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Membrane protein crystal structure

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https://www.readbyqxmd.com/read/28547763/new-approaches-towards-the-understanding-of-integral-membrane-proteins-a-structural-perspective-on-g-protein-coupled-receptors
#1
REVIEW
Reinhard Grisshammer
Three-dimensional structure determination of integral membrane proteins has advanced in unprecedented detail our understanding of mechanistic events of how ion channels, transporters, receptors and enzymes function. This exciting progress required a tremendous amount of methods development, as exemplified here with G protein-coupled receptors (GPCRs): Optimizing the production of GPCRs in recombinant hosts; increasing the probability of crystal formation using high-affinity ligands, nanobodies, and minimal G proteins for co-crystallization, thus stabilizing receptors into one conformation; using the T4 lysozyme technology and other fusion partners to promote crystal contacts; advancing crystallization methods including the development of novel detergents, and miniaturization and automation of the lipidic cubic phase crystallization method; the concept of conformational thermostabilization of GPCRs; and developing microfocus X-ray synchrotron technologies to analyze small GPCR crystals...
May 25, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28546512/wnt5a-promotes-frizzled-4-signalosome-assembly-by-stabilizing-cysteine-rich-domain-dimerization
#2
Zachary J DeBruine, Jiyuan Ke, Kaleeckal G Harikumar, Xin Gu, Peter Borowsky, Bart O Williams, Wenqing Xu, Laurence J Miller, H Eric Xu, Karsten Melcher
Wnt/β-catenin signaling is activated when extracellular Wnt ligands bind Frizzled (FZD) receptors at the cell membrane. Wnts bind FZD cysteine-rich domains (CRDs) with high affinity through a palmitoylated N-terminal "thumb" and a disulfide-stabilized C-terminal "index finger," yet how these binding events trigger receptor activation and intracellular signaling remains unclear. Here we report the crystal structure of the Frizzled-4 (FZD4) CRD in complex with palmitoleic acid, which reveals a CRD tetramer consisting of two cross-braced CRD dimers...
May 25, 2017: Genes & Development
https://www.readbyqxmd.com/read/28542288/structural-models-of-the-different-trimers-present-in-the-core-of-phycobilisomes-from-gracilaria-chilensis-based-on-crystal-structures-and-sequences
#3
Jorge Dagnino-Leone, Maximiliano Figueroa, Claudia Mella, María Alejandra Vorphal, Frédéric Kerff, Aleikar José Vásquez, Marta Bunster, José Martínez-Oyanedel
Phycobilisomes (PBS) are accessory light harvesting protein complexes that directionally transfer energy towards photosystems. Phycobilisomes are organized in a central core and rods radiating from it. Components of phycobilisomes in Gracilaria chilensis (Gch) are Phycobiliproteins (PBPs), Phycoerythrin (PE), and Phycocyanin (PC) in the rods, while Allophycocyanin (APC) is found in the core, and linker proteins (L). The function of such complexes depends on the structure of each component and their interaction...
2017: PloS One
https://www.readbyqxmd.com/read/28540724/pde%C3%AE-binding-to-ras-isoforms-provides-a-route-to-proper-membrane-localization
#4
Serena Muratcioglu, Hyunbum Jang, Attila Gursoy, Ozlem Keskin, Ruth Nussinov
To signal, Ras isoforms must be enriched at the plasma membrane (PM). It was suggested that phosphodiesterase-δ (PDEδ) can bind and shuttle some farnesylated Ras isoforms to the PM - but not all. Among these, interest focused on K-Ras4B, the most abundant oncogenic Ras isoform. To study PDEδ/Ras interactions, we modeled and simulated the PDEδ/K-Ras4B complex. We obtained structures which were similar to two subsequently determined crystal structures. We next modeled and simulated complexes of PDEδ with the farnesylated hypervariable regions (HVRs) of K-Ras4A and N-Ras...
