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BMC Structural Biology

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https://www.readbyqxmd.com/read/27809904/controlled-dehydration-improves-the-diffraction-quality-of-two-rna-crystals
#1
HaJeung Park, Tuan Tran, Jun Hyuck Lee, Hyun Park, Matthew D Disney
BACKGROUND: Post-crystallization dehydration methods, applying either vapor diffusion or humidity control devices, have been widely used to improve the diffraction quality of protein crystals. Despite the fact that RNA crystals tend to diffract poorly, there is a dearth of reports on the application of dehydration methods to improve the diffraction quality of RNA crystals. RESULTS: We use dehydration techniques with a Free Mounting System (FMS, a humidity control device) to recover the poor diffraction quality of RNA crystals...
November 3, 2016: BMC Structural Biology
https://www.readbyqxmd.com/read/27788689/combined-small-angle-x-ray-solution-scattering-with-atomic-force-microscopy-for-characterizing-radiation-damage-on-biological-macromolecules
#2
Luca Costa, Alexander Andriatis, Martha Brennich, Jean-Marie Teulon, Shu-Wen W Chen, Jean-Luc Pellequer, Adam Round
BACKGROUND: Synchrotron radiation facilities are pillars of modern structural biology. Small-Angle X-ray scattering performed at synchrotron sources is often used to characterize the shape of biological macromolecules. A major challenge with high-energy X-ray beam on such macromolecules is the perturbation of sample due to radiation damage. RESULTS: By employing atomic force microscopy, another common technique to determine the shape of biological macromolecules when deposited on flat substrates, we present a protocol to evaluate and characterize consequences of radiation damage...
October 27, 2016: BMC Structural Biology
https://www.readbyqxmd.com/read/27782824/the-c-terminal-domain-of-tpx2-is-made-of-alpha-helical-tandem-repeats
#3
Luis Sanchez-Pulido, Laurent Perez, Steffen Kuhn, Isabelle Vernos, Miguel A Andrade-Navarro
BACKGROUND: TPX2 (Targeting Protein for Xklp2) is essential for spindle assembly, activation of the mitotic kinase Aurora A and for triggering microtubule nucleation. Homologs of TPX2 in Chordata and plants were previously identified. Currently, proteins of the TPX2 family have little structural information and only small parts are covered by defined protein domains. METHODS: We have used computational sequence analyses and structural predictions of proteins of the TPX2 family, supported with Circular Dichroism (CD) measurements...
October 26, 2016: BMC Structural Biology
https://www.readbyqxmd.com/read/27719672/human-sex-hormone-binding-globulin-as-a-potential-target-of-alternate-plasticizers-an-in-silico-study
#4
Ishfaq A Sheikh, Muhammad Yasir, Muhammad Abu-Elmagd, Tanveer A Dar, Adel M Abuzenadah, Ghazi A Damanhouri, Mohammed Al-Qahtani, Mohd A Beg
BACKGROUND: Currently, alternate plasticizers are used to replace phthalate plasticizers in children's toys, medical equipments and food packaging, due to the adverse effects of phthalate compounds on human health and laws prohibiting their use. Current information regarding the safety and potential adverse effects of alternate plasticizers is limited and recent studies have found alternate plasticizers to display similar characteristics to those observed in phthalate plasticizers. This study was undertaken to evaluate and predict the potential endocrine disrupting activity of the three most commonly used alternate plasticizers: di(2-ethylhexyl)terephthalate (DEHT), tris(2-ethylhexyl)trimellitate (TOTM), and diisononyl hexahydrophthalate (DINCH) against human sex hormone-binding globulin (SHBG) using in silico approaches...
September 30, 2016: BMC Structural Biology
https://www.readbyqxmd.com/read/27719669/endocrine-disruption-in-silico-perspectives-of-interactions-of-di-2-ethylhexyl-phthalate-and-its-five-major-metabolites-with-progesterone-receptor
#5
Ishfaq A Sheikh, Muhammad Abu-Elmagd, Rola F Turki, Ghazi A Damanhouri, Mohd A Beg, Mohammed Al-Qahtani
BACKGROUND: Di-(2-ethylhexyl)phthalate (DEHP) is a common endocrine disrupting compound (EDC) present in the environment as a result of industrial activity and leaching from polyvinyl products. DEHP is used as a plasticizer in medical devices and many commercial and household items. Exposure occurs through inhalation, ingestion, and skin contact. DEHP is metabolized to a primary metabolite mono-(2-ethylhexyl)phthalate (MEHP) in the body, which is further metabolized to four major secondary metabolites, mono(2-ethyl-5-hydroxyhexyl)phthalate (5-OH-MEHP), mono(2-ethyl-5-oxyhexyl)phthalate (5-oxo-MEHP), mono(2-ethyl-5-carboxypentyl)phthalate (5-cx-MEPP) and mono[2-(carboxymethyl)hexyl]phthalate (2-cx-MMHP)...
