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BMC Structural Biology

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https://www.readbyqxmd.com/read/28774292/rosetta-broker-for-membrane-protein-structure-prediction-concentrative-nucleoside-transporter-3-and-corticotropin-releasing-factor-receptor-1-test-cases
#1
Dorota Latek
BACKGROUND: Membrane proteins are difficult targets for structure prediction due to the limited structural data deposited in Protein Data Bank. Most computational methods for membrane protein structure prediction are based on the comparative modeling. There are only few de novo methods targeting that distinct protein family. In this work an example of such de novo method was used to structurally and functionally characterize two representatives of distinct membrane proteins families of solute carrier transporters and G protein-coupled receptors...
August 3, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28545576/a-computational-assessment-of-ph-dependent-differential-interaction-of-t7-lysozyme-with-t7-rna-polymerase
#2
Subhomoi Borkotoky, Ayaluru Murali
BACKGROUND: T7 lysozyme (T7L), also known as N-acetylmuramoyl-L-alanine amidase, is a T7 bacteriophage gene product. It involves two functions: It can cut amide bonds in the bacterial cell wall and interacts with T7 RNA polymerase (T7RNAP) as a part of transcription inhibition. In this study, with the help of molecular dynamics (MD) calculations and computational interaction studies, we investigated the effect of varying pH conditions on conformational flexibilities of T7L and their influence on T7RNAP -T7L interactions...
May 25, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28521820/destabilization-of-the-twist1-e12-complex-dimerization-following-the-r154p-point-mutation-of-twist1-an-in-silico-approach
#3
Charlotte Bouard, Raphael Terreux, Agnès Tissier, Laurent Jacqueroud, Arnaud Vigneron, Stéphane Ansieau, Alain Puisieux, Léa Payen
BACKGROUND: The bHLH transcription factor TWIST1 plays a key role in the embryonic development and in tumorigenesis. Some loss-of-function mutations of the TWIST1 gene have been shown to cause an autosomal dominant craniosynostosis, known as the Saethre-Chotzen syndrome (SCS). Although the functional impacts of many TWIST1 mutations have been experimentally reported, little is known on the molecular mechanisms underlying their loss-of-function. In a previous study, we highlighted the predictive value of in silico molecular dynamics (MD) simulations in deciphering the molecular function of TWIST1 residues...
May 18, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28482831/molecular-dynamics-simulation-of-the-opposite-base-preference-and-interactions-in-the-active-site-of-formamidopyrimidine-dna-glycosylase
#4
Alexander V Popov, Anton V Endutkin, Yuri N Vorobjev, Dmitry O Zharkov
BACKGROUND: Formamidopyrimidine-DNA glycosylase (Fpg) removes abundant pre-mutagenic 8-oxoguanine (oxoG) bases from DNA through nucleophilic attack of its N-terminal proline at C1' of the damaged nucleotide. Since oxoG efficiently pairs with both C and A, Fpg must excise oxoG from pairs with C but not with A, otherwise a mutation occurs. The crystal structures of several Fpg-DNA complexes have been solved, yet no structure with A opposite the lesion is available. RESULTS: Here we use molecular dynamic simulation to model interactions in the pre-catalytic complex of Lactococcus lactis Fpg with DNA containing oxoG opposite C or A, the latter in either syn or anti conformation...
May 8, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28438161/refolddb-a-new-and-sustainable-gateway-to-experimental-protocols-for-protein-refolding
#5
Hisashi Mizutani, Hideaki Sugawara, Ashley M Buckle, Takeshi Sangawa, Ken-Ichi Miyazono, Jun Ohtsuka, Koji Nagata, Tomoki Shojima, Shohei Nosaki, Yuqun Xu, Delong Wang, Xiao Hu, Masaru Tanokura, Kei Yura
BACKGROUND: More than 7000 papers related to "protein refolding" have been published to date, with approximately 300 reports each year during the last decade. Whilst some of these papers provide experimental protocols for protein refolding, a survey in the structural life science communities showed a necessity for a comprehensive database for refolding techniques. We therefore have developed a new resource - "REFOLDdb" that collects refolding techniques into a single, searchable repository to help researchers develop refolding protocols for proteins of interest...
April 24, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28372592/a-comparative-analysis-of-the-foamy-and-ortho-virus-capsid-structures-reveals-an-ancient-domain-duplication
#6
William R Taylor, Jonathan P Stoye, Ian A Taylor
BACKGROUND: The Spumaretrovirinae (foamy viruses) and the Orthoretrovirinae (e.g. HIV) share many similarities both in genome structure and the sequences of the core viral encoded proteins, such as the aspartyl protease and reverse transcriptase. Similarity in the gag region of the genome is less obvious at the sequence level but has been illuminated by the recent solution of the foamy virus capsid (CA) structure. This revealed a clear structural similarity to the orthoretrovirus capsids but with marked differences that left uncertainty in the relationship between the two domains that comprise the structure...
April 4, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28148269/dynadom-structure-based-prediction-of-t-cell-receptor-inter-domain-and-t-cell-receptor-peptide-mhc-class-i-association-angles
#7
Thomas Hoffmann, Antoine Marion, Iris Antes
BACKGROUND: T cell receptor (TCR) molecules are involved in the adaptive immune response as they distinguish between self- and foreign-peptides, presented in major histocompatibility complex molecules (pMHC). Former studies showed that the association angles of the TCR variable domains (Vα/Vβ) can differ significantly and change upon binding to the pMHC complex. These changes can be described as a rotation of the domains around a general Center of Rotation, characterized by the interaction of two highly conserved glutamine residues...
February 2, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28143508/prokaryotic-ubiquitin-like-protein-remains-intrinsically-disordered-when-covalently-attached-to-proteasomal-target-proteins
#8
Jonas Barandun, Fred F Damberger, Cyrille L Delley, Juerg Laederach, Frédéric H T Allain, Eilika Weber-Ban
BACKGROUND: The post-translational modification pathway referred to as pupylation marks proteins for proteasomal degradation in Mycobacterium tuberculosis and other actinobacteria by covalently attaching the small protein Pup (prokaryotic ubiquitin-like protein) to target lysine residues. In contrast to the functionally analogous eukaryotic ubiquitin, Pup is intrinsically disordered in its free form. Its unfolded state allows Pup to adopt different structures upon interaction with different binding partners like the Pup ligase PafA and the proteasomal ATPase Mpa...
February 1, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/27809904/controlled-dehydration-improves-the-diffraction-quality-of-two-rna-crystals
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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