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Membrane protein crystal structure

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https://www.readbyqxmd.com/read/28634303/structural-characterization-of-the-rabphilin-3a-snap25-interaction
#1
Cristina Ferrer-Orta, María Dolores Pérez-Sánchez, Teresa Coronado-Parra, Cristina Silva, David López-Martínez, Jesús Baltanás-Copado, Juan Carmelo Gómez-Fernández, Senena Corbalán-García, Núria Verdaguer
Membrane fusion is essential in a myriad of eukaryotic cell biological processes, including the synaptic transmission. Rabphilin-3A is a membrane trafficking protein involved in the calcium-dependent regulation of secretory vesicle exocytosis in neurons and neuroendocrine cells, but the underlying mechanism remains poorly understood. Here, we report the crystal structures and biochemical analyses of Rabphilin-3A C2B-SNAP25 and C2B-phosphatidylinositol 4,5-bisphosphate (PIP2) complexes, revealing how Rabphilin-3A C2 domains operate in cooperation with PIP2/Ca(2+) and SNAP25 to bind the plasma membrane, adopting a conformation compatible to interact with the complete SNARE complex...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28623699/the-effect-of-the-protein-corona-on-the-interaction-between-nanoparticles-and-lipid-bilayers
#2
Desirè Di Silvio, Marco Maccarini, Roger Parker, Alan Mackie, Giovanna Fragneto, Francesca Baldelli Bombelli
HYPOTHESIS: It is known that nanoparticles (NPs) in a biological fluid are immediately coated by a protein corona (PC), composed of a hard (strongly bounded) and a soft (loosely associated) layers, which represents the real nano-interface interacting with the cellular membrane in vivo. In this regard, supported lipid bilayers (SLB) have extensively been used as relevant model systems for elucidating the interaction between biomembranes and NPs. Herein we show how the presence of a PC on the NP surface changes the interaction between NPs and lipid bilayers with particular care on the effects induced by the NPs on the bilayer structure...
May 29, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28621666/9%C3%A3-structure-of-the-copi-coat-reveals-that-the-arf1-gtpase-occupies-two-contrasting-molecular-environments
#3
Svetlana O Dodonova, Patrick Aderhold, Juergen Kopp, Iva Ganeva, Simone Röhling, Wim J Hagen, Irmgard Sinning, Felix Wieland, John Ag Briggs
COPI coated vesicles mediate trafficking within the Golgi apparatus and between the Golgi and the endoplasmic reticulum. Assembly of a COPI coated vesicle is initiated by the small GTPase Arf1 that recruits the coatomer complex to the membrane, triggering polymerization and budding. The vesicle uncoats before fusion with a target membrane. Coat components are structurally conserved between COPI and clathrin/adaptor proteins. Using cryo-electron tomography and subtomogram averaging, we determined the structure of the COPI coat assembled on membranes in vitro at 9 Å resolution...
June 16, 2017: ELife
https://www.readbyqxmd.com/read/28620035/molecular-interactions-shaping-the-tetraspanin-web
#4
REVIEW
Sjoerd J van Deventer, Vera-Marie E Dunlock, Annemiek B van Spriel
To facilitate the myriad of different (signaling) processes that take place at the plasma membrane, cells depend on a high degree of membrane protein organization. Important mediators of this organization are tetraspanin proteins. Tetraspanins interact laterally among themselves and with partner proteins to control the spatial organization of membrane proteins in large networks called the tetraspanin web. The molecular interactions underlying the formation of the tetraspanin web were hitherto mainly described based on their resistance to different detergents, a classification which does not necessarily correlate with functionality in the living cell...
June 15, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28617850/molecular-determinants-for-the-thermodynamic-and-functional-divergence-of-uniporter-glut1-and-proton-symporter-xyle
#5
Meng Ke, Yafei Yuan, Xin Jiang, Nieng Yan, Haipeng Gong
GLUT1 facilitates the down-gradient translocation of D-glucose across cell membrane in mammals. XylE, an Escherichia coli homolog of GLUT1, utilizes proton gradient as an energy source to drive uphill D-xylose transport. Previous studies of XylE and GLUT1 suggest that the variation between an acidic residue (Asp27 in XylE) and a neutral one (Asn29 in GLUT1) is a key element for their mechanistic divergence. In this work, we combined computational and biochemical approaches to investigate the mechanism of proton coupling by XylE and the functional divergence between GLUT1 and XylE...
