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Crystallization of membrane protein

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https://www.readbyqxmd.com/read/28441870/protein-nanocellulose-interactions-in-paper-filters-for-advanced-separation-applications
#1
Simon Johan Gustafsson, Levon Manukyan, Albert Mihranyan
Protein-based pharmaceutics are widely explored for healthcare applications, and six out of ten best selling drugs today are biologicals. The goal of this work was to evaluate the protein nanocellulose interactions in paper filter for advanced separation applications such as virus removal filtration and bioprocessing. The protein recovery was measured for bovine serum albumin (BSA), γ-Globulin and Lysozyme using biuret total protein reagent and polyacrylamide gel electrophoresis (SDS-PAGE), and the throughput was characterized in terms of flux values from fixed volume filtrations at various protein concentrations and under worst-case experimental conditions...
April 26, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28437696/different-toxicity-of-anatase-and-rutile-tio2-nanoparticles-on-macrophages-involvement-of-difference-in-affinity-to-proteins-and-phospholipids
#2
Qilin Yu, Honggang Wang, Qi Peng, Ye Li, Zhe Liu, Mingchun Li
TiO2 nanoparticles (NPs) are well-known nanomaterials (NMs), widely used in cosmetics, solar cells, photo-catalysts and additives. Anatase and rutile are the two main crystalline phases of TiO2 NPs and have distinct electrical and optical properties. However, their relative toxicity to organisms is a current topic of debate. In this study, we synthesize both anatase NPs (TiO2-A) and rutile NPs (TiO2-R) with similar particle sizes (20-40nm), surface areas (51-52m(2)/g) and Zeta potentials (-13.4 to -13.7mV), and investigate their toxicity to macrophages...
April 9, 2017: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/28430426/the-rosetta-all-atom-energy-function-for-macromolecular-modeling-and-design
#3
Rebecca Faye Alford, Andrew Leaver-Fay, Jeliazko R Jeliazkov, Matthew J O'Meara, Frank P DiMaio, Hahnbeom Park, Maxim V Shapovalov, P Douglas Renfrew, Vikram Khipple Mulligan, Kalli Kappel, Jason W Labonte, Michael Steven Pacella, Richard Bonneau, Philip Bradley, Roland L Dunbrack, Rhiju Das, David Baker, Brian Kuhlman, Tanja Kortemme, Jeffrey J Gray
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta's success is the energy function: a model parameterized from small molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta Energy Function, REF15...
April 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28420706/common-structural-features-of-cholesterol-binding-sites-in-crystallized-soluble-proteins
#4
Anna N Bukiya, Alejandro M Dopico
Cholesterol-protein interactions are essential for the architectural organization of cell membranes and for lipid metabolism. While cholesterol-sensing motifs in transmembrane proteins have been identified, little is known about cholesterol recognition by soluble proteins. We reviewed the structural characteristics of binding sites for cholesterol and cholesterol sulfate from crystallographic structures available in the Protein Data Bank. This analysis unveiled key features of cholesterol-binding sites that are present in either all or the majority of sites: i) the cholesterol molecule is generally positioned between protein domains that have an organized secondary structure; ii) the cholesterol hydroxyl/sulfo group is often partnered by Asn, Gln and/or Tyr while the hydrophobic part of cholesterol interacts with Leu, Ile, Val and/or Phe; iii) cholesterol hydrogen-bonding partners are often found on alpha-helices while amino acids that interact with cholesterol hydrophobic core have a slight preference for beta-strands and secondary structure-lacking protein areas; iv) the steroid C21 and 26 constitute the ″hot spots″ most often seen for steroid-protein hydrophobic interactions; v) common ″cold spots″ are C8, 9, 10, 13 and 17, at which contacts with the proteins were not detected...
April 18, 2017: Journal of Lipid Research
https://www.readbyqxmd.com/read/28410397/a-bis-sulphamoylated-estradiol-derivative-induces-ros-dependent-cell-cycle-abnormalities-and-subsequent-apoptosis
#5
Michelle Helen Visagie, Iman van den Bout, Anna Margaretha Joubert
Clinical trials have revealed that the potential anticancer agent, 2-methoxyestradiol (2ME2) has limitations due to its low bioavailability. Subsequently, 2ME2 derivatives including (8R,13S,14S,17S)-2-ethyl-13-methyl-7,8,9,11,12,13,14,15,16,17-decahydro-6H-cyclopenta[a]phenanthrane-3,17-diyl bis(sulphamate) (EMBS) have shown improved efficacies in inducing apoptosis. However, no conclusive data exist to explain the mode of action exerted by these drugs. This study investigated the mode of action used by EMBS as a representative of the sulphamoylated 2ME2 derivatives...