September 30, 2016: BMC Structural Biology
https://www.readbyqxmd.com/read/27619958/a-lack-of-peptide-binding-and-decreased-thermostability-suggests-that-the-caskin2-scaffolding-protein-sh3-domain-may-be-vestigial
#6
Jamie J Kwan, Logan W Donaldson
BACKGROUND: CASKIN2 is a neuronal signaling scaffolding protein comprised of multiple ankyrin repeats, two SAM domains, and one SH3 domain. The CASKIN2 SH3 domain for an NMR structural determination because its peptide-binding cleft appeared to deviate from the repertoire of aromatic enriched amino acids that typically bind polyproline-rich sequences. RESULTS: The structure demonstrated that two non-canonical basic amino acids (K290/R319) in the binding cleft were accommodated well in the SH3 fold...
2016: BMC Structural Biology
https://www.readbyqxmd.com/read/27578274/conservation-of-the-c-type-lectin-fold-for-accommodating-massive-sequence-variation-in-archaeal-diversity-generating-retroelements
#7
Sumit Handa, Blair G Paul, Jeffery F Miller, David L Valentine, Partho Ghosh
BACKGROUND: Diversity-generating retroelements (DGRs) provide organisms with a unique means for adaptation to a dynamic environment through massive protein sequence variation. The potential scope of this variation exceeds that of the vertebrate adaptive immune system. DGRs were known to exist only in viruses and bacteria until their recent discovery in archaea belonging to the 'microbial dark matter', specifically in organisms closely related to Nanoarchaeota. However, Nanoarchaeota DGR variable proteins were unassignable to known protein folds and apparently unrelated to characterized DGR variable proteins...
2016: BMC Structural Biology
https://www.readbyqxmd.com/read/27534744/3d-qsar-pharmacophore-and-molecular-docking-studies-of-known-inhibitors-and-designing-of-novel-inhibitors-for-m18-aspartyl-aminopeptidase-of-plasmodium-falciparum
#8
Madhulata Kumari, Subhash Chandra, Neeraj Tiwari, Naidu Subbarao
BACKGROUND: The Plasmodium falciparum M18 Aspartyl Aminopeptidase (PfM18AAP) is only aspartyl aminopeptidase which is found in the genome of P. falciparum and is essential for its survival. The PfM18AAP enzyme performs various functions in the parasite and the erythrocytic host such as hemoglobin digestion, erythrocyte invasion, parasite growth and parasite escape from the host cell. It is a valid target to develop antimalarial drugs. In the present work, we employed 3D QSAR modeling, pharmacophore modeling, and molecular docking to identify novel potent inhibitors that bind with M18AAP of P...
2016: BMC Structural Biology
https://www.readbyqxmd.com/read/27491540/comprehensive-analysis-of-the-co-structures-of-dipeptidyl-peptidase-iv-and-its-inhibitor
#9
Hiroyuki Nojima, Kazuhiko Kanou, Genki Terashi, Mayuko Takeda-Shitaka, Gaku Inoue, Koichiro Atsuda, Chihiro Itoh, Chie Iguchi, Hajime Matsubara
BACKGROUND: We comprehensively analyzed X-ray cocrystal structures of dipeptidyl peptidase IV (DPP-4) and its inhibitor to clarify whether DPP-4 alters its general or partial structure according to the inhibitor used and whether DPP-4 has a common rule for inhibitor binding. RESULTS: All the main and side chains in the inhibitor binding area were minimally altered, except for a few side chains, despite binding to inhibitors of various shapes. Some residues (Arg125, Glu205, Glu206, Tyr662 and Asn710) in the area had binding modes to fix a specific atom of inhibitor to a particular spatial position in DPP-4...