June 15, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28608415/crystal-structural-characterization-reveals-novel-oligomeric-interactions-of-human-voltage-dependent-anion-channel-1
#6
Toshiaki Hosaka, Masateru Okazaki, Tomomi Kimura-Someya, Yoshiko Ishizuka-Katsura, Kaori Ito, Shigeyuki Yokoyama, Kosuke Dodo, Mikiko Sodeoka, Mikako Shirouzu
Voltage-dependent anion channel 1 (VDAC1), which is located in the outer mitochondrial membrane, plays important roles in various cellular processes. For example, oligomerization of VDAC1 is involved in the release of cytochrome c to the cytoplasm, leading to apoptosis. However, it is unknown how VDAC1 oligomerization occurs in the membrane. In the present study, we determined high-resolution crystal structures of oligomeric human VDAC1 (hVDAC1) prepared by using an Escherichia coli cell-free protein synthesis system, which avoided the need for denaturation and refolding of the protein...
June 12, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28607049/crystal-structures-and-atomic-model-of-nadph-oxidase
#7
Francesca Magnani, Simone Nenci, Elisa Millana Fananas, Marta Ceccon, Elvira Romero, Marco W Fraaije, Andrea Mattevi
NADPH oxidases (NOXs) are the only enzymes exclusively dedicated to reactive oxygen species (ROS) generation. Dysregulation of these polytopic membrane proteins impacts the redox signaling cascades that control cell proliferation and death. We describe the atomic crystal structures of the catalytic flavin adenine dinucleotide (FAD)- and heme-binding domains of Cylindrospermum stagnale NOX5. The two domains form the core subunit that is common to all seven members of the NOX family. The domain structures were then docked in silico to provide a generic model for the NOX family...
June 12, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28605828/crystal-structures-of-claudins-insights-into-their-intermolecular-interactions
#8
REVIEW
Hiroshi Suzuki, Kazutoshi Tani, Yoshinori Fujiyoshi
Claudins are four-transmembrane proteins that constitute the backbone of tight junction strands via self-polymerization in the apicolateral membranes of epithelial cells. Together with their cell-cell adhesion function, claudin proteins form the paracellular barrier and/or channels through epithelial cell sheets whose permeability is primarily dependent on the claudin subtype. Recently determined crystal structures of several claudins revealed the unique claudin fold of four transmembrane helices in a left-handed helical bundle with an extracellular β-sheet domain...
June 12, 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28603929/lipid-like-peptides-can-stabilize-integral-membrane-proteins-for-biophysical-and-structural-studies
#9
Katharina Veith, Maria Martinez Molledo, Yasser Almeida Hernandez, Inokentijs Josts, Julius Nitsche, Christian Löw, Henning Tidow
A crucial bottleneck in membrane protein structural biology is the difficulty in identifying a detergent that can maintain the stability and functionality of integral membrane proteins (IMPs). Detergents are poor membrane mimics and their common use in membrane protein crystallography may be one reason for the challenges in obtaining high-resolution crystal structures of many IMP families. Lipid-like peptides (LLPs) have detergent-like properties and have been proposed as alternatives for the solubilization of GPCRs and other membrane proteins...
June 11, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28594323/epistatic-mutations-in-puma-bh3-drive-an-alternate-binding-mode-to-potently-and-selectively-inhibit-anti-apoptotic-bfl-1
#10
Justin M Jenson, Jeremy A Ryan, Robert A Grant, Anthony Letai, Amy E Keating
Overexpression of anti-apoptotic Bcl-2 family proteins contributes to cancer progression and confers resistance to chemotherapy. Small molecules that target Bcl-2 are used in the clinic to treat leukemia, but tight and selective inhibitors are not available for Bcl-2 paralog Bfl-1. Guided by computational analysis, we designed variants of the native BH3 motif PUMA that are > 150-fold selective for Bfl-1 binding. The designed peptides potently trigger disruption of the mitochondrial outer membrane in cells dependent on Bfl-1, but not in cells dependent on other anti-apoptotic homologs...