May 25, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28533415/mechanistic-insight-into-the-nucleus-vacuole-junction-based-on-the-vac8p-nvj1p-crystal-structure
#5
Hanbin Jeong, Jumi Park, Hye-In Kim, Miriam Lee, Young-Joon Ko, Sanghwa Lee, Youngsoo Jun, Changwook Lee
Formation of the nucleus-vacuole junction (NVJ) is mediated by direct interaction between the vacuolar protein Vac8p and the outer nuclear endoplasmic reticulum membrane protein Nvj1p. Herein we report the crystal structure of Vac8p bound to Nvj1p at 2.4-Å resolution. Vac8p comprises a flexibly connected N-terminal H1 helix followed by 12 armadillo repeats (ARMs) that form a right-handed superhelical structure. The extended 80-Å-long loop of Nvj1p specifically binds the highly conserved inner groove formed from ARM1-12 of Vac8p...
May 22, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28522226/electron-crystallography-reveals-that-substrate-release-from-the-pts-iic-glucose-transporter-is-coupled-to-a-subtle-conformational-change
#6
David Kalbermatter, Po-Lin Chiu, Jean-Marc Jeckelmann, Zöhre Ucurum, Thomas Walz, Dimitrios Fotiadis
The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) is a structurally and functionally complex system that mediates sugar uptake in bacteria. Besides several soluble subunits, the glucose-specific PTS includes the integral membrane protein IICB that couples the transmembrane transport of glucose to its phosphorylation. Here, we used electron crystallography of sugar-embedded tubular crystals of the glucose-specific IIC transport domain from Escherichia coli (ecIIC(glc)) to visualize the structure of the transporter in the presence and absence of its substrate...
May 15, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28518108/identification-of-plant-ice-binding-proteins-through-assessment-of-ice-recrystallization-inhibition-and-isolation-using-ice-affinity-purification
#7
Melissa Bredow, Heather E Tomalty, Virginia K Walker
Ice-binding proteins (IBPs) belong to a family of stress-induced proteins that are synthesized by certain organisms exposed to subzero temperatures. In plants, freeze damage occurs when extracellular ice crystals grow, resulting in the rupture of plasma membranes and possible cell death. Adsorption of IBPs to ice crystals restricts further growth by a process known as ice-recrystallization inhibition (IRI), thereby reducing cellular damage. IBPs also demonstrate the ability to depress the freezing point of a solution below the equilibrium melting point, a property known as thermal hysteresis (TH) activity...
May 5, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28515320/recognition-of-nectin-2-by-the-natural-killer-cell-receptor-tigit
#8
Felix A Deuss, Benjamin S Gully, Jamie Rossjohn, Richard Berry
T cell immunoglobulin and ITIM domain (TIGIT) is an inhibitory receptor expressed on the surface of natural killer (NK) cells. TIGIT recognizes nectin and nectin-like adhesion molecules and thus plays a critical role in the innate immune response to malignant transformation. While the TIGIT nectin-like protein-5 (necl-5) interaction is well understood, how TIGIT engages nectin-2, a receptor that is broadly over-expressed in breast and ovarian cancer, remains unknown. Here, we show that TIGIT bound to the immunoglobulin domain of nectin-2 that is most distal from the membrane with an affinity of 6 μM, which was moderately lower than the affinity observed for the TIGIT-necl-5 interaction (3...
May 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28514705/a-topologically-diverse-family-of-fluoride-channels
#9
REVIEW
Christian B Macdonald, Randy B Stockbridge
Dual-topology proteins are likely evolutionary antecedents to a common motif in membrane protein structures, the inverted repeat. A family of fluoride channels, the Flucs, which protect microorganisms, fungi, and plants against cytoplasmic fluoride accumulation, has representatives of all topologies along this evolutionary trajectory, including dual-topology homodimers, antiparallel heterodimers, and, in eukaryotes, fused two-domain proteins with an inverted repeat motif. Recent high-resolution crystal structures of dual-topology homodimers, coupled with extensive functional information about both the homodimers and two-domain Flucs, provide a case study of the co-evolution of fold and function...
May 14, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28512095/structure-based-mutations-in-the-herpes-simplex-virus-1-glycoprotein-b-ectodomain-arm-impart-a-slow-entry-phenotype
#10
Qing Fan, Sarah J Kopp, Sarah A Connolly, Richard Longnecker
Glycoprotein B (gB) is the conserved herpesvirus fusion protein, and it is required for the entry of herpesviruses. The structure of the postfusion conformation of gB has been solved for several herpesviruses; however, the gB prefusion crystal structure and the details of how the protein refolds from a prefusion to a postfusion form to mediate fusion have not been determined. Using structure-based mutagenesis, we previously reported that three mutations (I671A, H681A, and F683A) in the C-terminal arm of the gB ectodomain greatly reduced cell-cell fusion...