2016: BMC Structural Biology
https://www.readbyqxmd.com/read/27368374/investigation-of-allosteric-coupling-in-human-%C3%AE-2-adrenergic-receptor-in-the-presence-of-intracellular-loop-3
#10
Canan Ozgur, Pemra Doruker, E Demet Akten
BACKGROUND: This study investigates the allosteric coupling that exists between the intra- and extracellular parts of human β2-adrenergic receptor (β2-AR), in the presence of the intracellular loop 3 (ICL3), which is missing in all crystallographic experiments and most of the simulation studies reported so far. Our recent 1 μs long MD run has revealed a transition to the so-called very inactive state of the receptor, in which ICL3 packed under the G protein's binding cavity and completely blocked its accessibility to G protein...
2016: BMC Structural Biology
https://www.readbyqxmd.com/read/27368167/comparison-of-human-and-mouse-e-selectin-binding-to-sialyl-lewis-x
#11
Anne D Rocheleau, Thong M Cao, Tait Takitani, Michael R King
BACKGROUND: During inflammation, leukocytes are captured by the selectin family of adhesion receptors lining blood vessels to facilitate exit from the bloodstream. E-selectin is upregulated on stimulated endothelial cells and binds to several ligands on the surface of leukocytes. Selectin:ligand interactions are mediated in part by the interaction between the lectin domain and Sialyl-Lewis x (sLe(x)), a tetrasaccharide common to selectin ligands. There is a high degree of homology between selectins of various species: about 72 and 60 % in the lectin and EGF domains, respectively...
2016: BMC Structural Biology
https://www.readbyqxmd.com/read/27251136/crystal-structure-of-human-s100a8-in-complex-with-zinc-and-calcium
#12
Haili Lin, Gregers Rom Andersen, Laure Yatime
BACKGROUND: S100 proteins are a large family of calcium binding proteins present only in vertebrates. They function intra- and extracellularly both as regulators of homeostatic processes and as potent effectors during inflammation. Among these, S100A8 and S100A9 are two major constituents of neutrophils that can assemble into homodimers, heterodimers and higher oligomeric species, including fibrillary structures found in the ageing prostate. Each of these forms assumes specific functions and their formation is dependent on divalent cations, notably calcium and zinc...
2016: BMC Structural Biology
https://www.readbyqxmd.com/read/27246200/structural-determinant-for-inducing-rorgamma-specific-inverse-agonism-triggered-by-a-synthetic-benzoxazinone-ligand
#13
Douglas J Marcotte, YuTing Liu, Kevin Little, John H Jones, Noel A Powell, Craig P Wildes, Laura F Silvian, Jayanth V Chodaparambil
BACKGROUND: The nuclear hormone receptor RORγ regulates transcriptional genes involved in the production of the pro-inflammatory interleukin IL-17 which has been linked to autoimmune diseases such as rheumatoid arthritis, multiple sclerosis and inflammatory bowel disease. This transcriptional activity of RORγ is modulated through a protein-protein interaction involving the activation function 2 (AF2) helix on the ligand binding domain of RORγ and a conserved LXXLL helix motif on coactivator proteins...
2016: BMC Structural Biology
https://www.readbyqxmd.com/read/26969506/erratum-to-structuprint-a-scalable-and-extensible-tool-for-two-dimensional-representation-of-protein-surfaces
#14
Dimitrios Georgios Kontopoulos, Dimitrios Vlachakis, Georgia Tsiliki, Sofia Kossida
No abstract text is available yet for this article.
2016: BMC Structural Biology
https://www.readbyqxmd.com/read/26922638/structures-of-eccb1-and-eccd1-from-the-core-complex-of-the-mycobacterial-esx-1-type-vii-secretion-system
#15
Jonathan M Wagner, Sum Chan, Timothy J Evans, Sara Kahng, Jennifer Kim, Mark A Arbing, David Eisenberg, Konstantin V Korotkov
BACKGROUND: The ESX-1 type VII secretion system is an important determinant of virulence in pathogenic mycobacteria, including Mycobacterium tuberculosis. This complicated molecular machine secretes folded proteins through the mycobacterial cell envelope to subvert the host immune response. Despite its important role in disease very little is known about the molecular architecture of the ESX-1 secretion system. RESULTS: This study characterizes the structures of the soluble domains of two conserved core ESX-1 components - EccB1 and EccD1...
