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Membrane protein crystal structure

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https://www.readbyqxmd.com/read/28941661/molecular-analysis-of-human-solute-carrier-slc26-anion-transporter-disease-causing-mutations-using-3-dimensional-homology-modeling
#1
Chloe Rapp, Xiaoyun Bai, Reinhart A F Reithmeier
The availability of the first crystal structure of a bacterial member (SLC26Dg) of the solute carrier SLC26 family of anion transporters has allowed us to create 3-dimensional models of all 10 human members (SLC26A1-A11, A10 being a pseudogene) of these membrane proteins using the Phyre2 bioinformatic tool. The homology modeling predicted that the SLC26 human proteins, like the SLC26Dg template, all consist of 14 transmembrane segments (TM) arranged in a 7+7 inverted topology with the amino-termini of two half-helices (TM3 and 10) facing each other in the centre of the protein to create the anion-binding site, linked to a C-terminal cytosolic sulfate transporter anti-sigma factor antagonist (STAS) domain...
September 20, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28937994/modeling-of-annexin-a2-membrane-interactions-by-molecular-dynamics-simulations
#2
Davit Hakobyan, Volker Gerke, Andreas Heuer
The annexins are a family of Ca2+-regulated phospholipid binding proteins that are involved in membrane domain organization and membrane trafficking. Although they are widely studied and crystal structures are available for several soluble annexins their mode of membrane association has never been studied at the molecular level. Here we obtained molecular information on the annexin-membrane interaction that could serve as paradigm for the peripheral membrane association of cytosolic proteins by Molecular Dynamics simulations...
2017: PloS One
https://www.readbyqxmd.com/read/28932871/crystal-structures-of-eukaryote-glycosyltransferases-reveal-biologically-relevant-enzyme-homooligomers
#3
REVIEW
Deborah Harrus, Sakari Kellokumpu, Tuomo Glumoff
Glycosyltransferases (GTases) transfer sugar moieties to proteins, lipids or existing glycan or polysaccharide molecules. GTases form an important group of enzymes in the Golgi, where the synthesis and modification of glycoproteins and glycolipids take place. Golgi GTases are almost invariably type II integral membrane proteins, with the C-terminal globular catalytic domain residing in the Golgi lumen. The enzymes themselves are divided into 103 families based on their sequence homology. There is an abundance of published crystal structures of GTase catalytic domains deposited in the Protein Data Bank (PDB)...
September 20, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28930630/assessing-the-structure-and-stability-of-transmembrane-oligomeric-intermediates-of-an-%C3%AE-helical-toxin
#4
Rajat Desikan, Prabal K K Maiti, K Ganapathy Ayappa
Protein membrane interactions play an important role in our understanding of diverse phenomena ranging from membrane assisted protein aggregation to oligomerization and folding. Pore forming toxins (PFTs) form the primary vehicle for infection by several strains of bacteria. These proteins expressed in a water soluble form (monomers) bind to the target membrane (protomer) to form a transmembrane pore complex through a process of oligomerization. Based on the structure of the transmembrane domains, PFTs are broadly classified into β or α toxins...
September 20, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28926141/working-at-the-membrane-interface-ligand-induced-changes-in-dynamic-conformation-and-oligomeric-structure-in-human-aromatase
#5
Giovanna Di Nardo, Giuseppe Cimicata, Roberta Baravalle, Valentina Dell'Angelo, Alberto Ciaramella, Gianluca Catucci, Piero Ugliengo, Gianfranco Gilardi
Aromatase catalyses the biosynthesis of estrogens from androgens. Due to the physiological importance of this conversion of lipophilic substrates, the interaction with the lipid bilayer for this cytochrome P450 is crucial for its dynamics that must allow an easy access to substrates and inhibitors. Here, aromatase-anastrozole interaction is studied combining computational methods to identify possible access/egress routes with the protein inserted in the membrane and experimental tools aimed at the investigation of the effect of the inhibitor on the protein conformation...
