe a3). For this process to function properly, timing is essential: The channel must be closed after collection of the protons to be pumped and before Fe a oxidation. If the channel were to remain open, spontaneous backflow of the collected protons would occur...
July 2017: Science Advances
https://www.readbyqxmd.com/read/28739805/functional-insights-into-the-mode-of-dna-and-ligand-binding-of-the-tetr-family-regulator-tylp-from-streptomyces-fradiae
#8
Shamayeeta Ray, Anwesha Maitra, Anwesha Biswas, Santosh Panjikar, Jagannath Mondal, Ruchi Anand
Tetracycline Repressors (TetRs) modulate multi-drug efflux pathways in several pathogenic bacteria. In Streptomyces, they additionally regulate secondary metabolic pathways like antibiotic production. For instance, in the antibiotic producer Streptomyces fradiae, a layered network of TetRs regulate the levels of commercially important antibiotic tylosin, with TylP occupying the top of this cascading network. TetRs exist in two functional states; the DNA-bound and the ligand-bound form, which are allosterically regulated...
July 24, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28739483/structural-modeling-for-the-open-state-of-an-nmda-receptor
#9
Xiaodong Pang, Huan-Xiang Zhou
NMDA receptors are tetrameric ligand-gated ion channels that are crucial for neurodevelopment and higher order processes such as learning and memory, and have been implicated in numerous neurological disorders. The lack of a structure for the channel open state has greatly hampered the understanding of the normal gating process and mechanisms of disease-associated mutations. Here we report the structural modeling for the open state of an NMDA receptor. Staring from the crystal structure of the closed state, we repacked the pore-lining helices to generate an initial open model...
July 21, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28739266/identification-of-%C3%AE-helix-4-%C3%AE-4-of-rab11a-as-a-novel-rab11-binding-domain-rbd-interaction-of-rab11a-with-the-prostacyclin-receptor
#10
Eamon P Mulvaney, Fergal O'Meara, Amir R Khan, David J O'Connell, B Therese Kinsella
The cellular trafficking of numerous G protein-coupled receptors (GPCRs) is known to be regulated by Rab proteins that involves a direct protein:protein interaction between the receptor and the GTPase. In the case of the human prostacyclin receptor (hIP), it undergoes agonist-induced internalization and subsequent Rab11a-dependent recyclization involving an interaction between a Rab11-binding domain (RBD) localized within its carboxyl-tail domain with Rab11a. However, the GPCR-interacting domain on Rab11a itself is unknown...
July 21, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28738801/charged-residues-next-to-transmembrane-regions-revisited-positive-inside-rule-is-complemented-by-the-negative-inside-depletion-outside-enrichment-rule
#11
James Alexander Baker, Wing-Cheong Wong, Birgit Eisenhaber, Jim Warwicker, Frank Eisenhaber
BACKGROUND: Transmembrane helices (TMHs) frequently occur amongst protein architectures as means for proteins to attach to or embed into biological membranes. Physical constraints such as the membrane's hydrophobicity and electrostatic potential apply uniform requirements to TMHs and their flanking regions; consequently, they are mirrored in their sequence patterns (in addition to TMHs being a span of generally hydrophobic residues) on top of variations enforced by the specific protein's biological functions...
July 24, 2017: BMC Biology
https://www.readbyqxmd.com/read/28738244/dna-binding-and-unwinding-by-hel308-helicase-requires-dual-functions-of-a-winged-helix-domain
#12
Sarah J Northall, Ryan Buckley, Nathan Jones, J Carlos Penedo, Panos Soultanas, Edward L Bolt
Hel308 helicases promote genome stability linked to DNA replication in archaea, and have homologues in metazoans. In the crystal structure of archaeal Hel308 bound to a tailed DNA duplex, core helicase domains encircle single-stranded DNA (ssDNA) in a "ratchet" for directional translocation. A winged helix domain (WHD) is also present, but its function is mysterious. We investigated the WHD in full-length Hel308, identifying that mutations in a solvent exposed α-helix resulted in reduced DNA binding and unwinding activities...
July 16, 2017: DNA Repair
https://www.readbyqxmd.com/read/28737807/npy-binds-with-heme-to-form-a-npy-heme-complex-enhancing-peroxidase-activity-in-free-heme-and-promoting-npy-nitration-and-inactivation
#13
Huixian Ye, Zhen Yang, Hailing Li, Zhonghong Gao
Neuropeptide Y (NPY) is a member of the pancreatic peptide family of neuropeptides that play a crucial role in numerous central and peripheral nervous system responses. Recently, it has been shown that NPY protects cells against neurotoxic damage from β-amyloid peptides (Aβ) in Alzheimer's disease (AD). Heme is a common factor linking several metabolic perturbations in AD and altered heme metabolism has been shown to be related to the pathologies of AD. Thus, heme may have a chance to act on NPY and potentially counteract its function...
