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Membrane protein crystal structure

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https://www.readbyqxmd.com/read/28343125/structural-modeling-of-human-organic-cation-transporters
#1
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
#2
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...
March 22, 2017: Nature
https://www.readbyqxmd.com/read/28319136/structural-insights-into-the-regulation-of-bacillus-subtilis-sigw-activity-by-anti-sigma-rsiw
#3
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
#4
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 is function on dendritic cells and additional immune cells...
March 14, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28303107/localization-and-ordering-of-lipids-around-aquaporin-0-protein-and-lipid-mobility-effects
#5
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
https://www.readbyqxmd.com/read/28302513/expression-purification-and-enzymatic-characterization-of-undecaprenyl-pyrophosphate-phosphatase-from-vibrio-vulnificus
#6
Hsin-Yang Chang, Chia-Cheng Chou, Mao-Lun Wu, Andrew H J Wang
Undecaprenyl pyrophosphate phosphatase (UppP), a cell membrane integral enzyme, catalyzes the dephosphorylation of undecaprenyl pyrophosphate to undecaprenyl phosphate, which is an essential carrier lipid in bacterial cell wall synthesis. We previously purified E. coli UppP and concluded that its catalytic site is likely located in the periplasm. To search for additional natural UppP homologs to elucidate what constitutes a common catalytic mechanism and to gain a better chance of obtaining high-resolution crystal structural information, we expressed and purified recombinant Vibrio vulnificus UppP using E...
March 14, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28299732/structural-studies-of-matrix-metalloproteinase-by-x-ray-diffraction
#7
Elena Decaneto, Wolfgang Lubitz, Hideaki Ogata
Matrix Metalloproteinases (MMPs) are a family of proteolytic enzymes whose endopeptidase activity is dependent on the presence of specific metal ions. MT1-MMP (or MMP-14), which has been implicated in tumor progression and cellular invasion, contains a membrane-spanning region located C-terminal to a hemopexin-like domain and an N-terminal catalytic domain. We recombinantly expressed the catalytic domain of human MT1-MMP in E. coli and purified it from inclusion bodies using a refolding protocol that yielded significant quantities of active protein...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28291748/the-crystal-structure-of-mouse-lc3b-in-complex-with-the-fyco1-lir-reveals-the-importance-of-the-flanking-region-of-the-lir-motif
#8
Shunya Sakurai, Taisuke Tomita, Toshiyuki Shimizu, Umeharu Ohto
FYVE and coiled-coil domain-containing protein 1 (FYCO1), a multidomain autophagy adaptor protein, mediates microtubule plus-end-directed autophagosome transport by interacting with kinesin motor proteins and with the autophagosomal membrane components microtubule-associated protein 1 light chain 3 (LC3), Rab7 and phosphatidylinositol 3-phosphate (PI3P). To establish the structural basis for the recognition of FYCO1 by LC3, the crystal structure of mouse LC3B in complex with the FYCO1 LC3-interacting region (LIR) motif peptide was determined...
March 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28286332/two-alternative-binding-mechanisms-connect-the-protein-translocation-sec71-sec72-complex-with-heat-shock-proteins
#9
Arati Tripathi, Elisabet C Mandon, Reid Gilmore, Tom A Rapoport
The biosynthesis of many eukaryotic proteins requires accurate targeting to and translocation across the endoplasmic reticulum (ER) membrane. Post-translational protein translocation in yeast requires both the Sec61 translocation channel, and a complex of four additional proteins: Sec63, Sec62, Sec71, and Sec72. The structure and function of these proteins are largely unknown. This pathway also requires the cytosolic Hsp70 protein Ssa1, but whether Ssa1 associates with the translocation machinery to target protein substrates to the membrane is unclear...
March 12, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28272640/mutual-relationships-between-structural-and-functional-changes-in-a-psbm-deletion-mutant-of-photosystem-ii
#10
S Uto, K Kawakami, Y Umena, M Iwai, M Ikeuchi, J-R Shen, N Kamiya
Photosystem II (PSII) is a membrane protein complex that performs light-induced electron transfer and oxygen evolution from water. PSII consists of 19 or 20 subunits in its crystal form and binds various cofactors such as chlorophyll a, plastoquinone, carotenoid, and lipids. After initial light excitation, the charge separation produces an electron, which is transferred to a plastoquinone molecule (QA) and then to another plastoquinone (QB). PsbM is a low-molecular-weight subunit with one transmembrane helix, and is located in the monomer-monomer interface of the PSII dimer...