September 19, 2017: Biotechnology and Applied Biochemistry
https://www.readbyqxmd.com/read/28917834/hexameric-assembly-of-membrane-fusion-protein-yknx-of-the-sporulation-delaying-efflux-pump-from-bacillus-amyloliquefaciens
#6
Yongbin Xu, Inseong Jo, Lulu Wang, Jinli Chen, Shengdi Fan, Yuesheng Dong, Chun-Shan Quan, Nam-Chul Ha
Membrane fusion proteins (MFPs) play an essential role in the action of the drug efflux pumps and protein secretion systems in bacteria. The sporulation delaying protein (SDP) efflux pump YknWXYZ has been identified in diverse Bacillus species. The MFP YknX requires the ATP-binding cassette (ABC) transporter YknYZ and the Yip1 family protein YknW to form a functional complex. To date, the crystal structure, molecular function and mechanism of action of YknX remain unknown. In this study, to characterize the structural and biochemical roles of YknX in the functional assembly of YknWXYZ from B...
September 13, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28912275/nmr-reveals-the-intrinsically-disordered-domain-2-of-ns5a-protein-as-an-allosteric-regulator-of-the-hepatitis-c-virus-rna-polymerase-ns5b
#7
Luiza M Bessa, Hélène Launay, Marie Dujardin, François-Xavier Cantrelle, Guy Lippens, Isabelle Landrieu, Robert Schneider, Xavier Hanoulle
Non-structural protein 5B (NS5B) is the RNAdependent RNA polymerase that catalyses replication of the hepatitis C virus (HCV) RNA genome, and so is central for its life cycle. NS5B interacts with the intrinsically disordered domain 2 of NS5A (NS5A-D2), another essential multifunctional HCV protein that is required for RNA replication. As a result, these two proteins represent important targets for anti-HCV chemotherapies. Despite this importance and the existence of NS5B crystal structures, our understanding of the conformational and dynamic behaviour of NS5B in solution and its relationship with NS5A-D2 remain incomplete...
September 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28904193/mutations-in-the-fusion-protein-of-measles-virus-that-confer-resistance-to-the-membrane-fusion-inhibitors-carbobenzoxy-d-phe-l-phe-gly-and-as-48
#8
Michael N Ha, Sébastien Delpeut, Ryan S Noyce, Gary Sisson, Karen M Black, Liang-Tzung Lin, Darius Bilimoria, Richard K Plemper, Gilbert G Privé, Christopher D Richardson
The inhibitors Z-d-Phe-l-Phe Gly (fusion inhibitor peptide, FIP) and AS-48 have similar efficacy in blocking membrane fusion and syncytia formation mediated by measles virus. Other homologues such as Z-d-Phe are less effective, but may act through the same mechanism. In an attempt to map the site of action of these inhibitors, we generated mutant viruses which were resistant to the inhibitory effects of Z-d-Phe-l-Phe Gly. These 10 mutations were localized to the heptad repeat region (HRB) of the fusion protein and no changes were observed in the viral hemagglutinin, which is the receptor attachment protein...
September 13, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28885614/crystal-structure-of-e-coli-apolipoprotein-n-acyl-transferase
#9
Guangyuan Lu, Yingzhi Xu, Kai Zhang, Yong Xiong, He Li, Lei Cui, Xianping Wang, Jizhong Lou, Yujia Zhai, Fei Sun, Xuejun C Zhang
In Gram-negative bacteria, lipid modification of proteins is catalysed in a three-step pathway. Apolipoprotein N-acyl transferase (Lnt) catalyses the third step in this pathway, whereby it transfers an acyl chain from a phospholipid to the amine group of the N-terminal cysteine residue of the apolipoprotein. Here, we report the 2.6-Å crystal structure of Escherichia coli Lnt. This enzyme contains an exo-membrane nitrilase domain fused to a transmembrane (TM) domain. The TM domain of Lnt contains eight TM helices which form a membrane-embedded cavity with a lateral opening and a periplasmic exit...
July 4, 2017: Nature Communications
https://www.readbyqxmd.com/read/28880952/large-scale-expression-and-purification-of-secreted-mouse-hephaestin
#10
Chandrika N Deshpande, Vicky Xin, Yan Lu, Tom Savage, Gregory J Anderson, Mika Jormakka
Hephaestin is a large membrane-anchored multicopper ferroxidase involved in mammalian iron metabolism. Newly absorbed dietary iron is exported across the enterocyte basolateral membrane by the ferrous iron transporter ferroportin, but hephaestin increases the efficiency of this process by oxidizing the transported iron to its ferric form and promoting its release from ferroportin. Deletion or mutation of the hephaestin gene leads to systemic anemia with iron accumulation in the intestinal epithelium. The crystal structure of human ceruloplasmin, another multicopper ferroxidase with 50% sequence identity to hephaestin, has provided a framework for comparative analysis and modelling...