2017: PloS One
https://www.readbyqxmd.com/read/28398555/biophysical-and-functional-characterization-of-hippocalcin-mutants-responsible-for-human-dystonia
#6
Nordine Helassa, Svetlana V Antonyuk, Lu-Yun Lian, Lee P Haynes, Robert D Burgoyne
Dystonia is a neurological movement disorder that forces the body into twisting, repetitive movements or sometimes painful abnormal postures. With the advent of next-generation sequencing technologies, the homozygous mutations T71N and A190T in the neuronal calcium sensor (NCS) hippocalcin were identified as the genetic cause of primary isolated dystonia (DYT2 dystonia). However, the effect of these mutations on the physiological role of hippocalcin has not yet been elucidated. Using a multidisciplinary approach, we demonstrated that hippocalcin oligomerises in a calcium-dependent manner and binds to voltage-gated calcium channels...
April 7, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28394325/structural-basis-for-lipopolysaccharide-extraction-by-abc-transporter-lptb2fg
#7
Qingshan Luo, Xu Yang, Shan Yu, Huigang Shi, Kun Wang, Le Xiao, Guangyu Zhu, Chuanqi Sun, Tingting Li, Dianfan Li, Xinzheng Zhang, Min Zhou, Yihua Huang
After biosynthesis, bacterial lipopolysaccharides (LPS) are transiently anchored to the outer leaflet of the inner membrane (IM). The ATP-binding cassette (ABC) transporter LptB2FG extracts LPS molecules from the IM and transports them to the outer membrane. Here we report the crystal structure of nucleotide-free LptB2FG from Pseudomonas aeruginosa. The structure reveals that lipopolysaccharide transport proteins LptF and LptG each contain a transmembrane domain (TMD), a periplasmic β-jellyroll-like domain and a coupling helix that interacts with LptB on the cytoplasmic side...
April 10, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28393915/allosteric-inhibition-of-aminopeptidase-n-functions-related-to-tumor-growth-and-virus-infection
#8
César Santiago, Gaurav Mudgal, Juan Reguera, Rosario Recacha, Sébastien Albrecht, Luis Enjuanes, José M Casasnovas
Cell surface aminopeptidase N (APN) is a membrane-bound ectoenzyme that hydrolyzes proteins and peptides and regulates numerous cell functions. APN participates in tumor cell expansion and motility, and is a target for cancer therapies. Small drugs that bind to the APN active site inhibit catalysis and suppress tumor growth. APN is also a major cell entry receptor for coronavirus, which binds to a region distant from the active site. Three crystal structures that we determined of human and pig APN ectodomains defined the dynamic conformation of the protein...
April 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28375549/homology-based-modeling-of-rhodopsin-like-family-members-in-the-inactive-state-structural-analysis-and-deduction-of-tips-for-modeling-and-optimization
#9
Matteo Pappalardo, Mahmoud Rayan, Saleh Abu-Lafi, Martha E Leonardi, Danilo Milardi, Salvatore Guccione, Anwar Rayan
Modeling G-Protein Coupled Receptors (GPCRs) is an emergent field of research, since utility of high-quality models in receptor structure-based strategies might facilitate the discovery of interesting drug candidates. The findings from a quantitative analysis of eighteen resolved structures of rhodopsin family "A" receptors crystallized with antagonists and 153 pairs of structures are described. A strategy termed endeca-amino acids fragmentation was used to analyze the structures models aiming to detect the relationship between sequence identity and Root Mean Square Deviation (RMSD) at each trans-membrane-domain...
April 4, 2017: Molecular Informatics
https://www.readbyqxmd.com/read/28370548/formation-of-a-cubic-liquid-crystalline-nanostructure-with-%C3%AF-conjugated-fluorinated-rods-on-the-gyroid-minimal-surface
#10
Marko Poppe, Changlon Chen, Feng Liu, Silvio Poppe, Carsten Tschierske
Bicontinuous cubic phases are of significant importance for numerous applications, for example, for the crystallization of membrane proteins, as photonic materials and as templates for porous silica. A new variant of bicontinuous cubic liquid crystalline phase with Ia3¯d lattice is reported here for X-shaped bolapolyphiles. It is shown that in this class of compounds cubic phase induction can be achieved by proper aromatic core fluorination; in addition, the first cubic phases having π-conjugated oligo(phenylene ethynylene) rods on the gyroid minimal surface were obtained...