June 8, 2017: ELife
https://www.readbyqxmd.com/read/28584102/crystal-structures-of-the-burkholderia-multivorans-hopanoid-transporter-hpnn
#11
Nitin Kumar, Chih-Chia Su, Tsung-Han Chou, Abhijith Radhakrishnan, Jared A Delmar, Kanagalaghatta R Rajashankar, Edward W Yu
Strains of the Burkholderia cepacia complex (Bcc) are Gram-negative opportunisitic bacteria that are capable of causing serious diseases, mainly in immunocompromised individuals. Bcc pathogens are intrinsically resistant to multiple antibiotics, including β-lactams, aminoglycosides, fluoroquinolones, and polymyxins. They are major pathogens in patients with cystic fibrosis (CF) and can cause severe necrotizing pneumonia, which is often fatal. Hopanoid biosynthesis is one of the major mechanisms involved in multiple antimicrobial resistance of Bcc pathogens...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28581294/contrast-matched-isotropic-bicelles-a-versatile-tool-to-specifically-probe-the-solution-structure-of-peripheral-membrane-proteins-using-sans
#12
Raphael Dos Santos Morais, Olivier Delalande, Javier Pérez, Liza Mouret, Arnaud Bondon, Anne Martel, Marie-Sousai Appavou, Elisabeth Le Rumeur, Jean-François Hubert, Sophie Combet
Obtaining structural information on integral or peripheral membrane proteins is currently arduous due to the difficulty of their solubilization, purification, and crystallization (for X-ray crystallography (XRC) application). To overcome this challenge, bicelles are known to be a versatile tool for high-resolution structure determination, especially when using solution and/or solid state nuclear magnetic resonance (NMR) and, to a lesser extent, XRC. For proteins not compatible with these high-resolution methods, small-angle X-ray and neutron scattering (SAXS and SANS, respectively) are powerful alternatives to obtain structural information directly in solution...
June 16, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28580922/phosphate-binding-protein-from-polaromonas-js666-purification-characterization-crystallization-and-sulfur-sad-phasing
#13
Vanessa R Pegos, Louis Hey, Jacob LaMirande, Rachel Pfeffer, Rosalie Lipsh, Moshe Amitay, Daniel Gonzalez, Mikael Elias
Phosphate-binding proteins (PBPs) are key proteins that belong to the bacterial ABC-type phosphate transporters. PBPs are periplasmic (or membrane-anchored) proteins that capture phosphate anions from the environment and release them to the transmembrane transporter. Recent work has suggested that PBPs have evolved for high affinity as well as high selectivity. In particular, a short, unique hydrogen bond between the phosphate anion and an aspartate residue has been shown to be critical for selectivity, yet is not strictly conserved in PBPs...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28580915/the-potential-use-of-single-particle-electron-microscopy-as-a-tool-for-structure-based-inhibitor-design
#14
S Rawson, M J McPhillie, R M Johnson, C W G Fishwick, S P Muench
Recent developments in electron microscopy (EM) have led to a step change in our ability to solve the structures of previously intractable systems, especially membrane proteins and large protein complexes. This has provided new opportunities in the field of structure-based drug design, with a number of high-profile publications resolving the binding sites of small molecules and peptide inhibitors. There are a number of advantages of EM over the more traditional X-ray crystallographic approach, such as resolving different conformational states and permitting the dynamics of a system to be better resolved when not constrained by a crystal lattice...
June 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28580643/insights-into-pg-binding-conformational-change-and-dimerization-of-the-ompa-c-terminal-domains-from-salmonella-enterica-serovar-typhimurium-and-borrelia-burgdorferi
#15
Kemin Tan, Brooke L Deatherage Kaiser, Ruiying Wu, Marianne Cuff, Yao Fan, Lance Bigelow, Robert P Jedrzejczak, Joshua N Adkins, John R Cort, Gyorgy Babnigg, Andrzej Joachimiak
S. Typhimurium can induce both humoral and cell-mediated responses when establishing itself in the host. These responses are primarily stimulated against the lipopolysaccharide and major outer membrane (OM) proteins. OmpA is one of these major OM proteins. It comprises a N-terminal eight-stranded β-barrel trans membrane domain and a C-terminal domain (OmpA(CTD) ). The OmpA(CTD) and its homologs are believed to bind to peptidoglycan (PG) within the periplasm, maintaining bacterial osmotic homeostasis and modulating the permeability and integrity of the OM...