March 8, 2017: Faraday Discussions
https://www.readbyqxmd.com/read/28264013/structure-determination-of-a-major-facilitator-peptide-transporter-inward-facing-peptst-from-streptococcus-thermophilus-crystallized-in-space-group-p3121
#11
Esben M Quistgaard, Maria Martinez Molledo, Christian Löw
Major facilitator superfamily (MFS) peptide transporters (typically referred to as PepT, POT or PTR transporters) mediate the uptake of di- and tripeptides, and so play an important dietary role in many organisms. In recent years, a better understanding of the molecular basis for this process has emerged, which is in large part due to a steep increase in structural information. Yet, the conformational transitions underlying the transport mechanism are still not fully understood, and additional data is therefore needed...
2017: PloS One
https://www.readbyqxmd.com/read/28261000/a-versatile-system-for-high-throughput-in-situ-x-ray-screening-and-data-collection-of-soluble-and-membrane-protein-crystals
#12
Jana Broecker, Viviane Klingel, Wei-Lin Ou, Aidin R Balo, David J Kissick, Craig M Ogata, Anling Kuo, Oliver P Ernst
In recent years, in situ data collection has been a major focus of progress in protein crystallography. Here, we introduce the Mylar in situ method using Mylar-based sandwich plates that are inexpensive, easy to make and handle, and show significantly less background scattering than other setups. A variety of cognate holders for patches of Mylar in situ sandwich films corresponding to one or more wells makes the method robust and versatile, allows for storage and shipping of entire wells, and enables automated crystal imaging, screening, and goniometer-based X-ray diffraction data-collection at room temperature and under cryogenic conditions for soluble and membrane-protein crystals grown in or transferred to these plates...
November 2, 2016: Crystal Growth & Design
https://www.readbyqxmd.com/read/28258203/mechanism-of-single-and-double-sided-inhibition-of-dual-topology-fluoride-channels-by-synthetic-monobodies
#13
Daniel L Turman, Randy B Stockbridge
The Fluc family of proteins comprises small, electrodiffusive fluoride channels, which prevent accumulation of toxic F(-) ions in microorganisms. Recent crystal structures have confirmed their unusual architecture, in which a pair of antiparallel subunits convenes to form a dimer with a twofold symmetry axis parallel to the plane of the membrane. These structures have also revealed the interactions between Fluc channels and several different fibronectin domain monobodies that inhibit Fluc-mediated F(-) currents; in all structures, each channel binds to two monobodies symmetrically, one on either side of the membrane...
March 3, 2017: Journal of General Physiology
https://www.readbyqxmd.com/read/28256220/do-all-x-ray-structures-of-protein-ligand-complexes-represent-functional-states-epor-a-case-study
#14
Michael S P Corbett, Alan E Mark, David Poger
Based on differences between the x-ray crystal structures of ligand-bound and unbound forms, the activation of the erythropoietin receptor (EPOR) was initially proposed to involve a cross-action scissorlike motion. However, the validity of the motions involved in the scissorlike model has been recently challenged. Here, atomistic molecular dynamics simulations are used to examine the structure of the extracellular domain of the EPOR dimer in the presence and absence of erythropoietin and a series of agonistic or antagonistic mimetic peptides free in solution...
February 28, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28255005/international-union-of-basic-and-clinical-pharmacology-ci-structures-and-small-molecule-modulators-of-mammalian-adenylyl-cyclases
#15
REVIEW
Carmen W Dessauer, Val J Watts, Rennolds S Ostrom, Marco Conti, Stefan Dove, Roland Seifert
Adenylyl cyclases (ACs) generate the second messenger cAMP from ATP. Mammalian cells express nine transmembrane AC (mAC) isoforms (AC1-9) and a soluble AC (sAC, also referred to as AC10). This review will largely focus on mACs. mACs are activated by the G-protein Gαs and regulated by multiple mechanisms. mACs are differentially expressed in tissues and regulate numerous and diverse cell functions. mACs localize in distinct membrane compartments and form signaling complexes. sAC is activated by bicarbonate with physiologic roles first described in testis...
April 2017: Pharmacological Reviews
https://www.readbyqxmd.com/read/28252385/chlamydia-interfere-with-an-interaction-between-the-mannose-6-phosphate-receptor-and-sorting-nexins-to-counteract-host-restriction
#16
Cherilyn A Elwell, Nadine Czudnochowski, John von Dollen, Jeffrey R Johnson, Rachel Nakagawa, Kathleen Mirrashidi, Nevan J Krogan, Joanne N Engel, Oren S Rosenberg
Chlamydia trachomatis is an obligate intracellular pathogen that resides in a membrane-bound compartment, the inclusion. The bacteria secrete a unique class of proteins, Incs, which insert into the inclusion membrane and modulate the host-bacterium interface. We previously reported that IncE binds specifically to the Sorting Nexin 5 Phox domain (SNX5-PX) and disrupts retromer trafficking. Here, we present the crystal structure of the SNX5-PX:IncE complex, showing IncE bound to a unique and highly conserved hydrophobic groove on SNX5...