2016: BMC Structural Biology
https://www.readbyqxmd.com/read/26911476/structuprint-a-scalable-and-extensible-tool-for-two-dimensional-representation-of-protein-surfaces
#16
Dimitrios Georgios Kontopoulos, Dimitrios Vlachakis, Georgia Tsiliki, Sofia Kossida
BACKGROUND: The term 'molecular cartography' encompasses a family of computational methods for two-dimensional transformation of protein structures and analysis of their physicochemical properties. The underlying algorithms comprise multiple manual steps, whereas the few existing implementations typically restrict the user to a very limited set of molecular descriptors. RESULTS: We present Structuprint, a free standalone software that fully automates the rendering of protein surface maps, given - at the very least - a directory with a PDB file and an amino acid property...
2016: BMC Structural Biology
https://www.readbyqxmd.com/read/26865045/crystal-structure-and-functional-implications-of-the-tandem-type-universal-stress-protein-uspe-from-escherichia-coli
#17
Yongbin Xu, Jianyun Guo, Xiaoling Jin, Jin-Sik Kim, Ying Ji, Shengdi Fan, Nam-Chul Ha, Chun-Shan Quan
BACKGROUND: The universal stress proteins (USP) family member UspE is a tandem-type USP that consists of two Usp domains. The UspE expression levels of the Escherichia coli (E. coli) become elevated in response to oxidative stress and DNA damaging agents, including exposure to mitomycin C, cadmium, and hydrogen peroxide. It has been shown that UspA family members are survival factors during cellular growth arrest. The structures and functions of the UspA family members control the growth of E...
2016: BMC Structural Biology
https://www.readbyqxmd.com/read/26822308/a-direct-interaction-between-nqo1-and-a-chemotherapeutic-dimeric-naphthoquinone
#18
Lakshmi Swarna Mukhi Pidugu, J C Emmanuel Mbimba, Muqeet Ahmad, Edwin Pozharski, Edward A Sausville, Ashkan Emadi, Eric A Toth
BACKGROUND: Multimeric naphthoquinones are redox-active compounds that exhibit antineoplastic, antiprotozoal, and antiviral activities. Due to their multimodal effect on perturbation of cellular oxidative state, these compounds hold great potential as therapeutic agents against highly proliferative neoplastic cells. In our previous work, we developed a series of novel dimeric naphthoquinones and showed that they were selectively cytotoxic to human acute myeloid leukemia (AML), breast and prostate cancer cell lines...
2016: BMC Structural Biology
https://www.readbyqxmd.com/read/26449279/three-dimensional-structure-model-and-predicted-atp-interaction-rewiring-of-a-deviant-rna-ligase-2
#19
Sandrine Moreira, Emmanuel Noutahi, Guillaume Lamoureux, Gertraud Burger
BACKGROUND: RNA ligases 2 are scarce and scattered across the tree of life. Two members of this family are well studied: the mitochondrial RNA editing ligase from the parasitic trypanosomes (Kinetoplastea), a promising drug target, and bacteriophage T4 RNA ligase 2, a workhorse in molecular biology. Here we report the identification of a divergent RNA ligase 2 (DpRNL) from Diplonema papillatum (Diplonemea), a member of the kinetoplastids' sister group. METHODS: We identified DpRNL with methods based on sensitive hidden Markov Model...
October 9, 2015: BMC Structural Biology
https://www.readbyqxmd.com/read/26377800/the-crystal-structure-of-jnk-from-drosophila-melanogaster-reveals-an-evolutionarily-conserved-topology-with-that-of-mammalian-jnk-proteins
#20
Sarin Chimnaronk, Jatuporn Sitthiroongruang, Kanokporn Srisucharitpanit, Monrudee Srisaisup, Albert J Ketterman, Panadda Boonserm
BACKGROUND: The c-Jun N-terminal kinases (JNKs), members of the mitogen-activated protein kinase (MAPK) family, engage in diverse cellular responses to signals produced under normal development and stress conditions. In Drosophila, only one JNK member is present, whereas ten isoforms from three JNK genes (JNK1, 2, and 3) are present in mammalian cells. To date, several mammalian JNK structures have been determined, however, there has been no report of any insect JNK structure. RESULTS: We report the first structure of JNK from Drosophila melanogaster (DJNK)...
September 16, 2015: BMC Structural Biology
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