March 29, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28369529/human-apo-srp72-and-srp68-72-complex-structures-reveal-the-molecular-basis-of-protein-translocation
#11
Yina Gao, Qi Zhang, Yue Lang, Yang Liu, Xiaofei Dong, Zhenhang Chen, Wenli Tian, Jun Tang, Wei Wu, Yufeng Tong, Zhongzhou Chen
The co-translational targeting or insertion of secretory and membrane proteins into the endoplasmic reticulum (ER) is a key biological process mediated by the signal recognition particle (SRP). In eukaryotes, the SRP68-SRP72 (SRP68/72) heterodimer plays an essential role in protein translocation. However, structural information on the two largest SRP proteins, SRP68 and SRP72, is limited, especially regarding their interaction. Herein, we report the first crystal structures of human apo-SRP72 and the SRP68/72 complex at 2...
March 20, 2017: Journal of Molecular Cell Biology
https://www.readbyqxmd.com/read/28368278/crystallization-and-x-ray-analysis-of-the-extracellular-adhesion-domain-of-helicobacter-pylori-adhesin-a-the-significance-of-the-cation-composition-in-the-crystallization-precipitant
#12
Ling Guo, Jinyong Zhang, Liwei Cui, Dong Liu, Bo Ma, Shufeng Wang, Haibo Li, Yuzhang Wu, Wei Liu
Adherence to host cells is a crucial step in the process of bacterial infection, which is usually mediated by a number of outer membrane proteins identified as adhesins. Helicobacter pylori adhesin A (HpaA) is a member of the adhesin family that mediates the adherence of Helicobacter pylori to gastric epithelial cells, and consequently assists the bacteria in becoming a life-long colonizer of the human stomach. In this study, two constructs were made for the production of truncated HpaA proteins comprising residues 31-260 and 53-260, respectively...
April 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28362368/peptide-scanning-assisted-identification-of-a-monoclonal-antibody-recognized-linear-b-cell-epitope
#13
Chien-Wen Chen, Chi-Yao Chang
The identification of an antigenic epitope by the immune system allows for the understanding of the protective mechanism of neutralizing antibodies that may facilitate the development of vaccines and peptide drugs. Peptide scanning is a simple and efficient method that straightforwardly maps the linear epitope recognized by a monoclonal antibody (mAb). Here, the authors present an epitope determination methodology involving serially truncated recombinant proteins, synthetic peptide design, and dot-blot hybridization for the antigenic recognition of nervous necrosis virus coat protein using a neutralizing mAb...
March 24, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28348076/the-crystal-structure-of-a-membrane-bound-multi-domain-protease-inhibitor-reveals-the-mechanism-of-its-auto-inhibition
#14
Min Liu, Cai Yuan, Jan Jensen, Baoyu Zhao, Yunbin Jiang, Longguang Jiang, Mindong Huang
Hepatocyte growth factor activator inhibitor 1 (HAI-1) is a membrane-bound multi-domain protein essential to the integrity of the basement membrane during placental development and is also important in maintaining postnatal homeostasis in many tissues. HAI-1 is a Kunitz-type serine protease inhibitor, and soluble fragments of HAI-1 with variable lengths have been identified in vivo. The full-length extracellular portion of HAI-1 (sHAI-1) shows weaker inhibitory activity toward target proteases than do the smaller fragments, suggesting auto-inhibition of HAI-1...
March 27, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28343125/structural-modeling-of-human-organic-cation-transporters
#15
Tikam Chand Dakal, Rajender Kumar, Dindial Ramotar
Human organic cation transporters (hOCTs) belong to solute carriers (SLC) 22 family of membrane proteins that play a central role in transportation of chemotherapeutic drugs for several clinical and pathological conditions, including cancer and diabetes. These transporters mediate drug transport; however, the precise mechanism of drug-binding and transport by them is not fully uncovered yet, partly due to unavailability of any crystal structure record. In this work, we performed a multi-phasic approach to compute the 3D structural models of seven human organic cation transporters (hOCTs) starting from primary protein sequence...