July 24, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28737724/time-dependent-inhibition-of-cyp2c8-and-cyp2c19-by-hedera-helix-extracts-a-traditional-respiratory-herbal-medicine
#14
Shaheed Ur Rehman, In Sook Kim, Min Sun Choi, Seung Hyun Kim, Yonghui Zhang, Hye Hyun Yoo
The extract of Hedera helix L. (Araliaceae), a well-known folk medicine, has been popularly used to treat respiratory problems, worldwide. It is very likely that this herbal extract is taken in combination with conventional drugs. The present study aimed to evaluate the effects of H. helix extract on cytochrome P450 (CYP) enzyme-mediated metabolism to predict the potential for herb-drug interactions. A cocktail probe assay was used to measure the inhibitory effect of CYP. H. helix extracts were incubated with pooled human liver microsomes or CYP isozymes with CYP-specific substrates, and the formation of specific metabolites was investigated to measure the inhibitory effects...
July 24, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28737286/unexpected-chiro-thermoresponsive-behavior-of-helical-poly-phenylacetylene-s-bearing-elastin-based-side-chains
#15
Sandra Arias, Felix Freire, Marcelo Calderon, Julian Bergueiro
The thermoresponsive behavior of an elastin based polymer can be altered by the polymeric macromolecular conformation. Thus, when the elastin basic amino-acid sequence VPGVG is used as a pendant group of a poly(phenylacetylene) (PPA) its thermoresponsivity in water can be remotely detected due to conformational changes on the formed helix. Circular dichroism at different temperatures show an inversion of the first Cotton effect (450 nm) at 25.8 ºC that matches with the cloud point temperature. Interestingly, this elastin-based side-chain PPA shows an upper critical solution temperature with low pH and concentration dependency, not expected in elastin based polymers...
July 24, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28736040/structural-characteristics-and-prebiotic-effects-of-semen-coicis-resistant-starches-type-3-prepared-by-different-methods
#16
Chen Bao, Hongliang Zeng, Yi Zhang, Longtao Zhang, Xu Lu, Zebin Guo, Song Miao, Baodong Zheng
In order to investigate the effects of different preparation methods on Semen coicis resistant starch, the structural properties and prebiotic effects of autoclaving treatment-purified S. coicis resistant starch (GP-SRS3), ultrasonic-autoclaving treatment-purified S. coicis resistant starch (UP-SRS3), enzyme-autoclaving treatment-purified S. coicis resistant starch (EP-SRS3) and microwave-moisture treatment-purified S. coicis resistant starch (MP-SRS3) were studied compared to high-amylose maize starch (HAMS)...
July 20, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28735751/structure-of-the-nav1-4-%C3%AE-1-complex-from-electric-eel
#17
Zhen Yan, Qiang Zhou, Lin Wang, Jianping Wu, Yanyu Zhao, Gaoxingyu Huang, Wei Peng, Huaizong Shen, Jianlin Lei, Nieng Yan
Voltage-gated sodium (Nav) channels initiate and propagate action potentials. Here, we present the cryo-EM structure of EeNav1.4, the Nav channel from electric eel, in complex with the β1 subunit at 4.0 Å resolution. The immunoglobulin domain of β1 docks onto the extracellular L5I and L6IV loops of EeNav1.4 via extensive polar interactions, and the single transmembrane helix interacts with the third voltage-sensing domain (VSDIII). The VSDs exhibit "up" conformations, while the intracellular gate of the pore domain is kept open by a digitonin-like molecule...
July 15, 2017: Cell
https://www.readbyqxmd.com/read/28735540/the-n%C3%A2-%C3%AF-interaction
#18
Robert W Newberry, Ronald T Raines
The carbonyl group holds a prominent position in chemistry and biology not only because it allows diverse transformations but also because it supports key intermolecular interactions, including hydrogen bonding. More recently, carbonyl groups have been found to interact with a variety of nucleophiles, including other carbonyl groups, in what we have termed an n→π* interaction. In an n→π* interaction, a nucleophile donates lone-pair (n) electron density into the empty π* orbital of a nearby carbonyl group...
July 23, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28735167/first-observation-of-metal-ion-induced-structural-fluctuations-of-%C3%AE-helical-peptides-by-using-diffracted-x-ray-tracking
#19
Daiki Usui, Satomi Inaba, Hiroshi Sekiguchi, Yuji C Sasaki, Toshiki Tanaka, Masayuki Oda
In order to analyze protein structural dynamics, we designed simple model peptides whose structures changed from random-coil to helix-bundle structures by forming stable hydrophobic core in the presence of metal ions. The strategy involved destabilizing a de novo designed three helix-bundle protein by substituting the residues present in its hydrophobic core with histidine and small amino acids. The conformational changes of peptides induced upon binding of Zn(2+) to histidine were analyzed using circular dichroism spectroscopy, which revealed peptides, HA and HG, to be good candidates for further analyses...
July 14, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28734207/in-silico-designing-of-therapeutic-protein-enriched-with-branched-chain-amino-acids-for-the-dietary-treatment-of-chronic-liver-disease
#20
Sunil L, Prasanna Vasu
Leucine, isoleucine, and valine are three essential branched-chain amino acids (BCAA) account for 40-45% of total essential amino acids. BCAA stimulates protein synthesis primarily in skeletal muscles, and it can directly transport to circulatory blood stream bypassing the liver. Hence, a protein enriched with BCAA is an important therapeutic target for the dietary treatment of chronic liver disease. The present study is to design a synthetic protein enriched with BCAA and the challenge is to maximize the BCAA content, keeping the balanced ratio of leucine, isoleucine, valine - 2: 1: 1...
July 12, 2017: Journal of Molecular Graphics & Modelling
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