March 2, 2017: ELife
https://www.readbyqxmd.com/read/28251761/3d-structural-analysis-of-protein-o-mannosyl-kinase-pomk-a-causative-gene-product-of-dystroglycanopathy
#17
Masamichi Nagae, Sushil K Mishra, Makiko Neyazaki, Rika Oi, Akemi Ikeda, Naohiro Matsugaki, Satoko Akashi, Hiroshi Manya, Mamoru Mizuno, Hirokazu Yagi, Koichi Kato, Toshiya Senda, Tamao Endo, Terukazu Nogi, Yoshiki Yamaguchi
Orchestration of the multiple enzymes engaged in O-mannose glycan synthesis provides a matriglycan on α-dystroglycan (α-DG) which attracts extracellular matrix (ECM) proteins such as laminin. Aberrant O-mannosylation of α-DG leads to severe congenital muscular dystrophies due to detachment of ECM proteins from the basal membrane. Phosphorylation at C6-position of O-mannose catalyzed by protein O-mannosyl kinase (POMK) is a crucial step in the biosynthetic pathway of O-mannose glycan. Several mis-sense mutations of the POMK catalytic domain are known to cause a severe congenital muscular dystrophy, Walker-Warburg syndrome...
March 2, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28248291/structural-insights-into-the-coordination-of-plastid-division-by-the-arc6-pdv2-complex
#18
Wenhe Wang, Jinyu Li, Qingqing Sun, Xiaoyu Yu, Weiwei Zhang, Ning Jia, Chuanjing An, Yiqiong Li, Yanan Dong, Fengjiao Han, Ning Chang, Xiaomin Liu, Zhiling Zhu, You Yu, Shilong Fan, Maojun Yang, Shi-Zhong Luo, Hongbo Gao, Yue Feng
Chloroplasts divide by binary fission, which is accomplished by the simultaneous constriction of the FtsZ ring on the stromal side of the inner envelope membrane, and the ARC5 ring on the cytosolic side of the outer envelope membrane. The two rings are connected and coordinated mainly by the interaction between the inner envelope membrane protein ARC6 and the outer envelope membrane protein PDV2 in the intermembrane space. The underlying mechanism of this coordination is unclear to date. Here, we solved the crystal structure of the intermembrane space region of the ARC6-PDV2 complex...
March 1, 2017: Nature Plants
https://www.readbyqxmd.com/read/28246390/prl3-phosphatase-active-site-is-required-for-binding-the-putative-magnesium-transporter-cnnm3
#19
Huizhi Zhang, Guennadi Kozlov, Xinlu Li, Howie Wu, Irina Gulerez, Kalle Gehring
The phosphatases of regenerating liver (PRLs) are involved in tumorigenesis and metastatic cancer yet their cellular function remains unclear. Recent reports have shown PRL phosphatases bind tightly to the CNNM family of membrane proteins to regulate magnesium efflux. Here, we characterize the interactions between the CBS-pair (Bateman) domain of CNNM3 and either PRL2 or PRL3 using X-ray crystallography, isothermal titration calorimetry, and activity assays. We report four new crystal structures of PRL proteins bound to the CNNM3 CBS-pair domain that reveal the effects of cysteine disulphide formation and nucleotide binding on complex formation...
December 2017: Scientific Reports
https://www.readbyqxmd.com/read/28246117/probing-the-conformation-of-a-conserved-glutamic-acid-within-the-cl-pathway-of-a-clc-h-cl-exchanger
#20
Malvin Vien, Daniel Basilio, Lilia Leisle, Alessio Accardi
The CLC proteins form a broad family of anion-selective transport proteins that includes both channels and exchangers. Despite extensive structural, functional, and computational studies, the transport mechanism of the CLC exchangers remains poorly understood. Several transport models have been proposed but have failed to capture all the key features of these transporters. Multiple CLC crystal structures have suggested that a conserved glutamic acid, Gluex, can adopt three conformations and that the interconversion of its side chain between these states underlies H(+)/Cl(-) exchange...
February 28, 2017: Journal of General Physiology
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