March 18, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28329765/structural-insights-into-adiponectin-receptors-suggest-ceramidase-activity
#16
Ieva Vasiliauskaité-Brooks, Remy Sounier, Pascal Rochaix, Gaëtan Bellot, Mathieu Fortier, François Hoh, Luigi De Colibus, Chérine Bechara, Essa M Saied, Christoph Arenz, Cédric Leyrat, Sébastien Granier
Adiponectin receptors (ADIPORs) are integral membrane proteins that control glucose and lipid metabolism by mediating, at least in part, a cellular ceramidase activity that catalyses the hydrolysis of ceramide to produce sphingosine and a free fatty acid (FFA). The crystal structures of the two receptor subtypes, ADIPOR1 and ADIPOR2, show a similar overall seven-transmembrane-domain architecture with large unoccupied cavities and a zinc binding site within the seven transmembrane domain. However, the molecular mechanisms by which ADIPORs function are not known...
April 6, 2017: Nature
https://www.readbyqxmd.com/read/28324060/expression-of-pd-1-and-pd-l1-in-anaplastic-thyroid-cancer-patients-treated-with-multimodal-therapy-results-from-a-retrospective-study
#17
Ashish V Chintakuntlawar, Kandelaria M Rumilla, Carin Y Smith, Sarah M Jenkins, Robert L Foote, Jan L Kasperbauer, John C Morris, Mabel Ryder, Samer Alsidawi, Crystal Hilger, Keith C Bible
Context: Anaplastic thyroid cancer (ATC) is rare and a highly fatal malignancy. The role of PD-1 and PD-L1 as prognostic and/or predictive marker in ATC is unknown. Objective: Multimodal therapy offers the best chance at tumor control. Objective of this study was to detect potential associations of PD-1/PD-L1 axis variables with outcome data in ATC. Design: Retrospective study of a uniformly treated cohort. Setting: Single institution retrospective cohort study...
March 7, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28319136/structural-insights-into-the-regulation-of-bacillus-subtilis-sigw-activity-by-anti-sigma-rsiw
#18
Shankar Raj Devkota, Eunju Kwon, Sung Chul Ha, Hyeun Wook Chang, Dong Young Kim
Bacillus subtilis SigW is localized to the cell membrane and is inactivated by the tight interaction with anti-sigma RsiW under normal growth conditions. Whereas SigW is discharged from RsiW binding and thus initiates the transcription of its regulon under diverse stress conditions such as antibiotics and alkaline shock. The release and activation of SigW in response to extracytoplasmic signals is induced by the regulated intramembrane proteolysis of RsiW. As a ZAS (Zinc-containing anti-sigma) family protein, RsiW has a CHCC zinc binding motif, which implies that its anti-sigma activity may be regulated by the state of zinc coordination in addition to the proteolytic cleavage of RsiW...
2017: PloS One
https://www.readbyqxmd.com/read/28315353/crystal-structure-of-the-extracellular-domain-of-the-human-dendritic-cell-surface-marker-cd83
#19
Christiane S Heilingloh, Stefan Klingl, Claudia Egerer-Sieber, Benedikt Schmid, Sigrid Weiler, Petra Mühl-Zürbes, Jörg Hofmann, Joachim D Stump, Heinrich Sticht, Mirko Kummer, Alexander Steinkasserer, Yves A Muller
CD83 is a type-I membrane protein and an efficient marker for identifying mature dendritic cells. Whereas membrane-bound, full-length CD83 co-stimulates the immune system, a soluble variant (sCD83), consisting of the extracellular domain only, displays strong immune-suppressive activities. Besides a prediction that sCD83 adopts a V-set Ig-like fold, however, little is known about the molecular architecture of CD83 and the mechanism by which CD83 exerts its function on dendritic cells and additional immune cells...
April 21, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28303107/localization-and-ordering-of-lipids-around-aquaporin-0-protein-and-lipid-mobility-effects
#20
Rodolfo Briones, Camilo Aponte-Santamaría, Bert L de Groot
Hydrophobic matching, lipid sorting, and protein oligomerization are key principles by which lipids and proteins organize in biological membranes. The Aquaporin-0 channel (AQP0), solved by electron crystallography (EC) at cryogenic temperatures, is one of the few protein-lipid complexes of which the structure is available in atomic detail. EC and room-temperature molecular dynamics (MD) of dimyristoylglycerophosphocholine (DMPC) annular lipids around AQP0 show similarities, however, crystal-packing and temperature might affect the protein surface or the lipids distribution...
2017: Frontiers in Physiology
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