May 16, 2017: MBio
https://www.readbyqxmd.com/read/28508075/fast-iodide-sad-phasing-for-high-throughput-membrane-protein-structure-determination
#11
Igor Melnikov, Vitaly Polovinkin, Kirill Kovalev, Ivan Gushchin, Mikhail Shevtsov, Vitaly Shevchenko, Alexey Mishin, Alexey Alekseev, Francisco Rodriguez-Valera, Valentin Borshchevskiy, Vadim Cherezov, Gordon A Leonard, Valentin Gordeliy, Alexander Popov
We describe a fast, easy, and potentially universal method for the de novo solution of the crystal structures of membrane proteins via iodide-single-wavelength anomalous diffraction (I-SAD). The potential universality of the method is based on a common feature of membrane proteins-the availability at the hydrophobic-hydrophilic interface of positively charged amino acid residues with which iodide strongly interacts. We demonstrate the solution using I-SAD of four crystal structures representing different classes of membrane proteins, including a human G protein-coupled receptor (GPCR), and we show that I-SAD can be applied using data collection strategies based on either standard or serial x-ray crystallography techniques...
May 2017: Science Advances
https://www.readbyqxmd.com/read/28506671/modeling-of-flux-binding-and-substitution-of-urea-molecules-in-the-urea-transporter-dvut
#12
Hai-Tian Zhang, Zhe Wang, Tao Yu, Jian-Ping Sang, Xian-Wu Zou, Xiaoqin Zou
Urea transporters (UTs) are transmembrane proteins that transport urea molecules across cell membranes and play a crucial role in urea excretion and water balance. Modeling the functional characteristics of UTs helps us understand how their structures accomplish the functions at the atomic level, and facilitates future therapeutic design targeting the UTs. This study was based on the crystal structure of Desulfovibrio vulgaris urea transporter (dvUT). To model the binding behavior of urea molecules in dvUT, we constructed a cooperative binding model...
April 25, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28506526/molecular-simulation-and-biochemical-studies-support-an-elevator-type-transport-mechanism-in%C3%A2-eiic
#13
Jumin Lee, Zhenning Ren, Ming Zhou, Wonpil Im
Enzyme IIC (EIIC) is a membrane-embedded sugar transport protein that is part of the phosphoenolpyruvate-dependent phosphotransferases. Crystal structures of two members of the glucose EIIC superfamily, bcChbC in the inward-facing conformation and bcMalT in the outward-facing conformation, were previously solved. Comparing the two structures led us to the hypothesis that sugar translocation could be achieved by an elevator-type transport mechanism in which a transport domain binds to the substrate and, through rigid body motions, transports it across the membrane...
May 13, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28501786/qac-modified-pvdf-membranes-antibiofouling-performance-mechanisms-and-effects-on-microbial-communities-in-an-mbr-treating-municipal-wastewater
#14
Mei Chen, Xingran Zhang, Zhiwei Wang, Liang Wang, Zhichao Wu
Biofouling remains as a critical issue limiting the widespread applications of membrane bioreactors (MBRs). The use of antibiofouling membranes is an emerging method to tackle this issue. In this study, a polyvinylidene fluoride (PVDF) membrane was modified using a quaternary ammonium compound (QAC) to create an antibiofouling membrane. The membrane was used in an MBR and the performance, mechanisms, and effects on microbial communities of this membrane were compared to a control operated in parallel. Results showed that the membrane exhibited a significantly reduced transmembrane pressure increase rate of 0...