June 5, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28580138/plasma-membrane-association-facilitates-conformational-changes-in-the-marburg-virus-protein-vp40-dimer
#16
Nisha Bhattarai, Jeevan B Gc, Bernard S Gerstman, Robert V Stahelin, Prem P Chapagain
Filovirus infections cause hemorrhagic fever in humans and non-human primates that often results in high fatality rates. The Marburg virus is a lipid-enveloped virus from the Filoviridae family and is closely related to the Ebola virus. The viral matrix layer underneath the lipid envelope is formed by the matrix protein VP40 (VP40), which is also involved in other functions during the viral life-cycle. As in the Ebola virus VP40 (eVP40), the recently determined X-ray crystal structure of the Marburg virus VP40 (mVP40) features loops containing cationic residues that form a lipid binding basic patch...
April 26, 2017: RSC Advances
https://www.readbyqxmd.com/read/28573571/crystallization-of-membrane-proteins-an-overview
#17
Andrii Ishchenko, Enrique E Abola, Vadim Cherezov
Membrane proteins are crucial components of cellular membranes and are responsible for a variety of physiological functions. The advent of new tools and technologies for structural biology of membrane proteins has led to a significant increase in the number of structures deposited to the Protein Data Bank during the past decade. This new knowledge has expanded our fundamental understanding of their mechanism of function and contributed to the drug-design efforts. In this chapter we discuss current approaches for membrane protein expression, solubilization, crystallization, and data collection...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28569500/extreme-dynamics-in-the-bama-%C3%AE-barrel-seam
#18
Pamela Arden Doerner, Marcelo C Sousa
BamA is an essential component of the β-barrel assembly machine (BAM) that is responsible for insertion and folding of β-barrel outer membrane proteins (OMPs) in Gram-negative bacteria. BamA is an OMP itself, and its β-barrel transmembrane domain is thought to catalyze OMP insertion and folding, although the molecular mechanism remains poorly understood. Crystal structures of BamA and complementary molecular dynamics simulations have shown that its β-barrel seam (the interface between the first and last barrel strands) is destabilized...
June 12, 2017: Biochemistry
https://www.readbyqxmd.com/read/28566738/structural-insights-into-the-elevator-like-mechanism-of-the-sodium-citrate-symporter-cits
#19
Ji Won Kim, Subin Kim, Songwon Kim, Haerim Lee, Jie-Oh Lee, Mi Sun Jin
The sodium-dependent citrate transporter of Klebsiella pneumoniae (KpCitS) belongs to the 2-hydroxycarboxylate transporter (2-HCT) family and allows the cell to use citrate as sole carbon and energy source in anaerobic conditions. Here we present crystal structures of KpCitS in citrate-bound outward-facing, citrate-bound asymmetric, and citrate-free inward-facing state. The structures reveal that the KpCitS dimerization domain remains stationary throughout the transport cycle due to a hydrogen bond network as well as extensive hydrophobic interactions...
May 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28559490/adar-rna-editing-below-the-backbone
#20
Liam P Keegan, Anzer Khan, Dragana Vukic, Mary A O'Connell
ADAR RNA editing enzymes (Adenosine Deaminases acting on RNA), that convert adenosine bases to inosines were first identified biochemically thirty years ago. Since then studies on ADARs in genetic model organisms, and evolutionary comparisons between them, continue to reveal a surprising range of pleiotropic biological effects of ADARs. This review focuses on Drosophila melanogaster, which has a single Adar gene encoding a homolog of vertebrate ADAR2 that site-specifically edits hundreds of transcripts to change individual codons in ion channel subunits and membrane and cytoskeletal proteins...
May 30, 2017: RNA
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