2017: PloS One
https://www.readbyqxmd.com/read/28877507/crystal-structure-of-a-plant-multidrug-and-toxic-compound-extrusion-family-protein
#11
Yoshiki Tanaka, Shigehiro Iwaki, Tomoya Tsukazaki
The multidrug and toxic compound extrusion (MATE) family of proteins consists of transporters responsible for multidrug resistance in prokaryotes. In plants, a number of MATE proteins were identified by recent genomic and functional studies, which imply that the proteins have substrate-specific transport functions instead of multidrug extrusion. The three-dimensional structure of eukaryotic MATE proteins, including those of plants, has not been reported, preventing a better understanding of the molecular mechanism of these proteins...
September 5, 2017: Structure
https://www.readbyqxmd.com/read/28875161/crystal-structures-of-a-zip-zinc-transporter-reveal-a-binuclear-metal-center-in-the-transport-pathway
#12
Tuo Zhang, Jian Liu, Matthias Fellner, Chi Zhang, Dexin Sui, Jian Hu
Zrt/Irt-like proteins (ZIPs) play fundamental roles in metal metabolism/homeostasis and are broadly involved in numerous physiological and pathological processes. The lack of high-resolution structure of the ZIPs hinders understanding of the metal transport mechanism. We report two crystal structures of a prokaryotic ZIP in lipidic cubic phase with bound metal substrates (Cd(2+) at 2.7 Å and Zn(2+) at 2.4 Å). The structures revealed a novel 3+2+3TM architecture and an inward-open conformation occluded at the extracellular side...
August 2017: Science Advances
https://www.readbyqxmd.com/read/28875151/molecular-characterization-structural-modeling-and-evaluation-of-antimicrobial-activity-of-basrai-thaumatin-like-protein-against-fungal-infection
#13
Nusrat Yasmin, Mahjabeen Saleem, Mamoona Naz, Roquyya Gul, Hafiz Muzzammel Rehman
A thaumatin-like protein gene from Basrai banana was cloned and expressed in Escherichia coli. Amplified gene product was cloned into pTZ57R/T vector and subcloned into expression vector pET22b(+) and resulting pET22b-basrai TLP construct was introduced into E. coli BL21. Maximum protein expression was obtained at 0.7 mM IPTG concentration after 6 hours at 37°C. Western blot analysis showed the presence of approximately 20 kDa protein in induced cells. Basrai antifungal TLP was tried as pharmacological agent against fungal disease...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28875031/serial-millisecond-crystallography-of-membrane-and-soluble-protein-microcrystals-using-synchrotron-radiation
#14
Jose M Martin-Garcia, Chelsie E Conrad, Garrett Nelson, Natasha Stander, Nadia A Zatsepin, James Zook, Lan Zhu, James Geiger, Eugene Chun, David Kissick, Mark C Hilgart, Craig Ogata, Andrii Ishchenko, Nirupa Nagaratnam, Shatabdi Roy-Chowdhury, Jesse Coe, Ganesh Subramanian, Alexander Schaffer, Daniel James, Gihan Ketwala, Nagarajan Venugopalan, Shenglan Xu, Stephen Corcoran, Dale Ferguson, Uwe Weierstall, John C H Spence, Vadim Cherezov, Petra Fromme, Robert F Fischetti, Wei Liu
Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX)...
July 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28870806/structural-insights-into-the-functional-role-of-gmp-in-modulating-the-yfibnr-system
#15
Lei Zhou, Min Xu, Tao Jiang
YfiBNR, a tripartite cyclic-di-GMP (c-di-GMP) signalling system, plays an important role in biofilm formation of the gram-negative bacterium P. aeruginosa, which regulates the cellular processes strongly associated with chronic lung infections and drug resistance. The outer-membrane lipoprotein YfiB can release the inhibition of the inner membrane protein YfiR by sequestering the periplasmatic protein YfiR, resulting in the activation of diguanylate cyclase activity of YfiN and the production of c-di-GMP. In contrast to the extensive studies on c-di-GMP, little is known about how GMP acts in the YfiBNR system...