May 8, 2017: Water Research
https://www.readbyqxmd.com/read/28500528/bacterial-actins
#15
Izoré, Fusinita van den Ent
A diverse set of protein polymers, structurally related to actin filaments contributes to the organization of bacterial cells as cytomotive or cytoskeletal filaments. This chapter describes actin homologs encoded by bacterial chromosomes. MamK filaments, unique to magnetotactic bacteria, help establishing magnetic biological compasses by interacting with magnetosomes. Magnetosomes are intracellular membrane invaginations containing biomineralized crystals of iron oxide that are positioned by MamK along the long-axis of the cell...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28496122/structural-insights-into-a-20-8-kda-tegumental-allergen-like-tal-protein-from-clonorchis-sinensis
#16
Chang Hwa Jo, Jonghyeon Son, Sulhee Kim, Takashi Oda, Jaehoon Kim, Myoung-Ro Lee, Mamoru Sato, Hyun Tae Kim, Satoru Unzai, Sam-Yong Park, Kwang Yeon Hwang
Survival of Clonorchis sinensis, a cause of human clonorchiasis, requires tegument proteins, which are localized to the tegumental outer surface membrane. These proteins play an important role in a host response and parasite survival. Thus, these proteins are interesting molecular targets for vaccine and drug development. Here, we have determined two crystal structures of the calmodulin like domain (amino acid [aa] positions 1-81) and dynein light chain (DLC)-like domain (aa 83-177) of a 20.8-kDa tegumental-allergen-like protein from Clonorchis sinensis (CsTAL3)...
May 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28479252/crystal-structure-of-mdm12-and-combinatorial-reconstitution-of-mdm12-mmm1-ermes-complexes-for-structural-studies
#17
Andrew P AhYoung, Brian Lu, Duilio Cascio, Pascal F Egea
Membrane contact sites between organelles serve as molecular hubs for the exchange of metabolites and signals. In yeast, the Endoplasmic Reticulum - Mitochondrion Encounter Structure (ERMES) tethers these two organelles likely to facilitate the non-vesicular exchange of essential phospholipids. Present in Fungi and Amoebas but not in Metazoans, ERMES is composed of five distinct subunits; among those, Mdm12, Mmm1 and Mdm34 each contain an SMP domain functioning as a lipid transfer module. We previously showed that the SMP domains of Mdm12 and Mmm1 form a hetero-tetramer...
June 17, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28476631/gating-of-connexin-channels-by-transjunctional-voltage-conformations-and-models-of-open-and-closed-states
#18
Thaddeus A Bargiello, Seunghoon Oh, Qingxiu Tang, Nicholas K Bargiello, Terry L Dowd, Taekyung Kwon
Voltage is an important physiologic regulator of channels formed by the connexin gene family. Connexins are unique among ion channels in that both plasma membrane inserted hemichannels (undocked hemichannels) and intercellular channels (aggregates of which form gap junctions) have important physiological roles. The hemichannel is the fundamental unit of gap junction voltage-gating. Each hemichannel displays two distinct voltage-gating mechanisms that are primarily sensitive to a voltage gradient formed along the length of the channel pore (the transjunctional voltage) rather than sensitivity to the absolute membrane potential (Vm or Vi-o)...
May 2, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28471361/camelid-nanobodies-used-as-crystallization-chaperones-for-different-constructs-of-porm-a-component-of-the-type-ix-secretion-system-from-porphyromonas-gingivalis
#19
Yoan Duhoo, Jennifer Roche, Thi Trang Nhung Trinh, Aline Desmyter, Anaïs Gaubert, Christine Kellenberger, Christian Cambillau, Alain Roussel, Philippe Leone
PorM is a membrane protein that is involved in the assembly of the type IX secretion system (T9SS) in Porphyromonas gingivalis, a major bacterial pathogen that is responsible for periodontal disease in humans. In the context of structural studies of PorM to better understand T9SS assembly, four camelid nanobodies were selected, produced and purified, and their specific interaction with the N-terminal or C-terminal part of the periplasmic domain of PorM was investigated. Diffracting crystals were also obtained, and the structures of the four nanobodies were solved by molecular replacement...
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28470758/insights-into-links-between-autophagy-and-the-ubiquitin-system-from-the-structure-of-lc3b-bound-to-the-lir-motif-from-the-e3-ligase-nedd4
#20
Yu Qiu, Yumei Zheng, Kuen-Phon Wu, Brenda A Schulman
Members of the LC3/GABARAP family of ubiquitin-like proteins function during autophagy by serving as membrane linked protein-binding platforms. Their C-termini are physically attached to membranes through covalent linkage to primary amines on lipids such as phosphatidylethanolamine, while their ubiquitin-like fold domains bind "LIR" (LC3-Interacting Region) sequences found within an extraordinarily diverse array of proteins including regulators of autophagy, adaptors that recruit ubiquitinated cargoes to be degraded, and even proteins controlling processes at membranes that are not associated with autophagy...
May 3, 2017: Protein Science: a Publication of the Protein Society
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