September 1, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28867210/membrane-transporter-research-in-times-of-countless-structures
#16
REVIEW
Markus A Seeger
Structural biology has advanced our understanding of membrane proteins like no other scientific discipline in the past two decades and the number of high resolution membrane transporter structures solved by X-ray crystallography has increased exponentially over this time period. Currently, single particle cryo-EM is in full swing due to a recent resolution revolution and permits for structural insights of proteins that were refractory to crystallization. It is foreseeable that multiple structures of many human transporters will be solved in the coming five years...
August 31, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28865724/the-crystal-structures-of-a-copper-bound-metallochaperone-from-saccharomyces-cerevisiae
#17
Mihwa Lee, N Dinesha G Cooray, Megan J Maher
Atx1 is a metallochaperone protein from the yeast Saccharomyces cerevisiae (yAtx1) that plays a major role in copper homeostasis in this organism. yAtx1 functions as a copper transfer protein by shuttling copper to the secretory pathway to control intracellular copper levels. Here we describe the first crystal structures of yAtx1 that have been determined in the presence of Cu(I). The structures from two different crystal forms have been solved and refined to resolutions of 1.65 and 1.93Å. In contrast to the previous metallated crystal structure of yAtx1 where a single Hg(II) atom was coordinated by one yAtx1 molecule, the Cu(I)-yAtx1 was crystallised as a dimer in both crystal forms, sharing one Cu(I) atom between two yAtx1 molecules...
August 24, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28864654/exogenous-polyunsaturated-fatty-acids-pufas-impact-membrane-remodeling-and-affect-virulence-phenotypes-among-pathogenic-vibrio-species
#18
Anna R Moravec, Andrew W Siv, Chelsea R Hobby, Emily N Lindsay, Layla V Norbash, Daniel J Shults, Steven J K Symes, David K Giles
The pathogenic Vibrio species (cholerae, parahaemolyticus and vulnificus) represent a constant threat to human health, causing food-borne and skin wound infections as a result of ingestion or exposure to contaminated water and seafood. Recent studies have highlighted Vibrio's ability to acquire fatty acids from environmental sources and assimilate them into cell membranes. The possession and conservation of such machinery provokes consideration of fatty acids as important factors in the pathogenic lifestyle of Vibrio species...
September 1, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28863193/a-refined-model-of-claudin-15-tight-junction-paracellular-architecture-by-molecular-dynamics-simulations
#19
Giulio Alberini, Fabio Benfenati, Luca Maragliano
Tight-junctions between epithelial cells of biological barriers are specialized molecular structures that regulate the flux of solutes across the barrier, parallel to cell walls. The tight-junction backbone is made of strands of transmembrane proteins from the claudin family, but the molecular mechanism of its function is still not completely understood. Recently, the crystal structure of a mammalian claudin-15 was reported, displaying for the first time the detailed features of transmembrane and extracellular domains...
2017: PloS One
https://www.readbyqxmd.com/read/28835498/structural-transitions-of-the-conserved-and-metastable-hantaviral-glycoprotein-envelope
#20
Ilona Rissanen, Robert Stass, Antra Zeltina, Sai Li, Jussi Hepojoki, Karl Harlos, Robert J C Gilbert, Juha T Huiskonen, Thomas A Bowden
Hantaviruses are zoonotic pathogens with a near-global distribution that can cause severe hemorrhagic fever and pulmonary syndrome. The outer membrane of the hantavirus envelope displays a lattice of two glycoproteins, Gn and Gc, which orchestrate host cell recognition and entry. Here, we describe the crystal structure of the Gn glycoprotein ectodomain from the Asiatic Hantaan virus (HTNV), the most prevalent pathogenic hantavirus. Structural overlay analysis reveals that the HTNV Gn fold is highly similar to the Gn of Puumala virus (PUUV), a genetically and geographically distinct and less pathogenic hantavirus found predominantly in North-Eastern Europe, confirming that the hantaviral Gn fold is architecturally conserved across hantavirus clades...
August 23, 2017: Journal of Virology
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